diff options
262 files changed, 2508 insertions, 860 deletions
diff --git a/etc/spack/modules.yaml b/etc/spack/modules.yaml index 5f31cdd5c0..9ae54a2d09 100644 --- a/etc/spack/modules.yaml +++ b/etc/spack/modules.yaml @@ -13,6 +13,8 @@ modules: - PATH man: - MANPATH + share/man: + - MANPATH lib: - LIBRARY_PATH - LD_LIBRARY_PATH diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index d8d5a6a23a..90ba1164e6 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -114,13 +114,13 @@ that the packages is installed: $ spack install mpileaks ==> Installing mpileaks - ==> mpich is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4. - ==> callpath is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318. - ==> adept-utils is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da. + ==> mpich is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4. + ==> callpath is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318. + ==> adept-utils is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8da. ==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz ######################################################################## 100.0% - ==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=chaos_5_x86_64_ib-59f6ad23/mpileaks-1.0.tar.gz - ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=chaos_5_x86_64_ib-59f6ad23. + ==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23/mpileaks-1.0.tar.gz + ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23. ==> No patches needed for mpileaks. ==> Building mpileaks. @@ -128,7 +128,7 @@ that the packages is installed: ==> Successfully installed mpileaks. Fetch: 2.16s. Build: 9.82s. Total: 11.98s. - [+] /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpileaks@1.0-59f6ad23 + [+] /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpileaks@1.0-59f6ad23 The last line, with the ``[+]``, indicates where the package is installed. @@ -183,7 +183,7 @@ To uninstall a package and every package that depends on it, you may give the spack uninstall --dependents mpich -will display a list of all the packages that depends on `mpich` and, upon confirmation, +will display a list of all the packages that depend on `mpich` and, upon confirmation, will uninstall them in the right order. A line like @@ -230,7 +230,7 @@ Running ``spack find`` with no arguments lists installed packages: $ spack find ==> 74 installed packages. - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- ImageMagick@6.8.9-10 libdwarf@20130729 py-dateutil@2.4.0 adept-utils@1.0 libdwarf@20130729 py-ipython@2.3.1 atk@2.14.0 libelf@0.8.12 py-matplotlib@1.4.2 @@ -256,7 +256,7 @@ Running ``spack find`` with no arguments lists installed packages: lcms@2.6 pixman@0.32.6 xz@5.2.0 libdrm@2.4.33 py-dateutil@2.4.0 zlib@1.2.8 - -- chaos_5_x86_64_ib / gcc@4.9.2 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.9.2 -------------------------------- libelf@0.8.10 mpich@3.0.4 Packages are divided into groups according to their architecture and @@ -279,7 +279,7 @@ in more detail using ``spack find -d``, and by asking only to show $ spack find --deps libdwarf ==> 2 installed packages. - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- libdwarf@20130729-d9b90962 ^libelf@0.8.12 libdwarf@20130729-b52fac98 @@ -295,7 +295,7 @@ want to know whether two packages' dependencies differ, you can use $ spack find -l libdwarf ==> 2 installed packages. - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- libdwarf@20130729-d9b90962 libdwarf@20130729-b52fac98 Now the ``libwarf`` installs have hashes after their names. These are @@ -309,14 +309,14 @@ use ``spack find -p``: $ spack find -p ==> 74 installed packages. - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- - ImageMagick@6.8.9-10 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd - adept-utils@1.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da - atk@2.14.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/atk@2.14.0-3d09ac09 - boost@1.55.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/boost@1.55.0 - bzip2@1.0.6 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/bzip2@1.0.6 - cairo@1.14.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/cairo@1.14.0-fcc2ab44 - callpath@1.0.2 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318 + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- + ImageMagick@6.8.9-10 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd + adept-utils@1.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8da + atk@2.14.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/atk@2.14.0-3d09ac09 + boost@1.55.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/boost@1.55.0 + bzip2@1.0.6 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/bzip2@1.0.6 + cairo@1.14.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/cairo@1.14.0-fcc2ab44 + callpath@1.0.2 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318 ... And, finally, you can restrict your search to a particular package @@ -325,10 +325,10 @@ by supplying its name: .. code-block:: sh $ spack find -p libelf - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- - libelf@0.8.11 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11 - libelf@0.8.12 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12 - libelf@0.8.13 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.13 + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- + libelf@0.8.11 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.11 + libelf@0.8.12 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.12 + libelf@0.8.13 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.13 ``spack find`` actually does a lot more than this. You can use *specs* to query for specific configurations and builds of each @@ -338,7 +338,7 @@ package. If you want to find only libelf versions greater than version .. code-block:: sh $ spack find libelf@0.8.12: - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- libelf@0.8.12 libelf@0.8.13 Finding just the versions of libdwarf built with a particular version @@ -348,7 +348,7 @@ of libelf would look like this: $ spack find -l libdwarf ^libelf@0.8.12 ==> 1 installed packages. - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- libdwarf@20130729-d9b90962 We can also search for packages that have a certain attribute. For example, @@ -359,6 +359,7 @@ will find every installed package with a 'debug' compile-time option enabled. The full spec syntax is discussed in detail in :ref:`sec-specs`. +.. _compiler-config: Compiler configuration ----------------------------------- @@ -445,7 +446,7 @@ If you want to see specifics on a particular compiler, you can run fc = /usr/local/bin/ifort-15.0.090 This shows which C, C++, and Fortran compilers were detected by Spack. -Notice also that we didn't have to be too specific about the +Notice also that we didn\'t have to be too specific about the version. We just said ``intel@15``, and information about the only matching Intel compiler was displayed. @@ -460,19 +461,17 @@ editing your ``~/.spack/compilers.yaml`` file. You can do this by running Each compiler configuration in the file looks like this:: ... - chaos_5_x86_64_ib: - ... - intel@15.0.0: + compilers: + - compiler: + modules = [] + operating_system: OS + paths: cc: /usr/local/bin/icc-15.0.024-beta cxx: /usr/local/bin/icpc-15.0.024-beta f77: /usr/local/bin/ifort-15.0.024-beta fc: /usr/local/bin/ifort-15.0.024-beta - ... -The chaos_5_x86_64_ib string is an architecture string, and multiple -compilers can be listed underneath an architecture. The architecture -string may be replaced with the string 'all' to signify compilers that -work on all architectures. + spec: intel@15.0.0: For compilers, like ``clang``, that do not support Fortran, put ``None`` for ``f77`` and ``fc``:: @@ -488,10 +487,11 @@ list displayed by ``spack compilers``. You can also add compiler flags to manually configured compilers. The valid flags are ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, -``ldflags``, and ``ldlibs``. For example,:: +``ldflags``, and ``ldlibs``. For example:: ... - chaos_5_x86_64_ib: + compilers: + - compiler: ... intel@15.0.0: cc: /usr/local/bin/icc-15.0.024-beta @@ -518,10 +518,10 @@ Spack, that descriptor is called a *spec*. Spack uses specs to refer to a particular build configuration (or configurations) of a package. Specs are more than a package name and a version; you can use them to specify the compiler, compiler version, architecture, compile options, -and dependency options for a build. In this section, we'll go over +and dependency options for a build. In this section, we\'ll go over the full syntax of specs. -Here is an example of a much longer spec than we've seen thus far:: +Here is an example of a much longer spec than we\'ve seen thus far:: mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt arch=bgq_os ^callpath @1.1 %gcc@4.7.2 @@ -546,8 +546,8 @@ More formally, a spec consists of the following pieces: boolean variants * ``name=<value>`` Optional compiler flag specifiers. Valid flag names are ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``. -* ``arch=<value>`` Optional architecture specifier (``arch=bgq_os``) -* ``^`` Dependency specs (``^callpath@1.1``) +* ``target=<value> os=<value>`` Optional architecture specifier +(``target=haswell os=CNL10``) * ``^`` Dependency specs (``^callpath@1.1``) There are two things to notice here. The first is that specs are recursively defined. That is, each dependency after ``^`` is a spec @@ -626,7 +626,7 @@ compilers, variants, and architectures just like any other spec. Specifiers are associated with the nearest package name to their left. For example, above, ``@1.1`` and ``%gcc@4.7.2`` associates with the ``callpath`` package, while ``@1.2:1.4``, ``%gcc@4.7.5``, ``+debug``, -``-qt``, and ``arch=bgq_os`` all associate with the ``mpileaks`` package. +``-qt``, and ``target=haswell os=CNL10`` all associate with the ``mpileaks`` package. In the diagram above, ``mpileaks`` depends on ``mpich`` with an unspecified version, but packages can depend on other packages with @@ -758,14 +758,18 @@ in gnu autotools. If all flags are set, the order is Architecture specifiers ~~~~~~~~~~~~~~~~~~~~~~~ -.. Note:: +The architecture can be specified by using the reserved +words ``target`` and/or ``os`` (``target=x86-64 os=debian7``). You can also +use the triplet form of platform, operating system and processor. - Architecture specifiers are part of specs but are not yet - functional. They will be in Spack version 1.0, due in Q3 2015. +.. code-block:: sh + + spack install libelf arch=cray_xc-CNL10-haswell -The architecture specifier looks identical to a variant specifier for a -non-boolean variant. The architecture can be specified only using the -reserved name ``arch`` (``arch=bgq_os``). +Users on non-Cray systems won't have to worry about specifying the architecture. +Spack will autodetect what kind of operating system is on your machine as well +as the processor. For more information on how the architecture can be +used on Cray machines, check here :ref:`spack-cray` .. _sec-virtual-dependencies: @@ -985,7 +989,7 @@ of installed packages. $ module avail - ------- /home/gamblin2/spack/share/spack/modules/chaos_5_x86_64_ib -------- + ------- /home/gamblin2/spack/share/spack/modules/linux-debian7-x86_64 -------- adept-utils@1.0%gcc@4.4.7-5adef8da libelf@0.8.13%gcc@4.4.7 automaded@1.0%gcc@4.4.7-d9691bb0 libelf@0.8.13%intel@15.0.0 boost@1.55.0%gcc@4.4.7 mpc@1.0.2%gcc@4.4.7-559607f5 @@ -1056,7 +1060,7 @@ Spack. For example, this will add the ``mpich`` package built with $ spack use mpich %gcc@4.4.7 Prepending: mpich@3.0.4%gcc@4.4.7 (ok) $ which mpicc - ~/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4/bin/mpicc + ~/src/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc Or, similarly with modules, you could type: @@ -1089,8 +1093,8 @@ than one installed package matches it), then Spack will warn you: $ spack load libelf ==> Error: Multiple matches for spec libelf. Choose one: - libelf@0.8.13%gcc@4.4.7 arch=chaos_5_x86_64_ib - libelf@0.8.13%intel@15.0.0 arch=chaos_5_x86_64_ib + libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64 + libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64 You can either type the ``spack load`` command again with a fully qualified argument, or you can add just enough extra constraints to @@ -1150,7 +1154,7 @@ Modules may be loaded recursively with the command: More than one spec may be placed on the command line here. -Module Comamnds for Shell Scripts +Module Commands for Shell Scripts `````````````````````````````````` Although Spack is flexbile, the ``module`` command is much faster. @@ -1543,7 +1547,7 @@ an *extension*. Suppose you have Python installed like so: $ spack find python ==> 1 installed packages. - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- python@2.7.8 .. _spack-extensions: @@ -1556,7 +1560,7 @@ You can find extensions for your Python installation like this: .. code-block:: sh $ spack extensions python - ==> python@2.7.8%gcc@4.4.7 arch=chaos_5_x86_64_ib-703c7a96 + ==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96 ==> 36 extensions: geos py-ipython py-pexpect py-pyside py-sip py-basemap py-libxml2 py-pil py-pytz py-six @@ -1568,7 +1572,7 @@ You can find extensions for your Python installation like this: py-h5py py-numpy py-pyqt py-shiboken ==> 12 installed: - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2 py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10 py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1 @@ -1584,8 +1588,8 @@ prefixes, and you can see this with ``spack find -p``: $ spack find -p py-numpy ==> 1 installed packages. - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- - py-numpy@1.9.1 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/py-numpy@1.9.1-66733244 + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- + py-numpy@1.9.1 /g/g21/gamblin2/src/spack/opt/linux-debian7-x86_64/gcc@4.4.7/py-numpy@1.9.1-66733244 However, even though this package is installed, you cannot use it directly when you run ``python``: @@ -1646,9 +1650,9 @@ installation: .. code-block:: sh $ spack activate py-numpy - ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-3c74eb69 for python@2.7.8%gcc@4.4.7. - ==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=chaos_5_x86_64_ib-5f70f816 for python@2.7.8%gcc@4.4.7. - ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7. + ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=linux-debian7-x86_64-3c74eb69 for python@2.7.8%gcc@4.4.7. + ==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=linux-debian7-x86_64-5f70f816 for python@2.7.8%gcc@4.4.7. + ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7. Several things have happened here. The user requested that ``py-numpy`` be activated in the ``python`` installation it was built @@ -1663,7 +1667,7 @@ packages listed as activated: .. code-block:: sh $ spack extensions python - ==> python@2.7.8%gcc@4.4.7 arch=chaos_5_x86_64_ib-703c7a96 + ==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96 ==> 36 extensions: geos py-ipython py-pexpect py-pyside py-sip py-basemap py-libxml2 py-pil py-pytz py-six @@ -1675,14 +1679,14 @@ packages listed as activated: py-h5py py-numpy py-pyqt py-shiboken ==> 12 installed: - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2 py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10 py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1 py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0 ==> 3 currently activated: - -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- py-nose@1.3.4 py-numpy@1.9.1 py-setuptools@11.3.1 @@ -1711,7 +1715,7 @@ dependencies, you can use ``spack activate -f``: .. code-block:: sh $ spack activate -f py-numpy - ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7. + ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7. .. _spack-deactivate: @@ -1743,7 +1747,7 @@ Spack currently needs to be run from a filesystem that supports ``flock`` locking semantics. Nearly all local filesystems and recent versions of NFS support this, but parallel filesystems may be mounted without ``flock`` support enabled. You can determine how your -filesystems are mounted with ``mount -p``. The output for a Lustre + filesystems are mounted with ``mount -p``. The output for a Lustre filesystem might look like this: .. code-block:: sh @@ -1764,7 +1768,7 @@ This issue typically manifests with the error below: Traceback (most recent call last): File "./spack", line 176, in <module> main() - File "./spack", line 154, in main + File "./spack", line 154,' in main return_val = command(parser, args) File "./spack/lib/spack/spack/cmd/find.py", line 170, in find specs = set(spack.installed_db.query(**q_args)) @@ -1782,6 +1786,142 @@ This issue typically manifests with the error below: A nicer error message is TBD in future versions of Spack. + +.. _spack-cray: + +Spack on Cray +----------------------------- + +Spack differs slightly when used on a Cray system. The architecture spec +can differentiate between the front-end and back-end processor and operating system. +For example, on Edison at NERSC, the back-end target processor +is \"Ivy Bridge\", so you can specify to use the back-end this way: + +.. code-block:: sh + + spack install zlib target=ivybridge + +You can also use the operating system to build against the back-end: + +.. code-block:: sh + + spack install zlib os=CNL10 + +Notice that the name includes both the operating system name and the major +version number concatenated together. + +Alternatively, if you want to build something for the front-end, +you can specify the front-end target processor. The processor for a login node +on Edison is \"Sandy bridge\" so we specify on the command line like so: + +.. code-block:: sh + + spack install zlib target=sandybridge + +And the front-end operating system is: + +.. code-block:: sh + + spack install zlib os=SuSE11 + + + +Cray compiler detection +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Spack can detect compilers using two methods. For the front-end, we treat +everything the same. The difference lies in back-end compiler detection. +Back-end compiler detection is made via the Tcl module avail command. +Once it detects the compiler it writes the appropriate PrgEnv and compiler +module name to compilers.yaml and sets the paths to each compiler with Cray\'s +compiler wrapper names (i.e. cc, CC, ftn). During build time, Spack will load +the correct PrgEnv and compiler module and will call appropriate wrapper. + +The compilers.yaml config file will also differ. There is a +modules section that is filled with the compiler\'s Programming Environment +and module name. On other systems, this field is empty []:: + + ... + - compiler: + modules: + - PrgEnv-intel + - intel/15.0.109 + ... + +As mentioned earlier, the compiler paths will look different on a Cray system. +Since most compilers are invoked using cc, CC and ftn, the paths for each +compiler are replaced with their respective Cray compiler wrapper names:: + + ... + paths: + cc: cc + cxx: CC + f77: ftn + fc: ftn + ... + +As opposed to an explicit path to the compiler executable. This allows Spack +to call the Cray compiler wrappers during build time. + +For more on compiler configuration, check out :ref:`compiler-config`. + +Setting defaults and using Cray modules +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +If you want to use default compilers for each PrgEnv and also be able +to load cray external modules, you will need to set up a packages.yaml. + +Here\'s an example of an external configuration for cray modules: + +.. code-block:: yaml + + packages: + mpi: + modules: + mpich@7.3.1%gcc@5.2.0 arch=cray_xc-haswell-CNL10: cray-mpich + mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-haswell-CNL10: cray-mpich + +This tells Spack that for whatever package that depends on mpi, load the +cray-mpich module into the environment. You can then be able to use whatever +environment variables, libraries, etc, that are brought into the environment +via module load. + +You can set the default compiler that Spack can use for each compiler type. +If you want to use the Cray defaults, then set them under *all:* in packages.yaml. +In the compiler field, set the compiler specs in your order of preference. +Whenever you build with that compiler type, Spack will concretize to that version. + +Here is an example of a full packages.yaml used at NERSC + +.. code-block:: yaml + + packages: + mpi: + modules: + mpich@7.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-mpich + mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-SuSE11-ivybridge: cray-mpich + buildable: False + netcdf: + modules: + netcdf@4.3.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-netcdf + netcdf@4.3.3.1%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-netcdf + buildable: False + hdf5: + modules: + hdf5@1.8.14%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-hdf5 + hdf5@1.8.14%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-hdf5 + buildable: False + all: + compiler: [gcc@5.2.0, intel@16.0.0.109] + +Here we tell spack that whenever we want to build with gcc use version 5.2.0 or +if we want to build with intel compilers, use version 16.0.0.109. We add a spec +for each compiler type for each cray modules. This ensures that for each +compiler on our system we can use that external module. + + +For more on external packages check out the section :ref:`sec-external_packages`. + Getting Help ----------------------- diff --git a/lib/spack/docs/configuration.rst b/lib/spack/docs/configuration.rst index a6f876b2aa..f2ffa07264 100644 --- a/lib/spack/docs/configuration.rst +++ b/lib/spack/docs/configuration.rst @@ -53,6 +53,7 @@ in the first directory it finds to which it has write access. Add more elements to the list to indicate where your own site's temporary directory is. +.. _sec-external_packages: External Packages ---------------------------- @@ -70,20 +71,20 @@ directory. Here's an example of an external configuration: packages: openmpi: paths: - openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib: /opt/openmpi-1.4.3 - openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug - openmpi@1.6.5%intel@10.1 arch=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel + openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3 + openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug + openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel This example lists three installations of OpenMPI, one built with gcc, one built with gcc and debug information, and another built with Intel. If Spack is asked to build a package that uses one of these MPIs as a dependency, it will use the the pre-installed OpenMPI in -the given directory. +the given directory. Packages.yaml can also be used to specify modules Each ``packages.yaml`` begins with a ``packages:`` token, followed -by a list of package names. To specify externals, add a ``paths`` +by a list of package names. To specify externals, add a ``paths`` or ``modules`` token under the package name, which lists externals in a -``spec : /path`` format. Each spec should be as +``spec: /path`` or ``spec: module-name`` format. Each spec should be as well-defined as reasonably possible. If a package lacks a spec component, such as missing a compiler or package version, then Spack will guess the missing component based @@ -108,9 +109,9 @@ be: packages: openmpi: paths: - openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib: /opt/openmpi-1.4.3 - openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug - openmpi@1.6.5%intel@10.1 arch=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel + openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3 + openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug + openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel buildable: False The addition of the ``buildable`` flag tells Spack that it should never build @@ -118,6 +119,9 @@ its own version of OpenMPI, and it will instead always rely on a pre-built OpenMPI. Similar to ``paths``, ``buildable`` is specified as a property under a package name. +If an external module is specified as not buildable, then Spack will load the +external module into the build environment which can be used for linking. + The ``buildable`` does not need to be paired with external packages. It could also be used alone to forbid packages that may be buggy or otherwise undesirable. @@ -181,7 +185,6 @@ concretization rules. A provider lists a value that packages may dependency. - Profiling ------------------ diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 6cea4da14f..a0d0feabbd 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -36,10 +36,11 @@ Creating & editing packages ``spack create`` ~~~~~~~~~~~~~~~~~~~~~ -The ``spack create`` command generates a boilerplate package template -from a URL. The URL should point to a tarball or other software -archive. In most cases, ``spack create`` plus a few modifications is -all you need to get a package working. +The ``spack create`` command creates a directory with the package name and +generates a ``package.py`` file with a boilerplate package template from a URL. +The URL should point to a tarball or other software archive. In most cases, +``spack create`` plus a few modifications is all you need to get a package +working. Here's an example: @@ -47,12 +48,16 @@ Here's an example: $ spack create http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz -Spack examines the tarball URL and tries to figure out the name of the -package to be created. It also tries to determine what version strings -look like for this package. Using this information, it will try to -find *additional* versions by spidering the package's webpage. If it -finds multiple versions, Spack prompts you to tell it how many -versions you want to download and checksum: +Spack examines the tarball URL and tries to figure out the name of the package +to be created. Once the name is determined a directory in the appropriate +repository is created with that name. Spack prefers, but does not require, that +names be lower case so the directory name will be lower case when ``spack +create`` generates it. In cases where it is desired to have mixed case or upper +case simply rename the directory. Spack also tries to determine what version +strings look like for this package. Using this information, it will try to find +*additional* versions by spidering the package's webpage. If it finds multiple +versions, Spack prompts you to tell it how many versions you want to download +and checksum: .. code-block:: sh @@ -297,9 +302,10 @@ directories or files (like patches) that it needs to build. Package Names ~~~~~~~~~~~~~~~~~~ -Packages are named after the directory containing ``package.py``. So, -``libelf``'s ``package.py`` lives in a directory called ``libelf``. -The ``package.py`` file defines a class called ``Libelf``, which +Packages are named after the directory containing ``package.py``. It is +preferred, but not required, that the directory, and thus the package name, are +lower case. So, ``libelf``'s ``package.py`` lives in a directory called +``libelf``. The ``package.py`` file defines a class called ``Libelf``, which extends Spack's ``Package`` class. for example, here is ``$SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py``: @@ -562,7 +568,7 @@ The package author is responsible for coming up with a sensible name for each version to be fetched from a repository. For example, if you're fetching from a tag like ``v1.0``, you might call that ``1.0``. If you're fetching a nameless git commit or an older subversion -revision, you might give the commit an intuitive name, like ``dev`` +revision, you might give the commit an intuitive name, like ``develop`` for a development version, or ``some-fancy-new-feature`` if you want to be more specific. @@ -572,6 +578,17 @@ branches move forward over time and you aren't guaranteed to get the same thing every time you fetch a particular version. Life isn't always simple, though, so this is not strictly enforced. +When fetching from from the branch corresponding to the development version +(often called ``master``,``trunk`` or ``dev``), it is recommended to +call this version ``develop``. Spack has special treatment for this version so + that ``@develop`` will satisfy dependencies like +``depends_on(abc, when="@x.y.z:")``. In other words, ``@develop`` is +greater than any other version. The rationale is that certain features or +options first appear in the development branch. Therefore if a package author +wants to keep the package on the bleeding edge and provide support for new +features, it is advised to use ``develop`` for such a version which will +greatly simplify writing dependencies and version-related conditionals. + In some future release, Spack may support extrapolating repository versions as it does for tarball URLs, but currently this is not supported. @@ -587,6 +604,7 @@ Git fetching is enabled with the following parameters to ``version``: * ``tag``: name of a tag to fetch. * ``branch``: name of a branch to fetch. * ``commit``: SHA hash (or prefix) of a commit to fetch. + * ``submodules``: Also fetch submodules when checking out this repository. Only one of ``tag``, ``branch``, or ``commit`` can be used at a time. @@ -597,7 +615,7 @@ Default branch class Example(Package): ... - version('dev', git='https://github.com/example-project/example.git') + version('develop', git='https://github.com/example-project/example.git') This is not recommended, as the contents of the default branch change over time. @@ -643,6 +661,17 @@ Commits could just use the abbreviated commit hash. It's up to the package author to decide what makes the most sense. +Submodules + + You can supply ``submodules=True`` to cause Spack to fetch submodules + along with the repository at fetch