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2023-08-02Add qmake virtual provider (#38848)Adam J. Stewart4-1/+6
2023-08-02openmolcas: adding version 23.06 (#39195)snehring1-0/+1
2023-08-02bioconductor-dupradar, bioconductor-rsubread: add packages (#39206)pabloaledo2-0/+41
* bioconductor-dupradar, bioconductor-rsubread: add packages * [@spackbot] updating style on behalf of pabloaledo
2023-08-02tximeta: add package (#39207)pabloaledo1-0/+39
* tximeta: add package Signed-off-by: Pablo <pablo.aledo@seqera.io> * [@spackbot] updating style on behalf of pabloaledo --------- Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-02patchelf: 0.18 (#39215)Harmen Stoppels1-0/+1
2023-08-02CI: Refactor ci reproducer (#37088)kwryankrattiger5-95/+194
* CI: Refactor ci reproducer * Autostart container * Reproducer paths match CI paths * Generate start scripts for docker and reproducer * CI: Add interactive and gpg options to reproduce-build * Interactive will determine if the docker container persists after running reproduction. * GPG path/url allow downloading GPG keys needed for binary cache download validation. This is important for running reproducer for protected CI jobs. * Add exit_on_failure option to CI scripts * CI: Add runtime option for reproducer
2023-08-02version: move to module, avoid circular imports (#39077)Harmen Stoppels8-268/+358
2023-08-02buildcache extractall: extract directly into spec.prefix (#37441)Harmen Stoppels5-60/+159
- Run `mkdirp` on `spec.prefix` - Extract directly into `spec.prefix` 1. No need for `$store/tmp.xxx` where we extract the tarball directly, pray that it has one subdir `<name>-<version>-<hash>`, and then `rm -rf` the package prefix followed by `mv`. 2. No need to clean up this temp dir in `spack clean`. 3. Instead figure out package directory prefix from the tarball contents, and strip the tarinfo entries accordingly (kinda like tar --strip-components but more strict) - Set package dir permissions - Don't error during error handling when files cannot removed - No need to "enrich" spec.json with this tarball-toplevel-path After this PR, we can in fact tarball packages relative to `/` instead of `spec.prefix/..`, which makes it possible to use Spack tarballs as container layers, where relocation is impossible, and rootfs tarballs are expected.
2023-08-02feat: move -N/--namespace(s) to common args, allow in `buildcache list` (#36719)Wouter Deconinck9-45/+41
`spack buildcache list` did not have a way to display the namespace of packages in the buildcache. This PR adds that functionality. For consistency's sake, it moves the `-N/--namespace` arg definition to the `common/arguments.py` and modifies `find`, `solve`, `spec` to use the common definition. Previously, `find` was using `--namespace` (singular) to control whether to display the namespace (it doesn't restrict the search to that namespace). The other commands were using `--namespaces` (plural). For backwards compatibility and for consistency with `--deps`, `--tags`, etc, the plural `--namespaces` was chosen. The argument parser ensures that `find --namespace` will continue to behave as before. Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-08-02rust: disable build from downloading a version of LLVM from Rust CI (#39146)Alec Scott1-0/+3
2023-08-02Python: fix library/header error msg format (#39171)Adam J. Stewart1-4/+4
2023-08-01dcmtk: new version and pic configuration (#39161)Martin Aumüller1-8/+15
* dcmtk: checksum 3.6.7 compiles on macos * dcmtk: support pic configuration * [@spackbot] updating style on behalf of aumuell * dcmtk: use define_from_variant for shorter code * dcmtk: refine conflict it appears that dcmtk < 3.6.7 only fails on macos/aarch64: /Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/include/xmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture" --------- Co-authored-by: aumuell <aumuell@users.noreply.github.com>
2023-08-01py-gevent: add 23.7.0 and py-greenlet: add 3.0.0a1 (#39164)Manuela Kuhn2-9/+18
* py-gevent: add 23.7.0 and py-greenlet: add 3.0.0a1 * Update var/spack/repos/builtin/packages/py-gevent/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Remove version 1.3.a2 --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-01py-openai, py-pandas-stubs (#38912)sid4-9/+109
