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2023-01-25py-pytorch-lightning: add +extra variant (#35121)Adam J. Stewart17-16/+696
* py-pytorch-lightning: add +extra variant * Update dependencies * py-fsspec: add v2023.1.0
2023-01-25perl-math-symbolic: add 0.612 (#35145)Christopher Christofi1-0/+17
2023-01-25qperf: add verbs support (#35147)Michael Kuhn1-0/+4
2023-01-25py-cligj: add v0.7.2 (#35149)Adam J. Stewart1-6/+8
2023-01-25py-pycocotools: add v2.0.6 (#35150)Adam J. Stewart1-3/+6
2023-01-25py-scikit-learn: add v1.2.1 (#35152)Adam J. Stewart1-0/+1
2023-01-25spiner: add v1.6.0 (#35154)Richard Berger1-21/+35
2023-01-25amqp-cpp: added RabbitMQ C++ API (#35156)Loïc Pottier1-0/+39
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
2023-01-25Add Orca version 5.0.3-f.1 (#35157)Sebastian Ehlert1-2/+18
2023-01-25py-colorlover: new package with version 0.3.0 (#35144)Christopher Christofi1-0/+17
2023-01-25Add packages for scine modules (#34969)Sebastian Ehlert11-0/+585
* Add packages for scine modules - lbfgspp (dependency for scine-utilities) - scine-core - scine-utilities and py-scine-utilities (virtual) - scine-readuct and py-scine-readuct (virtual) - scine-sparrow and py-scine-sparrow (virtual) - scine-database and py-scine-database (virtual) - scine-molassembler and py-scine-molassembler (virtual) - scine-xtb and py-scine-xtb (virtual) - py-scine-chemoton - py-scine-puffin * Fix line-length for flake8 * Remove virtual dependencies * Update detection of boost, minor fixes in packages / dependencies * Correctly declare build-only dependencies, add git versions * Add sparrow dummy packages, fix dependencies * Rename latest version from develop to master * Restore original sparrow package * Also rename latest version for chemoton and puffin
2023-01-25py-flatten-dict: require poetry to build. (#35122)Matthias Wolf1-2/+2
* py-flatten-dict: require poetry to build. The sources seem to contain a bundled, auto-generated `setup.py`. Building with `pip` insist on using Poetry as mentioned in `pyproject.toml`, so require it as a build dependency. * Update var/spack/repos/builtin/packages/py-flatten-dict/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-flatten-dict/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-25py-lazy: add 1.4 and 1.5 (#35124)Erik Heeren1-0/+13
* py-lazy: add 1.4 and 1.5 * py-lazy: add url_for_version
2023-01-25Add package `py-continuum` (#35082)Thomas Bouvier2-0/+71
* Add package `py-continuum` * `py-continuum`: missing `py-pytest-mock` dependency * `py-continuum`: add missing python dependency * [@spackbot] updating style on behalf of thomas-bouvier * Patch to remove useless `prospector` package * Link to original PR Co-authored-by: thomas-bouvier <thomas-bouvier@users.noreply.github.com>
2023-01-25py-pyspark: new versions (#35129)Erik Heeren2-8/+29
* py-pyspark: new versions * py-py4j: new versions * py-py4j: more style * py-py4j: even more style * py-spark, py4j: review remarks
2023-01-25Print file summary on checksum validation failure (#35161)Harmen Stoppels2-4/+35
Currently we print "sha256 checksum failed for [file]. Expected X but got Y". This PR extends that message with file size and contents info: "... but got Y. File size = 123456 bytes. Contents = b'abc...def'" That way we can immediately see if the file was downloaded only partially, or if we downloaded a text page instead of a binary, etc. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-01-25libxc: 6.1.0 (#35159)Harmen Stoppels1-8/+5
Currently 6.0.0 fails on develop about incorrect shasum, but I can't reproduce; maybe the download was temporarily unavailable.
2023-01-25Update COSTA package (#35137)Rocco Meli1-5/+14
2023-01-24py-scipy: do not build 1.6 and older with python < 3.10.1 (#35120)Gilles Gouaillardet1-4/+4
py-scipy 1.6 and older come with pre cython-ized files that use the _PyGen_Send symbol that was removed from python 3.10.0.161, so do not build these old versions with python 3.10.1 and later
2023-01-24loki%gcc@11: -std=c++14 to avoid issue #32122 (#35148)eugeneswalker1-3/+4
2023-01-24LAMMPS: Add package ml-hdnnp. (#35133)Rémi Lacroix1-0/+21
First added as user-hdnnp in version 20210527.