time. + + .. code-block:: python + + version('1.0.1', git='https://github.com/example-project/example.git', + tag='v1.0.1', submdoules=True) + + Installing ^^^^^^^^^^^^^^ @@ -670,7 +699,7 @@ Default .. code-block:: python - version('hg-head', hg='https://jay.grs.rwth-aachen.de/hg/example') + version('develop', hg='https://jay.grs.rwth-aachen.de/hg/example') Note that this is not recommended; try to fetch a particular revision instead. @@ -702,7 +731,7 @@ Fetching the head .. code-block:: python - version('svn-head', svn='https://outreach.scidac.gov/svn/libmonitor/trunk') + version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk') This is not recommended, as the head will move forward over time. @@ -712,7 +741,7 @@ Fetching a revision .. code-block:: python - version('svn-head', svn='https://outreach.scidac.gov/svn/libmonitor/trunk', + version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk', revision=128) Subversion branches are handled as part of the directory structure, so @@ -1257,6 +1286,31 @@ command line to find installed packages or to install packages with particular constraints, and package authors can use specs to describe relationships between packages. +Additionally, dependencies may be specified for specific use cases: + +.. code-block:: python + + depends_on("cmake", type="build") + depends_on("libelf", type=("build", "link")) + depends_on("python", type="run") + +The dependency types are: + + * **"build"**: made available during the project's build. The package will + be added to ``PATH``, the compiler include paths, and ``PYTHONPATH``. + Other projects which depend on this one will not have these modified + (building project X doesn't need project Y's build dependencies). + * **"link"**: the project is linked to by the project. The package will be + added to the current package's ``rpath``. + * **"run"**: the project is used by the project at runtime. The package will + be added to ``PATH`` and ``PYTHONPATH``. + +If not specified, ``type`` is assumed to be ``("build", "link")``. This is the +common case for compiled language usage. Also available are the aliases +``alldeps`` for all dependency types and ``nolink`` (``("build", "run")``) for +use by dependencies which are not expressed via a linker (e.g., Python or Lua +module loading). + .. _setup-dependent-environment: ``setup_dependent_environment()`` @@ -1660,21 +1714,21 @@ the user runs ``spack install`` and the time the ``install()`` method is called. The concretized version of the spec above might look like this:: - mpileaks@2.3%gcc@4.7.3 arch=linux-ppc64 - ^callpath@1.0%gcc@4.7.3+debug arch=linux-ppc64 - ^dyninst@8.1.2%gcc@4.7.3 arch=linux-ppc64 - ^libdwarf@20130729%gcc@4.7.3 arch=linux-ppc64 - ^libelf@0.8.11%gcc@4.7.3 arch=linux-ppc64 - ^mpich@3.0.4%gcc@4.7.3 arch=linux-ppc64 + mpileaks@2.3%gcc@4.7.3 arch=linux-debian7-x86_64 + ^callpath@1.0%gcc@4.7.3+debug arch=linux-debian7-x86_64 + ^dyninst@8.1.2%gcc@4.7.3 arch=linux-debian7-x86_64 + ^libdwarf@20130729%gcc@4.7.3 arch=linux-debian7-x86_64 + ^libelf@0.8.11%gcc@4.7.3 arch=linux-debian7-x86_64 + ^mpich@3.0.4%gcc@4.7.3 arch=linux-debian7-x86_64 .. graphviz:: digraph { - "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-ppc64" - "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-ppc64" -> "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-ppc64" - "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-ppc64" -> "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64" - "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64" -> "libdwarf@20130729\n%gcc@4.7.3\n arch=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-ppc64" - "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-ppc64" + "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-debian7-x86_64" + "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-debian7-x86_64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-debian7-x86_64" + "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-debian7-x86_64" -> "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64" + "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libdwarf@20130729\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-debian7-x86_64" + "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-debian7-x86_64" } Here, all versions, compilers, and platforms are filled in, and there @@ -1703,9 +1757,9 @@ running ``spack spec``. For example: ^libdwarf ^libelf - dyninst@8.0.1%gcc@4.7.3 arch=linux-ppc64 - ^libdwarf@20130729%gcc@4.7.3 arch=linux-ppc64 - ^libelf@0.8.13%gcc@4.7.3 arch=linux-ppc64 + dyninst@8.0.1%gcc@4.7.3 arch=linux-debian7-x86_64 + ^libdwarf@20130729%gcc@4.7.3 arch=linux-debian7-x86_64 + ^libelf@0.8.13%gcc@4.7.3 arch=linux-debian7-x86_64 This is useful when you want to know exactly what Spack will do when you ask for a particular spec. @@ -2210,12 +2264,12 @@ example: def install(self, prefix): # Do default install - @when('arch=chaos_5_x86_64_ib') + @when('arch=linux-debian7-x86_64') def install(self, prefix): # This will be executed instead of the default install if # the package's sys_type() is chaos_5_x86_64_ib. - @when('arch=bgqos_0") + @when('arch=linux-debian7-x86_64") def install(self, prefix): # This will be executed if the package's sys_type is bgqos_0 @@ -2343,7 +2397,7 @@ build system. .. _sanity-checks: -Sanity checking an intallation +Sanity checking an installation -------------------------------- By default, Spack assumes that a build has failed if nothing is @@ -2706,15 +2760,15 @@ build process will start from scratch. ``spack purge`` ~~~~~~~~~~~~~~~~~ -Cleans up all of Spack's temporary and cached files. This can be used to -recover disk space if temporary files from interrupted or failed installs -accumulate in the staging area. +Cleans up all of Spack's temporary and cached files. This can be used to +recover disk space if temporary files from interrupted or failed installs +accumulate in the staging area. When called with ``--stage`` or ``--all`` (or without arguments, in which case -the default is ``--all``) this removes all staged files; this is equivalent to +the default is ``--all``) this removes all staged files; this is equivalent to running ``spack clean`` for every package you have fetched or staged. -When called with ``--cache`` or ``--all`` this will clear all resources +When called with ``--cache`` or ``--all`` this will clear all resources :ref:`cached <caching>` during installs. Keeping the stage directory on success @@ -2863,11 +2917,11 @@ build it: $ spack stage libelf ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz ######################################################################## 100.0% - ==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64/libelf-0.8.13.tar.gz - ==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64. + ==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64/libelf-0.8.13.tar.gz + ==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64. $ spack cd libelf $ pwd - /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64/libelf-0.8.13 + /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64/libelf-0.8.13 ``spack cd`` here changed he current working directory to the directory containing the expanded ``libelf`` source code. There are a diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index 20c9934704..d67585aac4 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -177,10 +177,11 @@ sys_type = None # should live. This file is overloaded for spack core vs. for packages. # __all__ = ['Package', 'StagedPackage', 'CMakePackage', \ - 'Version', 'when', 'ver'] + 'Version', 'when', 'ver', 'alldeps', 'nolink'] from spack.package import Package, ExtensionConflictError from spack.package import StagedPackage, CMakePackage from spack.version import Version, ver +from spack.spec import DependencySpec, alldeps, nolink from spack.multimethod import when import llnl.util.filesystem diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index fe5186a7d7..93fb0690f7 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -254,7 +254,8 @@ def set_build_environment_variables(pkg, env, dirty=False): env.set_path(SPACK_ENV_PATH, env_paths) # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES - dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)] + dep_prefixes = [d.prefix + for d in pkg.spec.traverse(root=False, deptype='build')] env.set_path(SPACK_DEPENDENCIES, dep_prefixes) # Add dependencies to CMAKE_PREFIX_PATH env.set_path('CMAKE_PREFIX_PATH', dep_prefixes) @@ -337,10 +338,6 @@ def set_module_variables_for_package(pkg, module): # Don't use which for this; we want to find it in the current dir. m.configure = Executable('./configure') - # TODO: shouldn't really use "which" here. Consider adding notion - # TODO: of build dependencies, as opposed to link dependencies. - # TODO: Currently, everything is a link dependency, but tools like - # TODO: this shouldn't be. m.cmake = Executable('cmake') m.ctest = Executable('ctest') @@ -388,9 +385,10 @@ def set_module_variables_for_package(pkg, module): def get_rpaths(pkg): """Get a list of all the rpaths for a package.""" rpaths = [pkg.prefix.lib, pkg.prefix.lib64] - rpaths.extend(d.prefix.lib for d in pkg.spec.dependencies.values() + deps = pkg.spec.dependencies(deptype='link') + rpaths.extend(d.prefix.lib for d in deps if os.path.isdir(d.prefix.lib)) - rpaths.extend(d.prefix.lib64 for d in pkg.spec.dependencies.values() + rpaths.extend(d.prefix.lib64 for d in deps if os.path.isdir(d.prefix.lib64)) # Second module is our compiler mod name. We use that to get rpaths from # module show output. @@ -449,7 +447,7 @@ def setup_package(pkg, dirty=False): load_external_modules(pkg) # traverse in postorder so package can use vars from its dependencies spec = pkg.spec - for dspec in pkg.spec.traverse(order='post', root=False): + for dspec in pkg.spec.traverse(order='post', root=False, deptype='build'): # If a user makes their own package repo, e.g. # spack.repos.mystuff.libelf.Libelf, and they inherit from # an existing class like spack.repos.original.libelf.Libelf, diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index f5f234d7a7..18c748e483 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -325,7 +325,7 @@ def create(parser, args): # Figure out a name and repo for the package. name, version = guess_name_and_version(url, args) spec = Spec(name) - name = spec.name # factors out namespace, if any + name = spec.name.lower() # factors out namespace, if any repo = find_repository(spec, args) tty.msg("This looks like a URL for %s version %s" % (name, version)) diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py index 39faf59a17..643e6374b2 100644 --- a/lib/spack/spack/cmd/diy.py +++ b/lib/spack/spack/cmd/diy.py @@ -50,7 +50,7 @@ def setup_parser(subparser): help="Do not display verbose build output while installing.") subparser.add_argument( 'spec', nargs=argparse.REMAINDER, - help="specs to use for install. Must contain package AND verison.") + help="specs to use for install. Must contain package AND version.") def diy(self, args): diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py index e40caaa234..1afc51d9fa 100644 --- a/lib/spack/spack/cmd/fetch.py +++ b/lib/spack/spack/cmd/fetch.py @@ -51,7 +51,7 @@ def fetch(parser, args): for spec in specs: if args.missing or args.dependencies: to_fetch = set() - for s in spec.traverse(): + for s in spec.traverse(deptype_query=spack.alldeps): package = spack.repo.get(s) if args.missing and package.installed: continue diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py index 64d0d20e24..5774034062 100644 --- a/lib/spack/spack/cmd/info.py +++ b/lib/spack/spack/cmd/info.py @@ -81,12 +81,14 @@ def print_text_info(pkg): print " " + fmt % (name, default, desc) - print - print "Dependencies:" - if pkg.dependencies: - colify(pkg.dependencies, indent=4) - else: - print " None" + for deptype in ('build', 'link', 'run'): + print + print "%s Dependencies:" % deptype.capitalize() + deps = pkg.dependencies(deptype) + if deps: + colify(deps, indent=4) + else: + print " None" print print "Virtual packages: " diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py index 3133e080d7..4c076322a9 100644 --- a/lib/spack/spack/cmd/install.py +++ b/lib/spack/spack/cmd/install.py @@ -58,6 +58,10 @@ def setup_parser(subparser): help="Install a package *without* cleaning the environment.") subparser.add_argument( 'packages', nargs=argparse.REMAINDER, help="specs of packages to install") + subparser.add_argument( + '--run-tests', action='store_true', dest='run_tests', + help="Run tests during installation of a package.") + def install(parser, args): @@ -80,6 +84,7 @@ def install(parser, args): keep_stage=args.keep_stage, ignore_deps=args.ignore_deps, make_jobs=args.jobs, + run_tests=args.run_tests, verbose=args.verbose, fake=args.fake, dirty=args.dirty, diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py index d5f7abe212..0cf682fc4f 100644 --- a/lib/spack/spack/cmd/mirror.py +++ b/lib/spack/spack/cmd/mirror.py @@ -179,7 +179,7 @@ def mirror_create(args): new_specs = set() for spec in specs: spec.concretize() - for s in spec.traverse(): + for s in spec.traverse(deptype_query=spack.alldeps): new_specs.add(s) specs = list(new_specs) diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 3cefb512c2..55826d133c 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -87,7 +87,7 @@ def module_find(mtype, flags, spec_array): return if flags.recurse_dependencies: - for dep in spec.dependencies.values(): + for dep in spec.dependencies(): _find_modules(dep, modules_list) mod = module_types[mtype](spec) @@ -108,7 +108,7 @@ def module_find(mtype, flags, spec_array): tty.die("No installed packages match spec %s" % raw_spec) if len(specs) > 1: - tty.error("Multiple matches for spec %s. Choose one:" % spec) + tty.error("Multiple matches for spec %s. Choose one:" % raw_spec) for s in specs: sys.stderr.write(s.tree(color=True)) sys.exit(1) diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py index 6c5c4ae8c6..bc64c77eab 100644 --- a/lib/spack/spack/cmd/package-list.py +++ b/lib/spack/spack/cmd/package-list.py @@ -80,11 +80,15 @@ def print_rst_package_list(): if pkg.versions: print "Versions:" print " " + ", ".join(str(v) for v in reversed(sorted(pkg.versions))) - if pkg.dependencies: - print "Dependencies" - print " " + ", ".join("`%s`_" % d if d != "mpi" else d - for d in pkg.dependencies) - print + + for deptype in ('build', 'link', 'run'): + deps = pkg.dependencies(deptype) + if deps: + print "%s Dependencies" % deptype.capitalize() + print " " + ", ".join("`%s`_" % d if d != "mpi" else d + for d in build_deps) + print + print "Description:" print pkg.format_doc(indent=2) print diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py index 02e9bfd281..04f3d663df 100644 --- a/lib/spack/spack/cmd/setup.py +++ b/lib/spack/spack/cmd/setup.py @@ -44,7 +44,7 @@ def setup_parser(subparser): help="Display verbose build output while installing.") subparser.add_argument( 'spec', nargs=argparse.REMAINDER, - help="specs to use for install. Must contain package AND verison.") + help="specs to use for install. Must contain package AND version.") def setup(self, args): diff --git a/lib/spack/spack/cmd/test-install.py b/lib/spack/spack/cmd/test-install.py index 45592a7dda..14c06d136d 100644 --- a/lib/spack/spack/cmd/test-install.py +++ b/lib/spack/spack/cmd/test-install.py @@ -133,7 +133,12 @@ def fetch_log(path): def failed_dependencies(spec): - return set(item for item in spec.dependencies.itervalues() if not spack.repo.get(item).installed) + def get_deps(deptype): + return set(item for item in spec.dependencies(deptype) + if not spack.repo.get(item).installed) + link_deps = get_deps('link') + run_deps = get_deps('run') + return link_deps.union(run_deps) def get_top_spec_or_die(args): diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py index f792008c49..386df08b2e 100644 --- a/lib/spack/spack/concretize.py +++ b/lib/spack/spack/concretize.py @@ -103,7 +103,7 @@ class DefaultConcretizer(object): usable.sort(cmp=cmp_externals) return usable - + # XXX(deptypes): Look here. def choose_virtual_or_external(self, spec): """Given a list of candidate virtual and external packages, try to find one that is most ABI compatible. @@ -166,7 +166,11 @@ class DefaultConcretizer(object): valid_versions.sort(key=prefer_key, reverse=True) if valid_versions: - spec.versions = ver([valid_versions[0]]) + # Disregard @develop and take the next valid version + if ver(valid_versions[0]) == ver('develop') and len(valid_versions) > 1: + spec.versions = ver([valid_versions[1]]) + else: + spec.versions = ver([valid_versions[0]]) else: # We don't know of any SAFE versions that match the given # spec. Grab the spec's versions and grab the highest @@ -390,8 +394,10 @@ def find_spec(spec, condition): """Searches the dag from spec in an intelligent order and looks for a spec that matches a condition""" # First search parents, then search children - dagiter = chain(spec.traverse(direction='parents', root=False), - spec.traverse(direction='children', root=False)) + deptype = ('build', 'link') + dagiter = chain( + spec.traverse(direction='parents', deptype=deptype, root=False), + spec.traverse(direction='children', deptype=deptype, root=False)) visited = set() for relative in dagiter: if condition(relative): @@ -399,7 +405,7 @@ def find_spec(spec, condition): visited.add(id(relative)) # Then search all other relatives in the DAG *except* spec - for relative in spec.root.traverse(): + for relative in spec.root.traverse(deptypes=spack.alldeps): if relative is spec: continue if id(relative) in visited: continue if condition(relative): diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index a4bbff3d5a..c95abd7423 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -215,9 +215,14 @@ class Database(object): # Add dependencies from other records in the install DB to # form a full spec. if 'dependencies' in spec_dict[spec.name]: - for dep_hash in spec_dict[spec.name]['dependencies'].values(): + for dep in spec_dict[spec.name]['dependencies'].values(): + if type(dep) == tuple: + dep_hash, deptypes = dep + else: + dep_hash = dep + deptypes = spack.alldeps child = self._read_spec_from_yaml(dep_hash, installs, hash_key) - spec._add_dependency(child) + spec._add_dependency(child, deptypes) # Specs from the database need to be marked concrete because # they represent actual installations. @@ -334,7 +339,10 @@ class Database(object): counts = {} for key, rec in self._data.items(): counts.setdefault(key, 0) - for dep in rec.spec.dependencies.values(): + # XXX(deptype): This checks all dependencies, but build + # dependencies might be able to be dropped in the + # future. + for dep in rec.spec.dependencies(): dep_key = dep.dag_hash() counts.setdefault(dep_key, 0) counts[dep_key] += 1 @@ -406,7 +414,7 @@ class Database(object): else: self._data[key] = InstallRecord(spec, path, True, explicit=explicit) - for dep in spec.dependencies.values(): + for dep in spec.dependencies(('link', 'run')): self._increment_ref_count(dep, directory_layout) def _increment_ref_count(self, spec, directory_layout=None): @@ -421,7 +429,7 @@ class Database(object): self._data[key] = InstallRecord(spec.copy(), path, installed) - for dep in spec.dependencies.values(): + for dep in spec.dependencies('link'): self._increment_ref_count(dep) self._data[key].ref_count += 1 @@ -466,7 +474,7 @@ class Database(object): if rec.ref_count == 0 and not rec.installed: del self._data[key] - for dep in spec.dependencies.values(): + for dep in spec.dependencies('link'): self._decrement_ref_count(dep) def _remove(self, spec): @@ -480,7 +488,7 @@ class Database(object): return rec.spec del self._data[key] - for dep in rec.spec.dependencies.values(): + for dep in rec.spec.dependencies('link'): self._decrement_ref_count(dep) # Returns the concrete spec so we know it in the case where a diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py index ca8f21dc08..88d2aaf472 100644 --- a/lib/spack/spack/directives.py +++ b/lib/spack/spack/directives.py @@ -171,7 +171,7 @@ def version(pkg, ver, checksum=None, **kwargs): pkg.versions[Version(ver)] = kwargs -def _depends_on(pkg, spec, when=None): +def _depends_on(pkg, spec, when=None, type=None): # If when is False do nothing if when is False: return @@ -180,10 +180,29 @@ def _depends_on(pkg, spec, when=None): when = pkg.name when_spec = parse_anonymous_spec(when, pkg.name) + if type is None: + # The default deptype is build and link because the common case is to + # build against a library which then turns into a runtime dependency + # due to the linker. + # XXX(deptype): Add 'run' to this? It's an uncommon dependency type, + # but is most backwards-compatible. + type = ('build', 'link') + + if isinstance(type, str): + type = (type,) + + for deptype in type: + if deptype not in spack.spec.alldeps: + raise UnknownDependencyTypeError('depends_on', pkg.name, deptype) + dep_spec = Spec(spec) if pkg.name == dep_spec.name: raise CircularReferenceError('depends_on', pkg.name) + pkg_deptypes = pkg._deptypes.setdefault(dep_spec.name, set()) + for deptype in type: + pkg_deptypes.add(deptype) + conditions = pkg.dependencies.setdefault(dep_spec.name, {}) if when_spec in conditions: conditions[when_spec].constrain(dep_spec, deps=False) @@ -191,13 +210,13 @@ def _depends_on(pkg, spec, when=None): conditions[when_spec] = dep_spec -@directive('dependencies') -def depends_on(pkg, spec, when=None): +@directive(('dependencies', '_deptypes')) +def depends_on(pkg, spec, when=None, type=None): """Creates a dict of deps with specs defining when they apply.""" - _depends_on(pkg, spec, when=when) + _depends_on(pkg, spec, when=when, type=type) -@directive(('extendees', 'dependencies')) +@directive(('extendees', 'dependencies', '_deptypes')) def extends(pkg, spec, **kwargs): """Same as depends_on, but dependency is symlinked into parent prefix. @@ -326,3 +345,13 @@ class CircularReferenceError(DirectiveError): directive, "Package '%s' cannot pass itself to %s" % (package, directive)) self.package = package + + +class UnknownDependencyTypeError(DirectiveError): + """This is raised when a dependency is of an unknown type.""" + def __init__(self, directive, package, deptype): + super(UnknownDependencyTypeError, self).__init__( + directive, + "Package '%s' cannot depend on a package via %s." % + (package, deptype)) + self.package = package diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index ee13e2dcbc..a5e76043ad 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -285,7 +285,7 @@ class YamlDirectoryLayout(DirectoryLayout): return path if spec.dag_hash() == installed_spec.dag_hash(): - raise SpecHashCollisionError(installed_hash, spec_hash) + raise SpecHashCollisionError(spec, installed_spec) else: raise InconsistentInstallDirectoryError( 'Spec file in %s does not match hash!' % spec_file_path) @@ -431,7 +431,7 @@ class SpecHashCollisionError(DirectoryLayoutError): def __init__(self, installed_spec, new_spec): super(SpecHashCollisionError, self).__init__( 'Specs %s and %s have the same SHA-1 prefix!' - % installed_spec, new_spec) + % (installed_spec, new_spec)) class RemoveFailedError(DirectoryLayoutError): diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 38133ee0ca..bcb33bd0e6 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -366,8 +366,8 @@ class CacheURLFetchStrategy(URLFetchStrategy): try: self.check() except ChecksumError: - # Future fetchers will assume they don't need to download if the - # file remains + # Future fetchers will assume they don't need to + # download if the file remains os.remove(self.archive_file) raise @@ -517,6 +517,7 @@ class GitFetchStrategy(VCSFetchStrategy): super(GitFetchStrategy, self).__init__( 'git', 'tag', 'branch', 'commit', **forwarded_args) self._git = None + self.submodules = kwargs.get('submodules', False) @property def git_version(self): @@ -595,6 +596,10 @@ class GitFetchStrategy(VCSFetchStrategy): self.git('pull', '--tags', ignore_errors=1) self.git('checkout', self.tag) + # Init submodules if the user asked for them. + if self.submodules: + self.git('submodule', 'update', '--init') + def archive(self, destination): super(GitFetchStrategy, self).archive(destination, exclude='.git') diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py index 22058d41d8..063e4647b6 100644 --- a/lib/spack/spack/graph.py +++ b/lib/spack/spack/graph.py @@ -80,12 +80,14 @@ def topological_sort(spec, **kwargs): """ reverse = kwargs.get('reverse', False) + # XXX(deptype): iterate over a certain kind of dependency. Maybe color + # edges based on the type of dependency? if not reverse: - parents = lambda s: s.dependents - children = lambda s: s.dependencies + parents = lambda s: s.dependents() + children = lambda s: s.dependencies() else: - parents = lambda s: s.dependencies - children = lambda s: s.dependents + parents = lambda s: s.dependencies() + children = lambda s: s.dependents() # Work on a copy so this is nondestructive. spec = spec.copy() diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index ce46047fa3..a2e528d295 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -120,7 +120,7 @@ def dependencies(spec, request='all'): return [] if request == 'direct': - return [xx for _, xx in spec.dependencies.items()] + return spec.dependencies() # FIXME : during module file creation nodes seem to be visited multiple # FIXME : times even if cover='nodes' is given. This work around permits diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 84bd99df54..7f53b461b2 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -311,6 +311,8 @@ class Package(object): parallel = True """# jobs to use for parallel make. If set, overrides default of ncpus.""" make_jobs = None + """By default do not run tests within package's install()""" + run_tests = False """Most packages are NOT extendable. Set to True if you want extensions.""" extendable = False """List of prefix-relative file paths (or a single path). If these do @@ -575,7 +577,7 @@ class Package(object): name = next(iter(self.extendees)) # If the extendee is in the spec's deps already, return that. - for dep in self.spec.traverse(): + for dep in self.spec.traverse(deptypes=('link', 'run')): if name == dep.name: return dep @@ -640,12 +642,13 @@ class Package(object): yield self for name in sorted(self.dependencies.keys()): - spec = self.dependencies[name] + dep_spec = self.get_dependency(name) + spec = dep_spec.spec - # currently, we do not descend into virtual dependencies, as this + # Currently, we do not descend into virtual dependencies, as this # makes doing a sensible traversal much harder. We just assume # that ANY of the virtual deps will work, which might not be true - # (due to conflicts or unsatisfiable specs). For now this is ok + # (due to conflicts or unsatisfiable specs). For now this is ok, # but we might want to reinvestigate if we start using a lot of # complicated virtual dependencies # TODO: reinvestigate this. @@ -683,7 +686,9 @@ class Package(object): for spec in spack.installed_db.query(): if self.name == spec.name: continue - for dep in spec.traverse(): + # XXX(deptype): Should build dependencies not count here? + #for dep in spec.traverse(deptype=('run')): + for dep in spec.traverse(deptype=spack.alldeps): if self.spec == dep: dependents.append(spec) return dependents @@ -881,6 +886,7 @@ class Package(object): skip_patch=False, verbose=False, make_jobs=None, + run_tests=False, fake=False, explicit=False, dirty=False, @@ -902,9 +908,10 @@ class Package(object): verbose -- Display verbose build output (by default, suppresses it) dirty -- Don't clean the build environment before installing. make_jobs -- Number of make jobs to use for install. Default is ncpus + run_tests -- Runn tests within the package's install() """ if not self.spec.concrete: - raise ValueError("Can only install concrete packages.") + raise ValueError("Can only install concrete packages: %s." % self.spec.name) # No installation needed if package is external if self.spec.external: @@ -932,7 +939,11 @@ class Package(object): fake=fake, skip_patch=skip_patch, verbose=verbose, - make_jobs=make_jobs) + make_jobs=make_jobs, + run_tests=run_tests) + + # Set run_tests flag before starting build. + self.run_tests = run_tests # Set parallelism before starting build. self.make_jobs = make_jobs @@ -1081,7 +1092,7 @@ class Package(object): def do_install_dependencies(self, **kwargs): # Pass along paths of dependencies here - for dep in self.spec.dependencies.values(): + for dep in self.spec.dependencies(): dep.package.do_install(**kwargs) @property @@ -1262,7 +1273,7 @@ class Package(object): (self.name, self.extendee.name)) def do_activate(self, force=False): - """Called on an etension to invoke the extendee's activate method. + """Called on an extension to invoke the extendee's activate method. Commands should call this routine, and should not call activate() directly. @@ -1274,7 +1285,7 @@ class Package(object): # Activate any package dependencies that are also extensions. if not force: - for spec in self.spec.traverse(root=False): + for spec in self.spec.traverse(root=False, deptype='run'): if spec.package.extends(self.extendee_spec): if not spec.package.activated: spec.package.do_activate(force=force) @@ -1320,7 +1331,7 @@ class Package(object): for name, aspec in activated.items(): if aspec == self.spec: continue - for dep in aspec.traverse(): + for dep in aspec.traverse(deptype='run'): if self.spec == dep: raise ActivationError( "Cannot deactivate %s because %s is activated and depends on it." # NOQA: ignore=E501 @@ -1406,9 +1417,10 @@ class Package(object): def rpath(self): """Get the rpath this package links with, as a list of paths.""" rpaths = [self.prefix.lib, self.prefix.lib64] - rpaths.extend(d.prefix.lib for d in self.spec.traverse(root=False) + deps = self.spec.dependencies(deptype='link') + rpaths.extend(d.prefix.lib for d in deps if os.path.isdir(d.prefix.lib)) - rpaths.extend(d.prefix.lib64 for d in self.spec.traverse(root=False) + rpaths.extend(d.prefix.lib64 for d in deps if os.path.isdir(d.prefix.lib64)) return rpaths diff --git a/lib/spack/spack/platforms/linux.py b/lib/spack/spack/platforms/linux.py index 4d8adac384..4d3f59c320 100644 --- a/lib/spack/spack/platforms/linux.py +++ b/lib/spack/spack/platforms/linux.py @@ -1,16 +1,23 @@ import subprocess +import platform from spack.architecture import Platform, Target from spack.operating_systems.linux_distro import LinuxDistro class Linux(Platform): priority = 90 - front_end = 'x86_64' - back_end = 'x86_64' - default = 'x86_64' def __init__(self): super(Linux, self).