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2018-01-10Keep track of source and versions for external libraries (#6803)Adam J. Stewart1-16/+98
* Keep track of source and versions for external libraries * Note source of more obscure libraries * We aren't upgrading jsonschema after all * Add note on modifications made to pytest
2018-01-10Update to pytest 3.2.5 (#6801)Adam J. Stewart48-2109/+3303
* Update to pytest 3.2.5 * Get pytest to pass Python 2.6 compatibility checks
2018-01-10Add suggestion to Contribution Guide to activate flake8 (#6886)Adam J. Stewart1-9/+19
2018-01-10Update to the latest version of jinja2 (#6790)Adam J. Stewart23-365/+728
2018-01-10Update to py 1.4.34 (#6789)Adam J. Stewart9-79/+25
* Update to the latest version of py * Revert back to py 1.4.34
2018-01-10Add unit tests for spack versions command (#6774)Adam J. Stewart2-1/+47
* Add unit tests for spack versions command * Fix bug in web spidering for Python 2.6
2018-01-10Update to the latest version of six (#6787)Adam J. Stewart1-3/+8
2018-01-10Fix bug in placeholder spack cd command and add unit tests (#6776)Adam J. Stewart3-3/+40
2018-01-10Add unit tests for spack arch command (#6775)Adam J. Stewart1-0/+34
2018-01-10Add unit tests for spack graph command (#6778)Adam J. Stewart1-0/+76
2018-01-10Fix a typo in fetch_strategy error message formatting (#6878)Adam J. Stewart1-1/+1
2018-01-07Add documentation on Codecov (#6842)Adam J. Stewart1-12/+60
2018-01-05Fixes the bug in spack configure spotted in #6833 (#6837)Massimiliano Culpo1-1/+1
2018-01-05Fix spack configure output (#6835)Adam J. Stewart1-1/+1
2018-01-02Fix HTML detection (#6394)Michael Kuhn1-1/+2
Some servers report a content-type header instead of Content-Type.
2018-01-02add OctavePackage (#6746)Denis Davydov4-9/+85
* add OctavePackage 1. remove import CudaPackage which is not needed anymore 2. mention CudaPackage and OctavePackage in packaging guide 3. adjust OctavePackageTemplate 4. add clue file for Octave build 5. sanity check on self.prefix * use setup_environment
2018-01-02Add more unit tests for spack clean command (#6777)Adam J. Stewart1-3/+5
2017-12-30Add unit tests for spack help command (#6779)Adam J. Stewart1-0/+75
* Add unit tests for spack help command * Work around issue with using `spack help` twice in tests
2017-12-30Update to the latest version of argparse (#6786)Adam J. Stewart1-53/+36
* Update to the latest version of argparse * Re-add colified logic
2017-12-30Update to distro 1.0.4 (#6788)Adam J. Stewart1-24/+39
* Update to the latest version of distro * Update distro to 1.0.4
2017-12-22Add more unit tests for spack list command (#6750)Adam J. Stewart1-2/+32
2017-12-22spack mirror remove: fix no-update error (#6559)Massimiliano Culpo1-9/+1
Fixes #4573 "spack mirror remove" was not actually removing mirrors from the configuration.
2017-12-21Fix python3 compatibility bug in spack edit command (#6748)Adam J. Stewart1-2/+2
In Python 2, filter() returns a list, but in Python 3, filter() returns an iterator, and iterators have no length.
2017-12-21separate stdout and stderr for module loading (#6713)becker331-1/+4
2017-12-20binary caching: handle files misidentified as needing relocation (#6679)Patrick Gartung3-25/+54
* Only specify a file as needing relocation if it contains the spack root as a text string (this constraint also applies to binaries) * Don't fail if there is an error retrieving RPATH information from a binary (even if it is specified as requiring relocation)
2017-12-20Compiler flag handlers (#6415)becker3312-1320/+372
This adds the ability for packages to apply compiler flags in one of three ways: by injecting them into the compiler wrapper calls (the default in this PR and previously the only automated choice); exporting environment variable definitions for variables with corresponding names (e.g. CPPFLAGS=...); providing them as arguments to the build system (e.g. configure). When applying compiler flags using build system arguments, a package must implement the 'flags_to_build_system_args" function. This is provided for CMake and autotools packages, so for packages which subclass those build systems, they need only update their flag handler method specify which compiler flags should be specified as arguments to the build system. Convenience methods are provided to specify that all flags be applied in one of the 3 available ways, so a custom implementation is only required if more than one method of applying compiler flags is needed. This also removes redundant build system definitions from tutorial examples
2017-12-19dealii: add GMSH, add CMAKE_FIND_APPBUNDLE to CMakePackage (#6723)Denis Davydov1-1/+4
* dealii: add GMSH dependency * CMakePackage: add CMAKE_FIND_APPBUNDLE to prevent picking up binaries from /Applications
2017-12-18spack install: make restaging the default (#6465)Massimiliano Culpo2-3/+9
Fixes #5940 This PR changes the option '--restage' of 'spack install' to '--dont-restage', inverting its meaning and the default behavior of the command.
2017-12-14Skip collection of compilers which report an empty version (#6684)scheibelp2-19/+39
Fixes #6200 For compilers that successfully run a version detection script but don't actually return a version, Spack was keeping track of the empty version and then failing when attempting to construct a compiler spec. This skips any attempt to add a compiler entry when no version is reported (but logs when a compiler fails to report a version).
