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2021-07-09mypy: move configuration to pyproject.toml (#24802)Todd Gamblin3-37/+46
This moves our `mypy` configuration from `.mypy.ini` to `.pyproject.toml` and increases the minimum `mypy` version in the tests. - [x] move `mypy` configuration to `pyproject.toml` - [x] remove `.mypy.ini` - [x] ensure that `mypy` version .900 or higher is used in tests
2021-07-09googletest: add v1.11 and "live at head", keep v1.10 the default (#24290)Seth R. Johnson2-11/+18
Ideally a test-only dependency won't be in the build, but until then mark the requirement of gtest up to 1.10. See e4s job failure at https://gitlab.spack.io/spack/spack/-/jobs/349959 . Looks like 1.11 introduces some breaking incompatibilities, so perhaps we should transition later.
2021-07-09flux: add latest tagged releases (#24687)Stephen Herbein2-0/+4
flux-core v0.21 requires jansson 2.10+ For more details, see: https://github.com/flux-framework/flux-core/commit/a6086e021ee9bf869663bc475d4311dc540486fe
2021-07-09abseil-cpp: add cxxstd variant (#24577)Nic McDonald1-4/+10
2021-07-08Update pox (#24635)Sebastian Schmitt1-2/+4
* Update pox * Add build and run
2021-07-08imports: sort imports everywhere in Spack (#24695)Todd Gamblin797-1394/+2000
* fix remaining flake8 errors * imports: sort imports everywhere in Spack We enabled import order checking in #23947, but fixing things manually drives people crazy. This used `spack style --fix --all` from #24071 to automatically sort everything in Spack so PR submitters won't have to deal with it. This should go in after #24071, as it assumes we're using `isort`, not `flake8-import-order` to order things. `isort` seems to be more flexible and allows `llnl` mports to be in their own group before `spack` ones, so this seems like a good switch.
2021-07-08hdf5: Fix compiler identification for warning flags (#24627)Paul Henning1-1/+2
* Fix compiler test Use `self.spec.satisfies` on compiler to determine if a flag should be applied or not. This approach avoids issues with the strings `gcc` or `clang` appearing in the full path to the compiler executables, as happens with spack-installed compilers (e.g. `nvhpc%gcc`). * Limit compiler name search to last path component @skosukhin pointed out that the cflag modification should happen for any clang or gcc compiler, regardless of what compiler spec provides them. This commit reverts to searching for a compiler name containing "gcc" or "clang", but limits the search to the last path component, which avoids matching spack-installed compilers built with gcc (e.g. `nvhpc%gcc`), which will have "gcc" in the compiler path. * Use `os.path` rather than `pathlib` Co-authored-by: Paul Henning <phenning@lanl.gov>
2021-07-08setup-env: allow users to skip slow parts (#24545)Adam J. Stewart2-87/+91
2021-07-07cvs tests: don't use dateutil at allTodd Gamblin2-24/+26
`dateutil.parser` was an optional dependency for CVS tests. It was failing on macOS beacuse the dateutil types were not being installed, and mypy was failing *even when the CVS tests were skipped*. This seems like it was an oversight on macOS -- `types-dateutil-parser` was not installed there, though it was on Linux unit tests. It takes 6 lines of YAML and some weird test-skipping logic to get `python-dateutil` and `types-python-dateutil` installed in all the tests where we need them, but it only takes 4 lines of code to write the date parser we need for CVS, so I just did that instead. Note that CVS date format can vary from system to system, but it seems like it's always pretty similar for the parts we care about. - [x] Replace dateutil.parser with a simpler date regex - [x] Lose the dependency on `dateutil.parser`
2021-07-07style: get close to full coverage of `spack style`Todd Gamblin3-95/+182
Previous tests of `spack style` didn't really run the tools -- they just ensure that the commands worked enough to get coverage. This adds several real tests and ensures that we hit the corner cases in `spack style`. This also tests sucess as well as failure cases.
2021-07-07style: clean up and restructure `spack style` commandTodd Gamblin3-96/+80
This consolidates code across tools in `spack style` so that each `run_<tool>` function can be called indirecty through a dictionary of handlers, and os that checks like finding the executable for the tool can be shared across commands. - [x] rework `spack style` to use decorators to register tools - [x] define tool order in one place in `spack style` - [x] fix python 2/3 issues to Get `isort` checks working - [x] make isort error regex more robust across versions - [x] remove unused output option - [x] change vestigial `TRAVIS_BRANCH` to `GITHUB_BASE_REF` - [x] update completion
2021-07-07style: Move isort configuration to pyproject.tomlTodd Gamblin5-21/+16
- [x] Remove flake8-import-order checks, as we only need isort for this - [x] Clean up configuration and requirements
2021-07-07style: add support for `isort` and `--fix`Danny McClanahan3-11/+68
2021-07-07xyce: Prefer master branch (#24733)Paul Kuberry1-2/+3
Adds 7.3.0 release of Xyce and makes a tag 'github.master' pointing at the master branch of the Xyce repository on github.com.
