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2020-04-16HAL: added new package at v2.1 (#16085)ilbiondo1-0/+102
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-15Add new package: zookeeper-benchmark (#16067)darmac1-0/+25
* Add new package: zookeeper-benchmark * refine zookeeper version * refine zookeeper version variant * remove unused variant
2020-04-15Neo4j (#16068)darmac1-0/+31
* Update var/spack/repos/builtin/packages/neo4j/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Add new package: neo4j * refine neo4j package * fix flake8 warning Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15update: memsurfer with python3 (#15636)Harsh Bhatia1-17/+19
* update: memsurfer with python3 * flake8 compliance * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * removed build_type preferences at adamjstewart's suggestion * Added build/run dependency on python3.7 as suggested by adam stewart * more flake8 horror! Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15Upgrade MSTK versions (#16079)Rao Garimella1-0/+3
2020-04-15netcdf-cxx4: bugfix (#16080)Carson Woods1-0/+1
* Add new variants * Fix missing config_args variable
2020-04-15x.org packages: mirror mixinAxel Huebl200-400/+401
overhaul all x.org packages to use available mirrors.
2020-04-15Added maintainers (#16078)wspear1-0/+1
Co-authored-by: Wyatt Spear <wspear@cs.uoregon.edu>
2020-04-15Sonlib (#16060)ilbiondo1-0/+47
* sonLib package as required by the HAL toolkit * cleanup * Update var/spack/repos/builtin/packages/sonlib/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/sonlib/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15New package: py-cmake-format (#16055)Kelly (KT) Thompson2-0/+21
* New package py-cmake-format * wrap long lines * Fix package description formatting.
2020-04-15Bump version of libtree (#16051)Harmen Stoppels1-1/+3
2020-04-15Tests: Mirror Mixin ClassesAxel Huebl7-0/+105
2020-04-15x.org: mirror mixinAxel Huebl1-2/+2
According to my nightly CI/CD tests, x.org is another large provider of software in common build chains that is often down. Added a hand-selected amount of mirrors that is well up-to-sync. Tested with `util-macros` that has a quite "recent" patch release. Other packages to follow in an individual PR.
2020-04-15Fix grcp@1.27.0: (#16052)Federico Ficarelli1-0/+5
Current default version was missing a dependency.
2020-04-15Add new package: mrbench (#16062)darmac1-0/+23
2020-04-15Add new package: kinesis (#16063)darmac1-0/+27
2020-04-15Added Laghos v3 to Proxy Apps v3 (#16070)Robert Pavel1-2/+3
Also fixed upper bound for v2 apps
2020-04-15julea: New package (#16071)Michael Kuhn1-0/+42
2020-04-15IQ-TREE: added new package at v1.6.12 (#16064)ilbiondo1-0/+51
2020-04-15Phylobayes MPI: added new package at v1.8b (#16065)ilbiondo1-0/+31
2020-04-15openfoam: set run environment by sourcing bashrc (#15949)Massimiliano Culpo1-11/+9
2020-04-15py-sonlib: added new package (#16058)ilbiondo1-0/+28
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-14Apply same patch to version 10. (#15963)Dan Lipsa1-1/+1
2020-04-14libssh2: fix linking on macOS (#16012)Adam J. Stewart2-0/+7
* libssh2: fix linking on macOS * Fix libgit2 linkage to libssh2
2020-04-14MAINT: Charliecloud OSX error (#16049)Tyler Reddy1-0/+2
* MAINT: Charliecloud OSX error * raise an appropriate error when attempting to build Charliecloud on Mac OSX, since it will otherwise fail with a more confusing configure stage link check failure * Update var/spack/repos/builtin/packages/charliecloud/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * MAINT: PR 16049 revision * remove an unused import Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-14fix typo (#16043)Sajid Ali1-1/+1
2020-04-14new package: py-torch-nvidia-apex (#16050)Andrew W Elble1-0/+41
2020-04-14Add new variants (#16047)Carson Woods1-0/+59
2020-04-14py-memory-profiler: add new version (#16048)Adam J. Stewart1-3/+4
2020-04-14cp2k: add version 7.1 (#16037)Tiziano Müller1-1/+16
* cp2k: add version 7.1 * cp2k: add option to use COSMA for CP2K 8+
2020-04-14tau: remove deprecated variants (#16041)Carson Woods1-16/+0
* Add more tau variants * Add more tau variants * Remove deprecated packages * Fix flake8 issue
2020-04-14Add support for pre-release builds of Rust (beta, master, nightly) (#16042)Andrew Gaspar1-3/+73
2020-04-14py-tokenizers: add 0.5.2 (#16039)Adam J. Stewart1-0/+7
2020-04-14libtree: new package at 1.0.3 (#16036)Harmen Stoppels1-0/+18
* Add new package libtree * Fix linter issues
2020-04-14pfft: fix to handle 'precision' variant in fftw (#16029)Tom Payerle1-12/+16
