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2017-04-15Fix flake8 changed files detection (#3855)Adam J. Stewart1-1/+1
2017-04-15Allow users to set parallel jobs in config.yaml (#3812)Adam J. Stewart5-6/+30
* Allow users to set parallel jobs in config.yaml * Undo change from endash to emdash * Remove parallel config, rename jobs to build_jobs
2017-04-14stage: remove a rogue period (#3846)Ben Boeckel1-1/+1
2017-04-14Add documentation on explicit param for do_install (#3823)Adam J. Stewart1-13/+15
2017-04-14Quick fix for #3153 (#3822)Mario Melara1-0/+3
2017-04-12Document commands that no longer work (#3781)Adam J. Stewart1-4/+37
2017-04-10doc: start with known issues section (#3722)Denis Davydov2-0/+38
2017-04-10Make it more clear that version ranges are inclusive (#3759)Adam J. Stewart1-43/+84
2017-04-07Abinit: a few modernizations for the package and its dependencies (#3699)Massimiliano Culpo1-5/+1
* libxc: added libs interface * hdf5: added libs interface, added conflicts * abinit: modernized package to use build interface * netcdf-fortran: added libs interface * abinit: added version 8.2.2
2017-04-06set_executable can set S_IX{GRP,OTH} (#3742)George Hartzell1-2/+8
`set_executable` now checks if a user/group.other had read permission on a file and if it does then it sets the corresponding executable bit. See #1483.
2017-04-06Correct uninstall -d to uninstall -R in tutorial (#3740)Max Katz1-2/+2
-d was changed to -R as of PR #1917
2017-04-05Update copyright on the docs. (#3718)Todd Gamblin1-2/+2
2017-04-05spack create MakefilePackage (#3710)Adam J. Stewart2-26/+38
* spack create MakefilePackage * Change default Perl template to match other build systems
2017-04-05Merge pull request #2789 from ↵scheibelp6-22/+112
paulhopkins/features/allow_package_installation_directory_to_be_configured Allow installation directory layout to be configured
2017-04-05Allow installation directory layout to be configured using either hashPaul Hopkins6-22/+112
length parameter or spec formatting.
2017-04-04Avoid null reference in arch concretization (#2596)scheibelp1-3/+18
Fixes #2587 The concretizer falls back on using the root architecture (followed by the default system architecture) to fill in unspecified arch properties for a spec. It failed to check cases where the root could be None.
2017-04-04Fixes #3675: Abinit: invalid spec on concretization #(3686)Massimiliano Culpo1-1/+1
2017-04-04Update getting_started.rst (#3685)Justin Cook1-1/+1
Fixed typo referring to .bashrc file
2017-04-03Overhaul Spack's URL parsing (#2972)Adam J. Stewart14-565/+1166
* Remove fake URLs from Spack * Ignore long lines for URLs that start with ftp: * Preliminary changes to version regexes * New redesign of version regexes * Allow letters in version-only * Fix detection of versions that end in Final * Rearrange a few regexes and add examples * Add tests for common download repositories * Add test cases for common tarball naming schemes * Finalize version regexes * spack url test -> spack url summary * Clean up comments * Rearrange suffix checks * Use query strings for name detection * Remove no longer necessary url_for_version functions * Strip off extraneous information after package name * Add one more test * Dot in square brackets does not need to be escaped * Move renaming outside of parse_name_offset * Fix versions for a couple more packages * Fix flake8 and doc tests * Correctly parse Python, Lua, and Bio++ package names * Use effective URLs for mfem * Add checksummed version to mitos * Remove url_for_version from STAR-CCM+ package * Revert changes to version numbers with underscores and dashes * Fix name detection for tbb * Correctly parse Ruby gems * Reverted mfem back to shortened URLs. * Updated instructions for better security * Remove preferred=True from newest version * Add tests for new `spack url list` flags * Add tests for strip_name_suffixes * Add unit tests for version