__init__('linux') - self.add_target(self.default, Target(self.default)) + self.add_target('x86_64', Target('x86_64')) + self.add_target('ppc64le', Target('ppc64le')) + + self.default = platform.machine() + self.front_end = platform.machine() + self.back_end = platform.machine() + + if self.default not in self.targets: + self.add_target(self.default, Target(self.default)) + linux_dist = LinuxDistro() self.default_os = str(linux_dist) self.front_os = self.default_os diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 77bc57147d..d3a5f66e57 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -155,6 +155,9 @@ _separators = '[%s]' % ''.join(color_formats.keys()) every time we call str()""" _any_version = VersionList([':']) +alldeps = ('build', 'link', 'run') +nolink = ('build', 'run') + def index_specs(specs): """Take a list of specs and return a dict of lists. Dict is @@ -292,6 +295,27 @@ class CompilerSpec(object): @key_ordering +class DependencySpec(object): + """ + Dependencies have conditions in which they apply. + + This stores both what is depended on and why it is a dependency. + """ + def __init__(self, spec, deptypes): + self.spec = spec + self.deptypes = deptypes + + def _cmp_key(self): + return self.spec + + def copy(self): + return DependencySpec(self.spec.copy(), self.deptype) + + def __str__(self): + return str(self.spec) + + +@key_ordering class VariantSpec(object): """Variants are named, build-time options for a package. Names depend @@ -440,11 +464,11 @@ class DependencyMap(HashableMap): The DependencyMap is keyed by name. """ @property def concrete(self): - return all(d.concrete for d in self.values()) + return all(d.spec.concrete for d in self.values()) def __str__(self): return ''.join( - ["^" + str(self[name]) for name in sorted(self.keys())]) + ["^" + str(self[name].spec) for name in sorted(self.keys())]) @key_ordering @@ -472,13 +496,13 @@ class Spec(object): # writes directly into this Spec object. other = spec_list[0] self.name = other.name - self.dependents = other.dependents self.versions = other.versions self.architecture = other.architecture self.compiler = other.compiler self.compiler_flags = other.compiler_flags self.compiler_flags.spec = self - self.dependencies = other.dependencies + self._dependencies = other._dependencies + self._dependents = other._dependents self.variants = other.variants self.variants.spec = self self.namespace = other.namespace @@ -500,7 +524,49 @@ class Spec(object): # Spec(a, b) will copy a but just add b as a dep. for dep in dep_like: spec = dep if isinstance(dep, Spec) else Spec(dep) - self._add_dependency(spec) + # XXX(deptype): default deptypes + self._add_dependency(spec, ('build', 'link')) + + def get_dependency(self, name): + dep = self._dependencies.get(name) + if dep is not None: + return dep + raise InvalidDependencyException( + self.name + " does not depend on " + comma_or(name)) + + def _deptype_norm(self, deptype): + if deptype is None: + return alldeps + # Force deptype to be a set object so that we can do set intersections. + if isinstance(deptype, str): + return (deptype,) + return deptype + + def _find_deps(self, where, deptype): + deptype = self._deptype_norm(deptype) + + return [dep.spec + for dep in where.values() + if deptype and any(d in deptype for d in dep.deptypes)] + + def dependencies(self, deptype=None): + return self._find_deps(self._dependencies, deptype) + + def dependents(self, deptype=None): + return self._find_deps(self._dependents, deptype) + + def _find_deps_dict(self, where, deptype): + deptype = self._deptype_norm(deptype) + + return [(dep.spec.name, dep) + for dep in where.values() + if deptype and any(d in deptype for d in dep.deptypes)] + + def dependencies_dict(self, deptype=None): + return dict(self._find_deps_dict(self._dependencies, deptype)) + + def dependents_dict(self, deptype=None): + return dict(self._find_deps_dict(self._dependents, deptype)) # # Private routines here are called by the parser when building a spec. @@ -609,13 +675,13 @@ class Spec(object): if self.architecture.platform: self.architecture.target = self.architecture.platform.target(value) - def _add_dependency(self, spec): + def _add_dependency(self, spec, deptypes): """Called by the parser to add another spec as a dependency.""" - if spec.name in self.dependencies: + if spec.name in self._dependencies: raise DuplicateDependencyError( "Cannot depend on '%s' twice" % spec) - self.dependencies[spec.name] = spec - spec.dependents[self.name] = self + self._dependencies[spec.name] = DependencySpec(spec, deptypes) + spec._dependents[self.name] = DependencySpec(self, deptypes) # # Public interface @@ -632,15 +698,15 @@ class Spec(object): installed). This will throw an assertion error if that is not the case. """ - if not self.dependents: + if not self._dependents: return self # If the spec has multiple dependents, ensure that they all # lead to the same place. Spack shouldn't deal with any DAGs # with multiple roots, so something's wrong if we find one. - depiter = iter(self.dependents.values()) - first_root = next(depiter).root - assert(all(first_root is d.root for d in depiter)) + depiter = iter(self._dependents.values()) + first_root = next(depiter).spec.root + assert(all(first_root is d.spec.root for d in depiter)) return first_root @property @@ -687,10 +753,21 @@ class Spec(object): and self.architecture.concrete and self.compiler and self.compiler.concrete and self.compiler_flags.concrete - and self.dependencies.concrete) + and self._dependencies.concrete) return self._concrete - def traverse(self, visited=None, d=0, **kwargs): + def traverse(self, visited=None, deptype=None, **kwargs): + traversal = self.traverse_with_deptype(visited=visited, + deptype=deptype, + **kwargs) + if kwargs.get('depth', False): + return [(s[0], s[1].spec) for s in traversal] + else: + return [s.spec for s in traversal] + + def traverse_with_deptype(self, visited=None, d=0, deptype=None, + deptype_query=None, _self_deptype=None, + **kwargs): """Generic traversal of the DAG represented by this spec. This will yield each node in the spec. Options: @@ -742,6 +819,12 @@ class Spec(object): direction = kwargs.get('direction', 'children') order = kwargs.get('order', 'pre') + if deptype is None: + deptype = alldeps + + if deptype_query is None: + deptype_query = ('link', 'run') + # Make sure kwargs have legal values; raise ValueError if not. def validate(name, val, allowed_values): if val not in allowed_values: @@ -759,30 +842,37 @@ class Spec(object): if key in visited and cover == 'nodes': return - # Determine whether and what to yield for this node. + def return_val(res): + return (d, res) if depth else res + yield_me = yield_root or d > 0 - result = (d, self) if depth else self # Preorder traversal yields before successors if yield_me and order == 'pre': - yield result + yield return_val(DependencySpec(self, _self_deptype)) + + deps = self.dependencies_dict(deptype) # Edge traversal yields but skips children of visited nodes if not (key in visited and cover == 'edges'): # This code determines direction and yields the children/parents - successors = self.dependencies + successors = deps if direction == 'parents': - successors = self.dependents + successors = self.dependents_dict() visited.add(key) for name in sorted(successors): child = successors[name] - for elt in child.traverse(visited, d + 1, **kwargs): + children = child.spec.traverse_with_deptype( + visited, d=d + 1, deptype=deptype_query, + deptype_query=deptype_query, + _self_deptype=child.deptypes, **kwargs) + for elt in children: yield elt # Postorder traversal yields after successors if yield_me and order == 'post': - yield result + yield return_val(DependencySpec(self, _self_deptype)) @property def short_spec(self): @@ -807,6 +897,7 @@ class Spec(object): if self._hash: return self._hash[:length] else: + # XXX(deptype): ignore 'build' dependencies here yaml_text = yaml.dump( self.to_node_dict(), default_flow_style=True, width=sys.maxint) sha = hashlib.sha1(yaml_text) @@ -819,11 +910,13 @@ class Spec(object): params = dict((name, v.value) for name, v in self.variants.items()) params.update(dict((name, value) for name, value in self.compiler_flags.items())) + deps = self.dependencies_dict(deptype=('link', 'run')) d = { - 'parameters' : params, - 'arch' : self.architecture, - 'dependencies' : dict((d, self.dependencies[d].dag_hash()) - for d in sorted(self.dependencies)) + 'parameters': params, + 'arch': self.architecture, + 'dependencies': dict((d, (deps[d].spec.dag_hash(), + deps[d].deptypes)) + for d in sorted(deps.keys())) } # Older concrete specs do not have a namespace. Omit for @@ -848,7 +941,7 @@ class Spec(object): def to_yaml(self, stream=None): node_list = [] - for s in self.traverse(order='pre'): + for s in self.traverse(order='pre', deptype=('link', 'run')): node = s.to_node_dict() node[s.name]['hash'] = s.dag_hash() node_list.append(node) @@ -889,6 +982,11 @@ class Spec(object): raise SpackRecordError( "Did not find a valid format for variants in YAML file") + # XXX(deptypes): why are dependencies not meant to be read here? + #for name, dep_info in node['dependencies'].items(): + # (dag_hash, deptypes) = dep_info + # spec._dependencies[name] = DependencySpec(dag_hash, deptypes) + return spec @staticmethod @@ -919,8 +1017,10 @@ class Spec(object): for node in yfile['spec']: name = next(iter(node)) - for dep_name in node[name]['dependencies']: - deps[name].dependencies[dep_name] = deps[dep_name] + for dep_name, (dep, deptypes) in \ + node[name]['dependencies'].items(): + deps[name]._dependencies[dep_name] = \ + DependencySpec(deps[dep_name], deptypes) return spec def _concretize_helper(self, presets=None, visited=None): @@ -940,8 +1040,9 @@ class Spec(object): changed = False # Concretize deps first -- this is a bottom-up process. - for name in sorted(self.dependencies.keys()): - changed |= self.dependencies[name]._concretize_helper(presets, visited) + for name in sorted(self._dependencies.keys()): + changed |= self._dependencies[ + name].spec._concretize_helper(presets, visited) if self.name in presets: changed |= self.constrain(presets[self.name]) @@ -965,13 +1066,16 @@ class Spec(object): def _replace_with(self, concrete): """Replace this virtual spec with a concrete spec.""" assert(self.virtual) - for name, dependent in self.dependents.items(): + for name, dep_spec in self._dependents.items(): + dependent = dep_spec.spec + deptypes = dep_spec.deptypes + # remove self from all dependents. - del dependent.dependencies[self.name] + del dependent._dependencies[self.name] # add the replacement, unless it is already a dep of dependent. - if concrete.name not in dependent.dependencies: - dependent._add_dependency(concrete) + if concrete.name not in dependent._dependencies: + dependent._add_dependency(concrete, deptypes) def _replace_node(self, replacement): """Replace this spec with another. @@ -982,13 +1086,15 @@ class Spec(object): to be normalized. """ - for name, dependent in self.dependents.items(): - del dependent.dependencies[self.name] - dependent._add_dependency(replacement) + for name, dep_spec in self._dependents.items(): + dependent = dep_spec.spec + deptypes = dep_spec.deptypes + del dependent._dependencies[self.name] + dependent._add_dependency(replacement, deptypes) - for name, dep in self.dependencies.items(): - del dep.dependents[self.name] - del self.dependencies[dep.name] + for name, dep_spec in self._dependencies.items(): + del dep_spec.spec.dependents[self.name] + del self._dependencies[dep.name] def _expand_virtual_packages(self): """Find virtual packages in this spec, replace them with providers, @@ -1008,13 +1114,14 @@ class Spec(object): a problem. """ # Make an index of stuff this spec already provides + # XXX(deptype): 'link' and 'run'? self_index = ProviderIndex(self.traverse(), restrict=True) changed = False done = False while not done: done = True - + # XXX(deptype): 'link' and 'run'? for spec in list(self.traverse()): replacement = None if spec.virtual: @@ -1054,10 +1161,10 @@ class Spec(object): # If replacement is external then trim the dependencies if replacement.external or replacement.external_module: - if (spec.dependencies): + if (spec._dependencies): changed = True - spec.dependencies = DependencyMap() - replacement.dependencies = DependencyMap() + spec._dependencies = DependencyMap() + replacement._dependencies = DependencyMap() replacement.architecture = self.architecture # TODO: could this and the stuff in _dup be cleaned up? @@ -1068,7 +1175,7 @@ class Spec(object): feq(replacement.versions, spec.versions) and feq(replacement.compiler, spec.compiler) and feq(replacement.architecture, spec.architecture) and - feq(replacement.dependencies, spec.dependencies) and + feq(replacement._dependencies, spec._dependencies) and feq(replacement.variants, spec.variants) and feq(replacement.external, spec.external) and feq(replacement.external_module, spec.external_module)): @@ -1116,7 +1223,7 @@ class Spec(object): changed = any(changes) force = True - for s in self.traverse(): + for s in self.traverse(deptype_query=alldeps): # After concretizing, assign namespaces to anything left. # Note that this doesn't count as a "change". The repository # configuration is constant throughout a spack run, and @@ -1146,7 +1253,7 @@ class Spec(object): Only for internal use -- client code should use "concretize" unless there is a need to force a spec to be concrete. """ - for s in self.traverse(): + for s in self.traverse(deptype_query=alldeps): s._normal = True s._concrete = True @@ -1159,6 +1266,13 @@ class Spec(object): return clone def flat_dependencies(self, **kwargs): + flat_deps = DependencyMap() + flat_deps_deptypes = self.flat_dependencies_with_deptype(**kwargs) + for name, depspec in flat_deps_deptypes.items(): + flat_deps[name] = depspec.spec + return flat_deps + + def flat_dependencies_with_deptype(self, **kwargs): """Return a DependencyMap containing all of this spec's dependencies with their constraints merged. @@ -1169,23 +1283,31 @@ class Spec(object): returns them. """ copy = kwargs.get('copy', True) + deptype_query = kwargs.get('deptype_query') flat_deps = DependencyMap() try: - for spec in self.traverse(root=False): + deptree = self.traverse_with_deptype(root=False, + deptype_query=deptype_query) + for depspec in deptree: + spec = depspec.spec + deptypes = depspec.deptypes + if spec.name not in flat_deps: if copy: - flat_deps[spec.name] = spec.copy(deps=False) + dep_spec = DependencySpec(spec.copy(deps=False), + deptypes) else: - flat_deps[spec.name] = spec + dep_spec = DependencySpec(spec, deptypes) + flat_deps[spec.name] = dep_spec else: - flat_deps[spec.name].constrain(spec) + flat_deps[spec.name].spec.constrain(spec) if not copy: - for dep in flat_deps.values(): - dep.dependencies.clear() - dep.dependents.clear() - self.dependencies.clear() + for depspec in flat_deps.values(): + depspec.spec._dependencies.clear() + depspec.spec._dependents.clear() + self._dependencies.clear() return flat_deps @@ -1200,17 +1322,11 @@ class Spec(object): """Return DependencyMap that points to all the dependencies in this spec.""" dm = DependencyMap() + # XXX(deptype): use a deptype kwarg. for spec in self.traverse(): dm[spec.name] = spec return dm - def flatten(self): - """Pull all dependencies up to the root (this spec). - Merge constraints for dependencies with the same name, and if they - conflict, throw an exception. """ - for dep in self.flat_dependencies(copy=False): - self._add_dependency(dep) - def _evaluate_dependency_conditions(self, name): """Evaluate all the conditions on a dependency with this name. @@ -1267,7 +1383,8 @@ class Spec(object): elif required: raise UnsatisfiableProviderSpecError(required[0], vdep) - def _merge_dependency(self, dep, visited, spec_deps, provider_index): + def _merge_dependency(self, dep, deptypes, visited, spec_deps, + provider_index): """Merge the dependency into this spec. This is the core of normalize(). There are some basic steps: @@ -1294,7 +1411,9 @@ class Spec(object): dep = provider else: index = ProviderIndex([dep], restrict=True) - for vspec in (v for v in spec_deps.values() if v.virtual): + for vspec in (v.spec + for v in spec_deps.values() + if v.spec.virtual): if index.providers_for(vspec): vspec._replace_with(dep) del spec_deps[vspec.name] @@ -1307,25 +1426,25 @@ class Spec(object): # If the spec isn't already in the set of dependencies, clone # it from the package description. if dep.name not in spec_deps: - spec_deps[dep.name] = dep.copy() + spec_deps[dep.name] = DependencySpec(dep.copy(), deptypes) changed = True # Constrain package information with spec info try: - changed |= spec_deps[dep.name].constrain(dep) + changed |= spec_deps[dep.name].spec.constrain(dep) except UnsatisfiableSpecError, e: e.message = "Invalid spec: '%s'. " e.message += "Package %s requires %s %s, but spec asked for %s" - e.message %= (spec_deps[dep.name], dep.name, e.constraint_type, - e.required, e.provided) + e.message %= (spec_deps[dep.name].spec, dep.name, + e.constraint_type, e.required, e.provided) raise e # Add merged spec to my deps and recurse dependency = spec_deps[dep.name] - if dep.name not in self.dependencies: - self._add_dependency(dependency) + if dep.name not in self._dependencies: + self._add_dependency(dependency.spec, dependency.deptypes) - changed |= dependency._normalize_helper( + changed |= dependency.spec._normalize_helper( visited, spec_deps, provider_index) return changed @@ -1351,10 +1470,11 @@ class Spec(object): for dep_name in pkg.dependencies: # Do we depend on dep_name? If so pkg_dep is not None. pkg_dep = self._evaluate_dependency_conditions(dep_name) + deptypes = pkg._deptypes[dep_name] # If pkg_dep is a dependency, merge it. if pkg_dep: changed |= self._merge_dependency( - pkg_dep, visited, spec_deps, provider_index) + pkg_dep, deptypes, visited, spec_deps, provider_index) any_change |= changed return any_change @@ -1385,11 +1505,13 @@ class Spec(object): # Ensure first that all packages & compilers in the DAG exist. self.validate_names() # Get all the dependencies into one DependencyMap - spec_deps = self.flat_dependencies(copy=False) + spec_deps = self.flat_dependencies_with_deptype(copy=False, + deptype_query=alldeps) # Initialize index of virtual dependency providers if # concretize didn't pass us one already - provider_index = ProviderIndex(spec_deps.values(), restrict=True) + provider_index = ProviderIndex([s.spec for s in spec_deps.values()], + restrict=True) # traverse the package DAG and fill out dependencies according # to package files & their 'when' specs @@ -1510,7 +1632,7 @@ class Spec(object): """Apply constraints of other spec's dependencies to this spec.""" other = self._autospec(other) - if not self.dependencies or not other.dependencies: + if not self._dependencies or not other._dependencies: return False # TODO: might want more detail than this, e.g. specific deps @@ -1526,13 +1648,17 @@ class Spec(object): # Update with additional constraints from other spec for name in other.dep_difference(self): - self._add_dependency(other[name].copy()) + dep_spec_copy = other.get_dependency(name) + dep_copy = dep_spec_copy.spec + deptypes = dep_spec_copy.deptypes + self._add_dependency(dep_copy.copy(), deptypes) changed = True return changed def common_dependencies(self, other): """Return names of dependencies that self an other have in common.""" + # XXX(deptype): handle deptypes via deptype kwarg. common = set( s.name for s in self.traverse(root=False)) common.intersection_update( @@ -1657,13 +1783,14 @@ class Spec(object): other = self._autospec(other) if strict: - if other.dependencies and not self.dependencies: + if other._dependencies and not self._dependencies: return False - if not all(dep in self.dependencies for dep in other.dependencies): + if not all(dep in self._dependencies + for dep in other._dependencies): return False - elif not self.dependencies or not other.dependencies: + elif not self._dependencies or not other._dependencies: # if either spec doesn't restrict dependencies then both are # compatible. return True @@ -1726,8 +1853,8 @@ class Spec(object): self.architecture = other.architecture self.compiler = other.compiler.copy() if other.compiler else None if kwargs.get('cleardeps', True): - self.dependents = DependencyMap() - self.dependencies = DependencyMap() + self._dependents = DependencyMap() + self._dependencies = DependencyMap() self.compiler_flags = other.compiler_flags.copy() self.variants = other.variants.copy() self.variants.spec = self @@ -1739,15 +1866,30 @@ class Spec(object): # If we copy dependencies, preserve DAG structure in the new spec if kwargs.get('deps', True): # This copies the deps from other using _dup(deps=False) - new_nodes = other.flat_dependencies() + # XXX(deptype): We can keep different instances of specs here iff + # it is only a 'build' dependency (from its parent). + # All other instances must be shared (due to symbol + # and PATH contention). These should probably search + # for any existing installation which can satisfy the + # build and latch onto that because if 3 things need + # the same build dependency and it is *not* + # available, we only want to build it once. + new_nodes = other.flat_dependencies(deptype_query=alldeps) new_nodes[self.name] = self - # Hook everything up properly here by traversing. - for spec in other.traverse(cover='nodes'): - parent = new_nodes[spec.name] - for child in spec.dependencies: - if child not in parent.dependencies: - parent._add_dependency(new_nodes[child]) + stack = [other] + while stack: + cur_spec = stack.pop(0) + new_spec = new_nodes[cur_spec.name] + + for depspec in cur_spec._dependencies.values(): + stack.append(depspec.spec) + + # XXX(deptype): add any new deptypes that may have appeared + # here. + if depspec.spec.name not in new_spec._dependencies: + new_spec._add_dependency( + new_nodes[depspec.spec.name], depspec.deptypes) # Since we preserved structure, we can copy _normal safely. self._normal = other._normal @@ -1790,7 +1932,7 @@ class Spec(object): raise KeyError("No spec with name %s in %s" % (name, self)) def __contains__(self, spec): - """True if this spec satisfis the provided spec, or if any dependency + """True if this spec satisfies the provided spec, or if any dependency does. If the spec has no name, then we parse this one first. """ spec = self._autospec(spec) @@ -1814,13 +1956,13 @@ class Spec(object): if self.ne_node(other): return False - if len(self.dependencies) != len(other.dependencies): + if len(self._dependencies) != len(other._dependencies): return False - ssorted = [self.dependencies[name] - for name in sorted(self.dependencies)] - osorted = [other.dependencies[name] - for name in sorted(other.dependencies)] + ssorted = [self._dependencies[name].spec + for name in sorted(self._dependencies)] + osorted = [other._dependencies[name].spec + for name in sorted(other._dependencies)] for s, o in zip(ssorted, osorted): visited_s = id(s) in vs @@ -1874,9 +2016,10 @@ class Spec(object): 1. A tuple describing this node in the DAG. 2. The hash of each of this node's dependencies' cmp_keys. """ + dep_dict = self.dependencies_dict(deptype=('link', 'run')) return self._cmp_node() + ( - tuple(hash(self.dependencies[name]) - for name in sorted(self.dependencies)),) + tuple(hash(dep_dict[name]) + for name in sorted(dep_dict)),) def colorized(self): return colorize_spec(self) @@ -2081,8 +2224,8 @@ class Spec(object): self.architecture, other.architecture) #Dependency is not configurable - if self.dependencies != other.dependencies: - return -1 if self.dependencies < other.dependencies else 1 + if self._dependencies != other._dependencies: + return -1 if self._dependencies < other._dependencies else 1 #Equal specs return 0 @@ -2196,10 +2339,13 @@ class SpecParser(spack.parse.Parser): specs.append(self.spec(None)) self.previous = None if self.accept(HASH): - specs[-1]._add_dependency(self.spec_by_hash()) + dep = self.spec_by_hash() else: self.expect(ID) - specs[-1]._add_dependency(self.spec(self.token.value)) + dep = self.spec(self.token.value) + # XXX(deptype): default deptypes + def_deptypes = ('build', 'link') + specs[-1]._add_dependency(dep, def_deptypes) else: # Attempt to construct an anonymous spec, but check that @@ -2263,8 +2409,8 @@ class SpecParser(spack.parse.Parser): spec.external = None spec.external_module = None spec.compiler_flags = FlagMap(spec) - spec.dependents = DependencyMap() - spec.dependencies = DependencyMap() + spec._dependents = DependencyMap() + spec._dependencies = DependencyMap() spec.namespace = spec_namespace spec._hash = None diff --git a/lib/spack/spack/test/cmd/test_install.py b/lib/spack/spack/test/cmd/test_install.py index d17e013ed2..a94d3c8bba 100644 --- a/lib/spack/spack/test/cmd/test_install.py +++ b/lib/spack/spack/test/cmd/test_install.py @@ -58,16 +58,39 @@ test_install = __import__("spack.cmd.test-install", fromlist=['test_install']) class MockSpec(object): def __init__(self, name, version, hashStr=None): - self.dependencies = {} + self._dependencies = {} self.name = name self.version = version self.hash = hashStr if hashStr else hash((name, version)) + def _deptype_norm(self, deptype): + if deptype is None: + return spack.alldeps + # Force deptype to be a tuple so that we can do set intersections. + if isinstance(deptype, str): + return (deptype,) + return deptype + + def _find_deps(self, where, deptype): + deptype = self._deptype_norm(deptype) + + return [dep.spec + for dep in where.values() + if deptype and any(d in deptype for d in dep.deptypes)] + + def dependencies(self, deptype=None): + return self._find_deps(self._dependencies, deptype) + + def dependents(self, deptype=None): + return self._find_deps(self._dependents, deptype) + def traverse(self, order=None): - for _, spec in self.dependencies.items(): - yield spec + for _, spec in self._dependencies.items(): + yield spec.spec yield self - #allDeps = itertools.chain.from_iterable(i.traverse() for i in self.dependencies.itervalues()) + #from_iterable = itertools.chain.from_iterable + #allDeps = from_iterable(i.traverse() + # for i in self.dependencies()) #return set(itertools.chain([self], allDeps)) def dag_hash(self): @@ -104,7 +127,7 @@ def mock_fetch_log(path): specX = MockSpec('X', "1.2.0") specY = MockSpec('Y', "2.3.8") -specX.dependencies['Y'] = specY +specX._dependencies['Y'] = spack.DependencySpec(specY, spack.alldeps) pkgX = MockPackage(specX, 'logX') pkgY = MockPackage(specY, 'logY') diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index ce02b08bc3..ae3ceecfc8 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -197,32 +197,36 @@ class ConcretizeTest(MockPackagesTest): def test_virtual_is_fully_expanded_for_callpath(self): # force dependence on fake "zmpi" by asking for MPI 10.0 spec = Spec('callpath ^mpi@10.0') - self.assertTrue('mpi' in spec.dependencies) + self.assertTrue('mpi' in spec._dependencies) self.assertFalse('fake' in spec) spec.concretize() - self.assertTrue('zmpi' in spec.dependencies) - self.assertTrue(all(not 'mpi' in d.dependencies for d in spec.traverse())) + self.assertTrue('zmpi' in spec._dependencies) + self.assertTrue(all('mpi' not in d._dependencies + for d in spec.traverse())) self.assertTrue('zmpi' in spec) self.assertTrue('mpi' in spec) - self.assertTrue('fake' in spec.dependencies['zmpi']) + self.assertTrue('fake' in spec._dependencies['zmpi'].spec) def test_virtual_is_fully_expanded_for_mpileaks(self): spec = Spec('mpileaks ^mpi@10.0') - self.assertTrue('mpi' in spec.dependencies) + self.assertTrue('mpi' in spec._dependencies) self.assertFalse('fake' in spec) spec.concretize() - self.assertTrue('zmpi' in spec.dependencies) - self.assertTrue('callpath' in spec.dependencies) - self.assertTrue('zmpi' in spec.dependencies['callpath'].dependencies) - self.assertTrue('fake' in spec.dependencies['callpath'].dependencies['zmpi'].dependencies) + self.assertTrue('zmpi' in spec._dependencies) + self.assertTrue('callpath' in spec._dependencies) + self.assertTrue('zmpi' in spec._dependencies['callpath']. + spec._dependencies) + self.assertTrue('fake' in spec._dependencies['callpath']. + spec._dependencies['zmpi']. + spec._dependencies) - self.assertTrue(all(not 'mpi' in d.dependencies for d in spec.traverse())) + self.assertTrue(all(not 'mpi' in d._dependencies for d in spec.traverse())) self.assertTrue('zmpi' in spec) self.assertTrue('mpi' in spec) diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py index e1acc32cb7..9d96622a6e 100644 --- a/lib/spack/spack/test/mock_packages_test.py +++ b/lib/spack/spack/test/mock_packages_test.py @@ -84,15 +84,6 @@ compilers: modules: 'None' - compiler: spec: clang@3.3 - operating_system: redhat6 - paths: - cc: /path/to/clang - cxx: /path/to/clang++ - f77: None - fc: None - modules: 'None' -- compiler: - spec: clang@3.3 operating_system: yosemite paths: cc: /path/to/clang @@ -124,15 +115,6 @@ compilers: cxx: /path/to/g++ f77: /path/to/gfortran fc: /path/to/gfortran - operating_system: redhat6 - spec: gcc@4.5.0 - modules: 'None' -- compiler: - paths: - cc: /path/to/gcc - cxx: /path/to/g++ - f77: /path/to/gfortran - fc: /path/to/gfortran operating_system: yosemite spec: gcc@4.5.0 modules: 'None' @@ -209,8 +191,7 @@ class MockPackagesTest(unittest.TestCase): # restore later. self.saved_deps = {} - - def set_pkg_dep(self, pkg_name, spec): + def set_pkg_dep(self, pkg_name, spec, deptypes=spack.alldeps): """Alters dependence information for a package. Adds a dependency on <spec> to pkg. @@ -224,7 +205,9 @@ class MockPackagesTest(unittest.TestCase): self.saved_deps[pkg_name] = (pkg, pkg.dependencies.copy()) # Change dep spec - pkg.dependencies[spec.name] = { Spec(pkg_name) : spec } + # XXX(deptype): handle deptypes. + pkg.dependencies[spec.name] = {Spec(pkg_name): spec} + pkg._deptypes[spec.name] = set(deptypes) def cleanmock(self): @@ -234,6 +217,7 @@ class MockPackagesTest(unittest.TestCase): shutil.rmtree(self.temp_config, ignore_errors=True) spack.config.clear_config_caches() + # XXX(deptype): handle deptypes. # Restore dependency changes that happened during the test for pkg_name, (pkg, deps) in self.saved_deps.items(): pkg.dependencies.clear() diff --git a/lib/spack/spack/test/mock_repo.py b/lib/spack/spack/test/mock_repo.py index a8098b8eec..386af282e7 100644 --- a/lib/spack/spack/test/mock_repo.py +++ b/lib/spack/spack/test/mock_repo.py @@ -103,6 +103,8 @@ class MockGitRepo(MockVCSRepo): def __init__(self): super(MockGitRepo, self).