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2020-02-29hpctoolkit: add version 2020.03.01 (#15277)Mark W. Krentel1-10/+14
Add version 2020.03.01, deprecate Blue Gene to 2019.12.28 and earlier, tighten a few dependencies.
2020-02-29Add kraken2 (#15053)Richard Berg1-0/+35
2020-02-29Caliper depends on python3. (#15260)Robert Blake1-1/+3
* Caliper depends on python3. The package needs to be told where to find it. * More flake8 formatting edits. * Change explicit python3 to spec['python'].command.path Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Removing defunct import for flake8 * Flake8 trailing whitespace warning. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-29opam: added versions up to v2.0.6 (#15178)Anthony Scemama1-2/+24
2020-02-29HPX: added v1.4.1 and "stable" branch (#15198)rtohid1-0/+3
2020-02-29MRCPP: New package. (#15201)Roberto Di Remigio1-0/+46
2020-02-29libhio: specify use of external json (#15209)plamborn1-0/+2
libhio has been building it's own json. With this change, libhio will rely on the json installed by spack.
2020-02-29Set http:// in homepage for a few packages (#15275)Glenn Johnson4-5/+5
This PR adds 'http://' to the homepage setting of a few packages that do not have it set. Not having that set can cause problems with some wiki apps when embedding the homepage value into markdown syntax. - bowtie2 - exuberant-ctags - perl-want - samtools
2020-02-28Update tree for v1.8.0 (#15272)George Hartzell1-0/+5
- add version info for v1.8.0 - v1.8.0 adds a new source file, `file.c`, which need to be included in our hardcoded list of objects to link. I discovered this while demonstrating "how easy it is to add a new package to Spack", only to scratch my head when it failed `spack install` but worked when I ran `make` in the stage dir. Finally looked at tree/package.py and it All Became Clear. Perhaps someone should rewrite this to use MakefilePackage, but the Makefile starts off with a bunch of twisty turny "uncomment these lines to run on this platform", so it might not be worth it.
2020-02-28Added package py-versioneer (#15130)Anthony Scemama1-0/+21
* Added package py-versioneer * Update python version * Added python2 to versioneer * Added python2 to versioneer * Update var/spack/repos/builtin/packages/py-versioneer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Cleaning comments * Removed temporarily @warner as a maintainer, waiting for answer * Removed line Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-28Add version info for the-silver-searcher@2.2.0 (#15270)George Hartzell1-0/+1
2020-02-28OpenMPI nolegacylaunchers: avoid a fork bomb (#15268)Rémi Lacroix1-3/+3
Due to the use of backquotes, the replacement script for mpirun/mpiexec commands would recursively call itself, effectively causing a fork bomb.
2020-02-28gromacs: add v2019.6 (#15267)Christoph Junghans1-1/+2
* gromacs: add v2019.6 * Update var/spack/repos/builtin/packages/gromacs/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-28Fix expect on linux (#15230) (#15269)iarspider1-4/+5
* Fix expect on linux * Flake8
2020-02-28ssht: Correct recipe (#15217)Erik Schnetter2-4/+38
- Tell make about the source code path - Install actual header files, not a wrapper with wrong paths - Add a patch to prevent compiler warnings - Improve description
2020-02-28Fix detection of redhat enterprise compute node (#15253)Adam J. Stewart1-0/+1
* Fix detection of redhat enterprise compute node * Add comma * Remove space
2020-02-28Add new version of libfabric that builds on macOS (#15254)Seth R. Johnson1-16/+17
* Add new version of libfabric that builds on macOS See https://github.com/ofiwg/libfabric/issues/5339 Fixes https://github.com/spack/spack/issues/15244 Also reduced copy-paste of URLs with `url_for_version`. * Address reviewer feedback
2020-02-28unifyfs depends on openssl (#15258)eugeneswalker1-0/+1
2020-02-28UCX: add 1.7.0 (#15266)Howard Pritchard1-0/+3
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2020-02-28Add @drbenmorgan as maintainer for core HEP packages (#15264)Ben Morgan15-1/+27
2020-02-27Fixups for jupyter (#15136)Glenn Johnson5-8/+25
* Fixups for jupyter This PR fixes a few things for some jupyter related packages. py-ipython: - make the python depends_on statements reflect needs of different versions - remove an unneeded conflicts directive py-ipywidgets: - add new version - set version constraints for py-widgetsnbextension py-jupyter-console - add new version - set python dependencies for versions as needed - set version constraint for py-ipython - set version constraints for py-prompt-toolkit py-pyqt5 - build with py-sip py-qtconsole - add dependency on py-pyqt5 * Update var/spack/repos/builtin/packages/py-jupyter-console/package.py Tweak version ranges. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-jupyter-console/package.py Tweak version range. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Make py-pyqt5 a run dependency Also, make formatting more consistent. * Fix site_packages_dir Change reference of site_packages_dir to self.site_packages_dir. Oddly, this did not show up as a problem until I regenerated the module. * Restore py-pyqt5 to previous state * Explicitly set path to site_packages_dir This change prevents an error when regenerating the py-pyqt5 module file. * Fix flake8 errors * Make sure prefix is in join_path * Fix flake8 errors Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-27Fixed url for SLEPc package (#15257)Anwar Koshakji1-2/+2
* Fixed url for SLEPc package * Fixed homepage url for SLEPc package
2020-02-27gsl: build against external cblas (#15261)Christoph Junghans2-0/+351
2020-02-27New package: py-librosa (#15223)Glenn Johnson7-4/+145
* New package: py-librosa This PR adds the py-librosa package, along with new dependency packages and some updates of existing dependency packages. - new package: py-audioread - new package: py-resampy - new package: py-soundfile - update package: py-numba - update package: py-llvmlite py-numba: - add updated version - adjust constraints py-llvmlite: - add updated version - adjust constraints - fix version specifications for llvm - add environment function to set PIC * Update var/spack/repos/builtin/packages/py-numba/package.py Ah, yes, I see that `setuptools` is listed in the `install_requires` array. I missed that before. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Fix dependency - Add dependency of py-soundfile depends on libsndfile - Add new libsndfile package * Add py-pytest-runner build dep * Make numpy a variant for py-soundfile Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-27Mark GCC7 and newer as conflicting with rhel6 without binutils (#14706)Seth R. Johnson1-0/+5
When building gcc7 and gcc8 on RHEL6 with Spack and installing it as a spack-available compiler, OpenBLAS will fail to compile because GCC generates newer instructions than rhel6's `as` assembler knows about (e.g. "vpermpd"). Building gcc8 with binutils succeeds, and it generates a GCC that can then successfully build OpenBLAS. This is also expected to work for gcc7 on RHEL6.
