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2017-07-31Add --color=[always|never|auto] argument; fix color when piping (#3013)paulhopkins13-44/+103
* Disable spec colorization when redirecting stdout and add command line flag to re-enable * Add command line `--color` flag to control output colorization * Add options to `llnl.util.tty.color` to allow color to be auto/always/never * Add `Spec.cformat()` function to be used when `format()` should have auto-coloring
2017-07-26Improve version detection for URLs with dynamic after version (#4902)Adam J. Stewart2-1/+4
2017-07-25Add universal build_type variant to CMakePackage (#4797)Adam J. Stewart1-15/+8
* Add universal build_type variant to CMakePackage * Override build_type in some packages with different possible values * Remove reference to no longer existent debug variant * Update CBTF packages with new build_type variant * Keep note on build size of LLVM
2017-07-25fix config.guess patch for ppc64le (#4858)Gregory Lee1-15/+3
* fix config.guess patch for ppc64le * explicit patch for config.guess not required
2017-07-24Change Version formatting properties and functions to return Version objects ↵Adam J. Stewart3-21/+132
(#4834) * Change version.up_to() to return Version() object * Add unit tests for Version.up_to() * Fix packages that expected up_to() to return a string * Ensure that up_to() preserves separator characters * Use version indexing instead of up_to * Make all Version formatting properties return Version objects * Update docs * Tests need to test string representation
2017-07-22Make testing spack commands simpler (#4868)Todd Gamblin10-388/+296
Adds SpackCommand class allowing Spack commands to be easily in Python Example usage: from spack.main import SpackCommand info = SpackCommand('info') out, err = info('mpich') print(info.returncode) This allows easier testing of Spack commands. Also: * Simplify command tests * Simplify mocking in command tests. * Simplify module command test * Simplify python command test * Simplify uninstall command test * Simplify url command test * SpackCommand uses more compatible output redirection
2017-07-19Allow packages to control handling of compiler flags (#4421)becker336-0/+169
* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler * Update packages so they do not obliterate flags * Added append to EnvironmentModifications class * changed EnvironmentModifications to have append_flags method * changed flag_val to be a tuple * Increased test coverage * added documentation of flag handling
2017-07-18Improve version detection of release versions (#4816)Adam J. Stewart2-0/+3
2017-07-18Open ended variants (#4746)becker331-1/+7
* Change directives to allow open-ended variants more easily * make None default to open-ended
2017-07-18Change path to CMakeLists.txt to be relative to root, not pwd (#4420)Adam J. Stewart1-4/+9
* Change path to CMakeLists.txt to be relative to root, not pwd * Changes requested during code review * Revert back to old naming of root_cmakelists_dir * Make relative directory more clear in docs * Revert change causing build_type AttributeError * Fix forgotten abs_path var * Update CLHEP with new relative path * Update more packages with new root_cmakelists_dir syntax
2017-07-18package: removed default no-op patch (#4103)Massimiliano Culpo1-4/+5
* package: removed default no-op patch fixes #4085 * do_patch: handles NoSuchMethodError nicely
2017-07-12Typo: submdoules -> submodules (#4716)George Hartzell1-1/+1
2017-07-06patch config.guess after autoreconf step (#4604)Gregory Lee1-18/+9
2017-07-04Parametrized lock test and make it work with MPITodd Gamblin2-46/+255
- Lock test can be run either as a node-local test or as an MPI test. - Lock test is now parametrized by filesystem, so you can test the locking capabilities of your NFS, Lustre, or GPFS filesystem. See docs for details.
2017-07-04Make filesytem more resilient to concurrent updates.Todd Gamblin1-2/+12
- Uses O_CREAT for touch (for guaranteed atomic open on NFS, multi-node) - Ignore concurrent create errors in mkdirp
2017-07-04Ported lock test to pytest.Todd Gamblin1-519/+630
2017-06-29Update hdfgroup packages to new URL structure (#4643)Adam J. Stewart1-14/+16
* Update hdfgroup packages to new URL structure * Update docs now that HDF5 URL isn't that complicated
2017-06-28add mpi to providers to remove virtual package error (#4608)EmreAtes1-2/+7
2017-06-27Added install option to read spec from file (#4611)becker331-1/+10
2017-06-25Don't immediately raise an error when an editor is not found (#4587)Adam J. Stewart1-5/+6
* Don't immediately raise an error when an editor is not found * If no editor is found, raise an error only if we try to use it.