separators * Fix bugs related to parseable name but in parseable version * Remove dead code, update docstring * Ignore 'binary' at end of version string * Remove platform from version * Flip libedit version numbers * Re-support weird NCO alpha/beta versions * Rebase and remove one new fake URL * Add / to beginning of regex to avoid picking up similarly named packages * Ignore weird tar versions * Fix bug in url parse --spider when no versions found * Less strict version matching for spack versions * Don't rename Python packages * Be a little more selective, version must begin with a digit * Re-add fake URLs * Fix up several other packages * Ignore more file endings * Add parsing support for Miniconda * Update tab completion * XFAILS are now PASSES for 2 web tests
2017-04-02new directive: conflicts() (#3125)Massimiliano Culpo4-1/+99
* Add conflicts(<spec>) directive * openblas: added conflicts for intel@16 refs #3119 * added brief docs and unit tests
2017-04-01Add epigraph in docs.Todd Gamblin1-1/+5
2017-04-01Add better tests for web.py; fix some bugs found with spidering.Todd Gamblin8-35/+283
- _spider in web.py was actually failing to spider deeper than a certain point. - Fixed multiprocessing pools to not use daemons and to allow recursive spawning. - Added detailed tests for spidering and for finding archive versions. - left some xfail URL finding exercises for the reader. - Fix noqa annotations for some @when decorators
2017-04-01Fix Python 3 support in spack versionsAdam J. Stewart2-4/+5
- Add missing import, fixes spack versions in Python 2 - Fix spack versions in Python 3
2017-04-01fix annoying 'fatal: Not a git repository' error message (#3657)Kenneth Hoste2-4/+8
fix annoying 'fatal: Not a git repository' error message produced by 'spack list' when Spack is not run from a Git repository (#3657)
2017-03-31fix flake8 ignore syntax (use E instead of ignore) (#3651)Gregory Lee1-1/+1
2017-03-31test/package_sanity.py: ported to pytest (#3474)Massimiliano Culpo1-34/+33
2017-03-31test/versions.py: ported to pytest (#3635)Massimiliano Culpo1-403/+443
2017-03-31Spack works with Python 3Todd Gamblin2-2/+2
- Update version guard in spack script to allow python 3 - Update min required version in the docs
2017-03-31Clean up tests and add Python3 to Travis.Todd Gamblin2-89/+155
- Clean up spec_syntax tests: don't dependend on DB order. - spec_syntax hash parsing tests were strongly dependent on the order the DB was traversed. - Tests now specifically grab the specs they want from the mock DB. - Tests are more readable as a result. - Add Python3 versions to Travis tests.
2017-03-31Fix concretization bugs with virtuals and deptypes.Todd Gamblin2-25/+39
1. Fix #2807: Can't depend on virtual and non-virtual package - This is tested by test_my_dep_depends_on_provider_of_my_virtual_dep in the concretize.py test. - This was actually working in the test suite, but it depended on the order the dependencies were resolved in. Resolving non-virtual then virtual worked, but virtual, then non-virtual did not. - Problem was that an unnecessary copy was made of a spec that already had some dependencies set up, and the copy lost half of some of the dependency relationships. This caused the "can'd depend on X twice error". - Fix by eliminating unnecessary copy and ensuring that dep parameter of _merge_dependency is always safe to own -- i.e. it's a defensive copy from somewhere else. 2. Fix bug and simplify concretization of deptypes. - deptypes weren't being accumulated; they were being set on each DependencySpec. This could cause concretization to get into an infinite loop. - Fixed by accumulating deptypes in DependencySpec.update_deptypes() - Also simplified deptype normalization logic: deptypes are now merged in constrain() like everything else -- there is no need to merge them specially or to look at dpeendents in _merge_dependency(). - Add some docstrings to deptype tests.
