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2023-07-11mypy: add more ignored modules to `pyproject.toml` (#38769)Todd Gamblin1-5/+22
`mypy` will check *all* imported packages, even optional dependencies outside your project, and this can cause issues if you are targeting python versions *older* than the one you're running in. `mypy` will report issues in the latest versions of dependencies as errors even if installing on some older python would have installed an older version of the dependency. We saw this problem before with `numpy` in #34732. We've started seeing it with IPython in #38704. This fixes the issue by exempting `IPython` and a number of other imports of Spack's from `mypy` checking.
2023-07-10py-gluoncv: switch to PyPI and add 0.10.5.post0 (#38814)Manuela Kuhn3-19/+29
* py-gluoncv: switch to PyPI and add 0.10.5.post0 * Fix style * Remove no-unicode-readme.patch
2023-07-10py-numpy: add v1.25.1 (#38799)Adam J. Stewart1-0/+1
2023-07-10[arrow] tuple has no method append (#38820)Jen Herting1-1/+1
2023-07-10mlpack: remove go variant from cmake_args (#38821)Wouter Deconinck1-1/+1
2023-07-10py-minkowskiengine: add missing openblas dependency (#38742)Manuela Kuhn1-0/+5
* py-minkowskiengine: add missing openblas dependency * Add comment about blas
2023-07-10Setting library path as lib similar to other rocm packages. (#37568)renjithravindrankannath3-2/+8
* Setting library path as lib similar to other rocm packages. * Fix style check failure * Restricting changes to 5.4.3 and above * Including comgr change
2023-07-10new hip-examples package (#35891)afzpatel3-0/+85
* initial commit for adding hip-examples package * adding test to hip-examples * fixed compile error on add4 * change standalone test to use new syntax
2023-07-10py-sacrebleu (#37159)Sangu Mbekelu1-0/+29
* new mosesdecoder package * "new py-sacrebleu package" * Delete package.py * [@spackbot] updating style on behalf of Sangu-Mbekelu * Update package.py updating package based on review --------- Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
2023-07-10Package:Openfoam-org version url using function (#37587)kjrstory1-41/+28
* Package:Openfoam-org version url using function * Package:Openfoam-org small style fix * openfoam-org: url_for_function
2023-07-10legion +rocm: set HIP_PATH to {hip.prefix}/hip (#38819)eugeneswalker1-1/+1
2023-07-10Perl package: detect opcode support in externals (#38618)Chris Green2-1/+6
Spack-installed Perl always has opcode support, but external Perl installations might not. This commit adds a +opcode variant and updates the external detection logic to check for opcode support. The postgresql package is updated to require perl+opcode (in combination with the above, this helps detect when an external Perl instance is sufficient for a Spack build of postgreqsql, or if Spack needs to build its own Perl).
2023-07-10glib: add 2.76.4 (#38813)Michael Kuhn1-0/+1
2023-07-10Update cp2k recipe to use cmake or the current build system (#35718)Taillefumier Mathieu3-28/+212
* Update cp2k recipe to use cmake or the current build system Offers the possibility to build cp2k with the new cmake build system. commands like this are now supported spack install cp2k@master build_system=cmake +..... the recipe supports the following optional functionalities - superlu, cosma, sirius, spglib, metis, spglib, libxc, libint, cuda/rocm, mkl/openblas/sci (and others), mpi, openmp, dbcsr - dbcsr is built separately using the currently available recipe. Two PRs need to be merged to be fully functional (cosma update in spack + one PR in cp2k github). * Fix indentation * Fix indentation * Update libvori * More typos * Simplify BLAS/LAPACK * Simplify BLAS/LAPACK * Add A100 gpu value * Fix typo * Add the enable_regtests option if -DCP2K_ENABLE_REGTESTS=ON (+enable_regtests with spack) then the location of the binary executables will be in the cp2k root directory under exe/build-cmake-*. This option is needed to run the regtests afterwards. * Minor update * more fixes * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi> * small changes * Remove any reference to nvidia architecture in the rocm list * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com> * Update var/spack/repos/builtin/packages/cp2k/package.py Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com> * Final reformating * Update py-fypp --------- Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi> Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