__init__('mock-git-stage', 'mock-git-repo') + self.url = 'file://' + self.path + with working_dir(self.path): git('init') @@ -140,8 +142,6 @@ class MockGitRepo(MockVCSRepo): self.r1 = self.rev_hash(self.branch) self.r1_file = self.branch_file - self.url = self.path - def rev_hash(self, rev): return git('rev-parse', rev, output=str).strip() diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py index c56c70b1fe..972e79aa20 100644 --- a/lib/spack/spack/test/spec_dag.py +++ b/lib/spack/spack/test/spec_dag.py @@ -148,10 +148,12 @@ class SpecDagTest(MockPackagesTest): # Normalize then add conflicting constraints to the DAG (this is an # extremely unlikely scenario, but we test for it anyway) mpileaks.normalize() - mpileaks.dependencies['mpich'] = Spec('mpich@1.0') - mpileaks.dependencies['callpath'].dependencies['mpich'] = Spec('mpich@2.0') + mpileaks._dependencies['mpich'].spec = Spec('mpich@1.0') + mpileaks._dependencies['callpath']. \ + spec._dependencies['mpich'].spec = Spec('mpich@2.0') - self.assertRaises(spack.spec.InconsistentSpecError, mpileaks.flatten) + self.assertRaises(spack.spec.InconsistentSpecError, + lambda: mpileaks.flat_dependencies(copy=False)) def test_normalize_twice(self): @@ -197,15 +199,17 @@ class SpecDagTest(MockPackagesTest): def check_links(self, spec_to_check): for spec in spec_to_check.traverse(): - for dependent in spec.dependents.values(): + for dependent in spec.dependents(): self.assertTrue( - spec.name in dependent.dependencies, - "%s not in dependencies of %s" % (spec.name, dependent.name)) + spec.name in dependent.dependencies_dict(), + "%s not in dependencies of %s" % + (spec.name, dependent.name)) - for dependency in spec.dependencies.values(): + for dependency in spec.dependencies(): self.assertTrue( - spec.name in dependency.dependents, - "%s not in dependents of %s" % (spec.name, dependency.name)) + spec.name in dependency.dependents_dict(), + "%s not in dependents of %s" % + (spec.name, dependency.name)) def test_dependents_and_dependencies_are_correct(self): @@ -442,3 +446,69 @@ class SpecDagTest(MockPackagesTest): orig_ids = set(id(s) for s in orig.traverse()) copy_ids = set(id(s) for s in copy.traverse()) self.assertFalse(orig_ids.intersection(copy_ids)) + + """ + Here is the graph with deptypes labeled (assume all packages have a 'dt' + prefix). Arrows are marked with the deptypes ('b' for 'build', 'l' for + 'link', 'r' for 'run'). + + use -bl-> top + + top -b-> build1 + top -bl-> link1 + top -r-> run1 + + build1 -b-> build2 + build1 -bl-> link2 + build1 -r-> run2 + + link1 -bl-> link3 + + run1 -bl-> link5 + run1 -r-> run3 + + link3 -b-> build2 + link3 -bl-> link4 + + run3 -b-> build3 + """ + def test_deptype_traversal(self): + dag = Spec('dtuse') + dag.normalize() + + names = ['dtuse', 'dttop', 'dtlink1', 'dtlink3', 'dtlink4', + 'dtrun1', 'dtlink5', 'dtrun3'] + + traversal = dag.traverse() + self.assertEqual([x.name for x in traversal], names) + + def test_deptype_traversal_with_builddeps(self): + dag = Spec('dttop') + dag.normalize() + + names = ['dttop', 'dtbuild1', 'dtlink2', 'dtrun2', 'dtlink1', + 'dtlink3', 'dtlink4', 'dtrun1', 'dtlink5', 'dtrun3'] + + traversal = dag.traverse() + self.assertEqual([x.name for x in traversal], names) + + def test_deptype_traversal_full(self): + dag = Spec('dttop') + dag.normalize() + + names = ['dttop', 'dtbuild1', 'dtbuild2', 'dtlink2', 'dtrun2', + 'dtlink1', 'dtlink3', 'dtlink4', 'dtrun1', 'dtlink5', + 'dtrun3', 'dtbuild3'] + + traversal = dag.traverse(deptype_query=spack.alldeps) + self.assertEqual([x.name for x in traversal], names) + + def test_deptype_traversal_pythonpath(self): + dag = Spec('dttop') + dag.normalize() + + names = ['dttop', 'dtbuild1', 'dtrun2', 'dtlink1', 'dtrun1', + 'dtrun3'] + + traversal = dag.traverse(deptype=spack.nolink, deptype_query='run') + self.assertEqual([x.name for x in traversal], names) diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py index 6d8c3ac67c..d3e3bf1383 100644 --- a/lib/spack/spack/test/stage.py +++ b/lib/spack/spack/test/stage.py @@ -35,8 +35,8 @@ from llnl.util.filesystem import * from spack.stage import Stage from spack.util.executable import which -test_files_dir = join_path(spack.stage_path, '.test') -test_tmp_path = join_path(test_files_dir, 'tmp') +test_files_dir = os.path.realpath(join_path(spack.stage_path, '.test')) +test_tmp_path = os.path.realpath(join_path(test_files_dir, 'tmp')) archive_dir = 'test-files' archive_name = archive_dir + '.tar.gz' diff --git a/lib/spack/spack/test/versions.py b/lib/spack/spack/test/versions.py index 4624f901c8..41d72e7c34 100644 --- a/lib/spack/spack/test/versions.py +++ b/lib/spack/spack/test/versions.py @@ -92,6 +92,9 @@ class VersionsTest(unittest.TestCase): self.assert_ver_eq('1.0', '1.0') self.assert_ver_lt('1.0', '2.0') self.assert_ver_gt('2.0', '1.0') + self.assert_ver_eq('develop', 'develop') + self.assert_ver_lt('1.0', 'develop') + self.assert_ver_gt('develop', '1.0') def test_three_segments(self): self.assert_ver_eq('2.0.1', '2.0.1') @@ -389,3 +392,39 @@ class VersionsTest(unittest.TestCase): self.assertEqual(v.dotted, '1.2.3') self.assertEqual(v.dashed, '1-2-3') self.assertEqual(v.underscored, '1_2_3') + + def test_repr_and_str(self): + + def check_repr_and_str(vrs): + a = Version(vrs) + self.assertEqual(repr(a), 'Version(\'' + vrs + '\')') + b = eval(repr(a)) + self.assertEqual(a, b) + self.assertEqual(str(a), vrs) + self.assertEqual(str(a), str(b)) + + check_repr_and_str('1.2.3') + check_repr_and_str('R2016a') + check_repr_and_str('R2016a.2-3_4') + + def test_get_item(self): + a = Version('0.1_2-3') + self.assertTrue(isinstance(a[1], int)) + # Test slicing + b = a[0:2] + self.assertTrue(isinstance(b, Version)) + self.assertEqual(b, Version('0.1')) + self.assertEqual(repr(b), 'Version(\'0.1\')') + self.assertEqual(str(b), '0.1') + b = a[0:3] + self.assertTrue(isinstance(b, Version)) + self.assertEqual(b, Version('0.1_2')) + self.assertEqual(repr(b), 'Version(\'0.1_2\')') + self.assertEqual(str(b), '0.1_2') + b = a[1:] + self.assertTrue(isinstance(b, Version)) + self.assertEqual(b, Version('1_2-3')) + self.assertEqual(repr(b), 'Version(\'1_2-3\')') + self.assertEqual(str(b), '1_2-3') + # Raise TypeError on tuples + self.assertRaises(TypeError, b.__getitem__, 1, 2) diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py index 858d581472..6f6c83b3d8 100644 --- a/lib/spack/spack/version.py +++ b/lib/spack/spack/version.py @@ -44,6 +44,7 @@ be called on any of the types:: concrete """ import re +import numbers from bisect import bisect_left from functools import wraps @@ -194,10 +195,24 @@ class Version(object): return iter(self.version) def __getitem__(self, idx): - return tuple(self.version[idx]) + cls = type(self) + if isinstance(idx, numbers.Integral): + return self.version[idx] + elif isinstance(idx, slice): + # Currently len(self.separators) == len(self.version) - 1 + extendend_separators = self.separators + ('',) + string_arg = [] + for token, sep in zip(self.version, extendend_separators)[idx]: + string_arg.append(str(token)) + string_arg.append(str(sep)) + string_arg.pop() # We don't need the last separator + string_arg = ''.join(string_arg) + return cls(string_arg) + message = '{cls.__name__} indices must be integers' + raise TypeError(message.format(cls=cls)) def __repr__(self): - return self.string + return 'Version(' + repr(self.string) + ')' def __str__(self): return self.string @@ -221,6 +236,14 @@ class Version(object): if self.version == other.version: return False + # dev is __gt__ than anything but itself. + if other.string == 'develop': + return True + + # If lhs is dev then it can't be < than anything + if self.string == 'develop': + return False + for a, b in zip(self.version, other.version): if a == b: continue diff --git a/share/spack/qa/run-flake8 b/share/spack/qa/run-flake8 index 57534eb6e2..595df417ec 100755 --- a/share/spack/qa/run-flake8 +++ b/share/spack/qa/run-flake8 @@ -18,7 +18,7 @@ if [[ ! $flake8 ]]; then fi # Check if changed files are flake8 conformant [framework] -changed=$(git diff --name-only develop... | grep '.py$') +changed=$(git diff --name-only --find-renames develop... | grep '.py$') # Add approved style exemptions to the changed packages. for file in $changed; do @@ -26,6 +26,7 @@ for file in $changed; do cp "$file" "$file~" # Exempt lines with urls and descriptions from overlong line errors. + perl -i -pe 's/^(\s*homepage\s*=.*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*url\s*=.*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*version\(.*\).*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*variant\(.*\).*)$/\1 # NOQA: ignore=E501/' $file diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py index 355689a2d2..c58430317a 100644 --- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py @@ -38,7 +38,7 @@ class CmakeClient(Package): version('1.0', '4cb3ff35b2472aae70f542116d616e63') - depends_on('cmake') + depends_on('cmake', type='build') def setup_environment(self, spack_env, run_env): diff --git a/var/spack/repos/builtin.mock/packages/dtbuild1/package.py b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py new file mode 100644 index 0000000000..7429b2a8ef --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py @@ -0,0 +1,18 @@ +from spack import * + + +class Dtbuild1(Package): + """Package for use as a build tool for deptypes testing which has its own + deptree""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtbuild1-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtbuild2', type='build') + depends_on('dtlink2') + depends_on('dtrun2', type='run') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtbuild2/package.py b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py new file mode 100644 index 0000000000..cf3bb82a10 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtbuild2(Package): + """Simple package which acts as a build dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtbuild2-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtbuild3/package.py b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py new file mode 100644 index 0000000000..6ba7e69a41 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtbuild3(Package): + """Simple package which acts as a build dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtbuild3-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink1/package.py b/var/spack/repos/builtin.mock/packages/dtlink1/package.py new file mode 100644 index 0000000000..2747dcf354 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink1/package.py @@ -0,0 +1,15 @@ +from spack import * + + +class Dtlink1(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink1-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtlink3') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink2/package.py b/var/spack/repos/builtin.mock/packages/dtlink2/package.py new file mode 100644 index 0000000000..b80bad053f --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink2/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtlink2(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink2-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink3/package.py b/var/spack/repos/builtin.mock/packages/dtlink3/package.py new file mode 100644 index 0000000000..bee8b4b8f8 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink3/package.py @@ -0,0 +1,16 @@ +from spack import * + + +class Dtlink3(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink3-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtbuild2', type='build') + depends_on('dtlink4') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink4/package.py b/var/spack/repos/builtin.mock/packages/dtlink4/package.py new file mode 100644 index 0000000000..3f05d5c0d6 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink4/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtlink4(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink4-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtlink5/package.py b/var/spack/repos/builtin.mock/packages/dtlink5/package.py new file mode 100644 index 0000000000..c8b1e97d37 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtlink5/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtlink5(Package): + """Simple package which acts as a link dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtlink5-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtrun1/package.py b/var/spack/repos/builtin.mock/packages/dtrun1/package.py new file mode 100644 index 0000000000..fb33b9b2f2 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtrun1/package.py @@ -0,0 +1,16 @@ +from spack import * + + +class Dtrun1(Package): + """Simple package which acts as a run dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtrun1-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtlink5') + depends_on('dtrun3', type='run') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtrun2/package.py b/var/spack/repos/builtin.mock/packages/dtrun2/package.py new file mode 100644 index 0000000000..e5d4b5e0b4 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtrun2/package.py @@ -0,0 +1,13 @@ +from spack import * + + +class Dtrun2(Package): + """Simple package which acts as a run dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtrun2-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtrun3/package.py b/var/spack/repos/builtin.mock/packages/dtrun3/package.py new file mode 100644 index 0000000000..70dacf45ff --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtrun3/package.py @@ -0,0 +1,15 @@ +from spack import * + + +class Dtrun3(Package): + """Simple package which acts as a run dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtrun3-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtbuild3', type='build') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dttop/package.py b/var/spack/repos/builtin.mock/packages/dttop/package.py new file mode 100644 index 0000000000..202a3b6883 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dttop/package.py @@ -0,0 +1,17 @@ +from spack import * + + +class Dttop(Package): + """Package with a complicated dependency tree""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dttop-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dtbuild1', type='build') + depends_on('dtlink1') + depends_on('dtrun1', type='run') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/dtuse/package.py b/var/spack/repos/builtin.mock/packages/dtuse/package.py new file mode 100644 index 0000000000..bd7391cee8 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/dtuse/package.py @@ -0,0 +1,15 @@ +from spack import * + + +class Dtuse(Package): + """Simple package which uses dttop""" + + homepage = "http://www.example.com" + url = "http://www.example.com/dtuse-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('dttop') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin/packages/ImageMagick/package.py b/var/spack/repos/builtin/packages/ImageMagick/package.py index f8173169e1..b0ccba1009 100644 --- a/var/spack/repos/builtin/packages/ImageMagick/package.py +++ b/var/spack/repos/builtin/packages/ImageMagick/package.py @@ -51,7 +51,7 @@ class Imagemagick(Package): url="http://sourceforge.net/projects/imagemagick/files/old-sources/6.x/6.8/ImageMagick-6.8.9-10.tar.gz/download") depends_on('jpeg') - depends_on('libtool') + depends_on('libtool', type='build') depends_on('libpng') depends_on('freetype') depends_on('fontconfig') diff --git a/var/spack/repos/builtin/packages/Mitos/package.py b/var/spack/repos/builtin/packages/Mitos/package.py index 83aca3dc6a..d577a1b285 100644 --- a/var/spack/repos/builtin/packages/Mitos/package.py +++ b/var/spack/repos/builtin/packages/Mitos/package.py @@ -41,6 +41,7 @@ class Mitos(Package): depends_on('dyninst@8.2.1:') depends_on('hwloc') depends_on('mpi') + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 001dde5329..11c5909efa 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -40,6 +40,7 @@ class R(Package): extendable = True + version('3.3.1', 'f50a659738b73036e2f5635adbd229c5') version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') version('3.2.3', '1ba3dac113efab69e706902810cc2970') version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') @@ -87,6 +88,29 @@ class R(Package): make() make('install') + self.filter_compilers(spec, prefix) + + def filter_compilers(self, spec, prefix): + """Run after install to tell the configuration files and Makefiles + to use the compilers that Spack built the package with. + + If this isn't done, they'll have CC and CXX set to Spack's generic + cc and c++. We want them to be bound to whatever compiler + they were built with.""" + + etcdir = join_path(prefix, 'rlib', 'R', 'etc') + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + + filter_file(env['CC'], self.compiler.cc, + join_path(etcdir, 'Makeconf'), **kwargs) + filter_file(env['CXX'], self.compiler.cxx, + join_path(etcdir, 'Makeconf'), **kwargs) + filter_file(env['F77'], self.compiler.f77, + join_path(etcdir, 'Makeconf'), **kwargs) + filter_file(env['FC'], self.compiler.fc, + join_path(etcdir, 'Makeconf'), **kwargs) + # ======================================================================== # Set up environment to make install easy for R extensions. # ======================================================================== @@ -99,7 +123,7 @@ class R(Package): # Set R_LIBS to include the library dir for the # extension and any other R extensions it depends on. r_libs_path = [] - for d in extension_spec.traverse(): + for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): if d.package.extends(self.spec): r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir)) diff --git a/var/spack/repos/builtin/packages/adept-utils/package.py b/var/spack/repos/builtin/packages/adept-utils/package.py index 7b6c3702af..592681bb82 100644 --- a/var/spack/repos/builtin/packages/adept-utils/package.py +++ b/var/spack/repos/builtin/packages/adept-utils/package.py @@ -35,6 +35,7 @@ class AdeptUtils(Package): depends_on("boost") depends_on("mpi") + depends_on('cmake', type='build') def install(self, spec, prefix): cmake(*std_cmake_args) diff --git a/var/spack/repos/builtin/packages/apex/package.py b/var/spack/repos/builtin/packages/apex/package.py index 20cbd8e8c6..59fbe50c93 100644 --- a/var/spack/repos/builtin/packages/apex/package.py +++ b/var/spack/repos/builtin/packages/apex/package.py @@ -33,7 +33,7 @@ class Apex(Package): depends_on("binutils+libiberty") depends_on("boost@1.54:") - depends_on("cmake@2.8.12:") + depends_on('cmake@2.8.12:', type='build') depends_on("activeharmony@4.5:") depends_on("ompt-openmp") diff --git a/var/spack/repos/builtin/packages/arpack-ng/make_install.patch b/var/spack/repos/builtin/packages/arpack-ng/make_install.patch new file mode 100644 index 0000000000..ad5cffcc19 --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/make_install.patch @@ -0,0 +1,24 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 607d221..50426c3 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -389,3 +389,19 @@ target_link_libraries(bug_1323 arpack ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) + add_test(bug_1323 Tests/bug_1323) + + add_dependencies(check dnsimp_test bug_1315_single bug_1315_double bug_1323) ++ ++############################ ++# install ++############################ ++# 'make install' to the correct location ++install(TARGETS arpack ++ ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib ++ RUNTIME DESTINATION bin) ++ ++if (MPI) ++ install(TARGETS parpack ++ ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib ++ RUNTIME DESTINATION bin) ++endif () diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index fcd5171a7d..d5dc703c06 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -27,7 +27,8 @@ from spack import * class ArpackNg(Package): """ - ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. + ARPACK-NG is a collection of Fortran77 subroutines designed to solve large + scale eigenvalue problems. Important Features: @@ -38,43 +39,76 @@ class ArpackNg(Package): Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. - * Example driver routines that may be used as templates to implement numerous - Shift-Invert strategies for all problem types, data types and precision. + * Example driver routines that may be used as templates to implement + numerous Shift-Invert strategies for all problem types, data types and + precision. - This project is a joint project between Debian, Octave and Scilab in order to - provide a common and maintained version of arpack. + This project is a joint project between Debian, Octave and Scilab in order + to provide a common and maintained version of arpack. - Indeed, no single release has been published by Rice university for the last - few years and since many software (Octave, Scilab, R, Matlab...) forked it and - implemented their own modifications, arpack-ng aims to tackle this by providing - a common repository and maintained versions. + Indeed, no single release has been published by Rice university for the + last few years and since many software (Octave, Scilab, R, Matlab...) + forked it and implemented their own modifications, arpack-ng aims to tackle + this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere. """ homepage = 'https://github.com/opencollab/arpack-ng' url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz' + version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4') version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5') variant('shared', default=True, description='Enables the build of shared libraries') variant('mpi', default=False, description='Activates MPI support') - # The function pdlamch10 does not set the return variable. This is fixed upstream + # The function pdlamch10 does not set the return variable. + # This is fixed upstream # see https://github.com/opencollab/arpack-ng/issues/34 - patch('pdlamch10.patch', when='@3.3:') + patch('pdlamch10.patch', when='@3.3.0') + + patch('make_install.patch', when='@3.4.0') + patch('parpack_cmake.patch', when='@3.4.0') depends_on('blas') depends_on('lapack') - depends_on('automake') - depends_on('autoconf') - depends_on('libtool@2.4.2:') + depends_on('automake', when='@3.3.0', type='build') + depends_on('autoconf', when='@3.3.0', type='build') + depends_on('libtool@2.4.2:', when='@3.3.0', type='build') + depends_on('cmake@2.8.6:', when='@3.4.0:', type='build') depends_on('mpi', when='+mpi') + @when('@3.4.0:') + def install(self, spec, prefix): + + options = ['-DEXAMPLES=ON'] + options.extend(std_cmake_args) + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) + + # TODO: + # Arpack calls directly find_package(BLAS REQUIRED) and + # find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are + # picked up. + + if '+mpi' in spec: + options.append('-DMPI=ON') + + # TODO: -DINTERFACE64=ON + + if '+shared' in spec: + options.append('-DBUILD_SHARED_LIBS=ON') + + cmake('.', *options) + make() + # TODO: make test does not work + # make('test') + + make('install') + + @when('@3.3.0') def install(self, spec, prefix): # Apparently autotools are not bootstrapped - # TODO: switch to use the CMake build in the next version - # rather than bootstrapping. which('libtoolize')() bootstrap = Executable('./bootstrap') @@ -83,7 +117,7 @@ class ArpackNg(Package): if '+mpi' in spec: options.extend([ '--enable-mpi', - 'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names + 'F77=%s' % spec['mpi'].mpif77 ]) if '~shared' in spec: diff --git a/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch new file mode 100644 index 0000000000..9b11bea6ac --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch @@ -0,0 +1,18 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 607d221..345b7fc 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -113,11 +113,12 @@ set_target_properties(arpack PROPERTIES OUTPUT_NAME arpack${LIBSUFFIX}) + + if (MPI) + # add_library(parpack SHARED +- add_library(parpack ++ add_library(parpack + ${parpacksrc_STAT_SRCS} + ${parpackutil_STAT_SRCS}) + + target_link_libraries(parpack ${MPI_Fortran_LIBRARIES}) ++ target_link_libraries(parpack arpack) + set_target_properties(parpack PROPERTIES OUTPUT_NAME parpack${LIBSUFFIX}) + endif () + diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index 770ceed48b..2de1c390db 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -35,7 +35,7 @@ class Autoconf(Package): version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b') version('2.62', '6c1f3b3734999035d77da5024aab4fbd') - depends_on('m4') + depends_on('m4', type='build') def _make_executable(self, name): return Executable(join_path(self.prefix.bin, name)) diff --git a/var/spack/repos/builtin/packages/automaded/package.py b/var/spack/repos/builtin/packages/automaded/package.py index fc65a04a06..2b4681778f 100644 --- a/var/spack/repos/builtin/packages/automaded/package.py +++ b/var/spack/repos/builtin/packages/automaded/package.py @@ -44,6 +44,7 @@ class Automaded(Package): depends_on('mpi') depends_on('boost') depends_on('callpath') + depends_on('cmake', type='build') def install(self, spec, prefix): cmake("-DSTATE_TRACKER_WITH_CALLPATH=ON", *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/bear/package.py b/var/spack/repos/builtin/packages/bear/package.py index 730a684ec5..a137fded08 100644 --- a/var/spack/repos/builtin/packages/bear/package.py +++ b/var/spack/repos/builtin/packages/bear/package.py @@ -31,7 +31,7 @@ class Bear(Package): version('2.0.4', 'fd8afb5e8e18f8737ba06f90bd77d011') - depends_on("cmake") + depends_on('cmake', type='build') depends_on("python") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py index 8d7da705e4..7dd17a062e 100644 --- a/var/spack/repos/builtin/packages/bertini/package.py +++ b/var/spack/repos/builtin/packages/bertini/package.py @@ -37,8 +37,8 @@ class Bertini(Package): variant('mpi', default=True, description='Compile in parallel') - depends_on('flex') - depends_on('bison') + depends_on('flex', type='build') + depends_on('bison', type='build') depends_on('gmp') depends_on('mpfr') depends_on('mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index 35d52128c3..e329e6fd7a 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -38,9 +38,9 @@ class Binutils(Package): version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') - depends_on('m4') - depends_on('flex') - depends_on('bison') + depends_on('m4', type='build') + depends_on('flex', type='build') + depends_on('bison', type='build') # Add a patch that creates binutils libiberty_pic.a which is preferred by # OpenSpeedShop and cbtf-krell diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index c5bc051c80..c7a125df15 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -34,7 +34,7 @@ class Bison(Package): version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8') - depends_on("m4") + depends_on("m4", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py index ec7db6c08e..216ae1ec12 100644 --- a/var/spack/repos/builtin/packages/boxlib/package.py +++ b/var/spack/repos/builtin/packages/boxlib/package.py @@ -35,6 +35,7 @@ class Boxlib(Package): version('master', git='https://ccse.lbl.gov/pub/Downloads/BoxLib.git') depends_on('mpi') + depends_on('cmake', type='build') def install(self, spec, prefix): args = std_cmake_args diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py index 3b6d1d830e..27303293d2 100644 --- a/var/spack/repos/builtin/packages/bzip2/package.py +++ b/var/spack/repos/builtin/packages/bzip2/package.py @@ -24,54 +24,59 @@ ############################################################################## from spack import * + class Bzip2(Package): """bzip2 is a freely available, patent free high-quality data - compressor. It typically compresses files to within 10% to 15% - of the best available techniques (the PPM family of statistical - compressors), whilst being around twice as fast at compression - and six times faster at decompression. + compressor. It typically compresses files to within 10% to 15% + of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression + and six times faster at decompression.""" - """ homepage = "http://www.bzip.org" url = "http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz" version('1.0.6', '00b516f4704d4a7cb50a1d97e6e8e15b') - def patch(self): - mf = FileFilter('Makefile-libbz2_so') - mf.filter(r'^CC=gcc', 'CC=cc') + # bzip2 comes with two separate Makefiles for static and dynamic builds + # Tell both to use Spack's compiler wrapper instead of GCC + filter_file(r'^CC=gcc', 'CC=cc', 'Makefile') + filter_file(r'^CC=gcc', 'CC=cc', 'Makefile-libbz2_so') - # Below stuff patches the link line to use RPATHs on Mac OS X. + # Patch the link line to use RPATHs on macOS if 'darwin' in self.spec.architecture: v = self.spec.version - v1, v2, v3 = (v.up_to(i) for i in (1,2,3)) + v1, v2, v3 = (v.up_to(i) for i in (1, 2, 3)) - mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3), - '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), string=True) + kwargs = {'ignore_absent': False, 'backup': False, 'string': True} - mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3), - '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), string=True) + mf = FileFilter('Makefile-libbz2_so') + mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3), # NOQA ignore=E501 + '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), **kwargs) # NOQA ignore=E501 + + mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3), # NOQA ignore=E501 + '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), **kwargs) # NOQA ignore=E501 mf.filter('rm -f libbz2.so.