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2019-09-13py-bleach package: add version 3.1.0 (#12814)Adam J. Stewart1-4/+5
2019-09-13py-cython package: fix --test (#12813)Adam J. Stewart1-1/+1
Fix bug in string conversion of "make_jobs"
2019-09-13py-emcee package: add version 2.2.1 (#12812)Adam J. Stewart1-1/+2
2019-09-13wcslib package: add version 6.4 (#12810)Adam J. Stewart1-1/+2
2019-09-13Add diamond dependencyGlenn P Johnson1-0/+1
2019-09-13Update braker packageGlenn P Johnson1-6/+33
- add version 2.1.4 - change url to github - add perl dependencies - new version has a new source layout - filter shebang to use spack perl
2019-09-13Fixes for augustus packageGlenn P Johnson1-13/+23
- add missing perl dependency - only filter Makefile if referred to dependency is in the spec - rewrite the shebang line of scripts to use spack perl - remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13Update genemark-et packageGlenn P Johnson1-1/+19
- add version 4.46 - add missing perl dependencies - new version has different source layout - filter shebang to use spack perl
2019-09-13New package: py-pykwalify (#12540)Sinan1-0/+28
2019-09-13preCICE: added versions 1.6.0 and 1.6.1 (#12809)Frédéric Simonis1-0/+2
2019-09-13diamond: added version 0.9.25 (#12805)Glenn Johnson1-0/+1
2019-09-12New package: py-ruamel-yaml (#12543)Sinan1-0/+29
2019-09-12Singularity package: add version 3.4.0 (#12785)Owen Solberg2-3/+22
This version in combination with the included patch can install without root.
2019-09-12New package: cryptsetup (#12762)Owen Solberg2-0/+60
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-12add compilation option to sqlite (#12794)Sinan1-0/+5
* add compilation option to sqlite * rename variant * fix bug * re-rename variant
2019-09-12Update legion gasnet config (#12523)ktsai72-12/+32
2019-09-12py-gpaw: Fixed broken fftw linking in newer versions of py-gpaw (#12795)Simo Tuomisto1-0/+2
2019-09-11fgsl: new version + fix for recent spack commit (#12790)brietzke1-0/+6
2019-09-11jsoncpp: new versions, support cxxstd variant. (#12780)Chris Green1-0/+20
2019-09-10create package popt (#12783)Owen Solberg1-0/+15
2019-09-10fix bug in p4est (don't use MPI spec if not compiling with MPI) (#12784)Jonas Lippuner1-5/+5
2019-09-10openmx: new package (#12768)Hironori-Yamaji1-0/+80
* openmx: new package * openmx: use copy method
2019-09-10cuda: New version 10.1.243 (#12777)Janne Blomqvist1-4/+14
* cuda: New version 10.1.243 Adds CUDA 10.1.243. The installer command-line arguments have slightly changed, hence in the install method the version needs to be inspected in order to give the correct arguments for the new installer. * cuda: Combine common command-line arguments The CUDA 10.1+ installer has slightly different command-line arguments than previous versions. Keep the common parts together and only split where they are different. * Make flake8 happy
2019-09-10py-atropos: new package (#12745)Owen Solberg1-0/+26
* create new package py-atropos * remove whitespace * make tqdm and pysam dependencies optional, exposed as variants
2019-09-10ccs-qcd: disable parallel builds (#12775)Hironori-Yamaji1-2/+2
2019-09-09update bbmap (#12721)xfzhao1-1/+6
* update bbmap * remove one extra comment line
2019-09-09Fix pkgconfig dependencies (#12714)Michael Kuhn3-3/+3
pkgconfig is the virtual dependency, pkg-config is an implementation.
