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2021-07-08imports: sort imports everywhere in Spack (#24695)Todd Gamblin468-529/+952
* 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>
2021-07-07xyce: 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
2021-07-07py-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 Danilin9-4/+46
2021-07-06qt: rework to use the when context manager (#24723)Massimiliano Culpo1-33/+39
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
2021-07-06py-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>
2021-07-05GDAL: add v3.3.1 (#24713)Adam J. Stewart1-0/+1
2021-07-05py-importlib-metadata: add 4.6.1 and 3.10.1 (#24701)Manuela Kuhn1-0/+2
2021-07-05py-whoosh: add new package (#24707)Manuela Kuhn1-0/+17
2021-07-05py-keyrings-alt: add new package (#24704)Manuela Kuhn1-0/+19
2021-07-05py-patool: add new package (#24703)Manuela Kuhn1-0/+18
2021-07-05py-iso8601: add new package (#24702)Manuela Kuhn1-0/+17
2021-07-05py-num2words: add new package (#24681)Manuela Kuhn1-0/+18
2021-07-05uriparser: add v0.9.5 (#24688)Sebastian Pipping1-0/+1
2021-07-05grpc: add versions up to 1.33.1 (#24693)figroc1-1/+4
2021-07-05py-pandas: add v1.3.0 (#24696)Adam J. Stewart1-0/+4
2021-07-05py-isort: add v5.9.1, +colors variant (#24699)Adam J. Stewart1-4/+9
2021-07-05py-colorama: add v0.4.4 (#24698)Adam J. Stewart1-0/+2
2021-07-02Update Z-checker and SZ (#24446)Robert Underwood2-7/+2
2021-07-02Rename cray compiler to cce (#24653)Joe Heaton1-3/+3
cp2k was using the outdated and Incorrect compiler name `cray`.