2017-06-24Allow arbitrary Prefix attributes (#4591)Adam J. Stewart4-103/+134
* Allow arbitrary Prefix attributes * Test attribute type as well * Flake8 fixes * Remove __new__ method * Fewer uses of join_path in the docs
2017-06-24Make LICENSE recognizable by GitHub. (#4598)Todd Gamblin228-229/+229
2017-06-23mv variants: packages are now needed only during normalization (#4129)Massimiliano Culpo4-158/+240
* mv variants: packages are now needed only during normalization The relationship among different types of variants have been weakened, in the sense that now it is permitted to compare MV, SV and BV among each other. The mechanism that permits this is an implicit conversion of the variant passed as argument to the type of the variant asking to execute a constrain, satisfies, etc. operation. * asbtract variant: added a new type of variant An abstract variant is like a multi valued variant, but behaves differently on "satisfies" requests, because it will reply "True" to requests that **it could** satisfy eventually. Tests have been modified to reflect the fact that abstract variants are now what get parsed from expressions like `foo=bar` given by users. * Removed 'concrete=' and 'normal=' kwargs from Spec.__init__ These two keyword arguments where only used in one test module to force a Spec to 'appear' concrete. I suspect they are just a leftover from another refactoring, as now there's the private method '_mark_concrete' that does essentially the same job. Removed them to reduce a bit the clutter in Spec. * Moved yaml related functions from MultiValuedVariant to AbstractVariant. This is to fix the erros that are occurring in epfl-scitas#73, and that I can't reproduce locally.
2017-06-21fix issue #4577 (#4579)becker331-1/+1
2017-06-21Module cmd fix (#3250)becker337-70/+346
* Parse modules in a way that works for both lmod and tcl * added test and made method more robust * refactoring for pythonic clarity * Improved detection of 'module' shell function + refactored module utilities into spack.util.module_cmd * Improved regex to reject nested parentheses we are not prepared to handle * make tests backwards compatible with python 2.6 * Improved regex to account for sh being aliased to bash and used in bash module definition on some systems * Improve test compatibility with lmod * Added error for None module_cmd * Add test for get_module_cmd_from_which() Add test for get_module_cmd_from_which(). Add -c argument to Popen call to typeset -f module in get_module_cmd_from_bash(). * Increased detection options Included BASH_FUNC_module() variable outside of typeset as a detection option This should work on bash even in restricted_shell mode Kept the typeset detection as an option in case the module function is not exported in bash Also added try statements to tests, with environment recreation in finally blocks. * More tests added; some hackiness * increased test coverage for util/module_cmd
2017-06-16System config (#4518)becker335-20/+40
* Code changes to enable system config scope in /etc Files will go in either /etc/spack or /etc/spack/<platform> Required minor changes to conftest. * Updated documentation to match new config scope
2017-06-16bugfix: support EDITOR values with spaces (#4523)Todd Gamblin1-8/+8
- previous code called `which` on $EDITOR, but that doesn't work for EDITORs like `emacs -nw` or `emacsclient -t -nw`. - This patch just trusts EDITOR if it is set (same as previous behavior), and only uses the defaults if it's not.
2017-06-16issue 4492: DependencyMap.concrete checks for unconditional dependencies (#4499)Massimiliano Culpo2-10/+96
* issue 4492: added xfailing test, added owner to DependencyMap * DependencyMap.concrete checks if we have unconditional dependencies This fixes #4492 and #4107 using some heuristics to avoid an infinite recursion among Spec.satisfies, Spec.concrete and DependencyMap.concrete The idea, as suggested by @becker33, is to check just for unconditional dependencies. This is not covering the whole space and a package with just conditional dependencies can still fail in the same way. It should cover though all the **real** packages we have in our repo so far.
2017-06-15Fix tests on cray (#4298)Mario Melara3-5/+4
* Check for CRAYPE_VERSION instead of path Architecture tests would fail on Cray since it would not find the expected path. To make the test correctly work on Cray search for the CRAYPE version instead. * Catch SystemExit error in case flake8 not in path On shared systems having flake8 can involve starting own virtual env. Skip the test if no flake8 is found to avoid failure reporting. * Add compatibility to 1.5 svnadmin create The flag added is needed to correctly create svn repos on NERSC systems. This could be unnecessary for other sites. I'd like to see others test before this change gets merged.