2017-12-14misc fixes, changed to EnvironmentModifications (issue #6501) (#6541)Mark Olesen1-11/+52
* Support pruning of vars with Env from_sourcing_file (issue #6501) - Blacklist string literals or regular expressions of environment variables that are to be removed from consideration as being affect by the sourcing of the file. Conversely, whitelist modifications that should not ignored. Whitelisted variables have priority over blacklisting. Eg, EnvironmentModifications.from_sourcing_file ( bashrc blacklist=['JUNK_ENV', 'OPTIONAL_.*'], whitelist=['OPTIONAL_REQUIRED.*'] ) This modification can be used to eliminate environment variables that are not generalized for modules (eg, user-specific variables). * BUG: module prepend-path in wrong order (fixes #6501) * STYLE: module variables in sorted order (issue #6501) - looks nicer and also helps when comparing the contents of different module files. * ENH: remove duplicates from env paths when creating modules (issue #6501) - this makes for a cleaner module environment and helps avoid some unnecessary changes to the environment that are only provoked by redundancies in the PATH. eg, before PATH=/usr/bin after PATH=/usr/bin:/usr/bin:/my/application/bin should only result in /my/application/bin being added to the PATH and not /usr/bin:/my/application/bin Activate via the 'clean' flag (default: False): EnvironmentModifications.from_sourcing_file(bashrc, clean=True,..
2017-12-11add -d option for edit command (#6416)becker331-3/+21
* add -d option for edit command and improve suffix extrapolation from '.py' to use glob
2017-12-11Simplified "Environment-Modules" section in getting started guide. (#6410)Massimiliano Culpo1-58/+21
Fixes #2440 The "Getting started" guide should be short and sweet. This commit simplifies the "Environment-Modules" section pruning: - outdated / wrong suggestions as noted in #2440 - uncommon setups that are better treated in a reference guide
2017-12-07config.py: fixed comments that refer to variables following them (#6585)Massimiliano Culpo1-11/+10
According to the documentation here: http://www.sphinx-doc.org/en/stable/ext/autodoc.html "For module data members and class attributes, documentation can either be put into a comment with special formatting (using a #: to start the comment instead of just #), or in a docstring after the definition."
2017-12-06CMAKE_INSTALL_RPATH is semicolon-separated. (#6577)Sergey Kosukhin1-1/+1
2017-12-01Buildcache: relocate fixes (#6512)Patrick Gartung3-27/+60
* Updated function which checks if a binary file needs relocation. Previously this was incorrectly identifying ELF binaries as symbolic links (so they were being excluded from relocation). Added test to check that ELF binaries are not considered symlinks. * relocate_text was not replacing paths in text files. Added test to check that text files are relocated properly (i.e. paths in the file are converted to the new prefix). * Exclude backup files created by filter_file when installing from binary cache. * Update write_buildinfo_file method signature to distinguish between the spec prefix and the working directory for the binary cache package.
2017-12-01Remove reference to deprecated spack md5 command (#6537)Adam J. Stewart1-2/+1
2017-11-30gpg creation: added suggestion on how to set-up rngd (#6483)Massimiliano Culpo1-0/+16
2017-11-30'spack install': make conflict messages as verbose as 'spack spec' (#6436)Massimiliano Culpo4-15/+37
"spack spec" was providing helpful error information about conflicts that was missing from "spack install", this updates "spack install" to provide the same information.
2017-11-29Improve docstring of spack.directives.extend (#6485)David Lukes1-2/+3
The original docstring had confusing wording re: what is going to symlinked and where when using the `extend` directive, and how exactly the symlinking is performed (not automatically on install, but using `spack activate`). See #5559.
2017-11-28Remove spack md5 and sha256 commands (#6428)Adam J. Stewart3-160/+0
2017-11-28add path to package.py in case of a syntax error (#6458)healther1-1/+8
2017-11-28spack spec: don't show normalize + no hash for non concrete specs (#6417)Massimiliano Culpo1-7/+2
Showing "Normalize" on output doesn't give users additional information, as this step is essentially an implementation detail of concretization. This PR skips it and shows just the input spec and the concretized one. Printing partial hashes for input spec has been disabled.
2017-11-26Use long flag in spack help message (#6429)Adam J. Stewart1-1/+1
2017-11-23Introduce virtual dependency pkgconfig (#5198)Michael Kuhn1-2/+2
There are two providers, pkgconf and pkg-config, with the former being the default provider.
2017-11-22Remove spack extensions from list of known issues (#6405)Adam J. Stewart1-20/+0
2017-11-19dealii: add cuda_arch variant via CudaPackage (#6070)Denis Davydov1-0/+88
2017-11-15git grep --files-with-matches github.com/llnl/spack | xargs sed -i ↵Christoph Junghans15-15/+15
'/github.com/s@llnl/spack@spack/spack@' (#6329)
2017-11-15Fix truncated error messages in directives (#6320)scheibelp1-4/+4
Fixes #6299 Error messages in 'directives' were split across multiple lines and not properly concatenated, which led to truncated messages.
2017-11-13Update tutorial slide links. (#6276)Todd Gamblin1-8/+7
2017-11-13basics tutorial: output updated (#6267)becker331-813/+1308
* basics tutorial: output updated through gcc * finished update for basics tutorial * missed two lines * doc error fix