2017-03-31Use key sorting instead of cmp()Todd Gamblin19-396/+318
- Get rid of pkgsort() usage for preferred variants. - Concretization is now entirely based on key-based sorting. - Remove PreferredPackages class and various spec cmp() methods. - Replace with PackagePrefs class that implements a key function for sorting according to packages.yaml. - Clear package pref caches on config test. - Explicit compare methods instead of total_ordering in Version. - Our total_ordering backport wasn't making Python 3 happy for some reason. - Python 3's functools.total_ordering and spelling the operators out fixes the problem. - Fix unicode issues with spec hashes, json, & YAML - Try to use str everywhere and avoid unicode objects in python 2.
2017-03-31Resolve Python2/Python3 unicode issues by using str()Todd Gamblin7-13/+15
- Remove ascii encoding assumption from spack_yaml - proc.communicate() returns bytes; convert to str before adding. - Fix various byte string/unicode issues for Python 2/3 support - Need to decode subprocess output as utf-8 in from_sourcing_files. - Fix comments in strify()
2017-03-31Convert Python 2 idioms to Python 2/3-compatible ones.Todd Gamblin73-321/+392
- convert print, StringIO, except as, octals, izip - convert print statement to print function - convert StringIO to six.StringIO - remove usage of csv reader in Spec, in favor of simple regex - csv reader only does byte strings - convert 0755 octal literals to 0o755 - convert `except Foo, e` to `except Foo as e` - fix a few places `str` is used. - may need to switch everything to str later. - convert iteritems usages to use six.iteritems - fix urllib and HTMLParser - port metaclasses to use six.with_metaclass - More octal literal conversions for Python 2/3 - Fix a new octal literal. - Convert `basestring` to `six.string_types` - Convert xrange -> range - Fix various issues with encoding, iteritems, and Python3 semantics. - Convert contextlib.nested to explicitly nexted context managers. - Convert use of filter() to list comprehensions. - Replace reduce() with list comprehensions. - Clean up composite: replace inspect.ismethod() with callable() - Python 3 doesn't have "method" objects; inspect.ismethod returns False. - Need to use callable in Composite to make it work. - Update colify to use future division. - Fix zip() usages that need to be lists. - Python3: Use line-buffered logging instead of unbuffered. - Python3 raises an error with unbuffered I/O - See https://bugs.python.org/issue17404
2017-03-31Update externals to work with Python 3Todd Gamblin42-131/+7062
- Update YAML version to support Python 3 - Python 3 support for ordereddict backport - Exclude Python3 YAML from version tests. - Vendor six into Spack. - Make Python version-check tests work with Python 3 - Add ability to add version check exceptions with '# nopyqver' line comments.
2017-03-31PythonPackage: Let There Be Tests! (#2869)Adam J. Stewart2-7/+75
* Run python setup.py test if --run-tests * Attempt to import the Python module after installation * Add testing support to numpy and scipy * Remove duplicated comments * Update to new run-tests callback methodology * Remove unrelated changes for another PR
2017-03-31Fix mxml (#3639)Michael Kuhn1-0/+1
mxml is now hosted on GitHub.
2017-03-30Extendable Perl (#3614)Milton Woods8-7/+179
* perl: make extendable and add Module::Build package * perl: allow 'spack create' to identify perl packages from their contents * perl-module-build: fix indenting of package docstring * perl: split install() method for extensions into phases * perl: auto-detect build method (Makefile.PL vs Build.PL) and define a 'check' method * PerlPackage: use import statements similar to those in AutotoolsPackage * PerlModule: fix detection of Build.PL * PerlPackageTemplate: remove extraneous lines to avoid flake8 warnings * PerlPackageTemplate: split into separate templates for Makefile.PL and Build.PL * PerlPackage: add cross-references to docstrings * AutotoolsPackage: fix ambiguous cross-references to avoid errors in doc tests * PerlbuildPackageTemplate: depend on perl-module-build if Build.PL exists
2017-03-28Fix bug in `spack find` for installations with unknown namespaces. (#3573)Todd Gamblin1-1/+7
- Spack find would fail with "unknown namespace" for some queries when a package from an unknown namespace was installed. - Solve by being conservative: assume unknown packages are NOT providers of virtual dependencies.