{0}'.format(v2), - 'rm -f libbz2.{0}.dylib'.format(v2), string=True) + 'rm -f libbz2.{0}.dylib'.format(v2), **kwargs) mf.filter('ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2), - 'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), string=True) - + 'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), **kwargs) # NOQA ignore=E501 def install(self, spec, prefix): + # Build the dynamic library first make('-f', 'Makefile-libbz2_so') - make('clean') - make("install", "PREFIX=%s" % prefix) + # Build the static library and everything else + make() + make('install', 'PREFIX={0}'.format(prefix)) install('bzip2-shared', join_path(prefix.bin, 'bzip2')) - v1, v2, v3 = (self.spec.version.up_to(i) for i in (1,2,3)) + v1, v2, v3 = (self.spec.version.up_to(i) for i in (1, 2, 3)) if 'darwin' in self.spec.architecture: lib = 'libbz2.dylib' - lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3)) + lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3)) # NOQA ignore=E501 else: lib = 'libbz2.so' - lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3)) + lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3)) # NOQA ignore=E501 install(lib3, join_path(prefix.lib, lib3)) with working_dir(prefix.lib): diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py index dee332be14..49f9861126 100644 --- a/var/spack/repos/builtin/packages/c-blosc/package.py +++ b/var/spack/repos/builtin/packages/c-blosc/package.py @@ -38,7 +38,7 @@ class CBlosc(Package): version('1.8.1', 'd73d5be01359cf271e9386c90dcf5b05') version('1.8.0', '5b92ecb287695ba20cc33d30bf221c4f') - depends_on("cmake") + depends_on("cmake", type='build') depends_on("snappy") depends_on("zlib") diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py index a424c73859..4a0fc54acc 100644 --- a/var/spack/repos/builtin/packages/caliper/package.py +++ b/var/spack/repos/builtin/packages/caliper/package.py @@ -41,6 +41,7 @@ class Caliper(Package): depends_on('libunwind') depends_on('papi') depends_on('mpi', when='+mpi') + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('build', create=True): diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py index 2ad2dc60e4..2f171fb9ce 100644 --- a/var/spack/repos/builtin/packages/callpath/package.py +++ b/var/spack/repos/builtin/packages/callpath/package.py @@ -39,6 +39,7 @@ class Callpath(Package): depends_on("dyninst") depends_on("adept-utils") depends_on("mpi") + depends_on('cmake', type='build') def install(self, spec, prefix): # TODO: offer options for the walker used. diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py index e9e5da4486..8e4f23046b 100644 --- a/var/spack/repos/builtin/packages/cantera/package.py +++ b/var/spack/repos/builtin/packages/cantera/package.py @@ -42,7 +42,7 @@ class Cantera(Package): variant('matlab', default=False, description='Build the Cantera Matlab toolbox') # Required dependencies - depends_on('scons') + depends_on('scons', type='build') # Recommended dependencies depends_on('blas', when='+lapack') @@ -52,10 +52,10 @@ class Cantera(Package): # Python module dependencies extends('python', when='+python') - depends_on('py-numpy', when='+python') - depends_on('py-scipy', when='+python') - depends_on('py-cython', when='+python') - depends_on('py-3to2', when='+python') + depends_on('py-numpy', when='+python', type=nolink) + depends_on('py-scipy', when='+python', type=nolink) + depends_on('py-cython', when='+python', type=nolink) + depends_on('py-3to2', when='+python', type=nolink) # TODO: these "when" specs don't actually work # depends_on('py-unittest2', when='+python^python@2.6') # depends_on('py-unittest2py3k', when='+python^python@3.1') diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py index 7ce90ce0db..321d02b556 100644 --- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py +++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py @@ -53,7 +53,7 @@ class CbtfArgonavis(Package): version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-argonavis.git') - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') depends_on("boost@1.50.0:") depends_on("papi") depends_on("mrnet@5.0.1:+lwthreads+krellpatch") diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py index 7506f78146..acb78a7395 100644 --- a/var/spack/repos/builtin/packages/cbtf-krell/package.py +++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py @@ -64,7 +64,7 @@ class CbtfKrell(Package): variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.") # Dependencies for cbtf-krell - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') # For binutils service depends_on("binutils@2.24+krellpatch") diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py index fa7de3d4a3..5694535fcc 100644 --- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py +++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py @@ -53,7 +53,7 @@ class CbtfLanl(Package): version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl') - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') # Dependencies for cbtf-krell depends_on("mrnet@5.0.1:+lwthreads+krellpatch") depends_on("xerces-c@3.1.1:") diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py index 2231cf1d45..017b897f3c 100644 --- a/var/spack/repos/builtin/packages/cbtf/package.py +++ b/var/spack/repos/builtin/packages/cbtf/package.py @@ -57,7 +57,7 @@ class Cbtf(Package): variant('runtime', default=False, description="build only the runtime libraries and collectors.") - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') depends_on("boost@1.50.0:") depends_on("mrnet@5.0.1:+lwthreads+krellpatch") depends_on("xerces-c@3.1.1:") diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py index c53c667efb..41dc9a274b 100644 --- a/var/spack/repos/builtin/packages/cereal/package.py +++ b/var/spack/repos/builtin/packages/cereal/package.py @@ -31,6 +31,7 @@ class Cereal(Package): homepage = "http://uscilab.github.io/cereal/" url = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz" + version('1.2.0', 'e372c9814696481dbdb7d500e1410d2b') version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9') version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27') version('1.1.0', '9f2d5f72e935c54f4c6d23e954ce699f') @@ -39,7 +40,7 @@ class Cereal(Package): patch("Werror.patch") - depends_on("cmake @2.6.2:") + depends_on('cmake@2.6.2:', type='build') def install(self, spec, prefix): # Don't use -Werror diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py index ea1b20e34f..5c87978339 100644 --- a/var/spack/repos/builtin/packages/cgal/package.py +++ b/var/spack/repos/builtin/packages/cgal/package.py @@ -46,7 +46,7 @@ class Cgal(Package): depends_on('mpfr') depends_on('gmp') depends_on('zlib') - depends_on('cmake') + depends_on('cmake', type='build') # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL) # FIXME : Optional third party libraries missing diff --git a/var/spack/repos/builtin/packages/cleverleaf/package.py b/var/spack/repos/builtin/packages/cleverleaf/package.py index 6b54d1bf26..c258e89514 100644 --- a/var/spack/repos/builtin/packages/cleverleaf/package.py +++ b/var/spack/repos/builtin/packages/cleverleaf/package.py @@ -40,6 +40,7 @@ class Cleverleaf(Package): depends_on("SAMRAI@3.8.0:") depends_on("hdf5+mpi") depends_on("boost") + depends_on('cmake', type='build') def install(self, spec, prefix): cmake(*std_cmake_args) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 7b2a125fe5..b39b086396 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -47,8 +47,8 @@ class Cmake(Package): depends_on('ncurses', when='+ncurses') depends_on('openssl', when='+openssl') depends_on('qt', when='+qt') - depends_on('python@2.7.11:', when='+doc') - depends_on('py-sphinx', when='+doc') + depends_on('python@2.7.11:', when='+doc', type='build') + depends_on('py-sphinx', when='+doc', type='build') def url_for_version(self, version): """Handle CMake's version-based custom URLs.""" diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py index 41f80d9761..aa2b3cc3bb 100644 --- a/var/spack/repos/builtin/packages/cmocka/package.py +++ b/var/spack/repos/builtin/packages/cmocka/package.py @@ -32,6 +32,8 @@ class Cmocka(Package): version('1.0.1', 'ed861e501a21a92b2af63e466df2015e') parallel = False + depends_on('cmake', type='build') + def install(self, spec, prefix): with working_dir('spack-build', create=True): cmake('..', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/cram/package.py b/var/spack/repos/builtin/packages/cram/package.py index 7e05587087..283bc5adea 100644 --- a/var/spack/repos/builtin/packages/cram/package.py +++ b/var/spack/repos/builtin/packages/cram/package.py @@ -33,6 +33,7 @@ class Cram(Package): extends('python') depends_on("mpi") + depends_on('cmake', type='build') def install(self, spec, prefix): cmake(".", *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py index d69f3e5009..a251a94470 100644 --- a/var/spack/repos/builtin/packages/czmq/package.py +++ b/var/spack/repos/builtin/packages/czmq/package.py @@ -32,10 +32,10 @@ class Czmq(Package): version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz') - depends_on('libtool') - depends_on('automake') - depends_on('autoconf') - depends_on('pkg-config') + depends_on('libtool', type='build') + depends_on('automake', type='build') + depends_on('autoconf', type='build') + depends_on('pkg-config', type='build') depends_on('zeromq') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py index 3a8ddf28ef..d0d22d9728 100644 --- a/var/spack/repos/builtin/packages/dakota/package.py +++ b/var/spack/repos/builtin/packages/dakota/package.py @@ -55,6 +55,7 @@ class Dakota(Package): depends_on('python') depends_on('boost') + depends_on('cmake', type='build') def url_for_version(self, version): return Dakota._url_str.format(version=version) diff --git a/var/spack/repos/builtin/packages/damselfly/package.py b/var/spack/repos/builtin/packages/damselfly/package.py index 42fab63f98..427997072c 100644 --- a/var/spack/repos/builtin/packages/damselfly/package.py +++ b/var/spack/repos/builtin/packages/damselfly/package.py @@ -31,6 +31,8 @@ class Damselfly(Package): version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895', git='https://github.com/llnl/damselfly.git', tag='v1.0') + depends_on('cmake', type='build') + def install(self, spec, prefix): with working_dir('spack-build', create=True): cmake('-DCMAKE_BUILD_TYPE=release', '..', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 068dbec10a..54604d351f 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -37,7 +37,7 @@ class Dealii(Package): version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa') version('8.2.1', '71c728dbec14f371297cd405776ccf08') version('8.1.0', 'aa8fadc2ce5eb674f44f997461bf668d') - version('dev', git='https://github.com/dealii/dealii.git') + version('develop', git='https://github.com/dealii/dealii.git') variant('mpi', default=True, description='Compile with MPI') variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)') @@ -60,7 +60,7 @@ class Dealii(Package): depends_on("boost@1.59.0:+thread+system+serialization+iostreams", when='~mpi') # NOQA: ignore=E501 depends_on("boost@1.59.0:+mpi+thread+system+serialization+iostreams", when='+mpi') # NOQA: ignore=E501 depends_on("bzip2") - depends_on("cmake") + depends_on("cmake", type='build') depends_on("lapack") depends_on("muparser") depends_on("suite-sparse") @@ -73,20 +73,21 @@ class Dealii(Package): depends_on("doxygen+graphviz", when='+doc') depends_on("graphviz", when='+doc') depends_on("gsl", when='@8.5.0:+gsl') - depends_on("gsl", when='@dev+gsl') depends_on("hdf5+mpi", when='+hdf5+mpi') depends_on("metis@5:", when='+metis') depends_on("netcdf+mpi", when="+netcdf+mpi") depends_on("netcdf-cxx", when='+netcdf+mpi') depends_on("oce", when='+oce') depends_on("p4est", when='+p4est+mpi') - depends_on("petsc@:3.6.4+mpi", when='+petsc+mpi') # FIXME: update after 3.7 is supported upstream. # NOQA: ignore=E501 - depends_on("slepc@:3.6.3", when='+slepc+petsc+mpi') + depends_on("petsc+mpi", when='@8.5.0:+petsc+mpi') + depends_on("slepc", when='@8.5.0:+slepc+petsc+mpi') + depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi') + depends_on("slepc@:3.6.3", when='@:8.4.1+slepc+petsc+mpi') depends_on("trilinos", when='+trilinos+mpi') # developer dependnecies - depends_on("numdiff", when='@dev') - depends_on("astyle@2.04", when='@dev') + depends_on("numdiff", when='@develop') + depends_on("astyle@2.04", when='@develop') def install(self, spec, prefix): options = [] @@ -119,6 +120,16 @@ class Dealii(Package): '-DZLIB_DIR=%s' % spec['zlib'].prefix ]) + # Set directory structure: + if spec.satisfies('@:8.2.1'): + options.extend(['-DDEAL_II_COMPONENT_COMPAT_FILES=OFF']) + else: + options.extend([ + '-DDEAL_II_EXAMPLES_RELDIR=share/deal.II/examples', + '-DDEAL_II_DOCREADME_RELDIR=share/deal.II/', + '-DDEAL_II_DOCHTML_RELDIR=share/deal.II/doc' + ]) + # MPI if '+mpi' in spec: options.extend([ @@ -193,115 +204,118 @@ class Dealii(Package): ]) cmake('.', *options) - make() - make("test") + if self.run_tests: + make("test") make("install") # run some MPI examples with different solvers from PETSc and Trilinos - env['DEAL_II_DIR'] = prefix - print('=====================================') - print('============ EXAMPLES ===============') - print('=====================================') - # take bare-bones step-3 - print('=====================================') - print('============ Step-3 =================') - print('=====================================') - with working_dir('examples/step-3'): - cmake('.') - make('release') - make('run', parallel=False) - - # An example which uses Metis + PETSc - # FIXME: switch step-18 to MPI - with working_dir('examples/step-18'): + if self.run_tests: + env['DEAL_II_DIR'] = prefix print('=====================================') - print('============= Step-18 ===============') + print('============ EXAMPLES ===============') print('=====================================') - # list the number of cycles to speed up - filter_file(r'(end_time = 10;)', ('end_time = 3;'), 'step-18.cc') - if '^petsc' in spec and '^metis' in spec: - cmake('.') - make('release') - make('run', parallel=False) - - # take step-40 which can use both PETSc and Trilinos - # FIXME: switch step-40 to MPI run - with working_dir('examples/step-40'): + # take bare-bones step-3 print('=====================================') - print('========== Step-40 PETSc ============') + print('============ Step-3 =================') print('=====================================') - # list the number of cycles to speed up - filter_file(r'(const unsigned int n_cycles = 8;)', - ('const unsigned int n_cycles = 2;'), 'step-40.cc') - cmake('.') - if '^petsc' in spec: + with working_dir('examples/step-3'): + cmake('.') make('release') make('run', parallel=False) - print('=====================================') - print('========= Step-40 Trilinos ==========') - print('=====================================') - # change Linear Algebra to Trilinos - # The below filter_file should be different for versions - # before and after 8.4.0 - if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'): - filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)', - ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc') - else: - filter_file(r'(#define USE_PETSC_LA.*)', - ('// #define USE_PETSC_LA'), 'step-40.cc') - if '^trilinos+hypre' in spec: - make('release') - make('run', parallel=False) + # An example which uses Metis + PETSc + # FIXME: switch step-18 to MPI + with working_dir('examples/step-18'): + print('=====================================') + print('============= Step-18 ===============') + print('=====================================') + # list the number of cycles to speed up + filter_file(r'(end_time = 10;)', ('end_time = 3;'), + 'step-18.cc') + if '^petsc' in spec and '^metis' in spec: + cmake('.') + make('release') + make('run', parallel=False) - # the rest of the tests on step 40 only works for - # dealii version 8.4.0 and after - if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'): + # take step-40 which can use both PETSc and Trilinos + # FIXME: switch step-40 to MPI run + with working_dir('examples/step-40'): print('=====================================') - print('=== Step-40 Trilinos SuperluDist ====') + print('========== Step-40 PETSc ============') print('=====================================') - # change to direct solvers - filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501 - filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', - (''), 'step-40.cc') - filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501 - (''), 'step-40.cc') - filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501 - (''), 'step-40.cc') - filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501 - filter_file(r'(preconditioner\);)', (''), 'step-40.cc') - if '^trilinos+superlu-dist' in spec: + # list the number of cycles to speed up + filter_file(r'(const unsigned int n_cycles = 8;)', + ('const unsigned int n_cycles = 2;'), 'step-40.cc') + cmake('.') + if '^petsc' in spec: make('release') - make('run', paralle=False) + make('run', parallel=False) print('=====================================') - print('====== Step-40 Trilinos MUMPS =======') + print('========= Step-40 Trilinos ==========') print('=====================================') - # switch to Mumps - filter_file(r'(Amesos_Superludist)', - ('Amesos_Mumps'), 'step-40.cc') - if '^trilinos+mumps' in spec: + # change Linear Algebra to Trilinos + # The below filter_file should be different for versions + # before and after 8.4.0 + if spec.satisfies('@8.4.0:'): + filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)', + ('#define FORCE_USE_OF_TRILINOS'), + 'step-40.cc') + else: + filter_file(r'(#define USE_PETSC_LA.*)', + ('// #define USE_PETSC_LA'), 'step-40.cc') + if '^trilinos+hypre' in spec: make('release') make('run', parallel=False) - print('=====================================') - print('============ Step-36 ================') - print('=====================================') - with working_dir('examples/step-36'): - if 'slepc' in spec: - cmake('.') - make('release') - make('run', parallel=False) + # the rest of the tests on step 40 only works for + # dealii version 8.4.0 and after + if spec.satisfies('@8.4.0:'): + print('=====================================') + print('=== Step-40 Trilinos SuperluDist ====') + print('=====================================') + # change to direct solvers + filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501 + filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', + (''), 'step-40.cc') + filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501 + (''), 'step-40.cc') + filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501 + (''), 'step-40.cc') + filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501 + filter_file(r'(preconditioner\);)', (''), 'step-40.cc') + if '^trilinos+superlu-dist' in spec: + make('release') + make('run', paralle=False) - print('=====================================') - print('============ Step-54 ================') - print('=====================================') - with working_dir('examples/step-54'): - if 'oce' in spec: - cmake('.') - make('release') - make('run', parallel=False) + print('=====================================') + print('====== Step-40 Trilinos MUMPS =======') + print('=====================================') + # switch to Mumps + filter_file(r'(Amesos_Superludist)', + ('Amesos_Mumps'), 'step-40.cc') + if '^trilinos+mumps' in spec: + make('release') + make('run', parallel=False) + + print('=====================================') + print('============ Step-36 ================') + print('=====================================') + with working_dir('examples/step-36'): + if 'slepc' in spec: + cmake('.') + make('release') + make('run', parallel=False) + + print('=====================================') + print('============ Step-54 ================') + print('=====================================') + with working_dir('examples/step-54'): + if 'oce' in spec: + cmake('.') + make('release') + make('run', parallel=False) def setup_environment(self, spack_env, env): env.set('DEAL_II_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py index 38742b7e7d..1685f0009f 100644 --- a/var/spack/repos/builtin/packages/dia/package.py +++ b/var/spack/repos/builtin/packages/dia/package.py @@ -31,7 +31,7 @@ class Dia(Package): version('0.97.3', '0e744a0f6a6c4cb6a089e4d955392c3c') - depends_on('intltool') + depends_on('intltool', type='build') depends_on('gtkplus@2.6.0:') depends_on('cairo') #depends_on('libart') # optional dependency, not yet supported by spack. diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py index 9c22174610..87137168f3 100644 --- a/var/spack/repos/builtin/packages/docbook-xml/package.py +++ b/var/spack/repos/builtin/packages/docbook-xml/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -import glob from spack import * @@ -35,9 +34,10 @@ class DocbookXml(Package): version('4.5', '03083e288e87a7e829e437358da7ef9e') def install(self, spec, prefix): - cp = which('cp') - - install_args = ['-a', '-t', prefix] - install_args.extend(glob.glob('*')) - - cp(*install_args) + for item in os.listdir('.'): + src = os.path.abspath(item) + dst = os.path.join(prefix, item) + if os.path.isdir(item): + install_tree(src, dst, symlinks=True) + else: + install(src, dst) diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py index b2e9582b5a..267ba61756 100644 --- a/var/spack/repos/builtin/packages/doxygen/package.py +++ b/var/spack/repos/builtin/packages/doxygen/package.py @@ -24,6 +24,8 @@ ############################################################################## from spack import * +import sys + class Doxygen(Package): """Doxygen is the de facto standard tool for generating documentation @@ -41,12 +43,12 @@ class Doxygen(Package): # graphviz appears to be a run-time optional dependency variant('graphviz', default=True, description='Build with dot command support from Graphviz.') # NOQA: ignore=E501 - depends_on("cmake@2.8.12:") - depends_on("flex") - depends_on("bison") + depends_on("cmake@2.8.12:", type='build') + depends_on("flex", type='build') + depends_on("bison", type='build') # optional dependencies - depends_on("graphviz", when="+graphviz") + depends_on("graphviz", when="+graphviz", type='run') def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py index 735936f087..efe4de4abf 100644 --- a/var/spack/repos/builtin/packages/dyninst/package.py +++ b/var/spack/repos/builtin/packages/dyninst/package.py @@ -43,6 +43,7 @@ class Dyninst(Package): depends_on("libelf") depends_on("libdwarf") depends_on("boost@1.42:") + depends_on('cmake', type='build') # new version uses cmake def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index 9ff4107619..97343f499b 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -47,7 +47,7 @@ class Eigen(Package): variant('mpfr', default=True, description='Enables support for multi-precisions floating points via mpfr') # TODO : dependency on googlehash, superlu, adolc missing - depends_on('cmake') + depends_on('cmake', type='build') depends_on('metis@5:', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py index fe7a5ee4f6..5d5bb3be02 100644 --- a/var/spack/repos/builtin/packages/environment-modules/package.py +++ b/var/spack/repos/builtin/packages/environment-modules/package.py @@ -35,7 +35,7 @@ class EnvironmentModules(Package): version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb') # Dependencies: - depends_on('tcl') + depends_on('tcl', type=alldeps) def install(self, spec, prefix): tcl_spec = spec['tcl'] diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py index 5e9227af46..eb6c23afeb 100644 --- a/var/spack/repos/builtin/packages/exodusii/package.py +++ b/var/spack/repos/builtin/packages/exodusii/package.py @@ -44,9 +44,7 @@ class Exodusii(Package): version('2016-02-08', git='https://github.com/gsjaardema/seacas.git', commit='dcf3529') - # TODO: Make this a build dependency once build dependencies are supported - # (see: https://github.com/LLNL/spack/pull/378). - depends_on('cmake@2.8.7:') + depends_on('cmake@2.8.7:', type='build') depends_on('hdf5~shared~mpi') depends_on('netcdf~mpi') diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py index 51e827b2c5..2a9ac123f3 100644 --- a/var/spack/repos/builtin/packages/expat/package.py +++ b/var/spack/repos/builtin/packages/expat/package.py @@ -31,7 +31,7 @@ class Expat(Package): version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd') - depends_on('cmake') + depends_on('cmake', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index b778538606..800e4b9d96 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -34,7 +34,7 @@ class Flex(Package): version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec') version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde') - depends_on("bison") + depends_on("bison", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/flux/package.py b/var/spack/repos/builtin/packages/flux/package.py index 2b972d63ae..dec339a6af 100644 --- a/var/spack/repos/builtin/packages/flux/package.py +++ b/var/spack/repos/builtin/packages/flux/package.py @@ -45,8 +45,8 @@ class Flux(Package): depends_on("py-cffi") # TODO: This provides a catalog, hacked with environment below for now - depends_on("docbook-xml") - depends_on("asciidoc") + depends_on("docbook-xml", type='build') + depends_on("asciidoc", type='build') def install(self, spec, prefix): # Bootstrap with autotools diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py index 4479fc9bee..0ff5765895 100644 --- a/var/spack/repos/builtin/packages/foam-extend/package.py +++ b/var/spack/repos/builtin/packages/foam-extend/package.py @@ -29,6 +29,7 @@ class FoamExtend(Package): depends_on('python') depends_on('flex@:2.5.99') depends_on('zlib') + depends_on('cmake', type='build') depends_on('scotch ~ metis', when='~ptscotch+scotch') depends_on('scotch ~ metis + mpi', when='+ptscotch') diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py index caff06bdd6..9ed83bc3be 100644 --- a/var/spack/repos/builtin/packages/gdal/package.py +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -62,7 +62,7 @@ class Gdal(Package): depends_on("libpng") depends_on("zlib") depends_on("proj") - depends_on("py-numpy") + depends_on("py-numpy", type=nolink) parallel = False diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index 58d8a545db..78ad4b307d 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -41,7 +41,7 @@ class Gdb(Package): version('7.9', '8f8ced422fe462a00e0135a643544f17') version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc') - depends_on('texinfo') + depends_on('texinfo', type='build') def install(self, spec, prefix): configure('--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/gflags/package.py b/var/spack/repos/builtin/packages/gflags/package.py index 9f3552d53d..47bbf369ef 100644 --- a/var/spack/repos/builtin/packages/gflags/package.py +++ b/var/spack/repos/builtin/packages/gflags/package.py @@ -37,6 +37,8 @@ class Gflags(Package): version('2.1.2', 'ac432de923f9de1e9780b5254884599f') + depends_on('cmake', type='build') + def install(self, spec, prefix): cmake("-DCMAKE_INSTALL_PREFIX=" + prefix, "-DBUILD_SHARED_LIBS=ON") diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 03e7d3e031..4cbbaac342 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -49,7 +49,7 @@ class Git(Package): depends_on("openssl") - depends_on("autoconf") + depends_on("autoconf", type='build') depends_on("curl") depends_on("expat") diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index 342a61a6a1..0a0a02f464 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -38,8 +38,8 @@ class Glib(Package): depends_on("libffi") depends_on("zlib") - depends_on("pkg-config") - depends_on('gettext', sys.platform == 'darwin') + depends_on("pkg-config", type='build') + depends_on('gettext', when=sys.platform == 'darwin') # The following patch is needed for gcc-6.1 patch('g_date_strftime.patch') diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py index 0c9212f17d..442c1cdf40 100644 --- a/var/spack/repos/builtin/packages/glm/package.py +++ b/var/spack/repos/builtin/packages/glm/package.py @@ -35,8 +35,8 @@ class Glm(Package): url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz" version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8') - - depends_on ("cmake") + + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/global/package.py b/var/spack/repos/builtin/packages/global/package.py index c144d6660b..f832834a28 100644 --- a/var/spack/repos/builtin/packages/global/package.py +++ b/var/spack/repos/builtin/packages/global/package.py @@ -34,7 +34,7 @@ class Global(Package): version('6.5', 'dfec818b4f53d91721e247cf7b218078') - depends_on('exuberant-ctags') + depends_on('exuberant-ctags', type=nolink) depends_on('ncurses') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index 3933788425..e2c2892f18 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -35,7 +35,7 @@ class Gmp(Package): version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470') version('6.0.0' , '6ef5869ae735db9995619135bd856b84') - depends_on("m4") + depends_on("m4", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index 