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2018-12-23xsdk-0.4.0: add/update package versions: (#10038)Satish Balay4-15/+57
* xsdk-0.4.0: add/update package versions: hypre@2.15.1 mfem@3.4.0 superlu-dist@6.1.0 trilinos@12.14.0-rc1 petsc@3.10.3 dealii@9.0.1 pflotran@xsdk-0.4.0 alquimia@xsdk-0.4.0 sundials@3.2.1 plasma@18.11.1 magma@2.4.0 amrex@18.10.1 slepc@3.10.1 omega-h@9.19.1 strumpack@3.1.1 pumi@2.2.0 tasmanian@6.0 phist@1.7.5 dtk-3.0 [via trilinos features '+dtk+intrepid2+shards'] add option to disable omega-h build [wrt gcc-8 conflict] spack install xsdk~omega-h add option to disable dealii build [wrt cori build error] spack install xsdk~dealii * trilinos: default version should be the prior release
2018-12-23py-cftime: new package (#10066)Neil Flood1-0/+21
* py-cftime: new package * Added dependency on py-setuptools, and version range for py-cython, thanks to the ever-vigilant @adamjstewart
2018-12-23openFOAM-paraview-catalyst (#10129)Simone Bnà6-60/+1176
* paraview: adding variants to use external packages as internal do not compile * paraview: add latest paraview version * catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5 * catalyst: add latest catalyst version * catalyst: added ParaView_DIR env variable to catalyst module * add paraview, catalyst patches - https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2433 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2436 * - Handle updated library paths for catalyst. Versions 5.4 and old places libraries under a paraview subdirectory. Eg, "lib/paraview-5.4", they are now placed directly under "lib" - Minor code style cleanup * Handle update library and python paths for ParaView-5.5 * catalyst: added ParaView_DIR path to spack_env * BUG: applied the patch to the extracted catalyst source files * paraview: added missing self to a member variable * paraview: added Paraview_DIR to env * catalyst: added osmesa variant * of-catalyst: added new package * add (FOAM,WM)_PROJECT_DIR also to spack_env environment * depends on first openfoam release supporting catalyst * openfoam-com: added missing env variables to module generation * openfoam: fixed flake8 errors * of-catalyst: added full variant and openfoam version dependency * paraview: adding variants to use external packages as internal do not compile * catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5 * catalyst: added ParaView_DIR env variable to catalyst module * add paraview, catalyst patches - https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2433 - https://gitlab.kitware.com/paraview/paraview/merge_requests/2436 * - Handle updated library paths for catalyst. Versions 5.4 and old places libraries under a paraview subdirectory. Eg, "lib/paraview-5.4", they are now placed directly under "lib" - Minor code style cleanup * Handle update library and python paths for ParaView-5.5 * catalyst: added ParaView_DIR path to spack_env * BUG: applied the patch to the extracted catalyst source files * of-catalyst: added new package * add (FOAM,WM)_PROJECT_DIR also to spack_env environment * depends on first openfoam release supporting catalyst * paraview: added missing self to a member variable * openfoam-com: added missing env variables to module generation * openfoam: fixed flake8 errors * paraview: added Paraview_DIR to env * catalyst: added osmesa variant * of-catalyst: added full variant and openfoam version dependency * paraview-catalyst: use always external expat and netcdf * of-catalyst: reformatted package description * paraview-catalyst: removed duplicated function * catalyst: fixed flake8 error * of-catalyst: fixed license header * of-catalyst: minor changes * of-catalyst: renamed gitrepo with git * of-catalyst: removed useless gitrepo parameter
2018-12-23Feature add breathe and m2r (#10180)Brian Van Essen3-0/+61
* Added a package for the MDAnalysis toolkit. * Added python packages for breathe and m2r. Updated versions and URL for the sphinx package. * Fixed flake8 error * Updated package requirements based on feedback. * Updated with requirements from the setup.py * Switched it back to pypi.