* simple build of py-openai * added variants to py-openai * py-pandas-stubs is a dependency for py-openai * fixed format and flake8 errors for py-openai * black format error for py-pandas-stubs * [@spackbot] updating style on behalf of sidpbury * made style and format changes to py-openai * made style and format changes to py-pandas-stubs * py-types-pytz is a dependency for py-openai * [@spackbot] updating style on behalf of sidpbury * updated py-openpyxl for ver 3.0.7 and 3.1.2 * Update var/spack/repos/builtin/packages/py-pandas-stubs/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * ajs requested changes for py-openai * updated py-openpyxl for supported python * [@spackbot] updating style on behalf of sidpbury * updated py-openpyxl * removed requirement.txt dependencies in py-openpyxl * removed python depends on from openpyxl --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-01Add two latest versions (#39182)mschouler1-0/+2
Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
2023-08-01amrex: add 23.08 (#39190)Weiqun Zhang1-0/+1
2023-08-01Mongodb: Add new package (#39085)Dax Lynch2-0/+142
* Added the package * added dependency * Update package.py * Update package.py Added xz as a dependency
2023-08-01remove CMAKE_GENERATOR from the host-config because it cannot be overwritten ↵Chris White1-11/+0
on the command line (#39044)
2023-08-01Fix source bootstrapping for Debian and derivatives (#39107)vucoda1-1/+15
* Fix Python package.py for Debian and derivatives to find the system Python library location When bootstrapping from source, find_library() does not contain any paths that work for Debian and derivatives. fixes #36666 * Update to pass styling * Update to styling * Update python package.py with fake config value for LIBPL * Update python package.py libpl config_vars entry to follow double quote standard * styling update
2023-07-31petsc, py-petsc4py: add v3.19.4 (#39169)Satish Balay2-0/+2
2023-07-31qt-base: add conflict for 6.5+ with GCC < 9 (#39158)Martin Aumüller1-0/+3
2023-07-31py-numpy: add v1.25.2 (#39172)Adam J. Stewart1-0/+1
2023-07-31Add `spack checksum --verify`, fix `--add` (#38458)Alec Scott8-117/+272
* Add rewrite of spack checksum to include --verify and better add versions to package.py files * Fix formatting and remove unused import * Update checksum unit-tests to correctly test multiple versions and add to package * Remove references to latest in stage.py * Update bash-completion scripts to fix unit tests failures * Fix docs generation * Remove unused url_dict argument from methods * Reduce chance of redundant remote_versions work * Add print() before tty.die() to increase error readablity * Update version regular expression to allow for multi-line versions * Add a few unit tests to improve test coverage * Update command completion * Add type hints to added functions and fix a few py-lint suggestions * Add @no_type_check to prevent mypy from failing on pkg.versions * Add type hints to format.py and fix unit test * Black format lib/spack/spack/package_base.py * Attempt ignoring type errors * Add optional dict type hint and declare versions in PackageBase * Refactor util/format.py to allow for url_dict as an optional parameter * Directly reference PackageBase class instead of using TypeVar * Fix comment typo --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-07-31update py-cupy to enable ROCm builds and add variant to control optional ↵eugeneswalker3-15/+125
dependencies (#38919) * py-cupy updates: add +rocm and +all * rocm deps are link only * set parallelism for both +rocm and +cuda * add missing deps; remove unnecessary deps; uncomment maintainers; get hipcc properly
2023-07-31py-terminado: add 0.17.1 (#39165)Manuela Kuhn1-8/+13
* py-terminado: add 0.17.1 * Fix style * Update var/spack/repos/builtin/packages/py-terminado/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-07-31added new packages (#39166)Andrey Perestoronin1-0/+11
2023-07-31libtiff: 4.5.1 (#39159)Martin Aumüller1-0/+1
2023-07-31libgeotiff: new versions (#39160)Martin Aumüller1-0/+2
2023-07-31py-rdflib: add 6.3.2 (#39065)Manuela Kuhn1-3/+10
* py-rdflib: add 6.3.2 * Update var/spack/repos/builtin/packages/py-rdflib/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Remove python dependency --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-31py-python-hostlist: package addition (#39035)mschouler1-0/+20
* Add recipe for py-hostlist * Fix style * Fix style * Add homepage, fix version url and remove unnecessary dependency * Fix version and remove url * Rename package and fix git link --------- Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
2023-07-31Remove Xcode mock-up (#39020)Adam J. Stewart3-227/+0
