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2020-05-09macOS nightly: +1hr py-jupyterAxel Huebl1-1/+1
check if failures ares actually a real timeout or an error that just causes a hang.
2020-05-09macOS nightly: two coresAxel Huebl1-0/+1
All GitHub actions provide two cores. Just make sure this does not get oversubscribed with potentially visible additional physical cores.
2020-05-09Add unit test on MacOS using Github Actions (#14220)Massimiliano Culpo4-22/+50
- Remove macos tests from travis - Add macos tests in github actions.
2020-05-09[dd4hep] variant and run env updates (#16524)vvolkl1-2/+8
* [dd4hep] variant and run env updates * address comments from #16524
2020-05-09Add maintainers and variants for building with default earlier api versions. ↵Larry Knox1-0/+12
(#16534) * Add maintainers. Add variants for building with default earlier api versions. * Update var/spack/repos/builtin/packages/hdf5/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-09New package: py-addict (#16535)Jen Herting1-0/+19
* [py-addict] created template * [py-addict] added homepage and description * [py-addict] cleaned up fixmes * [py-addict] depends on py-setuptools
2020-05-09QMCPACK Update May 2020 (#16542)Nichols A. Romero1-23/+2
* Add naromero77 as a maintainer for QMCPACK Spack package. * Add QMCPACK 3.9.2 * Remove QE-to-QMCPACK wave function converter from QMCPACK Spack package. Already been moved to QE Spack package.
2020-05-09Fix dependency of geant4 (amends #16497) (#16504)iarspider3-10/+14
* Fix dependency of geant4 (amends #16497) * Update geant4-data dependencies * Reviewer comments (part 1/2) * Reviewer comments (part 2/2) * Update var/spack/repos/builtin/packages/geant4-data/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-09Increase coverage of spack.relocate (#16475)Massimiliano Culpo3-120/+286
- add docstrings and make parameter names consistent in `relocate.py` - Make `replace_prefix_*` and other functions private (as they are implementation details) - remove unused function _replace_prefix_nullterm() - Add unit tests for `relocate.py` functions - add patchelf to Travis and use it during tests - add hello_world fixture with a compiled binary, so we can test relocation
2020-05-09update visit package with 3.1.1 release and add comments (#16498)Cyrus Harrison3-7/+154
2020-05-09bugfix: don't use sys.stdout as a default arg value (#16541)Todd Gamblin8-12/+25
After migrating to `travis-ci.com`, we saw I/O issues in our tests -- tests that relied on `capfd` and `capsys` were failing. We've also seen this in GitHub actions, and it's kept us from switching to them so far. Turns out that the issue is that using streams like `sys.stdout` as default arguments doesn't play well with `pytest` and output redirection, as `pytest` changes the values of `sys.stdout` and `sys.stderr`. if these values are evaluated before output redirection (as they are when used as default arg values), output won't be captured properly later. - [x] replace all stream default arg values with `None`, and only assign stream values inside functions. - [x] fix tests we didn't notice were relying on this erroneous behavior
2020-05-09ci: update Travis badge in README.md to point to travis-ci.comTodd Gamblin1-1/+1
2020-05-08spaCy: add new package for en_core_web_sm model (#16539)Adam J. Stewart1-0/+17
2020-05-08Metall: add version 0.2 (#16502)Keita Iwabuchi1-0/+2
2020-05-08Add new package:py-pytest-check-links (#16503)takanori-ihara1-0/+19
2020-05-08py-netcdf4: a couple of improvements (#16505)Sergey Kosukhin2-0/+30
* py-netcdf4: avoid recompilation and make the older versions to work with HDF5@1.10: * py-netcdf4: add a new version and introduce a maintainer list.
2020-05-08precice: Fix conflict with boost 1.73.0 (#16507)Frédéric Simonis1-0/+1
2020-05-08graphviz: fix cairo backend (#16511)Christoph Junghans1-1/+1
2020-05-08Gaudi: separate variant for building documentation (#16515)iarspider1-2/+4
* Gaudi: separate variant for building documentation * Update package.py
2020-05-08New package (#16519)h-denpo1-0/+26
Large Scale Assembly, Structural Correspondence, Multi Dynamics Simulator.In this program, a part of functions of ADVENTURE_Solid ver.1.1 module
2020-05-08Gaudi: syntax fix (#16523)iarspider1-3/+3
2020-05-08new version xrootd-4.12.0 (#16528)Amjad Kotobi1-0/+1
2020-05-08new version r-git2r-0.27.1 (#16529)Amjad Kotobi1-0/+1
2020-05-08all_urls: add urls[0] for versions (#16435)Axel Huebl1-0/+4
This adds the `url` alternative `urls` to `package.all_urls`. With this addition, one can find again new versions with `spack versions <package>` for packages that are populated with from mixin mirror `urls`. Example: `util-macros` from x.org mixin.
