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2017-04-26link_tree: ported to pytest (#4008)Massimiliano Culpo1-89/+98
2017-04-26Add latest version of libx11 (#4011)Adam J. Stewart1-1/+2
2017-04-26Add latest version of libxpm (#4012)Adam J. Stewart1-1/+2
2017-04-26Add latest version of libxrender (#4013)Adam J. Stewart1-2/+3
2017-04-26Add latest version of xproto (#4010)Adam J. Stewart1-1/+2
2017-04-26Add latest version of libpthread-stubs (#4009)Adam J. Stewart1-1/+2
2017-04-26Add latest version of fontconfig (#4007)Adam J. Stewart1-5/+7
2017-04-26Add missing readline dependency to sqlite (#4001)Adam J. Stewart1-7/+9
* Add missing readline dependency to sqlite * Fix typo
2017-04-26matplotlib and basemap require setuptools to run properly together (#3835)Gregory Lee2-78/+8
* matplotlib and basemap require setuptools to run properly together * flake 8 fix
2017-04-26Update checksum for dummy xsdk package (#4002)Barry Smith1-2/+2
Commit-type: bug-fix Funded-by: IDEAS Project: xSDK Reported-by: "Klinvex, Alicia Marie" <amklinv@sandia.gov>
2017-04-26Add __format__ support to version for fancy formatting. (#3996)Todd Gamblin1-0/+3
- add Version.__format__ to support new-style formatting. - Python3 doesn't handle this well -- it delegates to object.__format__(), which raises an error for fancy format strings. - not sure why it doesn't call str(self).__format__ instead, but that's hwo things are.
2017-04-26Add list_url for bzip2 (#3988)Adam J. Stewart1-0/+1
2017-04-26add kokkos package (#3997)Jeffrey Salmond1-0/+61
* add kokkos package * fix flake8 * add descriptions to kokkos variants
2017-04-26gasnet: build with fPIC for shared lib consumers (#3962)Christoph Junghans1-3/+9
2017-04-26Add ncurses as zsh dependency (#3991)jadoro1-0/+1
zsh build will fail with configure: error: "No terminal handling library was found on your system." if ncurses is not found.
2017-04-26perl: identify dependency on gdbm (#3896)Milton Woods1-1/+5
* perl: provide +gdbm variant for use when system dbm is missing or buggy * perl: remove gdbm variant; always depends on gdbm * perl: pass gdbm paths as Configure arguments
2017-04-26ipopt: fix build with Linux clang (#3995)futuretristan1-0/+1
2017-04-25Add API Docs for lib/spack/llnl (#3982)Adam J. Stewart10-101/+130
* Add API Docs for lib/spack/llnl * Clean up after previous builds * Better fix for purging API docs
2017-04-25Fix bug with '# noqa' filtering (#3993)Adam J. Stewart2-10/+9
2017-04-26Make perl and python variants (#3992)George Hartzell1-1/+20
The blast+ configure script supports building --with-{python,perl}=path and --without-{python,perl}. This commit makes the use of those two languages configurable via variants and adds dependencies and explicit --with-... or --without-... flags to configure. Python was a non-optional dependency, now it is a variant that defaults to `True`. Perl was not previously an explicit dependency but the configure script was likely to discover one on your system (`/usr/bin/perl`). It is now a variant that defaults to `True`. I am unable to accurately determine what these flags to the configure script enable. My users are frustrated by the dependency on Python in particular because it constrains the other modules that they can have loaded for new discernible benefit.
2017-04-25xsdk version 0.2.0 (#3928)Barry Smith8-25/+210
* xSDK: a bundle/meta package that simple installs a series of packages with suitable specs This is based on struggles with previous attempts at such a bundler Funded-by: IDEAS Project: IDEAS/xSDK Time: 12 hours * PETSc needs c++11 when built with Trilinos * Added alquimia package * remove direct setting of cpp in petsc/package.py since it doesn't work on some systems. Funded-by: IDEAS Project: IDEAS/xSDK Time: .3 hours Reported-by: Mark A. Berrill <berrillma@ornl.gov> * provide the MPI compilers to PETSc configure with --with-cc etc instead of --with-mpi-dir Funded-by: IDEAS Project: IDEAS/xSDK * Spack bug fix issue #3144 String could contain /n which resulting in spack generating warning message to stderr on each use of compiler which configure interpreted as failing compiler Thanks-to: Mark A. Berrill <berrillma@ornl.gov> * Fixed alquimia package Alquimia expects PETSC_DIR and PETSC_ARCH to be defined, and refuses to install if they are not. Spack does not define PETSC_ ARCH, so Alquimia will not install. This patch does two things to fix the alquimia build: 1. A patch has been added to remove the dependency on PETSC_ARCH. 2. Alquimia currently depends on old versions of PETSc and pflotran. @ghammond86 updated the alquimia interfaces to use more recent versions, but his patch is still sitting in an alquimia pull request. As a result, the spack installer now uses his fork of alquimia. This is a temporary fix until his pull request is accepted. * Need to pass to Alquimia the MPI compilers, not the raw compilers Otherwise the PETSc tests do not produce executables that can run because