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2019-09-08py-dnaio: new package need by py-cutadapt (#12743)Owen Solberg1-0/+20
* add new package py-dnaio * provide git url with https, not ssh, protocol Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-07flake8: make entire repository pass `spack flake8 -a`Todd Gamblin69-337/+346
- Fix trailing whitespace missed by the bug described in #12755. - Fix other style issues that have crept in over time (this can happen when flake8 adds new checks with new versions)
2019-09-07flake8: only add E501 exemptions when absolutely necessary (#12755)Todd Gamblin1-2/+13
E501 (line too long) exemptions are probably our most common ones -- we add them for directives, URLs, hashes, etc. in packages. But we currently add them even when a line *doesn't* need them, which can mask trailing whitespace errors. This changes `spack flake8` so that it will only add E501 exemptions if the line is *actually* too long. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-07patch boost version 1.54-1.55 when being built with ANY gcc version after ↵Owen Solberg1-1/+1
5.0 (#12718)
2019-09-07Updating TAU package. Fixing compiler specification for OSX (#12720)Kevin Huck1-5/+13
and making Fortran an option that can be disabled. Also added support for the POSIX I/O wrapper and OMPT for OpenMP.
2019-09-07mesa: disable use of libunwind for arm arch (#12735)Howard Pritchard1-0/+3
There are problems with libunwind for arm and trying to use it with mesa. See for example: https://github.com/grate-driver/mesa/issues/6 disabling use of libunwind for arm, allows the package to be built Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2019-09-07add mpi variant to p4est package to allow turning off MPI (#12739)Jonas Lippuner1-2/+7
2019-09-07ncurses: improve build time (#12621)Axel Huebl1-1/+3
Apply configure options to skip manpage generation and test builds for both wide and non-wide builts.
2019-09-07luarocks: Use `make` command instead of `install` (#12703)Ruben Di Battista2-2/+2
This way luarocks does not attempt to pull stuff from the internet. Fix #3909
2019-09-07Add py-numpy 1.17.2 (#12753)Adam J. Stewart1-1/+2
2019-09-07Add patches to work around CMake versions (#12744)Piotr Luszczek3-0/+38
- Use of symbol testing macro requires explicit include() - CMake policies are not version-portable and the support has to queried based on CMake version
2019-09-07font-util 1.3.2 (#12728)Owen Solberg1-0/+1
2019-09-07Update docs on module loads command (#12702)Adam J. Stewart1-2/+2
2019-09-07new package: py-pygdal (#12747)Sinan1-0/+31
2019-09-07adding shadow-uidmap (#12750)Vanessasaurus1-0/+18
Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
2019-09-06upcxx: new packageMathias Jacquelin1-0/+89
Adding a UPC++ spack package pointing to the default 2019.3.2 UPC++ version, and allowing to build UPC++ with the experimental CUDA variant.
2019-09-06openspeedshop: fixed build on arm. (#11861)Toyohisa Kameyama4-0/+52
* openspeedshop: fixed build on arm. * remove patch comment.
2019-09-06libpeas@1.22.0: new package (#12385)Geoffrey Oxberry1-0/+107
* libpeas@1.22.0: new package * libpeas: note more build dependencies Build and link dependencies were obtained through a combination of examining the `config.log` file from `configure` and looking at the pkg-config files of `libpeas`. * libpeas: add search path for GIR/typelib files
2019-09-06iso-codes: new package (#12389)Geoffrey Oxberry1-0/+23
2019-09-05make env view loading unconditional (#12719)Greg Becker1-4/+2
2019-09-05fftw: change default value of simd variant for other than x86_64 (#11627)Toyohisa Kameyama1-1/+38
* Use spec.architecture.target insted of platform. * remove default in simd variant value. simd variant change to archtecture independent values. * Add check simd values. * rewrite check simd values. * * flake8 * change aarch64 to arm (neon support only 32 bit arm.)
2019-09-05FIX Catalyst: corrected catalyst package for aarch64 targets (#12707)Matthieu Dorier1-0/+5
* corrected catalyst package for aarch64 targets * corrected syntax * corrected undefined variable
2019-09-05Add pixz package (#12698)Ruben Di Battista1-0/+18
2019-09-05[jemalloc] added version 5.2.1 (#12706)Jennifer Herting1-0/+1
2019-09-05textparser: new package (#12713)Hironori-Yamaji2-0/+112
* textparser: new package * textparser: use 'parallel = False'
2019-09-05mariadb: Add missing dependencies (#12715)Michael Kuhn1-0/+7
Found while building mariadb in a minimal build environment.
2019-09-05py-ase: New version 3.18 (#12697)Janne Blomqvist1-1/+7
* py-ase: New version 3.18 Add ASE version 3.18. ASE 3.18 has dropped support for python 2.x, hence add a dependency on python@3.5: for it. * Add more ASE dependencies Address review comments, add dependencies on py-scipy, py-matplotlib, py-flask, and also add type=('build', 'run') dependency specifiers.