2018-12-23py-pynio: new package (#10074)Neil Flood1-0/+71
* py-pynio: new package * Major re-working to add some of the optional dependencies, and make it conform to the approach described in the pynio setup.py comments. Much of it turned out to be too complicated, and I have added some notes in comments to explain this to future adventurers. * Added variants for the hdf5 and gdal dependencies, which do seem to be genuinely optional. Also added absolute dependencies for jpeg and zlib, which setup.py says it wants, but were being found as the os-installed versions. * Added descriptions for the new variants, and moved them to above the dependencies
2018-12-22Add missing module env variable setting causing OSS to fail. (#10182)Jim Galarowicz1-0/+11
2018-12-22r-corhmm: new package at 1.22 (#9859)Justin Stanley1-0/+31
2018-12-22petsc-3.10.3: syncs with superlu-dist-6.1. (#10166)Satish Balay1-2/+6
2018-12-21gpgme: new package (#10174)Levi Baber1-0/+19
2018-12-21add charliecloud 0.9.6 (#10176)Jordan Ogas1-0/+1
2018-12-21py-numba: fix py-llvmlite version (#10175)Matthias Wolf1-1/+1
2018-12-21Add libiconv variant to glib (#10165)George Hartzell1-0/+6
Enable explicitly building glib with or without libiconv. Heads up: if you build with ~iconv but there is something else in the spec that includes libiconv then glib will *still* automagically discover it and the build will fail.
2018-12-21Remove /nfs/tmp2 from default build_stage locations (#10170)Elsa Gonsiorowski, PhD2-7/+4
* Remove /nfs/tmp2 from default configuration * /nfs/tmp2 is going away from LC... and doesn’t exist for the rest of the world. * update documentation to remove /nfs/tmp2 as well
2018-12-20R3D spackage (#10164)Daryl W. Grunau1-0/+49
* r3d spackage * address Adam's review comments * fix flake8: too many blank lines
2018-12-20update h5py to 2.9.0 (#10169)Sajid Ali1-1/+2
* modified: var/spack/repos/builtin/packages/py-h5py/package.py * Update package.py * Update package.py
2018-12-20Update TFEL package (#9995)thelfer1-6/+39
* add the tfel package * fix the tfel package * fix the tfel package * fix the tfel package * Taking Adam J. Steward' remarks into account * fixes trailing white spaces * Update description * Update dependencies following @adamjstewart adices * Style fixes * Style fixes * Add java optional support * add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice) * flake8 fixes * Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL) * Style fixes * Style fixes * Fix test on python version * Follow @adamjstewart advices: code is much cleaner and readable * Small fix * Small fix * Add comment * Small fix in cmake option * try again (trying to overcome Travis CI unstable build process)
2018-12-20OpenFOAM-v1812 - new version (#10167)Mark Olesen1-0/+2
2018-12-20Fix docker builds (#9805)Omar Padron3-29/+67
* move docker test logic to share/spack/qa * update Dockerfile for archlinux
2018-12-20fix multiple issues with the docker images (#9718)Omar Padron5-8/+35
- fixed an issue where some undesirable parts of the spack source tree were being copied into the image context. - added a workaround for a tty ioctl warning on ubuntu - adjusted how the main images are built so that `RUN spack ...` works automatically for child images that base themselves on them.
2018-12-20Performance improvements for CDash reporterZack Galbreath1-9/+12
* Record build output as an array of lines rather than concatenating to a single large string. * Use string.find to avoid running re.search on every line of output.
2018-12-20Include accurate build time in CDash reportZack Galbreath1-6/+10
2018-12-20Report current git commit of Spack to CDashZack Galbreath2-10/+30
When using the CDash reporter, upload a Update.xml file that indicates the hash of Spack's current git commit.
2018-12-20Make sure to urlencode cdash submit parametersScott Wittenburg1-3/+9
2018-12-20Get buildId from CDash at submit timeZack Galbreath1-2/+21
Pass extra data when submitting to CDash. If CDash responds with a buildId, construct and display helpful URL that links to the uploaded report.
2018-12-20Allow more customization for CDash reporterZack Galbreath8-26/+65
Add new command line arguments to `spack install` that allow users to set the build name, site name, and track in their CDash report.
2018-12-20Avoid UnboundLocalErrorZack Galbreath1-0/+1
Make sure cdash_phase is defined before referring to it.