they are not linked against MPI libraries Funded-by: IDEAS Project: IDEAS/xSDK Time: .5 hours * Add alquimia to xSDK build Funded-by: IDEAS Project: IDEAS/xSDK * Fix flake8 errors for xsdk packages * Add xsdk support for xsdk version xsdk-0.2.0 Note that currently it is just dummy code, but will eventually use a xsdk-0.2.0 tag for each package it installs. Funded-by: IDEAS Project: IDEAS/xSDK Time: .7 hours * Do not build Mumps by default for PETSc since it is not portable, for example to Cray Allow alquimia to accept PETSc even if the PETSc test executable cannot run since this is a problem on Cray. Reported-by: Alicia Marie Klinvex <amklinv@sandia.gov> * Add xsdk-0.2.0-rc1 tag for xsdk-0.2.0 installs * Switch alquimia download site back to standard location since they have incorporated Glenn Hammond's fixes Also it no longer needs the patch to the Alquimia cmake Funded-by: IDEAS Project: IDEAS/xSDK Reported-by: Sergi Molins Rafa <smolins@lbl.gov> * update hypre to use the latest release candidate for xsdk 0.2.0 Funded-by: IDEAS Project: IDEAS/xSDK Reported-by: Ulrike Meier Yang <yang11@llnl.gov> * Re-added patch to alquimia The patch was out of date and has been updated accordingly. * Added Tpetra-free option to Trilinos The Tpetra stack takes forever to build and is not used by any of the IDEAS teams, so there should be an option to disable it. I have added this option and updated the xSDK accordingly. I also disabled xSDKTrilinos in the xSDK, since none of the apps teams currently use it, and it's largely Tpetra-based. * Removed alquimia patch from develop version The patch has been incorporated into alquimia and is no longer necessary for the develop version. The tagged version has not been updated accordingly and still needs the patch for now. (When the tagged version gets updated, the patch does need to be removed from spack altogether, or it will break the build.) * Removed patch from alquimia It has been incorporated into alquimia, both the develop and rc2 tagged versions. The 0.2.0 version of alquimia has been updated to tag rc2 rather than rc1. * update xsdk-0.2.0 to depend on PETSc xsdk-0.2.0-rc2 which fixes for Apple xcode 8.3 Commit-type: bug-fix Funded-by: IDEAS Project: IDEAS/xSDK * import sys got lost in merge with develop * Update xsdk packages to use xsdk-0.2.0 tag Commit-type: feature Funded-by: IDEAS Project: ECP * Fixes for Flake8 note, had to ignore some long lines due to a single string * simple improvements to XDK packages as suggested by Spack pull request reviewers Commit-type: style-fix Funded-by: IDEAS Project: xSDK * Removed unneeded : after develop as requested by Denis Davydov in pull request review Commit-type: style-fix Funded-by: IDEAS Project: xSDK Thanks-to: Denis Davydov * Removed change that may not be needed due to updates in PETSc spack file such as using mpicc etc directly Commit-type: bug-fix Funded-by: IDEAS Project: xSDK Thanks-to: Adam J. Stewart * Do not turn on xSDKTrilinos for xSDK builds since it requires tpetra Commit-type: bug-fix Funded-by: IDEAS Project: xSDK * comment why MUMPS is disabled by default for PETSc so that others won't try to enable it when modifying petsc package next time Commit-type: documentation Funded-by: IDEAS Project: xSDK Thanks-to: Denis Davydov
2017-04-25Add latest version of freetype (#3989)Adam J. Stewart1-3/+4
2017-04-25Add latest version of libpng (#3987)Adam J. Stewart1-1/+2
2017-04-25Mark 1.64.0 unstable until +mpi+python fixed. (#3984)Adam J. Stewart1-1/+8
2017-04-25Add list_url for fftw (#3985)Adam J. Stewart1-0/+1
2017-04-25New package: pax-utils (#3980)Christoph Junghans1-0/+35
2017-04-25spack flake8 should exempt line-wrapped directives (#3990)Todd Gamblin1-8/+8
- Omit final paren from regular expressions in cmd/flake8.py - Allows long directives to be exempted even if they are wrapped.
2017-04-25hooks take spec as an argument (instead of pkg) (#3967)Massimiliano Culpo6-23/+27
2017-04-25Properly ignore flake8 F811 redefinition errors (#3932)Adam J. Stewart8-41/+324
* Properly ignore flake8 F811 redefinition errors * Add unit tests for flake8 command * Allow spack flake8 to work on systems with older git * Skip flake8 unit tests for Python 2.6 and 3.3
2017-04-25Add latest version of NCO (#3978)Adam J. Stewart1-1/+2
2017-04-25Add patch to gettext to fix parallel make check (#3981)Adam J. Stewart2-10/+63
2017-04-25legion: add mpi interoperability and shared libs (#3959)Christoph Junghans1-2/+14
* legion: add mpi inoperability * legion: make +mpi the default * legion: add shared variant
2017-04-25A new package: CNTK. (#3578)健美猫6-0/+670
2017-04-24Add global arrays package (#3970)serbanmaerean2-0/+310
* Added magma package * Incorporated Serban's change * globalarrays: add global arrays package to Spack. * globalarray: remove extreaneous comment from package file
2017-04-24Rename tutorial_sc16.rst to tutorial.rst (#3974)Todd Gamblin5-4/+4
- make the name more generic for posterity.