2017-06-15Add latest version of JDK (#4317)Adam J. Stewart1-10/+0
* Add latest version of JDK * Use a more specific URL to get curl to work * Remove failing unit test
2017-06-15Fix dashes in variant parsing (#4498)Todd Gamblin2-8/+8
- Skip spack flake8 test when flake8 is not installed. - Fix parsing of dashes in specs broken by new help parser. - use argparse.REMAINDER instead of narg='?' - don't interpret parts of specs like -mpi as arguments.
2017-06-15Prefer vim to vi for default editor (#4230)Adam J. Stewart4-82/+94
* vim > vi * Allow which to accept multiple args * Update __init__ to use which with multiple args * Fix doc tests
2017-06-14Adding package namd (#4321)Nicolas Richart1-11/+12
* Initial version of the namd package * Modified charm to consider compile against intel/intel-mpi * Correction of namd to compile with intel-mkl and intel compiler * Adding inclue64 in the prefix * adding property for the build directory * removing useless function build
2017-06-13Override partial installs by default - part three (#4331)scheibelp4-3/+172
* During install, remove prior unfinished installs If a user performs an installation which fails, in some cases the install prefix is still present, and the stage path may also be present. With this commit, unless the user specifies '--keep-prefix', installs are guaranteed to begin with a clean slate. The database is used to decide whether an install finished, since a database record is not added until the end of the install process. * test updates * repair_partial uses keep_prefix and keep_stage * use of mock stage object to ensure that stage is destroyed when it should be destroyed (and otherwise not) * add --restage option to 'install' command; when this option is not set, the default is to reuse a stage if it is found.
2017-06-12Add an installcheck phase to MakefilePackage (#4476)Adam J. Stewart1-0/+12
* Add an installcheck phase to MakefilePackage * Minor changes to ESMF
2017-06-09Move description to top of `spack info` (#4475)Todd Gamblin1-7/+8
2017-06-09Add default list_url for GitLab, BitBucket, and CRAN (#4439)Adam J. Stewart1-5/+38
* Add default list_url for GitLab, BitBucket, and CRAN * Fix flake and doc tests
2017-06-09Move gpg section of docs to Getting Started (#4446)Adam J. Stewart2-64/+67
2017-06-09Fix url parse offset for SourceForge downloads (#4458)Adam J. Stewart2-1/+4
2017-06-07Supress output from gpg --version during tests (#4441)Adam J. Stewart1-2/+2
2017-06-07Fixed duplicated spec: nag@6.1 line in getting started guide (#4445)Stas Sergienko1-0/+1
2017-05-30Fix spack info bug for Python 3 (#4391)Adam J. Stewart1-2/+2
2017-05-27Document known issue with R concretization (#4313)Adam J. Stewart1-0/+40
2017-05-26Fix typo in mod_to_class docstring (#4371)Adam J. Stewart1-1/+1
2017-05-26Add --configure-args/vars support to RPackage (#4289)Adam J. Stewart2-5/+37
* Add --configure-args/vars support to RPackage * Docstring formatting change
2017-05-26gpg: add 'spack gpg subcommand (#3845)Ben Boeckel6-0/+541
- Add a `spack gpg` subcommand in anticipation of signed binaries. - GPG keys are stored in var/spack/gpg, and the spack gpg command manages them. - Docs are included on the command.
2017-05-25Touch up string expansion. (#4344)George Hartzell1-1/+2
* Touch up string expansion. I'm chasing this: ``` $ (module purge; spack install perl %gcc/5.4.0) ==> Error: No installed spec matches the hash: '%s' ``` There's something deeper going on, but the error message isn't helpful. After this change it tells me this: ``` $ (module purge; spack install perl %gcc/5.4.0) ==> Error: No installed spec matches the hash: '5.4.0' ``` Which is weird because `5.4.0` is not a hash... Whatever is going on here, the error message needs to be fixed. * Flake8 whitespace
2017-05-24Fix issues parsing multiple anonymous specs (#4199)becker332-18/+24
* fix parser * Removed xfails * cleaned up debug print statements * make use of these changes in gcc * Added comment explaining unreachable line, line left for added protection
2017-05-24Fix PGI version detection: 17.4-0 -> 17.4 (#4251)Adam J. Stewart1-1/+1
2017-05-17Move doc dependencies to requirements.txt for readthedocs (#4280)Todd Gamblin1-0/+5
* Move doc dependencies to requirements.txt for readthedocs * Move sphinx to doc requirements.