2018-12-20packages/phist: add maintainer (#10162)jthies1-0/+2
2018-12-19CGNS: Allow use of git branch versions (#10156)Greg Sjaardema1-0/+3
* CGNS: Allow use of git branch versions Add ability to use git `master` and `develop` branches of the CGNS library. The `seacas` package sometimes needs to use the `master` or `develop` branch due to some new changes to the parallel I/O implementation in CGNS which has not yet been released. * CGNS: Reorder to put newest version on top Based on review comments, place newest version (develop) first in list.
2018-12-19env: all commands that disambiguate specs should be env-awareTodd Gamblin19-26/+55
- some commands were missed in the rollout of spack environments - this makes all commands that need to disambiguate specs restrict the disambiguation to installed packages in the active environment, as users would expect
2018-12-19dyninst: patch to build dyninst with older gcc (#10160)Mark W. Krentel2-0/+74
* dyninst: patch to build dyninst with older gcc Add 'v9.3.2-auto.patch'. This patch changes some 'auto t: type' usage to the older but equivalent 'type.begin()'. This allows building dyninst 9.3.2 with gcc 4.4 which doesn't support the newer syntax. This patch is harmless with newer gcc. * Fix typo in patch. (My bad for sloppy cut-and-paste.) * Restrict the patch to gcc 4.7 and earlier. gcc 4.8 supports the newer usage and thus doesn't need the patch.
2018-12-19sqlite: add 3.26.0 (#10138)Michael Kuhn3-90/+4
2018-12-19updated checksum for kallisto (#10158)Owen Solberg1-1/+1
2018-12-19fetch_strategy: improve GitFetchStrategy (#10153)Michael Kuhn2-12/+17
Currently, only the Git repsository's URL shows up in the `spack info` output, which makes it hard to distinguish different versions: ``` Safe versions: develop [git] https://github.com/LLNL/H5Z-ZFP.git 0.8.0 [git] https://github.com/LLNL/H5Z-ZFP.git 0.7.0 [git] https://github.com/LLNL/H5Z-ZFP.git ``` This change adds additional information as shown when cloning a Git repository: ``` Safe versions: develop [git] https://github.com/LLNL/H5Z-ZFP.git on branch master 0.8.0 [git] https://github.com/LLNL/H5Z-ZFP.git at commit af165c4 0.7.0 [git] https://github.com/LLNL/H5Z-ZFP.git at commit 58ac811 ```
2018-12-19phist tag 1.7.5 was moved (#10155)jthies1-1/+1
2018-12-19Updated Dakota to 6.9 (#10157)sknigh1-1/+5
* Updated Dakota to 6.9 * Change comment wording
2018-12-19Add python bindings to libxslt (#10149)Adam J. Stewart1-9/+27
2018-12-19Add missing libiconv dependency to libxml2 (#10148)Adam J. Stewart1-5/+18
2018-12-19Add list_url to docbook-xml (#10146)Adam J. Stewart1-10/+7
2018-12-19Add latest version of docbook-xsl (#10147)Adam J. Stewart2-12/+48
2018-12-19Restrict patch to oldest version of libbsd (#10145)Adam J. Stewart1-2/+4
2018-12-19PETSc: add version 3.10.3 (#10154)Satish Balay1-0/+1
2018-12-19mapserver: new package (#10067)Neil Flood1-0/+100
2018-12-19Added labels in github issue templates (#10128)Massimiliano Culpo3-2/+3
2018-12-18Add additional info to MesonPackage docs (#10133)Adam J. Stewart1-0/+44
* Add additional info to MesonPackage docs * No Pygments lexer for Meson code, default to none
2018-12-18fix for mpifileutils package (#10142)Elsa Gonsiorowski, PhD1-8/+17
* proper include & linking of libarchive * due to linux headers, mfu can't build on mac * hard code deps in configure line rather than relying on pkg-config * +xattr during config * must also link the lib * find mfu.h * long lines
2018-12-18WarpX: Added dependency on fftw when +psatd (#10144)Dave1-0/+2
2018-12-18flatbuffers: add 1.10.0 (#10137)Matthias Wolf2-1/+2
Also unpin the version from the arrow package.
2018-12-18Add pdf variant to cairo (#10135)Adam J. Stewart1-12/+19
2018-12-18clp: add build_directory, remove old hack (#10112)Justin Stanley1-4/+1
* clp: add build_directory, remove old hack * clp: use spack-build for building
2018-12-17Add latest version of libxkbcommon (#10134)Adam J. Stewart1-12/+9
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