* pfft: fix to handle 'precision' variant in fftw pfft had been checking for +double, etc. in fftw spec, which no longer are present (replaced by Multivalued variant precision). * pfft: fix to handle 'precision' variant in fftw pfft had been checking for +double, etc. in fftw spec, which no longer are present (replaced by Multivalued variant precision). (amended to use more idiomatic checks as suggested by @alalazo)
2020-04-14muscle: add 3.8.31 (#15974)Justin S1-3/+24
* muscle: add 3.8.31 * muscle: use build_directory property * muscle: add url_for_version, fix version comparison
2020-04-14sourceware.org: mirror urls (#15992)Axel Huebl5-26/+11
sourceware.org is often quite overrun and times out or results in certificate errors. Since libffi, bzip2, elfutils, etc. are quite fundamental in build chains, lets add some official mirrors. libffi, bzip2, elfutils, lvm2, valgrind: add mirrors
2020-04-14add charliecloud 0.15 (#16023)Jordan Ogas1-0/+1
2020-04-14py-vcf-kit: new package at 0.1.6 (#15976)Justin S1-0/+42
2020-04-14VMD: added new package at v1.9.3 (#16022)Antonio Arena1-0/+42
2020-04-14httpress: added new package at v1.1.0 (#15935)darmac1-0/+24
2020-04-13Rust: add missing dependencies (#16015)Adam J. Stewart1-2/+6
* Rust: add missing dependencies * 1.43.X won't support Python 3 either
2020-04-13bazel: increase logging during build, set job limit (#16024)Andrew W Elble1-1/+11
To better help in troubleshooting build issues. Job limit might also help with the memory limit issues we've been seeing.
2020-04-13Patch Mathematica (#16019)Antonio Arena1-0/+6
* Patch Mathematica Mathematica installer moves all files and directories from installation directory to a backup one. The problem is that it also moves .spack to this backup location. Once it's done it does not move .spack back where it was. My patch creates a copy of .spack to /tmp then moves it back right before exiting the install call. * Make lint happy * Use Spack native copy() As suggested in peer-review let's: - Copy .spack to stage directory so I don't have to use random - Use Spack native copy() to do these operations * Use join_path to create paths As per peer-review suggestion: - Use join_path to create paths - Use copy_tree since we're copying a directory that could have sub-directories
2020-04-13suite-sparse: add version 5.7.2 (#16020)Kai Torben Ohlhus1-0/+1
Release notes: https://github.com/DrTimothyAldenDavis/SuiteSparse/releases/tag/v5.7.2
2020-04-13New version: py-notebook@6.0.3 (#15975)Jennifer Herting1-21/+35
* Update package.py to include py-notebook 6.0.3 and sha * Update package.py * [py-notebook] updated py-tornado version requirements * [py-notebook] reworked and reordered for readability * [py-notebook] updated version requirement for py-jupyter-client * [py-notebook] updated version requirements for py-jupyter-core Co-authored-by: ehdeec <ehdeec@rit.edu>
2020-04-12py-sacremoses: add new version (#16018)Adam J. Stewart1-2/+2
2020-04-12boost: Fix for Version Comparison on Newer Clang on Darwin (#16014)Dr. Christian Tacke2-0/+37
Applying to boost @1.56.0:1.72.0 as that's the version range, where this patch can be cleanly applied. I was not able to test this myself, but got positive feedback. See: https://github.com/boostorg/build/issues/440 See: https://github.com/macports/macports-ports/pull/6726
2020-04-12new package: BART (#16016)Glenn Johnson3-0/+221
* new package: BART This PR adds the BART (Berkeley Advanced Reconstruction Toolset) package. Despite the presence of CMake files, this package builds with a Makefile. It looks like the project is moving away from cmake. The patch for MKL has been committed upstream so should only be necessary for this version of BART. The Makefile patch is meant for working with Spack and would not be useful upstream. The bart scripts are still setup to use bart with the subcommands being individual binaries. This patches those to use the single binary with built-in subcommands and assumes that spack is providing the TOOLBOX environment variable and setting PATH. * Update var/spack/repos/builtin/packages/bart/package.py Yes, '==' make more sense for a single string. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * The python dependencies are run time only. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-12New patch release SLEPc 3.13.1 (#16013)Jose E. Roman1-1/+2
* New patch release SLEPc 3.13.1 * Update var/spack/repos/builtin/packages/slepc/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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