2023-01-24Add package `py-nvidia-dali` (#35058)Thomas Bouvier1-0/+56
* Add package `py-nvidia-dali` * Add linux check * Add missing deps
2023-01-24Fix dbcsr checksums (#35134)Taillefumier Mathieu1-3/+3
2023-01-24hip: add cuda variant (#33872)Cory Bloor2-124/+141
2023-01-24New package: srcml (#35097)Jen Herting1-0/+37
* Initial srcml * [srcml] - Fixed dependencies likely will need some more rework - Disabling packaging cmake file (for now) - Added patch to fix issue with source code library import * [srcml] updated copyright * [srcml] requires antlr complied with -fPIC * [srcml] cleaned up dependencies * [srcml] flake8 * [srcml] limiting boost versions Co-authored-by: Benjamin Meyers <bsmits@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2023-01-24py-planetary-computer: add new package (#35089)Adam J. Stewart2-0/+42
2023-01-24Add whip 0.1.0 and use in pika (#35073)Mikael Simberg2-4/+8
* Add whip 0.1.0 * Make pika depend on whip@0.1.0 Co-authored-by: msimberg <msimberg@users.noreply.github.com>
2023-01-24rmgdft: Update for version 5.0.1 (#35047)Emil Briggs1-5/+10
* Updated for RMG version 5.0.1 * Update var/spack/repos/builtin/packages/rmgdft/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-01-24ForTrilinos: new version 2.2.0 (#35138)Seth R. Johnson1-1/+3
2023-01-24libgcrypt: make sure flags go through env (#35135)Harmen Stoppels1-0/+6
Parts of libgcrypt should not be optimized with -O1/2/3, so it's best to let the build system do that; the build system cannot know the compiler wrapper would inject optimization flags
2023-01-24hdf5: remove direct dependency on msmpi on Windows (#35111)John W. Parent1-1/+0
2023-01-24mochi-margo: add v0.12 (#35132)Matthieu Dorier1-0/+1
2023-01-24Windows: conflict with Apple-GL (#35114)John W. Parent1-0/+2
2023-01-24Update dbcsr version (#35131)Taillefumier Mathieu1-0/+3
2023-01-24Avoid creating help.sh and test.sh in cwd (#35123)Massimiliano Culpo1-42/+35
When running unit-test the test/ci.py module is leaving garbage (help.sh, test.sh files) in the current working directory. This commit changes the current working directory to a temporary path before those files are created.
2023-01-23ParaView/VTK: Patch xdmf2 for HDF5 1.13 (#33930)kwryankrattiger7-2/+151
* ParaView/VTK: Patch xdmf2 for HDF5 1.13 * Meson: update meson build system for 0.64 * ParaView: Change HDF5 1.13 patch to 1.13.1/2 patchs * Mesa: Remove legacy mesa option from meson_args * Use append to assemble meson args
2023-01-23curl: New version 7.87.0 (#35088)Erik Schnetter1-0/+2
2023-01-23actually add samtools 1.16.1 and fix Copyright dates on samtools, bcftools, ↵downloadico3-3/+4
and htslib (#35118) * samtools: add version 1.16.1 (for real this time!) also, fix Copyright date * bcftools and htslib: fix Copyright date
2023-01-24Update: spack help --spec (#35115)Richarda Butler1-0/+9
* Update variant & compiler propagation * Add the info for non boolean variants * Add example for multi variants
2023-01-23Update qmd-progress package.py (#34841)Jean-Luc Fattebert1-5/+11
2023-01-23helics: Add version 3.4.0 (#35096)HELICS-bot1-0/+1
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
2023-01-23n2p2: Allow building shared libraries (#35080)Rémi Lacroix1-0/+4
2023-01-23Update parallelio from NOAA-EMC fork (#34837)Alex Richert2-8/+49
2023-01-23freeimage: fails to compile with c++17, use c++14 (#35067)Wouter Deconinck2-1/+13
* freeimage: fails to compile with c++17, use c++14 Only `opencascade` when a (non-default) variant depends on `freeimage`, which seems to have gone unmaintained. There are c++17 standard violations [[1]]( https://en.cppreference.com/w/cpp/language/except_spec) in the code, so we can at most expect c++14. Since some compilers default to c++17 (gcc-12) we need to be explicit. * freeimage: install directly in prefix * freeimage: fix inverted patch
2023-01-23update Samtools, bcftools, and htslib versions (#35043)downloadico3-3/+6
* samtools: add version 1.6.1 * htslib: update version to 1.6 * bcftools: update version to 1.6
2023-01-23perl-test-leaktrace: add 0.17 (#35063)Christopher Christofi1-0/+16
2023-01-23[antlr] added pic variant (#35091)Jen Herting1-8/+11
* [antlr] modernize config arg processing * [antlr] added pic variant * [antlr] flake8
2023-01-23hpcviewer: add version 2023.01 (#35036)Mark W. Krentel1-0/+5
2023-01-23environments: don't replace relative view path with absolute path on ↵Harmen Stoppels4-4/+48
concretize/install (#34958) * environments: don't rewrite relative view path, expand path on cli ahead of time Currently if you have a spack.yaml that specifies a view by relative path, Spack expands it to an absolute path on `spack -e . install` and persists that to disk. This is rather annoying when you have a `spack.yaml` file inside a git repo, cause you want to use relative paths to make it relocatable, but you constantly have to undo the changes made to spack.yaml by Spack. So, as an alternative: 1. Always stick to paths as they are provided in spack.yaml, never replace them with a canonicalized version 2. Turn relative paths on the command line into absolute paths before storing to spack.yaml. This way you can do `spack env create --dir ./env --with-view ./view` and both `./env` and `./view` are resolved to the current working dir, as expected (not `./env/view`). This corresponds to the old behavior of `spack env create`. * create --with-view always takes a value
2023-01-23apptainer: add v1.1.5 (#35075)Massimiliano Culpo1-0/+1
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