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2017-08-31Patch directive allows non-archives (#5197)Massimiliano Culpo5-1/+100
- Don't expand downloaded patch file if it is not gzipped/tar'd/zipped/etc.
2017-08-30mpich: fix MPI_Barrier segfault (#5235)Denis Davydov2-0/+18
* mpich: fix MPI_Barrier segfault * one more link
2017-08-30add optional maintainers property to package (#5230)Denis Davydov3-0/+11
* add optional package maintainers
2017-08-30hapcut2: new package (#5238)Audrey Thoma1-0/+44
2017-08-30Slightly better error matching when parsing spack logs (#5236)Andrey Prokopenko1-1/+1
2017-08-29Added unit tests for Spec.__init__ exceptional pathsalalazo1-0/+11
2017-08-29Fixed bug in Spec._dup, updated docstringalalazo1-7/+17
The private method `Spec._dup` was missing a line (when setting compiler flags the parent spec was not set to `self`). This resulted in an inconsistent state of the duplicated Spec. This problem has been fixed here. The docstring of `Spec._dup` has been updated.
2017-08-29Make Spec construction simpler (#5227)Todd Gamblin1-27/+26
2017-08-28lammps: install headers (#5226)Christoph Junghans1-2/+2
* lammps: install headers * use prefix.include.lammps
2017-08-28redundans: new package (#5217)Audrey Thoma3-0/+132
* redundans: new package * fixing url for fastaindex and adding dep for pyscaf
2017-08-28Add --show-full-compiler option to 'spack find'Matthew Scott Krafczyk3-5/+15
When 'spack find' is invoked with the '--show-full-compiler' option, the compiler flags and version are shown for each spec that is found.
2017-08-25Removed default value for 'dirty' function argument. (#5109)Massimiliano Culpo1-3/+3
This change is done to avoid inconsistencies during refactoring. The rationale is that functions at different levels in the call stack all define a default for the 'dirty' argument. This PR removes the default value for all the functions except the top-level one (`PackageBase.do_install`). In this way not defining 'dirty' will result in an error, instead of the default value being used. This will reduce the risk of having an inconsistent behavior after a refactoring.
2017-08-25Fix copyright years in spack create template (#5203)Michael Kuhn1-1/+1
2017-08-25go: Update to 1.9 (#5216)Michael Kuhn1-0/+1
2017-08-25Improve Ubuntu arch detection (#2649)Michael Kuhn1-1/+6
Ubuntu uses a YY.{04,10} release scheme, where YY.04 is not necessarily binary-compatible with YY.10.
2017-08-25Zfp shared libs (#5212)Mark C. Miller1-7/+18
2017-08-25Link extra_rpaths from compilers.yaml at build time (#5211)scheibelp1-0/+2
2017-08-25patch config.guess for any ppc64le arch (#5215)Gregory Lee1-1/+1
2017-08-25Improve grammar in build log error message. (#5214)Todd Gamblin1-2/+7
- "1 error found" instead of "1 errors found" - don't print any build log context if no errors were found; just refer the user to the build log.
2017-08-25Add contributors link to Sphinx docs (#5213)Mark C. Miller1-1/+1
2017-08-25Respect --insecure (-k) flag when fetching list_url. (#5178)Sergey Kosukhin1-3/+33
* Respect --insecure when fetching list_url. * Ensure support for Python 2.6, and that urlopen works for python versions prior 2.7.9 and between 3.0 and 3.4.3.
2017-08-24dealii: add nanoflann, sundials and adol-c plus fixes on macOS (#5175)Denis Davydov5-3/+76
* expat: fix build on macOS * nanoflann: add new package * sundials: fix compilation on macOS with clang+gfortran * adol-c: add 2.6.3 * dealii: add adol-c, nanoflann, sundials and 8.5.1 * sundials: minor cleanup
2017-08-24pkgconf: New package (#5202)Michael Kuhn1-0/+43
pkgconf is a new pkg-config implementation with additional features and no external dependencies. For a detailed comparison, see: http://pkgconf.org/features.html
2017-08-24ray: new package (#5200)Audrey Thoma1-0/+44
2017-08-24test/gpg: init from the testing key directoryBen Boeckel1-11/+2
The old testing pattern set an attribute on the parser directly. Now that there is a parsed flag, use it instead.
2017-08-24gpg: add an argument for the import directoryBen Boeckel1-2/+8
This is hidden because it is only meant for use by the tests.
2017-08-24Make jpeg a virtual dependency. (#5190)Sergey Kosukhin9-11/+50
* Make jpeg a virtual dependency. * Make 'libjpeg-turbo' the default implementation of 'jpeg'.
