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`py-deepsig-biocomp`), new packages (`py-pyhmmer`, `py-pyrodigal`) (#47277)
* added updated versions
* added pyhmmer
* updated infernal
* fix blast-plus for apple-clang
* fix py-biopython build on apple-clang
* remove erroneous biopython dep: build issue is with python 3.8, not biopython
* deepsig python 3.9: expanding unnecessary python restrictions
* add pyrodigal
* fix unnecessarily strict diamond version
* builds and updates: blast-plus indexing broken, still need to test db download and bakta pipeline
* builds and runs
* revert blast-plus changes: remove my personal hacks to get blast-plus to build
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* fix the build error during compilation of rocdecode.was dependent on libva-devel packag
* address review comment
* address review changes.commit the changes
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* Adding sha for 7.4 release of OSU Micro Benchmarks
* Adds the sha256sum for the OSU mirco benchmarks 7.5 release.
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* py-fsspec-xrootd: new package
* py-fsspec-xrootd: depends_on python@3.8:
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* Add two_level_namespace variant (default is disabled) for MacOS to enable building
executables and libraries with two level namespace enabled.
* Addressed reviewer comments.
* Moved two_level_namespace variant ahead of the patch that uses that variant to
get concretize to work properly.
* Removed extra print statements
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Fix typo wrt @xiaoyeli
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* rsyslog: add v8.2410.0
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* py-pyppeteer: new package
* py-pyee: new package (v11.1.1, v12.0.0)
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* pixman: add v0.44.0 (switch to meson)
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Co-authored-by: t. chantrait <teddy.chantrait@cea.fr>
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* soqt: Add SoQt package
The geomodel package needs this if visualization is turned on.
* make qt versions explicit
* use virtual dependency for qt
* pr feedback
Remove myself as maintainer
Remove v1.6.0
Remove unused qt variant
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Take a simpler approach to listing variant options -- store them in variables instead of trying to
roundtrip them through metadata dictionaries.
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-Wno-error=missing-template-arg-list-after-template-kw (#47477)
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* butterflypack: add v3.2.0
* strumpack: add v8.0.0
* restrict fj patch to @1.2.0
* Update var/spack/repos/builtin/packages/butterflypack/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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the py-oracledb package only has a single outdated version available in its recipe. this PR adds a much broader range of versions and their corresponding checksums.
* add more versions of py-oracledb
* update py-oracledb recipe
* add py-cython version dependencies
* tweak py-cython version dependencies
* remove older versions of py-oracledb
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value for --with-exodusii-lib] (#47506)
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* vbfnlo: depends on tcsh (build)
* vbfnlo: add v3.0
* vbfnlo: comment
Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
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Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
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This filters any selected executable ending with `-ocl` from the list of executables being probed as candidate for external `llvm` installations.
I couldn't reproduce the entire issue, but with a simple script:
```
#!/bin/bash
touch foo.o
echo "clang version 10.0.0-4ubuntu1 "
echo "Target: x86_64-pc-linux-gnu"
echo "Thread model: posix"
echo "InstalledDir: /usr/bin"
exit 0
```
I noticed the executable was still probed:
```
$ spack -d compiler find /tmp/ocl
[ ... ]
==> [2024-11-11-08:38:41.933618] '/tmp/ocl/bin/clang-ocl' '--version'
```
and `foo.o` was left in the working directory. With this change, instead the executable is filtered out of the list on which we run `--version`, so `clang-ocl --version` is not run by Spack.
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`conditional()`, which defines conditional variant values, and the other ways to declare
variant values should probably be in a layer above `spack.variant`. This does the simple
thing and moves *just* `conditional()` to `spack.directives` to avoid a circular import.
We can revisit the public variant interface later, when we split packages from core.
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
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* lua: add +pcfile support for @5.4: versions, without using a version-dependent patch
* lua: always generate pcfile, remove +pcfile variant from all packages
* lua: minor fixes
* rpm: minor fix
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* mbedtls: add v2.28.9, v3.6.1 (fix CVEs)
* mbedtls: add v3.6.2
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* Add 5.030 and remove the requirement to patch verilator, the problem has be fixed in this rev
* Update var/spack/repos/builtin/packages/verilator/package.py
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
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* benchmark: enable shared libraries by default
The existing behaviour of Google Benchmark yiels static objects which
are of little use for most projects. This PR changes the spec to use
dynamic libraries instead.
* Add shared variant
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* librdkafka: added missing dependency on curl
This PR adds a missing dependency on curl in librdkafka.
* librdkafka: added dependency on openssl and zlib
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* Added support for Codeplay AMD Plugin for Intel OneAPI Compilers
* [@spackbot] updating style on behalf of kaanolgu
* Adding 2025.0.0
* removed HOME and XDG_RUNTIME_DIR
* [@spackbot] updating style on behalf of kaanolgu
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Co-authored-by: Kaan Olgu <kaan.olgu@bristol.ac.uk>
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as flexiblas is not a depends and the entire build chain to support using flexibls is not setup. As this does not seem to be needed with the spack blas and lapack, it is easier to disable (#47514)
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Adds version 1.0.21 of lksctp-tools
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Co-authored-by: Patrick Bridges <patrickb314@gmail.com>
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-Wno-error=missing-template-arg-list-after-template-kw (#47503)" (#47512)
This reverts commit 4322cf56b15a0a088156f5702d44a04e8238b4b3.
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No ROOT `builtin` should ever be set to true if possible, because that
builds an existing library that spack may not know about.
Furthermore, using `builtin_glew` forces the package to be on, even when
not building x/gl/aqua on macos. This causes build failures.
Caused by https://github.com/spack/spack/pull/45632#issuecomment-2276311748 .
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This reverts commit da1d533877f90610571b72f070c01e13b9729108.
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Currently, if a package has a dependency from another repository and patches it,
generation of the patch cache will fail. Concretization succeeds if a fixed patch
cache is in place.
- [x] don't assume that patched dependencies are in the same repo when indexing
- [x] add some test fixtures to support multi-repo tests.
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Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
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