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Input/output/error streams not directed to None or 'str' were not being closed
because `close()` method was being called on the argument value (a string type)
instead of the open file descriptor object.
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exception. (#1916)
DIYFetchBugfix
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* cgal: build out of source.
* Simplify cmake out-of-source.
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* Fix bug in handling of precedence of preferred=True vs. versions given in packages.yaml (#1556)
* Standardized comparison of versions: numeric versions are always greater than non-numeric versions; and non-numeric versions are sorted alphabetically.
This is
a) simple
b) ensures that non-numeric versions (such as 'develop') in package.py are not chosen ahead of numeric versions, when nothing is specified in packages.yaml
Fixes Issue #1557
* Removed debugging output
* Fix variable shadowing bug
* Ensure develop < numeric version.
* Bug fix.
* Passes all unit tests in versions.py
* flake8 fixes
* flake8 fixes
* Changed type test to be more correct.
See http://stackoverflow.com/questions/8203336/difference-between-int-and-numbers-integral-in-python
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This closes #1757 which provides an example of a url scheme where the
version appears after the extension. Instead of extending the parsing
logic to handle this case, this commit allows the user to specify
their extension type. This helps Spack choose the appropriate
decompressor and mirror archive filename.
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* Transferred pending changes from efischer/develop
* 1. Rewrite of "Getting Started": everything you need to set up Spack, even on old/ornery systems. This is not a reference manual section; items covered here are covered more systematically elsewhere in the manual. Some sections were moved here from elsewhere.
2. Beginning to write three methods of application developer support. Two methods were moved from elsewhere.
* Edits...
* Moved sections in preparation for additional text to be added from old efischer/docs branch.
* Moved 2 more sections.
* Avoid accid
* Applied proofreading edits from @adamjstewart
* Fixed non-standard section characters.
* Moved section on profiling to the developer's guide.
* Still working on Spack workflows...
* Finished draft of packaging_guide.rst
* Renamed sample projects.
* Updates to docstrings
* Added documentation to resolve #638 (content taken from #846)
* Added section on resolving inconsistent run dependencies. Addresses #645
* Showed how to build Python extensions only compatible with certain versions of Python.
* Added examples of getting the right behavior from depends_on(). See #1035
* Added section on Intel compilers and their GCC masquerading feature. Addresses #638, #1687.
* Fixed formatting
* Added fixes to filesystem views. Added a caveats section to ``spack setup``.
* Updated section on Intel compiler configuration because compiler flags currently do not work (see #1687)
* Defined trusted downloads, and updated text based on them. (See #1696)
* Added workflow to deal with buggy upstream software. See #1683
* Added proper separation between Spack Docs vs. Reference Manual
* Renamed spack_workflows to workflows. Resolves a conflict with the .gitignore file.
* Removed repeated section.
* Created new "Vendor Specific Compiler Configuration" section and organized existing Intel section into it. Added new PGI and NAG sections; but they need to be expanded / rewritten based on the existing text plus research through Spack issues on GitHub.
* Fixed text on `spack load --dependencies` to conform to reality. See #1662
* Added patching as option for upstream bugfixes.
* Added section on using licensed compilers.
* Added section on non-downloadable tarballs.
* Wrote sections on NAG and PGI. Arranged compilers in alphabetical order.
* Fix indent.
* Fixed typos.
* Clarified dependency types.
* Applied edits from Adam J. Stewart. Spellchecked workflows and getting_started.
* Removed spurious header
* Fixed Sphinx errors
* Fixed erroneous symbol in docstring.
* Fix many typos and formatting problems.
* Spacing changes
* Added section on fixing Git problems. See #1779
* Fixed signature of install() method.
* Addressed system packages in greater detail. See #1794 #1795
* Fixed typos
* Fixed quotes
* Duplicate section on Spack profiling removed from configuration.rst. It had earlier been moved to developer_guide.rst, where it fits better.
* Minor edits
- Tweak supported platform language.
- Various small changes to the new getting started guide.
* Fixed bug with quotes.
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* 1. Renamed ignore_deps variable to install_deps (use positive logic). UI remains the same.
2. install_self kwarg added to do_install(). Enables installation of a package's dependencies without installing the package itself.
3. Added `spack install --dependencies-only <package>` command.
* Flak8 fixes
* Indentation problem
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* Added missing function for CMake builds.
* Update build_environment.py
* std_cmake_args
Changed std_cmake_args to use get_std_cmake_args().
* Update build_environment.py
Delete additional lines subsumed by get_std_cmake_args()
* flake8.