* Remove Xcode mock-up * Remove unused imports
2023-07-31fzf: add v0.42.0 (#39150)Alec Scott1-0/+1
2023-07-31py-lightning: add v2.0.6 (#39152)Adam J. Stewart1-1/+3
2023-07-31py-sphinx: add v7.1 (#39151)Adam J. Stewart1-3/+14
2023-07-31libjpeg-turbo: checksum 2.1.5.1 & 3.0.0 (#39157)Martin Aumüller1-0/+2
2023-07-30py-lightly: add v1.4.14 (#39153)Adam J. Stewart1-0/+1
2023-07-30py-chex: add 0.1.5 (#39102)Christopher Christofi1-0/+1
2023-07-30py-csvkit: add 1.1.1 (#39124)Manuela Kuhn1-10/+15
2023-07-30sourmash: new package @4.8.2 (#38571)George Young5-4/+84
* sourmash: new package @4.8.2 * sourmash: new package @4.8.2 * py-bitarray: add 2.7.6, 2.7.4 * Update var/spack/repos/builtin/packages/py-bitstring/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update setuptools dependency * Adding missing deps * Update var/spack/repos/builtin/packages/sourmash/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Correcting maturin dep Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/sourmash/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/sourmash/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/sourmash/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Adding dependency types * Add `@0.14.17` as the last pre-`@1:` release * Switch to use `python_platlib` * Update package.py * Update var/spack/repos/builtin/packages/py-screed/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-07-30PyPy: add new package (#38999)Adam J. Stewart2-0/+234
* PyPy: add new package * Typo fix Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-07-30py-pytest-html: Add version 3.2.0 (#38989)Jordan Galby1-2/+20
* py-pytest-html: add 3.2.0 * py-pytest-html: Add py-py version requirement See https://github.com/pytest-dev/pytest-html/blob/v3.2.0/setup.py#L16 * py-pytest-html: Add dependencies from setup.py and pyproject.toml * py-pytest-html: Add git url * py-pytest-html: Add conflict with py-pytest@7.2: pending py-pytest-html@4
2023-07-29Bugfix/ltrace: Add missing elf dependency (#39143)Tamara Dahlgren1-0/+2
2023-07-28Adding NVIDIA HPC SDK 23.7 (#39127)Filippo Spiga1-0/+14
2023-07-28HACCKernels git repository has changed URL. Updating. (#39129)dslarm1-2/+2
2023-07-28Adding optional hip test (#34907)afzpatel2-1/+124
* Adding optional hip test * Modifications to run every samples test * Skipping test directories without a Makefile * fix styling and cleaning code * fix styling and changed method of itterating through sample folders * changed to new syntax for standalone tests * Updates for changes in syntax
2023-07-28libffi: add -Wno-error=implicit-function-declaration for clang >= 16 (#38356)Julien Bigot1-1/+5
2023-07-28MOLGW package: fix dependence to threaded MKL (#39028)Fabien Bruneval1-0/+2
* molgw package.py * molgw package.py almost ready * bug fix in molgw package.py * MOLGW v3.2 * black pass * duplicated line eliminated * remove FIXME in the header * add me as a maintainer * fix previous commit * sort the imports in the order spack wants * chop the too-long lines * many fixes - variants before dependences - eliminate useless build and install stages - no openmp with intel-mkl was broken * after blackization * cleaning * Update var/spack/repos/builtin/packages/molgw/package.py Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Update var/spack/repos/builtin/packages/molgw/package.py Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Update var/spack/repos/builtin/packages/molgw/package.py Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Update var/spack/repos/builtin/packages/molgw/package.py Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Update var/spack/repos/builtin/packages/molgw/package.py Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * use threaded mkl when openmp is triggered --------- Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-07-28py-distributed: add missing tblib dependency. (#39123)Matthias Wolf1-0/+1
I noticed this as we run a `pip check` on all modules we generate. This dependeny seems to have been around for a long time: https://github.com/dask/distributed/blob/2020.12.0/requirements.txt#L8 https://github.com/dask/distributed/blob/2023.4.1/pyproject.toml#L39 While it does not seem essential, it would be nice to have consistent installations by including the missing dependency.
2023-07-28gcc: add 13.2.0 (#39119)Michael Kuhn1-0/+1
2023-07-27Added support for building with Caliper (#39116)Brian Van Essen1-0/+4
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