0951b86d57..fe26cb3bf2 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -53,7 +53,7 @@ class Gmsh(Package): depends_on('blas') depends_on('lapack') - depends_on('cmake@2.8:') + depends_on('cmake@2.8:', type='build') depends_on('gmp') depends_on('mpi', when='+mpi') # Assumes OpenGL with GLU is already provided by the system: diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gnu-prolog/package.py new file mode 100644 index 0000000000..f497ed3001 --- /dev/null +++ b/var/spack/repos/builtin/packages/gnu-prolog/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class GnuProlog(Package): + """A free Prolog compiler with constraint solving over finite domains.""" + homepage = "http://www.gprolog.org/" + url = "http://www.gprolog.org/gprolog-1.4.4.tar.gz" + + version('1.4.4', '37009da471e5217ff637ad1c516448c8') + + parallel = False + + def install(self, spec, prefix): + with working_dir('src'): + configure('--with-install-dir=%s' % prefix, + '--without-links-dir') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index 13b83517d1..ff2c2f6781 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -24,7 +24,7 @@ class Go(Package): # to-do, make non-c self-hosting compilers feasible without backflips # should be a dep on external go compiler - depends_on('go-bootstrap') + depends_on('go-bootstrap', type='build') depends_on('git') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py index 9444253c8c..1dc74fbcf4 100644 --- a/var/spack/repos/builtin/packages/googletest/package.py +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -31,7 +31,7 @@ class Googletest(Package): version('1.7.0', '5eaf03ed925a47b37c8e1d559eb19bc4') - depends_on("cmake") + depends_on("cmake", type='build') def install(self, spec, prefix): which('cmake')('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/graphlib/package.py b/var/spack/repos/builtin/packages/graphlib/package.py index f70f32cc8a..087a322acc 100644 --- a/var/spack/repos/builtin/packages/graphlib/package.py +++ b/var/spack/repos/builtin/packages/graphlib/package.py @@ -31,6 +31,8 @@ class Graphlib(Package): version('2.0.0', '43c6df84f1d38ba5a5dce0ae19371a70') + depends_on('cmake', type='build') + def install(self, spec, prefix): cmake(".", *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index 2f99015ba2..e5898a6e59 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -44,7 +44,7 @@ class Graphviz(Package): depends_on("swig") depends_on("python") depends_on("ghostscript") - depends_on("pkg-config") + depends_on("pkg-config", type='build') def install(self, spec, prefix): options = ['--prefix=%s' % prefix] diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index 1a50a42488..55eacc8d38 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -50,6 +50,7 @@ class Gromacs(Package): depends_on('mpi', when='+mpi') depends_on('fftw') + depends_on('cmake', type='build') # TODO : add GPU support diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py index 50f380083c..28b65711b0 100644 --- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py +++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py @@ -53,7 +53,7 @@ class Hdf5Blosc(Package): depends_on("c-blosc") depends_on("hdf5") - depends_on("libtool") + depends_on("libtool", type='build') parallel = False diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py new file mode 100644 index 0000000000..6a236e9fc9 --- /dev/null +++ b/var/spack/repos/builtin/packages/hmmer/package.py @@ -0,0 +1,76 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Hmmer(Package): + """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments. It implements methods using + probabilistic models called profile hidden Markov models (profile HMMs). + """ + homepage = 'http://www.hmmer.org' + url = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz' + + version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f') + version('3.0', '4cf685f3bc524ba5b5cdaaa070a83588') + version('2.4i', 'dab234c87e026ac1de942450750acd20') + version('2.3.2', '5f073340c0cf761288f961a73821228a') + version('2.3.1', 'c724413e5761c630892506698a4716e2') + + variant('mpi', default=True, description='Compile with MPI') + variant('gsl', default=False, description='Compile with GSL') + + depends_on('mpi', when='+mpi') + depends_on('gsl', when='+gsl') + + def url_for_version(self, version): + base_url = 'http://eddylab.org/software' + + if version >= Version('3.0'): + return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version) + else: + return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version) + + def install(self, spec, prefix): + configure_args = [ + '--prefix={0}'.format(prefix) + ] + + if '+gsl' in self.spec: + configure_args.extend([ + '--with-gsl', + 'LIBS=-lgsl -lgslcblas' + ]) + + if '+mpi' in self.spec: + configure_args.append('--enable-mpi') + + configure(*configure_args) + make() + + if self.run_tests: + make('check') + + make('install') diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py index 90d5107e3b..060cd0b713 100644 --- a/var/spack/repos/builtin/packages/hoomd-blue/package.py +++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py @@ -45,12 +45,12 @@ class HoomdBlue(Package): variant('doc', default=True, description='Generate documentation') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) depends_on('boost+python') - depends_on('cmake') + depends_on('cmake', type='build') depends_on('mpi', when='+mpi') depends_on('cuda', when='+cuda') - depends_on('doxygen', when='+doc') + depends_on('doxygen', when='+doc', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index 8e6cf429a7..ed1e6c6cbf 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -26,13 +26,13 @@ class Ibmisc(CMakePackage): depends_on('netcdf-cxx4', when='+netcdf') depends_on('udunits2', when='+udunits2') depends_on('googletest', when='+googletest') - depends_on('py-cython', when='+python') - depends_on('py-numpy', when='+python') + depends_on('py-cython', when='+python', type=nolink) + depends_on('py-numpy', when='+python', type=nolink) depends_on('boost', when='+boost') # Build dependencies - depends_on('cmake') - depends_on('doxygen') + depends_on('cmake', type='build') + depends_on('doxygen', type='build') def configure_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py index 47c5ca0c09..3bd21df89e 100644 --- a/var/spack/repos/builtin/packages/ipopt/package.py +++ b/var/spack/repos/builtin/packages/ipopt/package.py @@ -38,7 +38,7 @@ class Ipopt(Package): depends_on("blas") depends_on("lapack") - depends_on("pkg-config") + depends_on("pkg-config", type='build') depends_on("mumps+double~mpi") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 99d138dcff..536ce69236 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -44,16 +44,16 @@ class Julia(Package): patch('openblas.patch', when='@0.4:0.4.5') # Build-time dependencies: - # depends_on("awk") - # depends_on("m4") - # depends_on("pkg-config") + # depends_on("awk", type='build') + # depends_on("m4", type='build') + # depends_on("pkg-config", type='build') # Combined build-time and run-time dependencies: - depends_on("binutils") - depends_on("cmake @2.8:") - depends_on("git") - depends_on("openssl") - depends_on("python @2.7:2.999") + depends_on("binutils", type=nolink) + depends_on("cmake @2.8:", type=nolink) + depends_on("git", type=nolink) + depends_on("openssl", type=nolink) + depends_on("python @2.7:2.999", type=nolink) # I think that Julia requires the dependencies above, but it # builds fine (on my system) without these. We should enable them @@ -93,8 +93,8 @@ class Julia(Package): # USE_SYSTEM_LIBGIT2=0 # Run-time dependencies for Julia packages: - depends_on("hdf5") - depends_on("mpi") + depends_on("hdf5", type='run') + depends_on("mpi", type='run') def install(self, spec, prefix): # Explicitly setting CC, CXX, or FC breaks building libuv, one diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py index f256810005..8aa6d72727 100644 --- a/var/spack/repos/builtin/packages/launchmon/package.py +++ b/var/spack/repos/builtin/packages/launchmon/package.py @@ -33,9 +33,9 @@ class Launchmon(Package): version('1.0.2', '8d6ba77a0ec2eff2fde2c5cc8fa7ff7a') - depends_on('autoconf') - depends_on('automake') - depends_on('libtool') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') def install(self, spec, prefix): configure( diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py index 5e4e420842..938f4f6f3b 100644 --- a/var/spack/repos/builtin/packages/libgd/package.py +++ b/var/spack/repos/builtin/packages/libgd/package.py @@ -40,6 +40,7 @@ class Libgd(Package): version('2.1.1', 'e91a1a99903e460e7ba00a794e72cc1e') depends_on('libpng') + depends_on('cmake', type='build') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py index 8615b2ed83..d1239ba0d9 100644 --- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py +++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py @@ -35,8 +35,8 @@ class LibjpegTurbo(Package): version('1.3.1', '2c3a68129dac443a72815ff5bb374b05') # Can use either of these. - depends_on("yasm") - depends_on("nasm") + depends_on("yasm", type='build') + depends_on("nasm", type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/libjson-c/package.py b/var/spack/repos/builtin/packages/libjson-c/package.py index 75f3e130ad..662ed3cb5a 100644 --- a/var/spack/repos/builtin/packages/libjson-c/package.py +++ b/var/spack/repos/builtin/packages/libjson-c/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class LibjsonC(Package): """ A JSON implementation in C """ homepage = "https://github.com/json-c/json-c/wiki" @@ -34,5 +35,5 @@ class LibjsonC(Package): def install(self, spec, prefix): configure('--prefix=%s' % prefix) - make() + make(parallel=False) make("install") diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py index 0e410a5061..a0070d72d0 100644 --- a/var/spack/repos/builtin/packages/libtool/package.py +++ b/var/spack/repos/builtin/packages/libtool/package.py @@ -35,7 +35,7 @@ class Libtool(Package): version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e') version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50') - depends_on('m4') + depends_on('m4', type='build') def _make_executable(self, name): return Executable(join_path(self.prefix.bin, name)) diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py index 63565c7aea..0d29270b38 100644 --- a/var/spack/repos/builtin/packages/libuv/package.py +++ b/var/spack/repos/builtin/packages/libuv/package.py @@ -31,9 +31,9 @@ class Libuv(Package): version('1.9.0', '14737f9c76123a19a290dabb7d1cd04c') - depends_on('automake') - depends_on('autoconf') - depends_on('libtool') + depends_on('automake', type='build') + depends_on('autoconf', type='build') + depends_on('libtool', type='build') def install(self, spec, prefix): bash = which("bash") diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py index 746d4567e2..586eb970d8 100644 --- a/var/spack/repos/builtin/packages/libxcb/package.py +++ b/var/spack/repos/builtin/packages/libxcb/package.py @@ -36,9 +36,9 @@ class Libxcb(Package): version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb') version('1.11.1', '118623c15a96b08622603a71d8789bf3') - depends_on("python") + depends_on("python", type='build') depends_on("xcb-proto") - depends_on("pkg-config") + depends_on("pkg-config", type='build') depends_on("libpthread-stubs") depends_on('libxau') diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py index baaa2fc83d..a6dabd2c05 100644 --- a/var/spack/repos/builtin/packages/libxml2/package.py +++ b/var/spack/repos/builtin/packages/libxml2/package.py @@ -23,7 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class Libxml2(Package): """Libxml2 is the XML C parser and toolkit developed for the Gnome @@ -42,8 +42,8 @@ class Libxml2(Package): def install(self, spec, prefix): if '+python' in spec: - site_packages_dir = os.path.join(prefix, 'lib/python%s.%s/site-packages' %(spec['python'].version[:2])) - python_args = ["--with-python=%s" % spec['python'].prefix, "--with-python-install-dir=%s" % site_packages_dir] + python_args = ["--with-python=%s" % spec['python'].prefix, + "--with-python-install-dir=%s" % site_packages_dir] else: python_args = ["--without-python"] diff --git a/var/spack/repos/builtin/packages/llvm-lld/package.py b/var/spack/repos/builtin/packages/llvm-lld/package.py index 073c2d1b9e..127fe1204d 100644 --- a/var/spack/repos/builtin/packages/llvm-lld/package.py +++ b/var/spack/repos/builtin/packages/llvm-lld/package.py @@ -34,6 +34,8 @@ class LlvmLld(Package): version('3.4', '3b6a17e58c8416c869c14dd37682f78e') + depends_on('cmake', type='build') + def install(self, spec, prefix): env['CXXFLAGS'] = self.compier.cxx11_flag diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 7a6ea7401c..e79c123a7e 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -51,7 +51,7 @@ class Llvm(Package): variant('all_targets', default=True, description="Build all supported targets, default targets <current arch>,NVPTX,AMDGPU,CppBackend") # Build dependency - depends_on('cmake @2.8.12.2:') + depends_on('cmake@2.8.12.2:', type='build') # Universal dependency depends_on('python@2.7:2.8') # Seems not to support python 3.X.Y diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index 7d75866d52..efa235f646 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -42,8 +42,8 @@ class Lmod(Package): version('6.0.1', '91abf52fe5033bd419ffe2842ebe7af9') depends_on('lua@5.2:') - depends_on('lua-luaposix') - depends_on('lua-luafilesystem') + depends_on('lua-luaposix', type=nolink) + depends_on('lua-luafilesystem', type=nolink) parallel = False diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py index 761932361b..ca0a481a83 100644 --- a/var/spack/repos/builtin/packages/lua/package.py +++ b/var/spack/repos/builtin/packages/lua/package.py @@ -86,7 +86,7 @@ class Lua(Package): def setup_dependent_environment(self, spack_env, run_env, extension_spec): lua_paths = [] - for d in extension_spec.traverse(): + for d in extension_spec.traverse(deptypes=nolink, deptype_query='run'): if d.package.extends(self.spec): lua_paths.append(os.path.join(d.prefix, self.lua_lib_dir)) lua_paths.append(os.path.join(d.prefix, self.lua_share_dir)) @@ -140,11 +140,11 @@ class Lua(Package): @property def lua_lib_dir(self): - return os.path.join('lib', 'lua', '%d.%d' % self.version[:2]) + return os.path.join('lib', 'lua', self.version.up_to(2)) @property def lua_share_dir(self): - return os.path.join('share', 'lua', '%d.%d' % self.version[:2]) + return os.path.join('share', 'lua', self.version.up_to(2)) def setup_dependent_package(self, module, ext_spec): """ diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py index ae34d25691..13c0ce768f 100644 --- a/var/spack/repos/builtin/packages/mbedtls/package.py +++ b/var/spack/repos/builtin/packages/mbedtls/package.py @@ -37,7 +37,7 @@ class Mbedtls(Package): version('2.1.3' , '7eb4cf1dfa68578a2c8dbd0b6fa752dd') version('1.3.16', '4144d7320c691f721aeb9e67a1bc38e0') - depends_on('cmake') + depends_on('cmake', type='build') def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/memaxes/package.py b/var/spack/repos/builtin/packages/memaxes/package.py index 135384e2f7..31672abaec 100644 --- a/var/spack/repos/builtin/packages/memaxes/package.py +++ b/var/spack/repos/builtin/packages/memaxes/package.py @@ -32,7 +32,7 @@ class Memaxes(Package): version('0.5', '5874f3fda9fd2d313c0ff9684f915ab5', url='https://github.com/llnl/MemAxes/archive/v0.5.tar.gz') - depends_on("cmake@2.8.9:") + depends_on('cmake@2.8.9:', type='build') depends_on("qt@5:") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py index bd9c9eec4a..3bad17b5cb 100644 --- a/var/spack/repos/builtin/packages/mesa/package.py +++ b/var/spack/repos/builtin/packages/mesa/package.py @@ -44,8 +44,8 @@ class Mesa(Package): # mesa 10.x # depends_on("py-mako") - # depends_on("flex") - # depends_on("bison") + # depends_on("flex", type='build') + # depends_on("bison", type='build') # depends_on("dri2proto") # depends_on("libxcb") # depends_on("libxshmfence") diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index c4f2afaff2..2180f2cce2 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -50,7 +50,7 @@ class Metis(Package): variant('idx64', default=False, description='Use int64_t as default index type') variant('real64', default=False, description='Use double precision floating point types') - depends_on('cmake@2.8:', when='@5:') # build-time dependency + depends_on('cmake@2.8:', when='@5:', type='build') patch('install_gklib_defs_rename.patch', when='@5:') diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 1b4456380b..e7a1d96388 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -62,7 +62,7 @@ class Mfem(Package): depends_on('blas', when='+suite-sparse') depends_on('lapack', when='+suite-sparse') depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:') - depends_on('cmake', when='^metis@5:') + depends_on('cmake', when='^metis@5:', type='build') def check_variants(self, spec): if '+mpi' in spec and ('+hypre' not in spec or '+metis' not in spec): diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpibash/package.py index b328b98ecf..e659663d90 100644 --- a/var/spack/repos/builtin/packages/mpibash/package.py +++ b/var/spack/repos/builtin/packages/mpibash/package.py @@ -36,7 +36,7 @@ class Mpibash(Package): patch('mpibash-4.3.patch', level=1, when='@4.3') # above patch modifies configure.ac - depends_on('autoconf') + depends_on('autoconf', type='build') # uses MPI_Exscan which is in MPI-1.2 and later depends_on('mpi@1.2:') diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py index 925dceabed..d42ac255d0 100644 --- a/var/spack/repos/builtin/packages/msgpack-c/package.py +++ b/var/spack/repos/builtin/packages/msgpack-c/package.py @@ -31,6 +31,8 @@ class MsgpackC(Package): version('1.4.1', 'e2fd3a7419b9bc49e5017fdbefab87e0') + depends_on('cmake', type='build') + def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/muster/package.py b/var/spack/repos/builtin/packages/muster/package.py index 993f147245..64b7324415 100644 --- a/var/spack/repos/builtin/packages/muster/package.py +++ b/var/spack/repos/builtin/packages/muster/package.py @@ -39,6 +39,7 @@ class Muster(Package): depends_on("boost") depends_on("mpi") + depends_on('cmake', type='build') def install(self, spec, prefix): cmake(".", *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py index f8af76429b..0fb181a7b2 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -34,7 +34,7 @@ class NetcdfCxx4(Package): version('4.2.1', 'd019853802092cf686254aaba165fc81') depends_on('netcdf') - depends_on("autoconf") + depends_on("autoconf", type='build') def install(self, spec, prefix): # Rebuild to prevent problems of inconsistency in git repo diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index c2256d5e9f..063d38e4f9 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -39,7 +39,7 @@ class Netcdf(Package): variant('mpi', default=True, description='Enables MPI parallelism') variant('hdf4', default=False, description='Enable HDF4 support') - depends_on("m4") + depends_on("m4", type='build') depends_on("hdf", when='+hdf4') # Required for DAP support diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 47857eb713..70015baf1c 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -52,7 +52,7 @@ class NetlibLapack(Package): provides('blas', when='~external-blas') provides('lapack') - depends_on('cmake') + depends_on('cmake', type='build') depends_on('blas', when='+external-blas') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index f7fe26a42d..a8250a38de 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -42,9 +42,9 @@ class NetlibScalapack(Package): provides('scalapack') - depends_on('cmake') depends_on('mpi') depends_on('lapack') + depends_on('cmake', when='@2.0.0:', type='build') def install(self, spec, prefix): options = [ diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py index e15d60cb0b..97164165e0 100644 --- a/var/spack/repos/builtin/packages/numdiff/package.py +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -35,7 +35,7 @@ class Numdiff(Package): version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e') - depends_on('gettext', sys.platform=='darwin') + depends_on('gettext', when=sys.platform=='darwin', type='build') def install(self, spec, prefix): options = ['--prefix=%s' % prefix] diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 0f0fcfb733..108c8f8a41 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -23,24 +23,26 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import platform, sys +import platform + class Oce(Package): - """ - Open CASCADE Community Edition: - patches/improvements/experiments contributed by users over the official Open CASCADE library. + """Open CASCADE Community Edition: + patches/improvements/experiments contributed by users over the official + Open CASCADE library. """ homepage = "https://github.com/tpaviot/oce" url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz" + version('0.17.2', 'bf2226be4cd192606af677cf178088e5') version('0.17.1', '36c67b87093c675698b483454258af91') - version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') + version('0.17', 'f1a89395c4b0d199bea3db62b85f818d') version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') - version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') + version('0.16', '7a4b4df5a104d75a537e25e7dd387eca') variant('tbb', default=True, description='Build with Intel Threading Building Blocks') - depends_on('cmake@2.8:') + depends_on('cmake@2.8:', type='build') depends_on('tbb', when='+tbb') # There is a bug in OCE which appears with Clang (version?) or GCC 6.0 @@ -49,8 +51,7 @@ class Oce(Package): # http://tracker.dev.opencascade.org/view.php?id=26042 # https://github.com/tpaviot/oce/issues/605 # https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch - patch('null.patch',when='@0.16:0.17.1') - + patch('null.patch', when='@0.16:0.17.1') def install(self, spec, prefix): options = [] @@ -63,7 +64,8 @@ class Oce(Package): '-DOCE_DISABLE_X11:BOOL=ON', '-DOCE_DRAW:BOOL=OFF', '-DOCE_MODEL:BOOL=ON', - '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ('TBB' if '+tbb' in spec else 'NONE'), + '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ( + 'TBB' if '+tbb' in spec else 'NONE'), '-DOCE_OCAF:BOOL=ON', '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF', '-DOCE_VISUALISATION:BOOL=OFF', @@ -77,15 +79,8 @@ class Oce(Package): '-DOCE_OSX_USE_COCOA:BOOL=ON', ]) - cmake('.', *options) + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) + cmake('.', *options) make("install/strip") - - # OCE tests build is brocken at least on Darwin. - # Unit tests are linked against libTKernel.10.dylib isntead of /full/path/libTKernel.10.dylib - # see https://github.com/tpaviot/oce/issues/612 - # make("test") - - # The shared libraries are not installed correctly on Darwin; correct this - if (sys.platform == 'darwin'): - fix_darwin_install_name(prefix.lib) + make("test") diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index f97bfc7d12..aa521899e5 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -61,16 +61,16 @@ class Octave(Package): variant('qrupdate', default=False) variant('qscintilla', default=False) variant('qt', default=False) - variant('suiteparse', default=False) + variant('suitesparse', default=False) variant('zlib', default=False) # Required dependencies depends_on('blas') depends_on('lapack') # Octave does not configure with sed from darwin: - depends_on('sed', sys.platform == 'darwin') + depends_on('sed', when=sys.platform == 'darwin', type='build') depends_on('pcre') - depends_on('pkg-config') + depends_on('pkg-config', type='build') # Strongly recommended dependencies depends_on('readline', when='+readline') diff --git a/var/spack/repos/builtin/packages/ompt-openmp/package.py b/var/spack/repos/builtin/packages/ompt-openmp/package.py index e74dcf6c23..800c04ae0e 100644 --- a/var/spack/repos/builtin/packages/ompt-openmp/package.py +++ b/var/spack/repos/builtin/packages/ompt-openmp/package.py @@ -31,7 +31,7 @@ class OmptOpenmp(Package): version('0.1', '2334e6a84b52da41b27afd9831ed5370') - # depends_on("foo") + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir("runtime/build", create=True): diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py index 989c66316c..ff551d0b92 100644 --- a/var/spack/repos/builtin/packages/opencv/package.py +++ b/var/spack/repos/builtin/packages/opencv/package.py @@ -54,7 +54,8 @@ class Opencv(Package): depends_on('python') depends_on('py-numpy') - depends_on('eigen', when='+eigen') + depends_on('eigen', when='+eigen', type='build') + depends_on('cmake', type='build') # FIXME : GUI extensions missing # FIXME : CUDA extensions still missing diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py index 1d00edb06d..1bc5b04f6f 100644 --- a/var/spack/repos/builtin/packages/openjpeg/package.py +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -43,7 +43,7 @@ class Openjpeg(Package): version('1.5.2', '545f98923430369a6b046ef3632ef95c') version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e') - depends_on('cmake') + depends_on('cmake', type='build') def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py index c501ea063c..4e2694a53c 100644 --- a/var/spack/repos/builtin/packages/openspeedshop/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop/package.py @@ -80,7 +80,7 @@ class Openspeedshop(Package): variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.") variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.") - depends_on("cmake@3.0.2") + depends_on("cmake@3.0.2", type='build') # Dependencies for openspeedshop that are common to all the variants of the OpenSpeedShop build depends_on("bison") depends_on("flex") diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index d0db4f7f20..4bbf0c1311 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -34,9 +34,9 @@ class P4est(Package): variant('tests', default=True, description='Run small tests') # build dependencies - depends_on('automake') - depends_on('autoconf') - depends_on('libtool@2.4.2:') + depends_on('automake', type='build') + depends_on('autoconf', type='build') + depends_on('libtool@2.4.2:', type='build') # other dependencies depends_on('lua') # Needed for the submodule sc diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py index d6324b63e6..97d36d94a4 100644 --- a/var/spack/repos/builtin/packages/paradiseo/package.py +++ b/var/spack/repos/builtin/packages/paradiseo/package.py @@ -48,13 +48,13 @@ class Paradiseo(Package): variant('gnuplot', default=False, description='Enable GnuPlot support') # Required dependencies - depends_on ("cmake") + depends_on ("cmake", type='build') # Optional dependencies depends_on ("mpi", when="+mpi") - depends_on ("doxygen", when='+doc') + depends_on ("doxygen", when='+doc', type='build') depends_on ("gnuplot", when='+gnuplot') - depends_on ("eigen", when='+edo') + depends_on ("eigen", when='+edo', type='build') depends_on ("boost~mpi", when='+edo~mpi') depends_on ("boost+mpi", when='+edo+mpi') diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py index 59c44c8a4a..deee46df8f 100644 --- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py +++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py @@ -39,7 +39,7 @@ class ParallelNetcdf(Package): variant('fortran', default=True, description='Build the Fortran Interface') variant('fpic', default=True, description='Produce position-independent code (for use with shared libraries)') - depends_on("m4") + depends_on("m4", type='build') depends_on("mpi") # See: https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 711cbc98c9..75f5272006 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -43,12 +43,13 @@ class Paraview(Package): variant('opengl2', default=False, description='Enable OpenGL2 backend') depends_on('python@2:2.7', when='+python') - depends_on('py-numpy', when='+python') - depends_on('py-matplotlib', when='+python') + depends_on('py-numpy', when='+python', type='run') + depends_on('py-matplotlib', when='+python', type='run') depends_on('tcl', when='+tcl') depends_on('mpi', when='+mpi') depends_on('qt@:4', when='+qt') + depends_on('cmake', type='build') depends_on('bzip2') depends_on('freetype') #depends_on('hdf5+mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index 9b36f273e4..b2ceadc128 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -42,7 +42,7 @@ class Parmetis(Package): variant('debug', default=False, description='Builds the library in debug mode') variant('gdb', default=False, description='Enables gdb support') - depends_on('cmake@2.8:') # build dependency + depends_on('cmake@2.8:', type='build') # build dependency depends_on('mpi') depends_on('metis@5:') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 6a7bee9788..11f5c36c22 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -149,20 +149,22 @@ class Petsc(Package): make("install") # solve Poisson equation in 2D to make sure nothing is broken: - with working_dir('src/ksp/ksp/examples/tutorials'): - cc = os.environ['CC'] if '~mpi' in self.spec else self.spec['mpi'].mpicc # NOQA: ignore=E501 - os.system('%s ex50.c -I%s -L%s -lpetsc -o ex50' % ( - cc, prefix.include, prefix.lib)) - ex50 = Executable('./ex50') - ex50('-da_grid_x', '4', '-da_grid_y', '4') - if 'superlu-dist' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 - - if 'mumps' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 - - if 'hypre' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 + if ('mpi' in spec) and self.run_tests: + with working_dir('src/ksp/ksp/examples/tutorials'): + env['PETSC_DIR'] = self.prefix + cc = Executable(spec['mpi'].mpicc) + cc('ex50.c', '-I%s' % prefix.include, '-L%s' % prefix.lib, + '-lpetsc', '-lm', '-o', 'ex50') + run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun')) + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4') + if 'superlu-dist' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 + + if 'mumps' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 + + if 'hypre' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # set up PETSC_DIR for everyone using PETSc package diff --git a/var/spack/repos/builtin/packages/pidx/package.py b/var/spack/repos/builtin/packages/pidx/package.py index d38dcd7b96..e7b18ce7a8 100644 --- a/var/spack/repos/builtin/packages/pidx/package.py +++ b/var/spack/repos/builtin/packages/pidx/package.py @@ -36,6 +36,7 @@ class Pidx(Package): version('1.0', git='https://github.com/sci-visus/PIDX.git', commit='6afa1cf71d1c41263296dc049c8fabaf73c296da') + depends_on('cmake', type='build') depends_on("mpi") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py index fc77ba7412..192dd86e0e 100644 --- a/var/spack/repos/builtin/packages/psi4/package.py +++ b/var/spack/repos/builtin/packages/psi4/package.py @@ -41,8 +41,8 @@ class Psi4(Package): depends_on('lapack') depends_on('boost+chrono+filesystem+python+regex+serialization+system+timer+thread') depends_on('python') - depends_on('cmake') - depends_on('py-numpy') + depends_on('cmake', type='build') + depends_on('py-numpy', type=nolink) # Optional dependencies # TODO: add packages for these diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py index 8ba6696b0c..e1ea71fb67 100644 --- a/var/spack/repos/builtin/packages/py-astroid/package.py +++ b/var/spack/repos/builtin/packages/py-astroid/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -from spack import depends_on, extends, version +from spack import depends_on, extends, version, nolink from spack import Package @@ -37,9 +37,9 @@ class PyAstroid(Package): version('1.4.1', 'ed70bfed5e4b25be4292e7fe72da2c02') extends('python') - depends_on('py-logilab-common') - depends_on('py-setuptools') - depends_on('py-six') + depends_on('py-logilab-common', type=nolink) + depends_on('py-setuptools', type='build') + depends_on('py-six', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py index a9962777dc..25dce87e49 100644 --- a/var/spack/repos/builtin/packages/py-astropy/package.py +++ b/var/spack/repos/builtin/packages/py-astropy/package.py @@ -38,18 +38,18 @@ class PyAstropy(Package): # Required dependencies extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) # Optional dependencies - depends_on('py-h5py') - depends_on('py-beautifulsoup4') - depends_on('py-pyyaml') - depends_on('py-scipy') + depends_on('py-h5py', type=nolink) + depends_on('py-beautifulsoup4', type=nolink) + depends_on('py-pyyaml', type=nolink) + depends_on('py-scipy', type=nolink) depends_on('libxml2') - depends_on('py-matplotlib') - depends_on('py-pytz') - depends_on('py-scikit-image') - depends_on('py-pandas') + depends_on('py-matplotlib', type=nolink) + depends_on('py-pytz', type=nolink) + depends_on('py-scikit-image', type=nolink) + depends_on('py-pandas', type=nolink) # System dependencies depends_on('cfitsio') diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py index f2fd3cd683..507664949b 100644 --- a/var/spack/repos/builtin/packages/py-autopep8/package.py +++ b/var/spack/repos/builtin/packages/py-autopep8/package.py @@ -8,8 +8,8 @@ class PyAutopep8(Package): version('1.2.2', 'def3d023fc9dfd1b7113602e965ad8e1') extends('python') - depends_on('py-setuptools') - depends_on('py-pep8') + depends_on('py-setuptools', type='build') + depends_on('py-pep8', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-basemap/package.py b/var/spack/repos/builtin/packages/py-basemap/package.py index 13f604bacd..9c7f6454df 100644 --- a/var/spack/repos/builtin/packages/py-basemap/package.py +++ b/var/spack/repos/builtin/packages/py-basemap/package.py @@ -35,10 +35,10 @@ class PyBasemap(Package): version('1.0.7', '48c0557ced9e2c6e440b28b3caff2de8') extends('python') - depends_on('py-setuptools') - depends_on('py-numpy') - depends_on('py-matplotlib+gui') - depends_on('pil') + depends_on('py-setuptools', type='build') + depends_on('py-numpy', type=nolink) + depends_on('py-matplotlib+gui', type=nolink) + depends_on('pil', type=nolink) depends_on("geos") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py index 26f42e060b..bcc889756e 100644 --- a/var/spack/repos/builtin/packages/py-biopython/package.py +++ b/var/spack/repos/builtin/packages/py-biopython/package.py @@ -32,8 +32,8 @@ class PyBiopython(Package): version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67') extends('python') - depends_on('py-mx') - depends_on('py-numpy') + depends_on('py-mx', type=nolink) + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-blessings/package.py b/var/spack/repos/builtin/packages/py-blessings/package.py index 05a1f5bcbb..8d7a2343d1 100644 --- a/var/spack/repos/builtin/packages/py-blessings/package.py +++ b/var/spack/repos/builtin/packages/py-blessings/package.py @@ -31,7 +31,7 @@ class PyBlessings(Package): version('1.6', '4f552a8ebcd4982693c92571beb99394') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends("python") diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py index 1a186b219c..2483fab85f 100644 --- a/var/spack/repos/builtin/packages/py-bottleneck/package.py +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -32,7 +32,7 @@ class PyBottleneck(Package): version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py index 58d0a81990..e54d50fa50 100644 --- a/var/spack/repos/builtin/packages/py-cffi/package.py +++ b/var/spack/repos/builtin/packages/py-cffi/package.py @@ -33,8 +33,8 @@ class PyCffi(Package): version('1.1.2', 'ca6e6c45b45caa87aee9adc7c796eaea') extends('python') - depends_on('py-setuptools') - depends_on('py-pycparser') + depends_on('py-setuptools', type='build') + depends_on('py-pycparser', type=nolink) depends_on('libffi') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py index 92a5bd0088..b7eaf58cd6 100644 --- a/var/spack/repos/builtin/packages/py-coverage/package.py +++ b/var/spack/repos/builtin/packages/py-coverage/package.py @@ -32,7 +32,7 @@ class PyCoverage(Package): version('4.0a6', '1bb4058062646148965bef0796b61efc') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends('python') diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py index 7fe2f953f7..2deaa2f74e 100644 --- a/var/spack/repos/builtin/packages/py-csvkit/package.py +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -35,12 +35,12 @@ class PyCsvkit(Package): extends('python') - depends_on('py-dateutil') - depends_on('py-dbf') - depends_on('py-xlrd') - depends_on('py-SQLAlchemy') - depends_on('py-six') - depends_on('py-openpyxl') + depends_on('py-dateutil', type=nolink) + depends_on('py-dbf', type=nolink) + depends_on('py-xlrd', type=nolink) + depends_on('py-SQLAlchemy', type=nolink) + depends_on('py-six', type=nolink) + depends_on('py-openpyxl', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py index 831f86e81c..b7dbab3d97 100644 --- a/var/spack/repos/builtin/packages/py-dask/package.py +++ b/var/spack/repos/builtin/packages/py-dask/package.py @@ -33,7 +33,7 @@ class PyDask(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py index eb8eb09e75..dfd1e143d9 100644 --- a/var/spack/repos/builtin/packages/py-dateutil/package.py +++ b/var/spack/repos/builtin/packages/py-dateutil/package.py @@ -34,8 +34,8 @@ class PyDateutil(Package): version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6') extends('python') - depends_on('py-setuptools') - depends_on('py-six') + depends_on('py-setuptools', type='build') + depends_on('py-six', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py index 90a95cd0cb..bd78f262f4 100644 --- a/var/spack/repos/builtin/packages/py-decorator/package.py +++ b/var/spack/repos/builtin/packages/py-decorator/package.py @@ -33,7 +33,7 @@ class PyDecorator(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py index d57ef4bd76..397f737cb1 100644 --- a/var/spack/repos/builtin/packages/py-emcee/package.py +++ b/var/spack/repos/builtin/packages/py-emcee/package.py @@ -35,7 +35,7 @@ class PyEmcee(Package): version('2.1.0', 'c6b6fad05c824d40671d4a4fc58dfff7') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-flake8/package.py b/var/spack/repos/builtin/packages/py-flake8/package.py index b261467d84..2fabe03d66 100644 --- a/var/spack/repos/builtin/packages/py-flake8/package.py +++ b/var/spack/repos/builtin/packages/py-flake8/package.py @@ -34,7 +34,7 @@ class PyFlake8(Package): version('2.5.4', 'a4585b3569b95c3f66acb8294a7f06ef') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-funcsigs/package.py b/var/spack/repos/builtin/packages/py-funcsigs/package.py index 9d987b284e..11ba639b85 100644 --- a/var/spack/repos/builtin/packages/py-funcsigs/package.py +++ b/var/spack/repos/builtin/packages/py-funcsigs/package.py @@ -34,7 +34,7 @@ class PyFuncsigs(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-genshi/package.py b/var/spack/repos/builtin/packages/py-genshi/package.py index cba479a88f..ea8d26c796 100644 --- a/var/spack/repos/builtin/packages/py-genshi/package.py +++ b/var/spack/repos/builtin/packages/py-genshi/package.py @@ -36,7 +36,7 @@ class PyGenshi(Package): version('0.6', '604e8b23b4697655d36a69c2d8ef7187') extends("python") - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-gnuplot/package.py b/var/spack/repos/builtin/packages/py-gnuplot/package.py index 3381c4a5ac..b08b03d1f1 100644 --- a/var/spack/repos/builtin/packages/py-gnuplot/package.py +++ b/var/spack/repos/builtin/packages/py-gnuplot/package.py @@ -32,7 +32,7 @@ class PyGnuplot(Package): version('1.8', 'abd6f571e7aec68ae7db90a5217cd5b1') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index 0180b658f5..c1950a91ac 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -41,17 +41,17 @@ class PyH5py(Package): extends('python') # Build dependencies - depends_on('py-cython@0.19:') - depends_on('pkg-config') - depends_on('hdf5@1.8.4:+mpi', when='+mpi') - depends_on('hdf5@1.8.4:~mpi', when='~mpi') + depends_on('py-cython@0.19:', type='build') + depends_on('pkg-config', type='build') + depends_on('hdf5@1.8.4:') + depends_on('hdf5+mpi', when='+mpi') depends_on('mpi', when='+mpi') # Build and runtime dependencies - depends_on('py-numpy@1.6.1:') + depends_on('py-numpy@1.6.1:', type=nolink) # Runtime dependencies - depends_on('py-six') + depends_on('py-six', type=nolink) def install(self, spec, prefix): python('setup.py', 'configure', diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py index 47751a702d..d7446c06d4 100644 --- a/var/spack/repos/builtin/packages/py-iminuit/package.py +++ b/var/spack/repos/builtin/packages/py-iminuit/package.py @@ -35,12 +35,12 @@ class PyIminuit(Package): # Required dependencies extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') # Optional dependencies - depends_on('py-numpy') - depends_on('py-matplotlib') - depends_on('py-cython') + depends_on('py-numpy', type=nolink) + depends_on('py-matplotlib', type=nolink) + depends_on('py-cython', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py index 7a94f90b38..b583609953 100644 --- a/var/spack/repos/builtin/packages/py-ipython/package.py +++ b/var/spack/repos/builtin/packages/py-ipython/package.py @@ -33,8 +33,8 @@ class PyIpython(Package): version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f') extends('python') - depends_on('py-pygments') - depends_on('py-setuptools') + depends_on('py-pygments', type=nolink) + depends_on('py-setuptools', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py index 48312d9baf..57f26e3b90 100644 --- a/var/spack/repos/builtin/packages/py-jinja2/package.py +++ b/var/spack/repos/builtin/packages/py-jinja2/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -from spack import depends_on, extends, version +from spack import depends_on, extends, version, nolink from spack import Package @@ -43,8 +43,8 @@ class PyJinja2(Package): version('2.7', 'ec70433f325051dcedacbb2465028a35') extends("python") - depends_on("py-setuptools") - depends_on("py-markupsafe") + depends_on("py-setuptools", type='build') + depends_on("py-markupsafe", type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-lockfile/package.py b/var/spack/repos/builtin/packages/py-lockfile/package.py index 998b41abc6..38cc81b895 100644 --- a/var/spack/repos/builtin/packages/py-lockfile/package.py +++ b/var/spack/repos/builtin/packages/py-lockfile/package.py @@ -41,7 +41,7 @@ class PyLockfile(Package): version('0.10.2', '1aa6175a6d57f082cd12e7ac6102ab15') extends("python") - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-logilab-common/package.py b/var/spack/repos/builtin/packages/py-logilab-common/package.py index 8675c48e9a..6dab4a40e4 100644 --- a/var/spack/repos/builtin/packages/py-logilab-common/package.py +++ b/var/spack/repos/builtin/packages/py-logilab-common/package.py @@ -22,7 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -from spack import depends_on, extends, version +from spack import depends_on, extends, version, nolink from spack import Package @@ -34,8 +34,8 @@ class PyLogilabCommon(Package): version('1.2.0', 'f7b51351b7bfe052746fa04c03253c0b') extends("python") - depends_on("py-setuptools") - depends_on("py-six") + depends_on("py-setuptools", type='build') + depends_on("py-six", type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-mako/package.py b/var/spack/repos/builtin/packages/py-mako/package.py index a03ef4defb..56741ec11f 100644 --- a/var/spack/repos/builtin/packages/py-mako/package.py +++ b/var/spack/repos/builtin/packages/py-mako/package.py @@ -33,7 +33,7 @@ class PyMako(Package): version('1.0.1', '9f0aafd177b039ef67b90ea350497a54') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends('python') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py index 58c9f70066..ee396de7be 100644 --- a/var/spack/repos/builtin/packages/py-markupsafe/package.py +++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py @@ -44,7 +44,7 @@ class PyMarkupsafe(Package): version('0.19', '64b05361adb92c11839fc470e308c593') extends("python") - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 14f9716ae6..b5eb8a53c4 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -38,19 +38,20 @@ class PyMatplotlib(Package): extends('python', ignore=r'bin/nosetests.*$|bin/pbr$') - depends_on('py-pyside', when='+gui') - depends_on('py-ipython', when='+ipython') - depends_on('py-pyparsing') - depends_on('py-six') - depends_on('py-dateutil') - depends_on('py-pytz') - depends_on('py-nose') - depends_on('py-numpy') - depends_on('py-mock') - depends_on('py-pbr') - depends_on('py-funcsigs') + depends_on('py-setuptools', type='build') + depends_on('py-pyside', when='+gui', type=nolink) + depends_on('py-ipython', when='+ipython', type=nolink) + depends_on('py-pyparsing', type=nolink) + depends_on('py-six', type=nolink) + depends_on('py-dateutil', type=nolink) + depends_on('py-pytz', type=nolink) + depends_on('py-nose', type=nolink) + depends_on('py-numpy', type=nolink) + depends_on('py-mock', type=nolink) + depends_on('py-pbr', type=nolink) + depends_on('py-funcsigs', type=nolink) - depends_on('pkg-config') + depends_on('pkg-config', type='build') depends_on('freetype') depends_on('qt', when='+gui') depends_on('bzip2') diff --git a/var/spack/repos/builtin/packages/py-mistune/package.py b/var/spack/repos/builtin/packages/py-mistune/package.py index 9bcbb5a927..399c10005e 100644 --- a/var/spack/repos/builtin/packages/py-mistune/package.py +++ b/var/spack/repos/builtin/packages/py-mistune/package.py @@ -40,7 +40,7 @@ class PyMistune(Package): version('0.5', '997736554f1f95eea78c66ae339b5722') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py index 0587131b88..f4c178de67 100644 --- a/var/spack/repos/builtin/packages/py-mock/package.py +++ b/var/spack/repos/builtin/packages/py-mock/package.py @@ -35,8 +35,8 @@ class PyMock(Package): version('1.3.0', '73ee8a4afb3ff4da1b4afa287f39fdeb') extends('python') - depends_on('py-pbr') - depends_on('py-setuptools@17.1:') + depends_on('py-pbr', type=nolink) + depends_on('py-setuptools@17.1:', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py index 2764b8b3c6..a749e16779 100644 --- a/var/spack/repos/builtin/packages/py-mpi4py/package.py +++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py @@ -33,7 +33,7 @@ class PyMpi4py(Package): version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') depends_on('mpi') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-mysqldb1/package.py b/var/spack/repos/builtin/packages/py-mysqldb1/package.py index 9918ba3e64..46b44f34dd 100644 --- a/var/spack/repos/builtin/packages/py-mysqldb1/package.py +++ b/var/spack/repos/builtin/packages/py-mysqldb1/package.py @@ -32,7 +32,7 @@ class PyMysqldb1(Package): version('1.2.5', '332c8f4955b6bc0c79ea15170bf7321b') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py index 16506e3eca..81f9fe4d09 100644 --- a/var/spack/repos/builtin/packages/py-nestle/package.py +++ b/var/spack/repos/builtin/packages/py-nestle/package.py @@ -35,10 +35,10 @@ class PyNestle(Package): # Required dependencies extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) # Optional dependencies - depends_on('py-scipy') + depends_on('py-scipy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-netcdf/package.py b/var/spack/repos/builtin/packages/py-netcdf/package.py index e3f857a0ce..9a354cb1c1 100644 --- a/var/spack/repos/builtin/packages/py-netcdf/package.py +++ b/var/spack/repos/builtin/packages/py-netcdf/package.py @@ -32,8 +32,8 @@ class PyNetcdf(Package): version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af') extends('python') - depends_on('py-numpy') - depends_on('py-cython') + depends_on('py-numpy', type=nolink) + depends_on('py-cython', type=nolink) depends_on('netcdf') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index 6bdb24e36e..d545717628 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -33,7 +33,7 @@ class PyNetworkx(Package): extends('python') - depends_on('py-decorator') + depends_on('py-decorator', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index abb2d500a2..d15a1784d1 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -37,7 +37,7 @@ class PyNose(Package): version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b') extends('python', ignore=r'bin/nosetests.*$') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index d8bacd179f..fd8d7dc0c6 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -34,7 +34,7 @@ class PyNumexpr(Package): version('2.5', '84f66cced45ba3e30dcf77a937763aaa') extends('python') - depends_on('py-numpy') + depends_on('py-numpy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index e9672b7bb0..273f5bfd8d 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -43,7 +43,7 @@ class PyNumpy(Package): variant('lapack', default=True) extends('python') - depends_on('py-nose') + depends_on('py-nose', type='build') depends_on('blas', when='+blas') depends_on('lapack', when='+lapack') diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py index 30cb52348f..624da58ff3 100644 --- a/var/spack/repos/builtin/packages/py-openpyxl/package.py +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -34,8 +34,8 @@ class PyOpenpyxl(Package): extends('python') - depends_on('py-jdcal') - depends_on('py-setuptools') + depends_on('py-jdcal', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 7f54fc5d76..8bd4227faf 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -35,12 +35,12 @@ class PyPandas(Package): version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') extends('python') - depends_on('py-dateutil') - depends_on('py-numpy') - depends_on('py-setuptools') - depends_on('py-pytz') - depends_on('py-numexpr') - depends_on('py-bottleneck') + depends_on('py-dateutil', type=nolink) + depends_on('py-numpy', type=nolink) + depends_on('py-setuptools', type='build') + depends_on('py-pytz', type=nolink) + depends_on('py-numexpr', type=nolink) + depends_on('py-bottleneck', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py index 336ea37144..8502b0b364 100644 --- a/var/spack/repos/builtin/packages/py-pbr/package.py +++ b/var/spack/repos/builtin/packages/py-pbr/package.py @@ -34,7 +34,7 @@ class PyPbr(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pep8/package.py b/var/spack/repos/builtin/packages/py-pep8/package.py index 987783b392..ffcc2b318c 100644 --- a/var/spack/repos/builtin/packages/py-pep8/package.py +++ b/var/spack/repos/builtin/packages/py-pep8/package.py @@ -8,7 +8,7 @@ class PyPep8(Package): version('1.7.0', '31070a3a6391928893cbf5fa523eb8d9') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-periodictable/package.py b/var/spack/repos/builtin/packages/py-periodictable/package.py index 7d8a635979..608f4e16c1 100644 --- a/var/spack/repos/builtin/packages/py-periodictable/package.py +++ b/var/spack/repos/builtin/packages/py-periodictable/package.py @@ -33,8 +33,8 @@ class PyPeriodictable(Package): version('1.4.1', '7246b63cc0b6b1be6e86b6616f9e866e') - depends_on('py-numpy') - depends_on('py-pyparsing') + depends_on('py-numpy', type=nolink) + depends_on('py-pyparsing', type=nolink) extends('python') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py index 68774c90c2..a3a4b7a9f7 100644 --- a/var/spack/repos/builtin/packages/py-phonopy/package.py +++ b/var/spack/repos/builtin/packages/py-phonopy/package.py @@ -33,10 +33,10 @@ class PyPhonopy(Package): version('1.10.0', '973ed1bcea46e21b9bf747aab9061ff6') extends('python') - depends_on('py-numpy') - depends_on('py-scipy') - depends_on('py-matplotlib') - depends_on('py-pyyaml') + depends_on('py-numpy', type=nolink) + depends_on('py-scipy', type=nolink) + depends_on('py-matplotlib', type=nolink) + depends_on('py-pyyaml', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--home=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index 25cf412b31..13a09f63cf 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -62,8 +62,8 @@ class PyPillow(Package): # Required dependencies extends('python') - depends_on('binutils') - depends_on('py-setuptools') + depends_on('binutils', type='build') + depends_on('py-setuptools', type='build') # Recommended dependencies depends_on('jpeg', when='+jpeg') diff --git a/var/spack/repos/builtin/packages/py-prettytable/package.py b/var/spack/repos/builtin/packages/py-prettytable/package.py index e3edc7b706..cf814733d4 100644 --- a/var/spack/repos/builtin/packages/py-prettytable/package.py +++ b/var/spack/repos/builtin/packages/py-prettytable/package.py @@ -38,7 +38,7 @@ class PyPrettytable(Package): version('0.7.2', 'a6b80afeef286ce66733d54a0296b13b') extends("python") - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py index da3a65c22e..dd2b5651de 100644 --- a/var/spack/repos/builtin/packages/py-protobuf/package.py +++ b/var/spack/repos/builtin/packages/py-protobuf/package.py @@ -44,7 +44,7 @@ class PyProtobuf(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py index 9c6e219264..02f37d8b78 100644 --- a/var/spack/repos/builtin/packages/py-py2neo/package.py +++ b/var/spack/repos/builtin/packages/py-py2neo/package.py @@ -38,7 +38,7 @@ class PyPy2neo(Package): version('2.0.5', '143b1f9c0aa22faf170c1b9f84c7343b') version('2.0.4', 'b3f7efd3344dc3f66db4eda11e5899f7') - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') extends("python") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py index c33769c526..9afba50077 100644 --- a/var/spack/repos/builtin/packages/py-pycparser/package.py +++ b/var/spack/repos/builtin/packages/py-pycparser/package.py @@ -33,7 +33,7 @@ class PyPycparser(Package): extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pydatalog/package.py b/var/spack/repos/builtin/packages/py-pydatalog/package.py new file mode 100644 index 0000000000..da157d3679 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pydatalog/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PyPydatalog(Package): + """pyDatalog adds logic programming to Python.""" + homepage = 'https://pypi.python.org/pypi/pyDatalog/' + url = 'https://pypi.python.org/packages/09/0b/2670eb9c0027aacfb5b5024ca75e5fee2f1261180ab8797108ffc941158a/pyDatalog-0.17.1.zip' + + version('0.17.1', '6b2682301200068d208d6f2d01723939') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py index fedf3d068d..0ca15dd10d 100644 --- a/var/spack/repos/builtin/packages/py-pygments/package.py +++ b/var/spack/repos/builtin/packages/py-pygments/package.py @@ -33,7 +33,7 @@ class PyPygments(Package): version('2.0.2', '238587a1370d62405edabd0794b3ec4a') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py index 66118e8228..7107b2987f 100644 --- a/var/spack/repos/builtin/packages/py-pylint/package.py +++ b/var/spack/repos/builtin/packages/py-pylint/package.py @@ -34,8 +34,8 @@ class PyPylint(Package): version('1.4.3', '5924c1c7ca5ca23647812f5971d0ea44') extends('python') - depends_on('py-nose') - depends_on('py-setuptools') + depends_on('py-nose', type='build') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pyqt/package.py b/var/spack/repos/builtin/packages/py-pyqt/package.py index b090e25682..05fb7aa22c 100644 --- a/var/spack/repos/builtin/packages/py-pyqt/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt/package.py @@ -34,7 +34,7 @@ class PyPyqt(Package): version('4.11.3', '997c3e443165a89a559e0d96b061bf70') extends('python') - depends_on('py-sip') + depends_on('py-sip', type=nolink) # TODO: allow qt5 when conditional deps are supported. # TODO: Fix version matching so that @4 works like @:4 diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py index affee6c55a..cd174ce658 100644 --- a/var/spack/repos/builtin/packages/py-pyside/package.py +++ b/var/spack/repos/builtin/packages/py-pyside/package.py @@ -32,11 +32,10 @@ class PyPyside(Package): version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d') - # TODO: make build dependency - # depends_on("cmake") + depends_on('cmake', type='build') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') depends_on('qt@:4') def patch(self): diff --git a/var/spack/repos/builtin/packages/py-pytables/package.py b/var/spack/repos/builtin/packages/py-pytables/package.py index 47592fb3d1..58ed067b21 100644 --- a/var/spack/repos/builtin/packages/py-pytables/package.py +++ b/var/spack/repos/builtin/packages/py-pytables/package.py @@ -34,9 +34,9 @@ class PyPytables(Package): extends('python') depends_on('hdf5') - depends_on('py-numpy') - depends_on('py-numexpr') - depends_on('py-cython') + depends_on('py-numpy', type=nolink) + depends_on('py-numexpr', type=nolink) + depends_on('py-cython', type=nolink) def install(self, spec, prefix): env["HDF5_DIR"] = spec['hdf5'].prefix diff --git a/var/spack/repos/builtin/packages/py-python-daemon/package.py b/var/spack/repos/builtin/packages/py-python-daemon/package.py index ae6393986d..c2c7c4de4f 100644 --- a/var/spack/repos/builtin/packages/py-python-daemon/package.py +++ b/var/spack/repos/builtin/packages/py-python-daemon/package.py @@ -42,8 +42,8 @@ class PyPythonDaemon(Package): version('2.0.5', '73e7f49f525c51fa4a995aea4d80de41') extends("python") - depends_on("py-setuptools") - depends_on("py-lockfile") + depends_on("py-setuptools", type='build') + depends_on("py-lockfile", type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-restview/package.py b/var/spack/repos/builtin/packages/py-restview/package.py index 91b1db993e..047214c58e 100644 --- a/var/spack/repos/builtin/packages/py-restview/package.py +++ b/var/spack/repos/builtin/packages/py-restview/package.py @@ -34,8 +34,8 @@ class PyRestview(Package): version('2.6.1', 'ac8b70e15b8f1732d1733d674813666b') extends('python') - depends_on('py-docutils') - depends_on('py-pygments') + depends_on('py-docutils', type=nolink) + depends_on('py-pygments', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py index 03fd2b4a06..8f4771f0eb 100644 --- a/var/spack/repos/builtin/packages/py-rpy2/package.py +++ b/var/spack/repos/builtin/packages/py-rpy2/package.py @@ -33,7 +33,7 @@ class PyRpy2(Package): version('2.5.6', 'a36e758b633ce6aec6a5f450bfee980f') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') depends_on('R') diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index 4c8fd0942a..26c286e4be 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -36,12 +36,12 @@ class PyScikitImage(Package): extends('python', ignore=r'bin/.*\.py$') - depends_on('py-dask') - depends_on('pil') - depends_on('py-networkx') - depends_on('py-six') - depends_on('py-scipy') - depends_on('py-matplotlib') + depends_on('py-dask', type=nolink) + depends_on('pil', type=nolink) + depends_on('py-networkx', type=nolink) + depends_on('py-six', type=nolink) + depends_on('py-scipy', type=nolink) + depends_on('py-matplotlib', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py index 7bb5853b19..1a6112bcf3 100644 --- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py @@ -35,9 +35,9 @@ class PyScikitLearn(Package): extends('python') - depends_on('py-setuptools') - depends_on('py-numpy') - depends_on('py-scipy') + depends_on('py-setuptools', type='build') + depends_on('py-numpy', type=nolink) + depends_on('py-scipy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index f7c372b345..ea3731cf1b 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -34,8 +34,8 @@ class PyScipy(Package): version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') extends('python') - depends_on('py-nose') - depends_on('py-numpy+blas+lapack') + depends_on('py-nose', type='build') + depends_on('py-numpy+blas+lapack', type=nolink) def install(self, spec, prefix): if 'atlas' in spec: diff --git a/var/spack/repos/builtin/packages/py-shiboken/package.py b/var/spack/repos/builtin/packages/py-shiboken/package.py index a2240c68a4..27188e1417 100644 --- a/var/spack/repos/builtin/packages/py-shiboken/package.py +++ b/var/spack/repos/builtin/packages/py-shiboken/package.py @@ -32,11 +32,10 @@ class PyShiboken(Package): version('1.2.2', '345cfebda221f525842e079a6141e555') - # TODO: make build dependency - # depends_on("cmake") + depends_on('cmake', type='build') extends('python') - depends_on("py-setuptools") + depends_on("py-setuptools", type='build') depends_on("libxml2") depends_on("qt@:4.8") diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py index 3efb3d4317..eb4846d5af 100644 --- a/var/spack/repos/builtin/packages/py-six/package.py +++ b/var/spack/repos/builtin/packages/py-six/package.py @@ -33,7 +33,7 @@ class PySix(Package): version('1.10.0', '34eed507548117b2ab523ab14b2f8b55') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py index 82ae2a2e69..feb3856e8b 100644 --- a/var/spack/repos/builtin/packages/py-sncosmo/package.py +++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py @@ -37,15 +37,15 @@ class PySncosmo(Package): # Required dependencies # py-sncosmo binaries are duplicates of those from py-astropy extends('python', ignore=r'bin/.