2017-08-23Added options to libfabrics (#5191)sknigh1-0/+29
2017-08-23Improve Spec literals, add Spec.from_dict() (#5151)Massimiliano Culpo4-199/+472
* Simplified Spec.__init__ signature by removing the *dep_like argument. The `*dep_like` argument of `Spec.__init__` is used only for tests. This PR removes it from the call signature and introduces an equivalent fixture to be used in tests. * Refactored ``spec_from_dict`` to be a static method of ``Spec`` The fixture ``spec_from_dict`` has been refactored to be a static method of ``Spec``. Test code has been updated accordingly. Added tests for exceptional paths. * Renamed argument `unique` to `normal` + added LazySpecCache class As requested in the review the argument `unique` of `Spec.from_literal` has been renamed to `normal`. To avoid eager evaluations of `Spec(spec_like)` expressions a subclass of `collections.defaultdict` has been introduced. * Spec object can be keys of the dictionary for a spec literal. Added back the possibility use a spec directly as a key. This permits to build DAGs that are partially normalized.
2017-08-23Add --source option to spack install (#4102)Christoph Junghans4-1/+28
- -- source will copy source into prefix along with the package. - added a test for --source, as well
2017-08-23pgdspider: new package (#5186)Audrey Thoma2-0/+60
* pgdspider: new package * couple of fixes
2017-08-23Boost: develop (#5184)Axel Huebl1-0/+5
Adds a development version of boost, based on their github master repo. Git clones the submodules forever, but installs! :) Useful for testing since boost tends to break complex software dependencies quite often. This helps testing it before releases.
2017-08-23add test for lua and node patching in sbang (#5169)healther1-6/+42
* add test for lua and node handling in sbang patching (cf #5086)
2017-08-22Add testing for new build output.Todd Gamblin3-2/+55
- Update handling of ChildError so that its output is capturable from a SpackCommand - Update cmd/install test to make sure Python and build log output is being displayed properly.
2017-08-22Make install command reusable within single Spack runTodd Gamblin3-21/+48
- install and probably other commands were designed to run once, but now we can to test them from within Spack with SpackCommand - cmd/install.py assumed that it could modify do_install in PackageBase and leave it that way; this makes the decorator temporary - package.py didn't properly initialize its stage if the same package had been built successfully before (and the stage removed). - manage stage lifecycle better and remember when Package needs to re-create the stage
2017-08-22SpackCommand uses log_output to capture command output.Todd Gamblin5-43/+29
2017-08-22log_ouptut can take either a filename or a file objectTodd Gamblin1-55/+93
2017-08-22Display build output on ProcessError, instead of Python context.Todd Gamblin2-29/+200
- If a failure comes from an external command and NOT the Python code, display errors highlighted with some context. - Add some rudimentary support for parsing errors out of the build log (not very sophisticated yet). - Build errors in Python code will still display with Python context.
2017-08-22Limit package context to 3 lines and colorize in error output.Todd Gamblin1-4/+16
2017-08-22Config scopes are now returning OrderedDicts instead of dicts. (#5183)Massimiliano Culpo3-3/+73
It seems 8f21332fec4c8adb5349ff90e30bb0e4f75e090e introduced a bug in that normal dictionaries are returned from ConfigScope objects instead of OrderedDicts. This is fixed here.
2017-08-22tcoffee: new package (#5185)Audrey Thoma4-0/+142
2017-08-22Boost: 1.65.0 (#5182)Axel Huebl1-0/+3
Adds the latest boost release. Downloads seem to be pointing to bintray from the official homepage.
2017-08-22Package 'libaec': no need to specify per version urls. (#5176)Sergey Kosukhin1-6/+6
2017-08-22Updates for package 'cdo'. (#5179)Sergey Kosukhin1-39/+39
* Package 'cdo': removed obsolete version 1.6.9. * Package 'cdo': updated urls. * Package 'cdo': added version 1.9.0. * Package 'cdo': no need to specify per version urls. * Package 'cdo': switched from Package to AutotoolsPackage. * Package 'cdo': added new variant 'openmp'. * Package 'cdo': variants 'curl' and 'magics' by default.
2017-08-21Add environment variables to path substitutionMatthew Scott Krafczyk3-22/+52
Update documentation on config file variable substitutions and add expansion of environment variables in config files.
2017-08-21py-pyrad: new package (#5181)Audrey Thoma1-0/+41
2017-08-21Added custom messages for conflicts directive. fixes #4965 (#5083)Massimiliano Culpo3-10/+37
Users can now add an optional custom message to the conflicts directive. Layout on screen has been changed to improve readability and the long spec is shown in tree format. Two conflicts in `espresso` have been modified to showcase the feature.
2017-08-21Protobuf: 3.4 (#5177)Axel Huebl1-0/+1
2017-08-20Unbuffer so that output from packages appears when redirectingTodd Gamblin3-2/+110
- Python I/O would not properly interleave (or appear) with output from subcommands. - Add a flusing wrapper around sys.stdout and sys.stderr when redirecting, so that Python output is synchronous with that of subcommands.
2017-08-20Add tests for output redirection.Todd Gamblin1-0/+95