2019-09-09Update py-bokeh: new version & dependencies" (#12724)brietzke1-9/+12
* update py-bokeh: new version & dependencies * Revert "update py-bokeh: new version & dependencies" This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f. * update py-bokeh: new version & dependencies * trigger travis-ci * adjust python dependency-type to br
2019-09-09New package: py-fsspec (#12725)brietzke1-0/+18
* update py-bokeh: new version & dependencies * Revert "update py-bokeh: new version & dependencies" This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f. * new package: py-fsspec: add package.py * trigger travis-ci * adjust python dependency-type to br
2019-09-09Paraview version (#12766)Dan Lipsa1-5/+10
* Update paraview * Paraview 5.6.2 provides only .xz (no .gz) * Add list_url and list_depth
2019-09-09binutils: fix undefined symbol libintl_dgettext (#12770)viniciusvgp1-0/+1
2019-09-08CGNS: Add setting of RPATH on Darwin (#9984)Greg Sjaardema1-0/+7
* CGNS: Add setting of RPATH on Darwin This should go in the CGNS CMakeLists.txt, but it isn't there yet and won't be in previous versions, so best to handle it here. If building on darwin/MacOSX, need to set the RPATH so applications can find shared library correctly. * Restrict MACOSX_RPATH setting This has now been added to the CGNS distribution, so the setting of `CMAKE_MACOSX_RPATH` should be restricted to current and previous releases and not upcoming releases.
2019-09-08fribidi@1.0.5: new package (#12386)Geoffrey Oxberry1-0/+22
2019-09-08new package: py-iniparse (#12638)Sinan1-0/+20
* new package: py-iniparse * add git version supporting python3 * redo python dependency
2019-09-08Package/py configobj (#12639)Sinan1-0/+30
* new package: py-configojb * add version 4.7.2 * improve dependencies * fix url for versions > 5.0.0 * Update var/spack/repos/builtin/packages/py-configobj/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-configobj/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * use format to create url strings * fix typo * improve style * Update var/spack/repos/builtin/packages/py-configobj/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08for fakeroot support, add "shadow" dependency (#12754)Owen Solberg1-3/+4
* adding checksum for singularity 3.4, adding dep for shadow * make v3.4 a TODO for now -- needs cryptsetup package first
2019-09-08Fix PyQt installation (#12479)Adam J. Stewart4-15/+47
* Fix PyQt installation * Switch dependency type * Replace SIP dependency with resource * Relax py-pyqt4 Qt dependency
2019-09-08py-gpaw: Fixing missing numpy include path, adding newer version of p… ↵Simo Tuomisto2-3/+28
(#12737) * py-gpaw: Fixing missing numpy include path, adding newer version of py-gpaw and fixing a bug with libxc.c in older py-gpaw * py-gpaw: Fix Python and ASE version dependencies - GPAW 19.8.1 requires Python 3.x, add dependency on python@3.5: - GPAW releases are associated with a corresponding ASE release, add matching ASE version dependencies. * py-gpaw: Enable the scalapack variant by default GPAW installation instructions say scalapack is optional but "highly recommended". Thus enable it by default.
2019-09-08py-cutadapt: Updated version checksum (#12741)Owen Solberg1-2/+7
* add new cutadapt release 2.5, and adjust dependencies conditional on version * use https, not ssh, for git url Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08new package: py-bz2file (#12761)Owen Solberg1-0/+15
* update py-xopen (add 0.8.2 checksum) * refine version specific dependencies add py-bz2file, which needs to be created * create py-bz2file * Revert "refine version specific dependencies" This reverts commit 70649da98851fefb2f936ca99a012fe6bef07b70. * Revert "update py-xopen (add 0.8.2 checksum)" This reverts commit 7400f44caa6e98419eb4bc3107704b91e8a2018b.
2019-09-08py-xopen: update release 0.8.2 checksum (#12742)Owen Solberg1-1/+4
* update py-xopen (add 0.8.2 checksum) * refine version specific dependencies add py-bz2file, which needs to be created * py-bz2file needed when built with python 2.7 Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * space after comma
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 Gamblin61-292/+300
- 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)
2019-09-07patch 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
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