*') - depends_on('py-numpy') - depends_on('py-scipy') - depends_on('py-astropy') + depends_on('py-numpy', type=nolink) + depends_on('py-scipy', type=nolink) + depends_on('py-astropy', type=nolink) # Recommended dependencies - depends_on('py-matplotlib') - depends_on('py-iminuit') - depends_on('py-emcee') - depends_on('py-nestle') + depends_on('py-matplotlib', type=nolink) + depends_on('py-iminuit', type=nolink) + depends_on('py-emcee', type=nolink) + depends_on('py-nestle', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-storm/package.py b/var/spack/repos/builtin/packages/py-storm/package.py index 53af720c50..0e972480f3 100644 --- a/var/spack/repos/builtin/packages/py-storm/package.py +++ b/var/spack/repos/builtin/packages/py-storm/package.py @@ -34,7 +34,7 @@ class PyStorm(Package): version('0.20', '8628503141f0f06c0749d607ac09b9c7') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tappy/package.py index a1026a9b4b..b10244acdd 100644 --- a/var/spack/repos/builtin/packages/py-tappy/package.py +++ b/var/spack/repos/builtin/packages/py-tappy/package.py @@ -33,7 +33,7 @@ class PyTappy(Package): version('1.6', 'c8bdb93ad66e05f939905172a301bedf') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py index 200a33a676..56056ebad1 100644 --- a/var/spack/repos/builtin/packages/py-tuiview/package.py +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -35,8 +35,8 @@ class PyTuiview(Package): version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30') extends("python") - depends_on("py-pyqt") - depends_on("py-numpy") + depends_on("py-pyqt", type=nolink) + depends_on("py-numpy", type=nolink) depends_on("gdal") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-twisted/package.py b/var/spack/repos/builtin/packages/py-twisted/package.py index 27db4adff4..2ce83cd24c 100644 --- a/var/spack/repos/builtin/packages/py-twisted/package.py +++ b/var/spack/repos/builtin/packages/py-twisted/package.py @@ -32,7 +32,7 @@ class PyTwisted(Package): version('15.4.0', '5337ffb6aeeff3790981a2cd56db9655') version('15.3.0', 'b58e83da2f00b3352afad74d0c5c4599') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends('python') diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py index f669a500ec..174ab0ca5f 100644 --- a/var/spack/repos/builtin/packages/py-unittest2/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2/package.py @@ -35,7 +35,7 @@ class PyUnittest2(Package): version('1.1.0', 'f72dae5d44f091df36b6b513305ea000') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py index ca857395fb..95e6dcbff0 100644 --- a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py +++ b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py @@ -36,7 +36,7 @@ class PyUnittest2py3k(Package): version('0.5.1', '8824ff92044310d9365f90d892bf0f09') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-urwid/package.py b/var/spack/repos/builtin/packages/py-urwid/package.py index 0accc72df8..48ba84e7bc 100644 --- a/var/spack/repos/builtin/packages/py-urwid/package.py +++ b/var/spack/repos/builtin/packages/py-urwid/package.py @@ -31,7 +31,7 @@ class PyUrwid(Package): version('1.3.0', 'a989acd54f4ff1a554add464803a9175') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') extends("python") diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index d42cb96eb7..d6b33ae175 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -35,7 +35,7 @@ class PyVirtualenv(Package): version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py index b0adbe3658..9588b879fa 100644 --- a/var/spack/repos/builtin/packages/py-wcsaxes/package.py +++ b/var/spack/repos/builtin/packages/py-wcsaxes/package.py @@ -35,9 +35,9 @@ class PyWcsaxes(Package): version('0.8', 'de1c60fdae4c330bf5ddb9f1ab5ab920') extends('python', ignore=r'bin/pbr') - depends_on('py-numpy') - depends_on('py-matplotlib') - depends_on('py-astropy') + depends_on('py-numpy', type=nolink) + depends_on('py-matplotlib', type=nolink) + depends_on('py-astropy', type=nolink) def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py index 68b6f3d679..9e383a9a19 100644 --- a/var/spack/repos/builtin/packages/py-wheel/package.py +++ b/var/spack/repos/builtin/packages/py-wheel/package.py @@ -33,7 +33,7 @@ class PyWheel(Package): version('0.26.0', '4cfc6e7e3dc7377d0164914623922a10') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-yapf/package.py b/var/spack/repos/builtin/packages/py-yapf/package.py index 60f740c98d..f7fe4037a1 100644 --- a/var/spack/repos/builtin/packages/py-yapf/package.py +++ b/var/spack/repos/builtin/packages/py-yapf/package.py @@ -33,7 +33,7 @@ class PyYapf(Package): version('0.2.1', '348ccf86cf2057872e4451b204fb914c') extends('python') - depends_on('py-setuptools') + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 8033c52b91..516b5c6cfe 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -38,15 +38,30 @@ class Python(Package): homepage = "http://www.python.org" url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz" + version('3.5.2', '3fe8434643a78630c61c6464fe2e7e72') version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe') version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36') - version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True) + version('3.4.3', '4281ff86778db65892c05151d5de738d') + version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9') + version('3.2.6', '23815d82ae706e9b781ca65865353d39') + version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab') + version('2.7.12', '88d61f82e3616a4be952828b3694109d', preferred=True) + version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b') version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521') version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') extendable = True + variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings') + # From https://docs.python.org/2/c-api/unicode.html: Python's default + # builds use a 16-bit type for Py_UNICODE and store Unicode values + # internally as UCS2. It is also possible to build a UCS4 version of Python + # (most recent Linux distributions come with UCS4 builds of Python). These + # builds then use a 32-bit type for Py_UNICODE and store Unicode data + # internally as UCS4. Note that UCS2 and UCS4 Python builds are not binary + # compatible. + depends_on("openssl") depends_on("bzip2") depends_on("readline") @@ -82,6 +97,15 @@ class Python(Package): "LDFLAGS=-L{0}".format(ldflags) ] + if '+ucs4' in spec: + if spec.satisfies('@:2.7'): + config_args.append('--enable-unicode=ucs4') + elif spec.satisfies('@3.0:3.2'): + config_args.append('--with-wide-unicode') + elif spec.satisfies('@3.3:'): + # https://docs.python.org/3.3/whatsnew/3.3.html + raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond') # NOQA: ignore=E501 + if spec.satisfies('@3:'): config_args.append('--without-ensurepip') @@ -141,7 +165,7 @@ class Python(Package): extension and any other python extensions it depends on.""" python_paths = [] - for d in extension_spec.traverse(): + for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): if d.package.extends(self.spec): python_paths.append(join_path(d.prefix, self.site_packages_dir)) diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py index 280c9cc12c..f7cbcc2736 100644 --- a/var/spack/repos/builtin/packages/qhull/package.py +++ b/var/spack/repos/builtin/packages/qhull/package.py @@ -45,7 +45,7 @@ class Qhull(Package): # https://github.com/qhull/qhull/pull/5 patch('qhull-iterator.patch', when='@1.0') - depends_on('cmake') + depends_on('cmake', type='build') def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 0c91a5ce87..f33e5c2d0e 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -60,8 +60,8 @@ class Qt(Package): # Webkit # depends_on("gperf") - # depends_on("flex") - # depends_on("bison") + # depends_on("flex", type='build') + # depends_on("bison", type='build') # depends_on("ruby") # depends_on("icu4c") diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py new file mode 100644 index 0000000000..4070b6fe8d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RAssertthat(Package): + """assertthat is an extension to stopifnot() that makes it easy to declare + the pre and post conditions that you code should satisfy, while also + producing friendly error messages so that your users know what they've done + wrong.""" + + homepage = "https://cran.r-project.org/web/packages/assertthat/index.html" + url = "https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz" + + version('0.1', '59f9d7f7c00077ea54d763b78eeb5798') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py new file mode 100644 index 0000000000..b065e0b817 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDplyr(Package): + """A fast, consistent tool for working with data frame like objects, both + in memory and out of memory.""" + + homepage = "https://github.com/hadley/dplyr" + url = "https://cran.r-project.org/src/contrib/dplyr_0.5.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/dplyr" + + version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef') + + extends('R') + depends_on('r-assertthat') + depends_on('r-R6') + depends_on('r-rcpp') + depends_on('r-tibble') + depends_on('r-magrittr') + depends_on('r-lazyeval') + depends_on('r-dbi') + depends_on('r-bh') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py new file mode 100644 index 0000000000..8fc1f397c8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGgvis(Package): + """An implementation of an interactive grammar of graphics, taking the best + parts of 'ggplot2', combining them with the reactive framework from 'shiny' + and web graphics from 'vega'.""" + + homepage = "http://ggvis.rstudio.com/" + url = "https://cran.r-project.org/src/contrib/ggvis_0.4.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggvis" + + version('0.4.2', '039f45e5c7f1e0652779163d7d99f922') + + extends('R') + + depends_on('r-assertthat') + depends_on('r-jsonlite') + depends_on('r-shiny') + depends_on('r-magrittr') + depends_on('r-dplyr') + depends_on('r-lazyeval') + depends_on('r-htmltools') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py new file mode 100644 index 0000000000..0aea564372 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RHtmltools(Package): + """Tools for HTML generation and output.""" + + homepage = "https://github.com/rstudio/htmltools" + url = "https://cran.r-project.org/src/contrib/htmltools_0.3.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/htmltools" + + version('0.3.5', '5f001aff4a39e329f7342dcec5139724') + + extends('R') + + depends_on('r-digest') + depends_on('r-rcpp') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py new file mode 100644 index 0000000000..6ab12bcf9d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RHttpuv(Package): + """Provides low-level socket and protocol support for handling HTTP and + WebSocket requests directly from within R. It is primarily intended as a + building block for other packages, rather than making it particularly easy + to create complete web applications using httpuv alone. httpuv is built on + top of the libuv and http-parser C libraries, both of which were developed + by Joyent, Inc. (See LICENSE file for libuv and http-parser license + information.)""" + + homepage = "https://github.com/rstudio/httpuv" + url = "https://cran.r-project.org/src/contrib/httpuv_1.3.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/httpuv" + + version('1.3.3', 'c78ae068cf59e949b9791be987bb4489') + + extends('R') + + depends_on('r-rcpp') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py new file mode 100644 index 0000000000..f80fb4d272 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RLazyeval(Package): + """An alternative approach to non-standard evaluation using formulas. + Provides a full implementation of LISP style 'quasiquotation', making it + easier to generate code with other code.""" + + homepage = "https://cran.r-project.org/web/packages/lazyeval/index.html" + url = "https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lazyeval" + + version('0.2.0', 'df1daac908dcf02ae7e12f4335b1b13b') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py new file mode 100644 index 0000000000..88576911f0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RLubridate(Package): + """Functions to work with date-times and timespans: fast and user friendly + parsing of date-time data, extraction and updating of components of a + date-time (years, months, days, hours, minutes, and seconds), algebraic + manipulation on date-time and timespan objects. The 'lubridate' package has + a consistent and memorable syntax that makes working with dates easy and + fun.""" + + homepage = "https://cran.r-project.org/web/packages/lubridate/index.html" + url = "https://cran.r-project.org/src/contrib/lubridate_1.5.6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lubridate" + + version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') + + extends('R') + depends_on('r-stringr') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py new file mode 100644 index 0000000000..a9a9532910 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -0,0 +1,52 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RShiny(Package): + """Makes it incredibly easy to build interactive web applications with R. + Automatic "reactive" binding between inputs and outputs and extensive + pre-built widgets make it possible to build beautiful, responsive, and + powerful applications with minimal effort.""" + + homepage = "http://shiny.rstudio.com/" + url = "https://cran.r-project.org/src/contrib/shiny_0.13.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/shiny" + + version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611') + + extends('R') + + depends_on('r-httpuv') + depends_on('r-mime') + depends_on('r-jsonlite') + depends_on('r-xtable') + depends_on('r-digest') + depends_on('r-htmltools') + depends_on('r-R6') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py new file mode 100644 index 0000000000..837c3df603 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RTibble(Package): + """Provides a 'tbl_df' class that offers better checking and printing + capabilities than traditional data frames.""" + + homepage = "https://github.com/hadley/tibble" + url = "https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/tibble" + + version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') + + extends('R') + + depends_on('r-assertthat') + depends_on('r-lazyeval') + depends_on('r-rcpp') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py new file mode 100644 index 0000000000..2db7b174c2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RTidyr(Package): + """An evolution of 'reshape2'. It's designed specifically for data tidying + (not general reshaping or aggregating) and works well with 'dplyr' data + pipelines.""" + + homepage = "https://github.com/hadley/tidyr" + url = "https://cran.r-project.org/src/contrib/tidyr_0.5.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/tidyr" + + version('0.5.1', '3cadc869510c054ed93d374ab44120bd') + + extends('R') + depends_on('r-tibble') + depends_on('r-dplyr') + depends_on('r-stringi') + depends_on('r-lazyeval') + depends_on('r-magrittr') + depends_on('r-rcpp') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py new file mode 100644 index 0000000000..46434b4842 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xtable/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RXtable(Package): + """Coerce data to LaTeX and HTML tables.""" + + homepage = "http://xtable.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/xtable" + + version('1.8-2', '239e4825cd046156a67efae3aac01d86') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/ravel/package.py b/var/spack/repos/builtin/packages/ravel/package.py index 763ec1b9a2..96692ac7c1 100644 --- a/var/spack/repos/builtin/packages/ravel/package.py +++ b/var/spack/repos/builtin/packages/ravel/package.py @@ -33,8 +33,7 @@ class Ravel(Package): version('1.0.0', 'b25fece58331c2adfcce76c5036485c2') - # TODO: make this a build dependency - depends_on('cmake@2.8.9:') + depends_on('cmake@2.8.9:', type='build') depends_on('muster@1.0.1:') depends_on('otf') diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py index b8a65e8574..bcd317eb8f 100644 --- a/var/spack/repos/builtin/packages/rose/package.py +++ b/var/spack/repos/builtin/packages/rose/package.py @@ -40,9 +40,9 @@ class Rose(Package): patch('add_spack_compiler_recognition.patch') - depends_on("autoconf@2.69") - depends_on("automake@1.14") - depends_on("libtool@2.4") + depends_on("autoconf@2.69", type='build') + depends_on("automake@1.14", type='build') + depends_on("libtool@2.4", type='build') depends_on("boost@1.54.0") depends_on("jdk@8u25-linux-x64") diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index 2f6e42c439..c2bad20c2f 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -45,8 +45,8 @@ class Scotch(Package): variant('shared', default=True, description='Build a shared version of the library') variant('metis', default=True, description='Build metis and parmetis wrapper libraries') - depends_on('flex') - depends_on('bison') + depends_on('flex', type='build') + depends_on('bison', type='build') depends_on('mpi', when='+mpi') depends_on('zlib', when='+compression') diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py index ff6fd2da9b..ebca74a3ab 100644 --- a/var/spack/repos/builtin/packages/serf/package.py +++ b/var/spack/repos/builtin/packages/serf/package.py @@ -36,7 +36,7 @@ class Serf(Package): depends_on('apr') depends_on('apr-util') - depends_on('scons') + depends_on('scons', type='build') depends_on('expat') depends_on('openssl') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/slepc/install_name_371.patch b/var/spack/repos/builtin/packages/slepc/install_name_371.patch new file mode 100644 index 0000000000..d02ca88657 --- /dev/null +++ b/var/spack/repos/builtin/packages/slepc/install_name_371.patch @@ -0,0 +1,32 @@ +From 7489a3f3d569e2fbf5513ac9dcd769017d9f7eb7 Mon Sep 17 00:00:00 2001 +From: Lisandro Dalcin <dalcinl@gmail.com> +Date: Thu, 2 Jun 2016 21:57:38 +0300 +Subject: [PATCH] OS X: Fix library path in invocation of install_name_tool + +--- + config/install.py | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/config/install.py b/config/install.py +index 09acd03..6ce98ae 100755 +--- a/config/install.py ++++ b/config/install.py +@@ -25,6 +25,7 @@ class Installer: + + def setupDirectories(self): + self.installDir = self.destDir ++ self.archDir = os.path.join(self.rootDir, self.arch) + self.rootIncludeDir = os.path.join(self.rootDir, 'include') + self.archIncludeDir = os.path.join(self.rootDir, self.arch, 'include') + self.rootConfDir = os.path.join(self.rootDir, 'lib','slepc','conf') +@@ -220,7 +221,7 @@ for dir in dirs: + if os.path.splitext(dst)[1] == '.dylib' and os.path.isfile('/usr/bin/install_name_tool'): + (result, output) = commands.getstatusoutput('otool -D '+src) + oldname = output[output.find("\n")+1:] +- installName = oldname.replace(self.destDir, self.installDir) ++ installName = oldname.replace(self.archDir, self.installDir) + (result, output) = commands.getstatusoutput('/usr/bin/install_name_tool -id ' + installName + ' ' + dst) + # preserve the original timestamps - so that the .a vs .so time order is preserved + shutil.copystat(src,dst) +-- +2.7.4.1.g5468f9e diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index d3739bf6a6..fd6c42d9fc 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -28,7 +28,7 @@ from spack import * class Slepc(Package): """ - Scalable Library for Eigenvalue Computations. + Scalable Library for Eigenvalue Problem Computations. """ homepage = "http://www.grycap.upv.es/slepc" @@ -45,9 +45,13 @@ class Slepc(Package): depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi') depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi') + patch('install_name_371.patch', when='@3.7.1') + def install(self, spec, prefix): # set SLEPC_DIR for installation - os.environ['SLEPC_DIR'] = self.stage.source_path + # Note that one should set the current (temporary) directory instead + # its symlink in spack/stage/ ! + os.environ['SLEPC_DIR'] = os.getcwd() options = [] @@ -67,9 +71,10 @@ class Slepc(Package): configure('--prefix=%s' % prefix, *options) make('MAKE_NP=%s' % make_jobs, parallel=False) - # FIXME: - # make('test') - make('install') + if self.run_tests: + make('test', parallel=False) + + make('install', parallel=False) def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # set up SLEPC_DIR for everyone using SLEPc package diff --git a/var/spack/repos/builtin/packages/spot/package.py b/var/spack/repos/builtin/packages/spot/package.py index 59535dcc4c..21bb6f03a7 100644 --- a/var/spack/repos/builtin/packages/spot/package.py +++ b/var/spack/repos/builtin/packages/spot/package.py @@ -32,7 +32,7 @@ class Spot(Package): version('1.99.3', 'd53adcb2d0fe7c69f45d4e595a58254e') - #depends_on("gcc@4.8:") + #depends_on("gcc@4.8:", type='build') depends_on("python@3.2:") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py index 80d27e149f..a03713397b 100644 --- a/var/spack/repos/builtin/packages/stat/package.py +++ b/var/spack/repos/builtin/packages/stat/package.py @@ -39,7 +39,7 @@ class Stat(Package): depends_on('libdwarf') depends_on('dyninst') depends_on('graphlib') - depends_on('graphviz') + depends_on('graphviz', type=alldeps) depends_on('launchmon') depends_on('mrnet') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index dd0dfa3e23..2cc89b843f 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -33,6 +33,7 @@ class SuiteSparse(Package): url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + version('4.5.3', '8ec57324585df3c6483ad7f556afccbd') # FIXME: (see below) # variant('tbb', default=True, description='Build with Intel TBB') @@ -40,34 +41,35 @@ class SuiteSparse(Package): depends_on('blas') depends_on('lapack') - depends_on('metis@5.1.0', when='@4.5.1') + depends_on('metis@5.1.0', when='@4.5.1:') # FIXME: - # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags - # does not seem to be used, which leads to linking errors on Linux. + # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng + # flags does not seem to be used, which leads to linking errors on Linux. # Try re-enabling in future versions. # depends_on('tbb', when='+tbb') def install(self, spec, prefix): - # The build system of SuiteSparse is quite old-fashioned - # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) - # with a lot of convoluted logic in it. - # Any kind of customization will need to go through filtering of that file + # The build system of SuiteSparse is quite old-fashioned. + # It's basically a plain Makefile which include an header + # (SuiteSparse_config/SuiteSparse_config.mk)with a lot of convoluted + # logic in it. Any kind of customization will need to go through + # filtering of that file make_args = ['INSTALL=%s' % prefix] # inject Spack compiler wrappers make_args.extend([ - 'AUTOCC=no', - 'CC=cc', - 'CXX=c++', - 'F77=f77', + 'AUTOCC=no', + 'CC=cc', + 'CXX=c++', + 'F77=f77', ]) # use Spack's metis in CHOLMOD/Partition module, # otherwise internal Metis will be compiled make_args.extend([ - 'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib, - 'MY_METIS_INC=%s' % spec['metis'].prefix.include, + 'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib, + 'MY_METIS_INC=%s' % spec['metis'].prefix.include, ]) # Intel TBB in SuiteSparseQR @@ -78,10 +80,13 @@ class SuiteSparse(Package): ]) # BLAS arguments require path to libraries - # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make_args.extend([ - 'BLAS=-lblas', - 'LAPACK=-llapack' - ]) + # FIXME: (blas/lapack always provide libblas and liblapack as aliases) + if '@4.5.1' in spec: + # adding -lstdc++ is clearly an ugly way to do this, but it follows + # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk + make_args.extend([ + 'BLAS=-lblas -lstdc++', + 'LAPACK=-llapack' + ]) make('install', *make_args) diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py index c55198a850..e52b90eb8a 100644 --- a/var/spack/repos/builtin/packages/sundials/package.py +++ b/var/spack/repos/builtin/packages/sundials/package.py @@ -42,6 +42,7 @@ class Sundials(Package): variant('openmp', default=False, description='Enable OpenMP support') variant('pthread', default=True, description='Enable POSIX threads support') + depends_on('cmake', type='build') depends_on('mpi', when='+mpi') depends_on('blas', when='+lapack') depends_on('lapack', when='+lapack') diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py index f8bb91acd9..620d658a10 100644 --- a/var/spack/repos/builtin/packages/swiftsim/package.py +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -43,10 +43,10 @@ class Swiftsim(Package): variant('mpi', default=True, description='Enable distributed memory parallelism') # Build dependencies - depends_on('autoconf') - depends_on('automake') - depends_on('libtool') - depends_on('m4') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') # link-time / run-time dependencies depends_on('mpi', when='+mpi') depends_on('metis') diff --git a/var/spack/repos/builtin/packages/task/package.py b/var/spack/repos/builtin/packages/task/package.py index dc52c4f9f6..8c3b412f48 100644 --- a/var/spack/repos/builtin/packages/task/package.py +++ b/var/spack/repos/builtin/packages/task/package.py @@ -31,6 +31,7 @@ class Task(Package): version('2.4.4', '517450c4a23a5842df3e9905b38801b3') + depends_on('cmake', type='build') depends_on("gnutls") depends_on("libuuid") # depends_on("gcc@4.8:") diff --git a/var/spack/repos/builtin/packages/taskd/package.py b/var/spack/repos/builtin/packages/taskd/package.py index 8a022b4fe9..1d7f9ed49e 100644 --- a/var/spack/repos/builtin/packages/taskd/package.py +++ b/var/spack/repos/builtin/packages/taskd/package.py @@ -32,6 +32,7 @@ class Taskd(Package): version('1.1.0', 'ac855828c16f199bdbc45fbc227388d0') + depends_on('cmake', type='build') depends_on("libuuid") depends_on("gnutls") diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py index c301a5b4e5..97aa68be65 100644 --- a/var/spack/repos/builtin/packages/tetgen/package.py +++ b/var/spack/repos/builtin/packages/tetgen/package.py @@ -38,9 +38,7 @@ class Tetgen(Package): version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18') version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz') - # TODO: Make this a build dependency once build dependencies are supported - # (see: https://github.com/LLNL/spack/pull/378). - depends_on('cmake@2.8.7:', when='@1.5.0:') + depends_on('cmake@2.8.7:', when='@1.5.0:', type='build') def install(self, spec, prefix): make('tetgen', 'tetlib') diff --git a/var/spack/repos/builtin/packages/the_platinum_searcher/package.py b/var/spack/repos/builtin/packages/the_platinum_searcher/package.py index 9c9a66cdef..0d2c2918c4 100644 --- a/var/spack/repos/builtin/packages/the_platinum_searcher/package.py +++ b/var/spack/repos/builtin/packages/the_platinum_searcher/package.py @@ -12,7 +12,7 @@ class ThePlatinumSearcher(Package): version('head', go=package) - extends("go") + extends("go", deptypes='build') def install(self, spec, prefix): env = os.environ diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py index e289b6d783..988619df30 100644 --- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py +++ b/var/spack/repos/builtin/packages/the_silver_searcher/package.py @@ -33,7 +33,7 @@ class TheSilverSearcher(Package): depends_on('pcre') depends_on('xz') - depends_on('pkg-config') + depends_on('pkg-config', type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index 6d834c6321..025ee2b885 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -41,12 +41,12 @@ class Thrift(Package): variant('python', default=True, description="Build support for python") depends_on('jdk') - depends_on('autoconf') - depends_on('automake') - depends_on('libtool') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') depends_on('boost@1.53:') - depends_on('bison') - depends_on('flex') + depends_on('bison', type='build') + depends_on('flex', type='build') depends_on('openssl') # Variant dependencies diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 3a53ac5c01..56499af8d9 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -68,6 +68,8 @@ class Trilinos(Package): variant('debug', default=False, description='Builds a debug version of the libraries') variant('boost', default=True, description='Compile with Boost') + depends_on('cmake', type='build') + # Everything should be compiled with -fpic depends_on('blas') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py index f66c20894b..e0dfb64879 100644 --- a/var/spack/repos/builtin/packages/vim/package.py +++ b/var/spack/repos/builtin/packages/vim/package.py @@ -60,7 +60,7 @@ class Vim(Package): depends_on('ruby', when='+ruby') variant('cscope', default=False, description="build with cscope support") - depends_on('cscope', when='+cscope') + depends_on('cscope', when='+cscope', type='run') variant('gui', default=False, description="build with gui (gvim)") # virtual dependency? diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index d2296dbc26..5c196b5ea8 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -37,6 +37,7 @@ class Vtk(Package): version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d') + depends_on('cmake', type='build') depends_on("qt") # VTK7 defaults to OpenGL2 rendering backend |