2017-04-24Caffe (#3948)Brian Van Essen2-1/+7
* Added a package for the MDAnalysis toolkit. * Added the hash for the 1.0 release of caffe and put in a conflict statemet indicating that protobuf requires a c++11 compiler. * Changed minimum version number. * Tweaked the minimum version number. * Fixed flake8 error.
2017-04-23Use six.moves.input instead of raw_input (#3961)Adam J. Stewart2-3/+4
* Use six.moves.input instead of raw_input * Remove comment mentioning raw_input
2017-04-23Do not require license for new Intel libraries (#3931)Gregory Lee3-11/+34
* new Intel libs do not require license to install * updated Intel library package URLs * disable license_required for new Intel libraries
2017-04-23Update ECWMF packages: grib-api, libemos and magics (#3901)Milton Woods3-2/+15
* grib-api: add version 1.21.0 * libemos: add version 4.4.7 and allow choice of eccodes or grib-api * magics: add version 2.32.0 * libemos: add description for eccodes variant
2017-04-23eccodes: new package for encoding and decoding meteorological data (#3900)Milton Woods1-0/+67
* eccodes: new package for encoding and decoding meteorological data * eccodes: remove line breaks from package docstring * eccodes: simplify names of variants * eccodes: give a description for each variant * eccodes: use succinct code for cmake_args * eccodes: found extra dependency for python variant * eccodes: add URL for a list of available releases
2017-04-22External packages are now registered in the DB (#1167)Massimiliano Culpo15-57/+230
* treats correctly a change from `explicit=False` to `explicit=True` in an external package DB entry. * added unit tests * fixed issues raised by @tgamblin . In particular the PR is no more hash-changing for packages that are not external. * added a test to check correctness of a spec/yaml round-trip for things that involve an external * Don't find external module path at each step of concretization * it's not necessary.. The paths are retrieved at the end of concretizaion * Don't find replacements for external packages. * Test root of the DAG if external * No reason not to test if the root of the DAG is external when external packages are now first class citizens! * Create `external` property for Spec (for external_path and external_module) * Allow users to specify external package paths relative to spack * Canonicalize external package paths so that users may specify their locations relative to spack's directory. * Update tests to use new external_path and external properly. * skip license hooks on external
2017-04-22Hack to fix python dependency ranges (#3938)Adam J. Stewart41-48/+46
* Hack to fix python dependency ranges * Flake8
2017-04-22Find more versions from GitHub (#3952)Adam J. Stewart1-1/+1
2017-04-22Add version info for emacs@25.2 (#3957)George Hartzell1-0/+1
2017-04-22add Intel mpi package and add MPI wrappers to Intel parallel studio (#3905)Denis Davydov3-0/+90
* intel-mpi: add new package * fix hashes * fix typo * flake8 * add install * blank line * error * add bin64 * fix MPI wrappers in intel-parallel-studio * add missing I_MPI_FC * use shorter hashes
2017-04-21more fixes for use of setuptools in python packagesMatthew Krafczyk3-1/+37
- py-setuptools is required by py-yt for importing yt in jupyter notebooks. - add two dependencies needed for python 2.7 - add the py-subprocess32 package
2017-04-21Fix setuptools handling in Python packages.Paul Hopkins12-5/+8
- add setuptools dependencies to packages that need it. - remove setuptools from packages that do not need it.
2017-04-21PythonPackage builds flat installs instead of egg directories.Todd Gamblin19-27/+63
- Spack doesn't need eggs -- it manages its own directories - Simplify install layout and reduce sys.path searches by installing all packages flat (eggs are deprecated for wheels, and this is also what wheels do). - We now supply the --single-version-externally-managed argument to `setup.py install` for setuptools packages and setuptools. - modify packages to only use setuptools args if setuptools is an immediate dependency - Remove setuptools from packages that do not need it. - Some packages use setuptools *only* when certain args (likeb 'develop' or 'bdist') are supplied to setup.py, and they specifically do not use setuptools for installation. - Spack never calls setup.py this way, so just removing the setuptools dependency works for these packages.
2017-04-21fetch git submodules recursively (#3779)Christoph Junghans2-5/+16
* fetch git submodules recursively This is useful if the submodules have submodules themselves. On the other hand doing a recursive update doesn't hurt if there is only one level. * fetch submodules with depth=1 as well (fix #2190) * use git submodule with depth only for git>=1.8.4
2017-04-21Coverage for multiple Python versions. (#3951)Todd Gamblin2-2/+4
Update tests to use codecov for multiple python versions.
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