2020-05-07Documentation: typo in option description (#16518)Erik Schnetter1-1/+1
2020-05-07Config option to disable setting S_ISGID bit when creating installation ↵iarspider3-1/+6
directory (#14479) * Add config option to disable setting S_ISGID bit when creating installation directory. Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-05-07"spack checksum" QoL (#14311)iarspider4-5/+19
* Non-interactive mode for spack checksum; allow passing 'package@version' to spack checksum * Flake8 fixes * Update checksum.py Fix typo * Update spack-completion script * Automatically set non-interactive mode if more than one version passed * Update lib/spack/spack/cmd/checksum.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Add documentation and update spack-completion * Flake8 * Rename option * Update spack-completion * Update lib/spack/spack/cmd/checksum.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update checksum.py * Update stage.py * Update create.py Use batch mode when adding a new package Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-07Revert changes to `qt` (#16516)Elizabeth Fischer1-3/+0
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-07Testing: fix unintended interactions between tests, part 2 (#16429)Peter Scheibel6-12/+47
This fixes some errors with setting up test configuration. These errors do not cause current Spack tests to fail but do create red herring issues elsewhere (see #15666). Fixing these errors leads to more errors in tests that depended on the original misconfigured state, so those are also addressed here. This is an update to #16003 which accounts for some unit tests with conflicting config/mutable_config fixtures. These conflicts were not exposed until the mutable_config fixture was fixed. Details are included below. The change which builds on #16003 is prefixed with "(new)". * For tests that use the real Spack package repository, the config needs to avoid using MPI providers that are not intended to be installed by Spack. Without this, it is possible that Spack tests which concretize the MPI virtual will end up trying to use an implementation that it shouldn't (e.g. one that is always provided externally). See #15666 for an example. * The mutable_config test fixture was not initializing the scope roots to the right directories (so the resulting config was empty). * The current_host fixture in the concretize.py tests was using the config fixture rather than mutable_config, and was polluting the config cache for other tests. * One test in concretize.py was clearing a nonexistent cache (PackagePrefs._packages_config_cache). This reference has been removed. * The test 'test_preferred_compilers' was was depending on cross test config pollution to succeed. The initial spec before concretization has been updated to updated to be explicit about the desired result. * (new) For tests that use install_mockery and mutable_config, replace install_mockery with a separate install_mockery_mutable_config fixture that is exactly the same as install_mockery but uses the mutable_config fixture to avoid conflicts.
2020-05-07GDAL: add 3.1.0 (#16509)Adam J. Stewart1-0/+1
2020-05-07NAG Compiler 7.0 (Build 7017) download checksum (#16510)Themos Tsikas1-1/+1
2020-05-07Add Rust 1.43.1 (#16512)Andrew Gaspar1-0/+7
2020-05-07ADD New package revocap-refiner (#16499)h-denpo1-0/+57
* ADD New package revocap-refiner """The University of Tokyo, CISS Project: Geometric processing, mesh processing, mesh generation""" * Modify homepage = "https://github.com/FrontISTR/REVOCAP_Refiner" Modify version('master', branch='master') Modify depends_on('swig', type='build') Modify install_tree('Refiner', prefix.include.refine) Delete mkdirp(prefix.include)
2020-05-07Add new package: ganglia (#16382)darmac1-0/+35
* Add new package: ganglia * ganglia: fix the libexpat depends
2020-05-07Adapt to the latest Acts developments (#16385)Hadrien G1-16/+56