2019-09-04cctools: fixed to build on ARM. (#11862)Toyohisa Kameyama2-0/+29
2019-09-04Add Go 1.13Paul Bryant1-0/+1
2019-09-04openblas: Add route to f_check for Fujitsu compiler. (#11804)t-karatsu2-0/+17
2019-09-04Improve mock_archive versatility; Remove unwanted ALLOWED_ARCHIVE_TYPES. ↵Chris Green3-7/+15
(#12513) mock_archive can now take multiple extension / tar option pairs (default matches old behavior). url_fetch.test_fetch tests more archive types. compression.EXTS split into EXTS and NOTAR_EXTS to avoid unwanted, non-meaningful combinatoric extensions such as .tar.tbz2.
2019-09-04Add gams recipe (#12700)asmaahassan901-0/+37
* Add gams recipe * Break down lines to pass lint
2019-09-04boost: add -c option to C/C++ compile commands for clang. (#12694)t-karatsu3-0/+44
2019-09-04cppflags point to ncurses headers (#12691)Mario Melara1-0/+5
While debugging this package on our Cray machine, tmux was throwing an error involving the ncurses headers. Tmux would look for headers in system locations rather than where spack installed ncurses. Tested only on a Cray.
2019-09-04Add tecplot recipe (#12688)asmaahassan901-0/+30
* Add tecplot recipe * break down description to pass lint * fix format to match python 2.6 requiremnets * importing os
2019-09-04Boost: fixed problem when requesting ~signals for boost >= 1.69 (#12627)Matthieu Dorier1-7/+7
* fixed problem when requesting ~signals for boost >= 1.69 * added checks for all libs in with_libs
2019-09-04new package: liblas (#12619)Sinan1-0/+54
* new package: liblas * explicitly disable build options * fix indentation
2019-09-04specs: better lookup by hash; allow references to missing dependency hashesTodd Gamblin3-16/+155
- previously spec parsing didn't allow you to look up missing (but still known) specs by hash - This allows you to reference and potentially reinstall force-uninstalled dependencies - add testing for force uninstall and for reference by spec - cmd/install tests now use mutable_database
2019-09-03Use spack/user-specific stage root by default; stage cleaning (#12516)Tamara Dahlgren8-79/+178
* When cleaning the stage root, only remove directories that appear to be used for staging Spack packages. Previously Spack was clearing all directories in the stage root, which could remove content not related to Spack if the user chose a staging root which contains files/directories not managed by Spack. * The documentation is updated with warnings about choosing a stage directory that is only managed by Spack (although generally the check added in this PR for "spack clean" should avoid removing content that was not created by Spack) * The default stage directory (in config.yaml) is now $tempdir/$user/spack-stage and the logic is updated to omit the $user portion of this path if $tempdir already contains a $user directory. * When creating stage root assign user read/write permissions to all directories in the path under $user. Previously Spack was assigning the permissions of the first existing parent directory
2019-09-03py-chardet package: add py-pytest-runner dependency (#12692)Peter Scheibel1-0/+1
This required dependency was missing
2019-09-03new package: protobuf-c (#12634)Sinan1-0/+20
* new package: protobuf-c * Update var/spack/repos/builtin/packages/protobuf-c/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-03perf: spack find -p now does only one DB transactionTodd Gamblin1-9/+12
`spec.prefix` reads from Spack's database, and if you do this with multiple consecutive read transactions, it can take a long time. Or, at least, you can see the paths get written out one by one. This uses an outer read transaction to ensure that actual disk locks are acquired only once for the whole `spack find` operation, and that each transaction inside `spec.prefix` is an in-memory operation. This speeds up `spack find -p` a lot.
2019-09-03Boost/Change the method for analysis version (#12676)t-karatsu2-0/+14
* boost:Change the method for analysis version when using Fujitsu compiler. * Change version to apply patch for Fujitsu. * fix typo
2019-09-03pmlib: new package (#12625)Hironori-Yamaji2-0/+132
* pmlib: new package * pmlib: fix options and add patch * pmlib: fix the patch file
2019-09-03ccs-qcd: new package (#12681)Hironori-Yamaji1-0/+68
* ccs-qcd: new package * ccs-qcd: fix variant and replacement string
2019-09-02tests: add tests for `spack extensions` commandTodd Gamblin6-88/+132
- add tests for `spack extensions` - refactor `test_activations` test to use real extensions.
2019-09-02tests and completions for `spack find --json` and `spack find --format`Todd Gamblin5-19/+217
2019-09-02tests: remove extraneous print statementTodd Gamblin1-4/+0
2019-09-02refactor: clean up `spack find`, make `spack find -dp` work properlyTodd Gamblin4-153/+132
Refactor `spack.cmd.display_specs()` and `spack find` so that any options can be used together with -d. This cleans up the display logic considerably, as there are no longer multiple "modes".
2019-09-02docs: add docs for `spack find --format` and `spack find --json`Todd Gamblin3-9/+119
- add docs for `spack find --format` - add docs for `spack find --json` - update references to Spec.format() docs and add links
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