2023-07-10Removing inactive maintainer (#38773)Massimiliano Culpo7-7/+8
2023-07-10find: add `--hashes` shortcut for piping to other commands (#38663)Todd Gamblin2-1/+9
People frequently ask us how to pipe `spack find` output to other commands, and we tell them to do things like this: ```console $ spack find --format "/{hash}" | spack uninstall -ay ``` Sometimes users don't know about hash references and come up with potentially ambiguous formulations like this: ```console spack find --format {name}@{version}%{compiler} | spack uninstall -ay ``` Since this is a common enough thing to want to do, and to make it more obvious how, this PR adds a `-H` / `--hashes` as a shortcut, so you can now just do: ```console spack find -H | spack uninstall -ay ```
2023-07-09Added package py-bitstruct (#38761)Dax Lynch1-0/+21
* Added packages bitstruct, callmonitor, and PYnvtx * Revert "Added packages bitstruct, callmonitor, and PYnvtx" This reverts commit 76d25aa76bf4655a85c78725fe5c76c1792717c9. * py-bitstruct: This module is intended to have a similar interface as the python struct module, but working on bits instead of primitive data types (char, int, …) * Update package.py To pass the style prechecks * PyNVTX: new package * Delete package.py Accidentally added this package. * Update var/spack/repos/builtin/packages/py-bitstruct/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-09py-triangle: restrict Python version (#38808)Manuela Kuhn1-1/+3
2023-07-09openssl: prefer 3.x (#36729)Harmen Stoppels7-51/+99
* openssl: prefer 3.x This PR is not intended to be merged immediately, but it would be good to see what packages fail to build in CI so that we can get proper version constraints on openssl (before all packages update and support both openssl 1 and 3) * Disable assembly for 3.x %oneapi * cmake: depend on spack curl, to deal with curl - openssl compat * also make zlib external * remove overly strict & unsafe requirement on py-cryptographty patch version number * update openssl compat bounds in py-cryptography * smaller diff * Make libssh2 an autotools/cmake package * fix weird upperbound in libssh2 as there is not openssl v2 * libssh2: pc file lists plain -lssl -lcrypto w/o leading -L flag, confusing libgit2 parsing of pkg-config output * Actually fix the issue in libssh2: its pc file looks broken
2023-07-09ci: Fix broken SPACK_CHECKOUT_VERSION (#38778)Jonathon Anderson2-17/+13
2023-07-09Automated deployment to update package flux-core 2023-07-08 (#38790)Vanessasaurus1-0/+1
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-07-09Don’t call spec.format in Database._get_matching_spec_key (#38792)Harmen Stoppels1-1/+15
`"%s" % spec` formats the spec with deps included, which produces sometimes KBs of data and is slow to run in pure Python. It can delay otherwise very short-lived read/write locks on the database. Discovered in #38762 where profile output showed about 2 seconds is spent in `spec.format`, which is significant overhead when using multiprocessing to install from binary cache in parallel (installation often takes <5s for small packages). With this change, `spec.format` no longer shows up in profile output. (This line hasn't changed since Spack v0.9 ;p) * move format() call to custom NoSuchSpecError exception * add a comment saying why, so we can eventually change `Spec.__str__`
2023-07-09pkgconf: Update to new upstream URL (#38800)Jonathon Anderson1-1/+1
See https://github.com/pkgconf/pkgconf/commit/437c2a3218bfcb1cae7fa38a4ccd0cb29575ff07
2023-07-09gcc: add 10.5.0 (#38784)Michael Kuhn1-1/+2
2023-07-08qt-* (Qt6 pkgs): new versions 6.5.0, 6.5.1 (#36705)Wouter Deconinck5-0/+10
* qt-base: new version 6.5.0 * qt-declarative: new version 6.5.0 * qt-quick3d: new version 6.5.0 * qt-quicktimeline: new version 6.5.0 * qt-shadertools: new version 6.5.0 * qt-*: new version 6.5.1 * qt-base: new version 6.5.1
2023-07-07PyNVTX: added new package (#38763)Dax Lynch1-0/+26
2023-07-07py-pyarrow: disable dataset variant by default (#38775)Manuela Kuhn1-1/+4