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* everytrace: New package
Everytrace ensures that stack trace is obtained every time a program exits, for whatever reason.
* everytrace: Change CMake to build dependency
* Renamed to everytrace-example, flake8 and copyright issues.
* flake8
* Missing type=build
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* Warn user if flake8 can't find setuptools
* Add missing dependencies of flake8
* Updates to py-autopep8, make packages activateable
* Check for presence of setuptools for Sphinx too
* Fix bug in order of commands
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* PNGwriter, libSplash: Add `master` version
* PNGwriter, libSplash: Add `dev` versions
Can be used for now, `develop` is currently discouraged.
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features/install_with_phases_rebase
Conflicts:
lib/spack/spack/cmd/setup.py
lib/spack/spack/package.py
var/spack/repos/builtin/packages/gmp/package.py
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- Fixes bad file descriptor error in lock acquire, #1904
- Fix bug introduced in previous PR #1857
- Backported fix from soon-to-be merged fine-grained DB locking branch.
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- Fix issue with package_list.py regeneration confusing Sphinx.
- Add -E option to avoid caching and make Sphinx happy.
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- Fixed up dependency management so that:
- build deps go in PATH and -I
- link deps go in -L args
- only *immediate* link deps are RPATH'd
The latter reduces the number of libraries that need to be added to
DT_NEEDED / LC_RPATH. This removes redundant RPATHs to transitive
dependencies.
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(#1317)
* Update grib-api: switched to cmake building system.
* Update harfbuzz: added pkg-config dependency.
* Update pango: added pkg-config dependency.
* Add libemos package.
* Add Magics (from ECMWF) package.
* Revert "Variant for building cdo without mpi (#1638)":
CDO does not use MPI.
This reverts commit 079d063c6d94be84974f1ddd6eb880e902c95b4a.
* Update CDO package: full featured implementation.
* Update magics: added python as build dependency.
* Update cdo: added disabling configuration options.
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* Spack package for HPCToolkit (performance analysis tool)
* Correction for PR comments, make flake8 happy
* update note / comments
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Fixes #1203. Apple ships headers in Yosemite (and possibly earlier) that
are gcc-incompatible, but compile fine with clang. The fix is to copy
the offending system header from /usr/include/${REST_OF_HEADER_PATH} to
${GCC_PREFIX}/include/${REST_OF_HEADER_PATH} and replace the non-gcc-
compatible features with gcc-compatible equivalents.
See https://github.com/hashdist/hashstack/pull/771/files for
inspiration, and
http://hamelot.io/programming/osx-gcc-dispatch_block_t-has-not-been-declared-invalid-typedef/
for a description of the header issue.
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* Adding last version of fenics and making trilinos not ambiguous on hdf5
* forcing fenics to ignore hdf5 cxx
* Adding deptypes and correcting the hdf5 patch
* flake8 corrections
* cleaning some useless code
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* Run make clean to prevent warning messages
* Don't delete temporary files after completion
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* Provide new versions of llvm.
+ Provide file list and md5 hashes for 3.8.1 and 3.9.0.
+ Clean up indentation for the 'releases' data structure to improve
consistency.
* Adding a block of code to the 'resources' structure for cfe.
* Merge cfe and clang resources into single entity.
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* Added hadoop, spark, and variant spark+hadoop
* Docstrings, dependency types, urls, copyright
* Flake8 fixes, link dependency for hadoop
* Build type for spark, env problem setting JAVA_HOME
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There is no librt on Darwin, and it's not necessary either.
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* New package: libquo
libquo is a high-level, easy to use programming interface tailored specifically
for MPI/MPI+X codes that may benefit from evolving process binding policies
during their execution. QUO allows for arbitrary process binding policies to
be enacted and reverted during the execution of an MPI/MPI+X application as
different computational phases are entered and exited, respectively.
https://github.com/losalamos/libquo
* Remove use of 'which' and fix style non-conformance.
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supported (#1525)
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packages are no longer available for download) (#1523)
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* Add libint package
* Add Intel optimization flags recommended by CP2K
* Add new version and Intel compiler optimization flags for libxc
* Add older version of libint
* Libint depends on GMP C++ library
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Pro tips from @adamjstewart:
* line too long in package description
* name it grib-api instead of grib_api
* depend on netcdf without reference to unnecessary constraints
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* py-pil: Does not build with Python3.
* Set py-pillow to be the default pil provider
* Update package.py
* Change to comments requested by adamjstewart
* Remove version constraint from extends(), avoid a Spack bug.
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