2021-07-07New package: git-annex (#24721)Manuela Kuhn1-0/+79
2021-07-07Configure docbook packages (#24300)Glenn Johnson2-6/+200
This PR configures the spack docbook packages - docbook-xsl - docbook-xml The public entities are now mapped to the locally installed files of the respective packages. The example catalogs are left in place and XML_CATALOG_FILES points to the newly created catalogs.
2021-07-07zziplib: add v0.13.72(#24462)Olivier Cessenat1-1/+34
2021-07-07m4 package: only apply nvhpc.patch for version 1.4.18 (#24730)Gregory Lee1-1/+1
The patch as-is does not apply to 1.4.19
2021-07-07magma package: fix bugs in cuda_arch variant (#24735)Adam J. Stewart1-2/+0
2021-07-07py-mypy: add version 0.910 (#24738)Adam J. Stewart1-1/+6
2021-07-07perl: bzip2 and zlib may be installed under <prefix>/lib64 (#24752)Massimiliano Culpo1-2/+2
2021-07-07py-torch: +magma requires +cuda (#24736)Adam J. Stewart1-0/+1
2021-07-07add e4s-on-power stack (#24734)eugeneswalker2-0/+406
2021-07-07py-seaborn: add 0.11.1 (#24748)Manuela Kuhn1-3/+16
2021-07-07charliecloud: add v0.24 (#24728)Jordan Ogas1-0/+1
2021-07-07py-neurokit2: add new package (#24749)Manuela Kuhn1-0/+29
2021-07-07libtree: add v1.2.2 (#24747)Harmen Stoppels1-0/+1
2021-07-07netpbm: new package (#24063)Olivier Cessenat1-0/+208
2021-07-07New Package: visit-ffp (#22903)Olivier Cessenat1-0/+82
2021-07-07sleef: disable optional dependencies (#24742)Adam J. Stewart1-0/+7
2021-07-07perl: add dependencies for bzip2 and zlib (#24743)Mark W. Krentel1-3/+14
Perl keeps copies of the bzip2 and zlib source code in its own source tree and by default uses them in favor of outside libraries. Instead, put these dependencies under control of spack and tell perl to use the spack-built versions.
2021-07-06trilinos: enable +teko gotype=long (#24722)Seth R. Johnson1-1/+7
2021-07-06Magma: add ROCm support and v2.6.0 (#24663)G-Ragghianti1-5/+33
2021-07-06oneAPI packages: add 2021.3 release (#24617)Vasily Danilin11-16/+81
2021-07-06qt: rework to use the when context manager (#24723)Massimiliano Culpo1-33/+39
2021-07-06fix buffered download (#24623)Harmen Stoppels1-8/+8
* Use shutil to do a buffered copy from http response to file * Fix flake8... * Somehow flake8 still complains about unrelated files
2021-07-06qt+webkit: fix missing dependencies and gcc11 compatibility (#24366)Manuela Kuhn1-4/+28
2021-07-06json-fortran: add version v6.0.11 (#24720)Jianwen1-0/+1
2021-07-06openfoam: add v2106 (#24579)Mark Olesen1-2/+3
Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2021-07-06py-torch: fix bug in libs/headers attributes (#24624)Adam J. Stewart1-2/+4
2021-07-06xyce: clean and fix trilinos dependencies (#24673)Seth R. Johnson1-7/+10
2021-07-06abseil-cpp: add versions up to 20210324.2 (#24692)figroc1-1/+5
2021-07-06tensorflow-serving-client: add v2.3.0 (#24694)figroc1-1/+4
2021-07-06installer: fix double print of exception (#24697)eugeneswalker1-0/+1
2021-07-06py-black: add v21.6b0 (#24715)Adam J. Stewart1-3/+15
2021-07-06hpcx-mpi: new package (#24194)Mark W. Krentel1-0/+43
This is a virtual package for Nvidia's HPC-X MPI implementation for external specs only.
2021-07-06OpenCV: various package updates (#24553)Adam J. Stewart1-82/+168
2021-07-05py-sphinx: add v4.0.2 (#24602)Adam J. Stewart1-1/+4
2021-07-05py-secretstorage: add 3.3.1 (#24705)Manuela Kuhn1-4/+10
2021-07-05py-keyring: fix installation on linux (#24706)Manuela Kuhn1-1/+4
* py-keyring: fix installation on linux * Update var/spack/repos/builtin/packages/py-keyring/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-keyring/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>