2017-03-28Bugfix: allow deactivating installs that don't have packages anymore. (#3572)Todd Gamblin1-5/+4
- deactivate -a wouldn't work if the installation's package was no longer available. - Fix installed_extensions_for so that it doesn't need to look at the package.py file.
2017-03-24make git fetching quite (#3180)Denis Davydov1-12/+31
also output repo and branch/commit/tag in one line
2017-03-23Add Expect package (#3517)Adam J. Stewart1-1/+2
* Add Expect package * Ignore patches during flake8 tests for package.py files * Remove controversial changes
2017-03-21Fix for `find --explicit` #3374 (#3492)George Hartzell1-1/+1
This fixes the problem described in #3374, which describes `spack find` ignore explicit/implicit. I believe that this was broken in #2626. This restores the behavior of implicit/explicit for me. I believe that it does not screw anything else up, but ....
2017-03-20Improve output for compiler commands (#3480)scheibelp2-1/+14
* Order listed compiler sections "spack compiler list" output compiler sections in an arbitrary order. With this commit compiler sections are ordered primarily by compiler name and then by operating system and target. * Compiler search lists config files with compilers If a compiler entry is already defined in a configuration file that the user does not know about, they may be confused when that compiler is not added by "spack compiler find". This commit adds a message at the end of "spack compiler find" to inform the user of the locations of all config files where compilers are defined.
2017-03-20Fix issue with config.guess patching when the overwritten config.guess did ↵Matthew LeGendre1-9/+5
not have write permissions. (#3494)
2017-03-18Use byte-encoded UTF-8 for sourced environment in Python 2 (#3489)Todd Gamblin3-9/+52
- Fixes recurring errors on develop with unicode commit characters. - still Python3-proof: python3 will use str instead of bytestrings.
2017-03-17Don't use @system in packages.yaml (#3472)Adam J. Stewart3-73/+19
2017-03-16Detect when OS updates affect compiler selection (#3410)scheibelp3-21/+77
Fixes #1476 Concretization uses compilers defined in config files and if those are not available defaults to searching typical paths where the detected operating system would have a compiler. If there is an OS update, the detected OS can change; in this case all compilers defined in the config files would no longer match (because they would be associated with the previous OS version). The error message in this case was too vague. This commit adds logic for detecting when it is likely that the OS has been updated (in particular when that affects compiler concretization) and improves the information provided to the user in the error message.
2017-03-16Dont propagate flags between different compilers (#3379)scheibelp2-41/+28
* Dont propagate flags between different compilers Fixes #2786 Previously when a spec had no parents with an equivalent compiler, Spack would default to adding the compiler flags associated with the root of the DAG. This eliminates that default. * added test for compiler flag propagation * simplify compiler flag propagation logic
2017-03-16Dont auto-init compiler conf for 'compiler find' (#3439)scheibelp2-8/+9
Fixes #3428 Users can run 'spack compiler find' to automatically initialize their compilers.yaml configuration file. It also turns out that Spack will implicitly initialize the compilers configuration file as part of detecting compilers if none are found (so if a user were to attempt to concretize a spec without running 'spack compiler find' it would not fail). However, in this case Spack was overlooking its own implicit initialization of the config files and would report that no new compilers were found. This commit removes implicit initialization when the user calls 'spack compiler find'. This did not surface until #2999 because the 'spack compiler' command defaulted to using a scope 'user/platform' that was not accounted for in get_compiler_config (where the implicit initialization logic predates the addition of this new scope); #2999 removed the scope specification when checking through config files, leading to the implicit initialization.
2017-03-14Consistent docs and usage of env mod methods (#3351)Adam J. Stewart2-81/+61