2020-02-27Added version 0.12.0 to py-pyfftw (#15252)L. Diana Amorim1-4/+5
* Added version 0.12.0 to fix issue #15218 * Added dependencies specs with compatible versions * Switched py-scipy dependency to variant (default F) * Removed variant py-scipy and didn't add py-dask * Fixed typo: missing ' * Update var/spack/repos/builtin/packages/py-pyfftw/package.py Fixing typos from version ranges in dependencies. Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update var/spack/repos/builtin/packages/py-pyfftw/package.py Removed repeating dependency option. Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update var/spack/repos/builtin/packages/py-pyfftw/package.py Limited version of py-numpy dependency to <2.0. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-27portage: needs to be linked against lapack:c (#15259)Christoph Junghans1-1/+1
2020-02-27Fix Trilinos 12.18.1 build when using Apple Clang 8.0.0Jean-Paul Pelteret2-0/+40
2020-02-27Update package: Trilinos + MesquiteJean-Paul Pelteret1-0/+21
2020-02-27Adding an option to build the C api for Umpire. (#15238)Robert Blake1-1/+13
* Adding an option to build the C api for Umpire. This is useful if you need to link to a C code and you're using a compiler suite that doesn't support fortran. * Also updating the versions while I'm here. * Adding conflict: Fortran requires C. To ease transition and confusion, default to C-bindings being present. This shouldn't hurt anyone who is upgrading an existing installation.
2020-02-27new package: py-auxlib (#15221)Glenn Johnson1-0/+20
2020-02-27Remove "triage" label from feature requestMassimiliano Culpo1-1/+1
2020-02-27Use checkout v2 to avoid issues on retriggeringMassimiliano Culpo1-1/+1
2020-02-27Improved the feature request templateMassimiliano Culpo1-9/+14
2020-02-27Improved the build error templateMassimiliano Culpo1-7/+18
2020-02-27Improved the bug report templateMassimiliano Culpo1-7/+22
2020-02-27hpcviewer: add version 2020.02Mark W. Krentel1-0/+6
2020-02-27New package: XCFun (#15199)Roberto Di Remigio1-0/+37
2020-02-27Add new timeout fetch_optionMichael Kuhn3-10/+21
This allows packages to override the global connect_timeout.
2020-02-27Generalize curl_options into fetch_optionsMichael Kuhn2-19/+22
This allows us to support higher-level concepts such as 'cookie' and 'timeout' without users having to specify curl options.
2020-02-27config: Add a new option connect_timeoutMichael Kuhn4-2/+14
connect_timeout can be used to increase the time Spack waits for the server to answer. This can be used to work around slow connections or servers. Fixes #14700
2020-02-27release sz 2.1.8.3 (#15250)Sheng Di1-0/+1
2020-02-27CudaPackage: add support for Tesla K80 and older CUDA (#15031)Adam J. Stewart1-30/+46
* CudaPackage: add support for Tesla K80 and older CUDA * Flake8 fixes * Fix cuda_arch when no arch is set * Fine-tune cuda_arch=37,50 supported CUDA versions * CUDA 6.5+ supports SM_37 * Add @svenevs as a maintainer
2020-02-27new package: py-cnvkit and py-pomegranate (#15222)Glenn Johnson2-0/+51
The py-pomegranate package is a dependency of py-cnvkit
2020-02-27new package: py-pycifrw (#15224)Glenn Johnson1-0/+18
2020-02-27new package: py-pycosat (#15225)Glenn Johnson1-0/+20
2020-02-27New packages: py-pymc3 and py-arviz (#15226)Glenn Johnson2-0/+55
This PR adds py-pymc3 and py-arviz as a dependency.
2020-02-27Added go 1.14 (#15249)Paul1-0/+1
2020-02-27Docs: "spack env" is in the meantime called "spack build-env" (#15233)TZ1-10/+10
2020-02-27arpack-ng: ILP64 support (#15103)Kai Torben Ohlhus1-1/+5
Details about ILP64 support: `INTERFACE64=1` are described on the [ARPACK-NG GitHub website](https://github.com/opencollab/arpack-ng).
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