* Adapt to the latest Acts developments A long time ago, the Acts project (whose name was then capitalized ACTS) used to maintain multiple software repositories: - The heart of the tracking toolkit was located in the `acts-core` repository - Fast simulation extensions were located in the `acts-fatras` repository - Advanced usage examples were located in the `acts-framework` repository This multi-repository organization, however, has been a source of constant pain, which is why the various projects were gradually merged into a single mono-repo, called `acts`. Today, with the integration of `acts-framework`, this merging process is reaching completion. The present pull request adapts the Acts package to this evolution by... - Renaming the package to `acts`, reflecting the new repository name - Renaming the `test` variant to `unit_tests`, reflecting current CMake naming - Adding the new build variants that were inherited from `acts-framework` - Acknowledging the change of semantics of the `examples` variant, and only supporting the new ones (as the former variant was almost unused) - Liberally using alphabetical order to make the package code more readable - Recording a large number of conflicts, some of which are introduced by the merging of `acts-framework` and some of which already existed before - Using the new capitalization of "Acts" * Add acts v0.23 * Update dd4hep version requirement * Add acts v0.22.1 bugfix
2020-05-07Add PGI version 19.7 and export OMPI variables (#16484)asmaahassan901-0/+11
* add PGI version 19.7 * use openmpi in pgi exporting openmpi enviroment variables when installed with pgi * fix lint
2020-05-07 bugfix: spack shouldn't fail in an incomplete environment (#16473)Todd Gamblin2-9/+49
Fixed #15884. Spack asks every package linked into an environment to tell us how environment variables should be modified when a spack environment is activated. As part of this, specs in an environment are symlinked into the environment's view (see #13249), and the package calculates environment modifications with *the default view as the prefix*. All of this works nicely for pointing the user's environment at the view *if* every package is successfully linked. Unfortunately, right now we only track what specs "should" be in a view, not which specs actually are. So we end up calculating environment modifications on things that aren't linked into thee view, and the exception isn't caught, so lots of spack commands end up failing. This fixes the issue by ignoring and warning about specs where calculating environment modifications fails. So we can still keep using Spack even if the current environment is incomplete. We should probably also just avoid computing env modifications *entirely* for unlinked packages, but right now that is a slow operation (requires a lot of YAML parsing). We should revisit that when we have some better state management for views, but the fix adopted here will still be necessary, as we want spack commands to be resilient to other types of bugs in `setup_run_environment()` and friends. That code is in packages and we have to assume it could be buggy when we call it outside of builds (as it might fail more than just the build).
2020-05-07neovim: added v0.4.3 (#16410)Eisuke Kawashima1-16/+37
Use neovim's vendored dependencies for 0.4 and later
2020-05-06openfoam: correspond to build with Fujitsu compiler. (#15941)Tomoki, Karatsu1-4/+32
* openfoam: correspond to build with Fujitsu compiler. * openfoam: add rules for Fujitsu compiler (on linuxARM64) - the Fujitsu compiler is a clang derivative, so use a modified version of the clang rules if upstream does not supply anything
2020-05-06Add new package:py-json5 (#16273)takanori-ihara1-0/+19
* Add new package:py-json5 * Remove unnecessary line
2020-05-06New version of pylint + fix dependencies (#16443)iarspider1-3/+10
* New version of pylint + fix dependencies * Update package.py * Update package.py
2020-05-06Install RMPISNOW wrapper in prefix.bin for r-snow (#16479)Glenn Johnson1-0/+5
If using mpirun, the R sessions can be started with a wrapper script that helps set up the R session cluster. Put this wrapper in the PATH so it is easily accessible.
2020-05-06py-shapely: fix unit tests (#16500)Adam J. Stewart1-4/+13
2020-05-06py-netcdf4: make sure we don't use system hdf5. (#16492)Sergey Kosukhin2-0/+13
2020-05-06Bazel: add new versions (#16493)Adam J. Stewart2-2/+29
2020-05-06TensorFlow: add new version (#16494)Adam J. Stewart1-8/+15
2020-05-06OpenMPI - Update to 3.1.6 (#16496)Kevin Manalo1-1/+2
2020-05-06Add new version of Geant4 (#16497)iarspider1-0/+1
2020-05-06PyTorch/Torchvision: fix deptype (#16495)Adam J. Stewart2-4/+4
2020-05-06blis: FIX threads option, HPL: enable opemp variant for 2.3 (#16476)yellowhat2-4/+12
* blis: FIX threads option * HPL: openmp variant is ignored for 2.3 * blis: FIX flake8 * blis: FIX spacing * Update var/spack/repos/builtin/packages/hpl/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * hpl: FIX spec --> self.spec, FIX blas with amdblis * HPL: fix flake8 * HPL: FIX flake8 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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