* py-pyarrow: enable parquet variant by default * Disable parquet variant by default * Add conflict to enable parquet when dataset is active * Disable dataset variant by default
2023-07-07py-matplotlib: add v3.7.2 (#38745)Adam J. Stewart1-0/+3
* py-matplotlib: add v3.7.2 * Update dep versions
2023-07-07New package: py-nanobind (#38327)Chris Richardson1-0/+34
* initial commit of nanobind package * style fixes * Update package.py Typo * addressed PR comments * add v1.4.0 * Update var/spack/repos/builtin/packages/py-nanobind/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Matthew Archer <ma595@cam.ac.uk> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-07py-astropy: fix import tests and restrict py-pip version (#38731)Manuela Kuhn7-25/+151
* py-astropy: fix import tests and restrict py-pip version * Fix --install-option name in comments * Rename variant and fix variant dependencies * Remove parquet variant from py-pyarrow
2023-07-07Remove "node_compiler" from the list of unknown atoms (#38753)Massimiliano Culpo1-0/+1
2023-07-07Fix multiple quadratic complexity issues in environments (#38771)Harmen Stoppels3-63/+57
1. Fix O(n^2) iteration in `_get_overwrite_specs` 2. Early exit `get_by_hash` on full hash 3. Fix O(n^2) double lookup in `all_matching_specs` with hashes 4. Fix some legibility issues
2023-07-07Prevent "spack external find" to error out on wrong permissions (#38755)Massimiliano Culpo2-4/+36
fixes #38733
2023-07-07add info about spack env from spack-configs for oneAPI build tools (#38751)Andrey Parfenov1-0/+47
Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>
2023-07-06add cgns 4.4.0 (#38530)Mickael PHILIT1-0/+1
2023-07-06freesurfer: add 7.4.1, 7.4.0, 7.3.2 (#38544)Carlos Bederián1-0/+3
2023-07-06mlpack: new package (#38277)Wouter Deconinck1-0/+81
* mlpack: new package mlpack is an intuitive, fast, and flexible header-only C++ machine learning library with bindings to other languages. It is meant to be a machine learning analog to LAPACK, and aims to implement a wide array of machine learning methods and functions as a "swiss army knife" for machine learning researchers. * mlpack: upstream merged patch to allow python installation in spack
2023-07-06Curl Package: Fixup bugs preventing build on Win (#38757)John W. Parent1-4/+1
2023-07-06Add new version 5.0.0 of PyAMG (#38674)Ben Cowan2-1/+7
* Added v5.0.0 of PyAMG. This required v7.1.0 of setuptools_scm due to a bug in 7.0.5. * Added comment about version requirement. * Loosened dependency based on build experiments. * Updated tomli deps. * Update var/spack/repos/builtin/packages/py-setuptools-scm/package.py Dependence for 7.0 only. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyamg/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Swapped lines. --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-06Disable fortran in openblas for darwin ci, fix variant default value (#38752)Harmen Stoppels2-1/+3
2023-07-06`py-torch`: fix build (#38730)Thomas Bouvier1-0/+14
2023-07-06py-scikit-learn: add v1.3.0 (#38660)Adam J. Stewart1-9/+13
2023-07-06openfoam.org: add a maintainer(#37280) (#37697)kjrstory1-0/+1
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
2023-07-06[py-blis] added versions 0.7.9 and 0.9.1 (#38269)Jen Herting1-0/+3
* [py-blis] added version 0.7.9 * [py-blis] added version 0.9.1 * [py-blis] - removed type run for dependency py-cython
2023-07-06namd: add maintainer (#38740)Jim Phillips1-0/+2
2023-07-06py-abipy: add 0.9.3 (#38716)Manuela Kuhn1-16/+39
* py-abipy: add 0.9.3 * Remove py-cython dependency * Remove dep version restrictions for new release
2023-07-06[py-cymem] added version 2.0.7 (#38267)Jen Herting1-1/+3
* [py-cymem] added version 2.0.3 * [py-cymem] added restriction to py-wheel limitation
2023-07-06`py-dm-tree`: add v0.1.8 (#38606)Thomas Bouvier1-2/+5
* `py-dm-tree`: add v0.1.8 * Update dependencies * Fix hash
2023-07-05`py-horovod`: update to v0.28.1 (#38732)Thomas Bouvier1-0/+1
2023-07-05py-pip: add 23.1.2 (#38608)Manuela Kuhn13-5/+35
* py-pip: add 23.1.2 * Restrict py-pip version for py-protobuf * Restrict py-pip version for straightforward packages * Restrict py-pip version for nrm * Fix --install-option name in comments * Simplify py-pip restriction for py-scs * nrm: fix wrong comment
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