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2020-04-15x.org: mirror mixinAxel Huebl3-2/+40
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.
2020-04-15`spack install` terminal output handling in foreground/background (#15723)Todd Gamblin7-224/+1155
Makes the following changes: * (Fixes #15620) tty configuration was failing when stdout was redirected. The implementation now creates a pseudo terminal for stdin and checks stdout properly, so redirections of stdin/out/err should be handled now. * Handles terminal configuration when the Spack process moves between the foreground and background (possibly multiple times) during a build. * Spack adjusts terminal settings to allow users to to enable/disable build process output to the terminal using a "v" toggle, abnormal exit cases (like CTRL-C) could leave the terminal in an unusable state. This is addressed here with a special-case handler which restores terminal settings. Significantly extend testing of process output logger: * New PseudoShell object for setting up a master and child process and configuring file descriptor inheritance between the two * Tests for "v" verbosity toggle making use of the added PseudoShell object * Added `uniq` function which takes a list of elements and replaces any consecutive sequence of duplicate elements with a single instance (e.g. "112211" -> "121") Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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
2020-04-14Package extensions: fixed a link in docs (#16040)Massimiliano Culpo3-7/+9
* Moved link to the right place in the docs * Fixed a few minor issues in extensions docs Fixed a typo, added a subsubsection for better navigation, reworded "modules in Python" as "Python packages"
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 Huebl7-26/+49
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>
2020-04-12database: maintain in-memory consistency on remove (#15777)Massimiliano Culpo2-1/+21
The performance improvements done in #14693 where leaving the DB in an inconsistent state when specs were removed from it. This PR updates the DB internal state whenever the DB is written to a file. Note that we still cannot properly enumerate installed dependents, so there is a TODO in this code. Fixing that will require the dependents dictionaries in specs to be re-keyed (either by hash, or not keyed at all -- a list would do). See #11983 for details.
2020-04-12new package: py-youtube-dl + fixes for dependencies (#15978)Glenn Johnson2-11/+130
* new package: py-youtube-dl + fixes for dependencies This PR adds the py-youtube-dl program. In addition, there are a couple of dependency packages that needed to be updated. * ffmpeg This is needed by py-youtube-dl. However, the spack ffmpeg recipe does not include a lot of options, specifically, a dependency on openssl for working with the https protocol. - Added updated version. - Added variants for the different licensing options. - Added "meta" variants for X and drawtext. These turn on/off several options. - Set variants and dependencies for many options. The defaults are based on the configuration settings in ffmpeg. - Set dependencies that were missing or that will likely get pulled in from the system. * libxml2 The ffmpeg+libxml2 variant initially failed to build. The issue is that libxml2 sets the headers property to include_dir = self.spec.prefix.include.libxml2 The ffmpeg configure looks for prefix.include and fills in the rest. This could probably be patched in ffmpeg but the headers property in the libxml2 recipe is not consistent with the environment module or the pkgconfig file, both of which set the headers path to prefix.include. This PR sets the libxml2 headers property to include_dir = self.spec.prefix.include A spot check of a few libxml2 dependents did not rreveal any problems with this change. * Comment out libxml2 dependency in ffmpeg The header property issue of the spack libxml2 package will need to be resolved in another PR before libxml2 can be enabled in ffmpeg.
2020-04-12py-transformers: add new package (#16011)Adam J. Stewart1-0/+29
2020-04-12py-tokenizers: add new package (#16010)Adam J. Stewart1-0/+16
2020-04-12py-sacremoses: add new package (#16009)Adam J. Stewart1-0/+20
2020-04-12py-setuptools-rust: add new package (#16008)Adam J. Stewart1-0/+18
2020-04-11tau: added new variants (#16005)Carson Woods1-0/+20
* Add more tau variants * Add more tau variants
2020-04-11new package: openmm (#16002)Andrew W Elble1-0/+48
* new package: openmm * dependency adjustments * 1. modify dependencies 2. openmm dynamically compiles cuda kernels during runtime, attempt to set up an environment that will work. * Update var/spack/repos/builtin/packages/openmm/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-10[py-jupyter-core] added version 4.6.3 (#15991)Jennifer Herting1-0/+3
* [py-jupyter-core] added version 4.6.3 * [py-jupyter-core] updated python version requirement
2020-04-10votca-tools: add mkl support (#15997)Christoph Junghans1-0/+8
* votca-tools: add mkl support * Update package.py
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