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Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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Currently, the `python` package tries to set `CPATH` in `setup_run_environment()`.
We no longer set `CPATH` and other destructive environment variables (like
`LD_LIBRARY_PATH`) in modules, so we shouldn't do something special for Python.
Also, the way `python` sets `CPATH` causes issues. Because it does a header search to
find directories containing headers, if you bootstrap `mypy` or other style tools on a
fresh Ubuntu image with *no* python devel headers installed, you'll get an error like
this when trying to load the thing you just installed:
```console
[root@980de539843d /]# spack -b load py-mypy
==> Error: Unable to locate python headers in any of these locations:
/usr/include/python3.6m
/usr/include/3.6
/usr/Headers
```
The headers and includes aren't needed to get `mypy` in the path or for `mypy` to work,
so we're failing unnecessarily here.
- [x] remove `setup_run_environment()` from `python/package.py`
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Co-Authored-By: Alec Scott <scott112@llnl.gov>
Co-authored-by: Alec Scott <scott112@llnl.gov>
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1. add variant cray-static, older crays build hpcprof-mpi static,
newer ones build dynamic.
2. move URL patches from github to gitlab.
3. add workaround for a bug where a file is mistakenly overwritten.
4. add conflict for hpcprof-mpi at 2022.10.01.
* [@spackbot] updating style on behalf of mwkrentel
Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
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* VTK: add missing dependencies
* Deal with missing verdict dep
* http -> https
* Add patch to fix failing cmake
* Update netcdf-cxx usage in build recipe
* netcdf-cxx4 doesn't work
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* license bump year
* fix black issues of modified files
* mypy
* fix 2021 -> 2023
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* npm: Add latest version, update build
The `npm` package had gotten a bit long in the tooth and only suported the last version
for which running `configure` / `make` / `make install` actually worked.
- [x] Update the package to support npm@9, in which `npm install .` works properly and
installation is easier.
- [x] Update the package so that `npm@6:8` also install successfullly. The incantation
that is *supposed* to work on these versions is `node bin/npm-cli.js install $(node
bin/npm-cli.js pack . | tail -1)`, but depending on the version one of `npm install`
or `npm pack` will fail when run straight from the install directory. So now we just
manually copies things over.
This seems to make the `npm` install much more reliable for all of `npm@6:9` (at least
for me).
udpates the `npm` build to support versions 6-9 and fixes the install for all of
them on macos.
* update for review
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* [armpl-gcc] Make pkg-config files available
ARMpl pkgconfig files are located in a non-default location and do not have the
.pc extension. Changing those both helps pkgconfig pick them up correctly, e.g.
in the meson build of `py-scipy`.
* Address @annop-w comments
* symlink instead of cp.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
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* py-itk: add version 5.3.0
* Remove wheels for unsupported python versions
* Fill out the version specs
* Drop th 'm' from the cp37 version strings
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-Wno-error=incompatible-function-pointer-types,pointer-types-discards-qualifiers (#34984)
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* py-sphinx-immaterial: new package
This is a new-ish theme for Sphinx that's based on MkDocs's `immaterial` theme. More on
the theme here: https://jbms.github.io/sphinx-immaterial/, but it seems to be very clear
and readable. We *might* consider switching to it for Spack's docs.
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add note about node.js requirements
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* Forward lookup of "test_log_file" and "test_failures"
refers #34531
closes #34487
fixes #34440
* Add unit test
* py-libensemble: fix tests
* Support stand-alone tests with cached files as install-time tests
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
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* gnupg: 2.4.0
* libksba: 1.6.3 (CVE-2022-47629)
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This is only a work-around for the actual problem that Python is used to install libraries instead of CMake, so we end up with BUILD_RPATH not INSTALL_RPATHs.
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
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* Add new file for MVAPICH 3.0a release
Creating this as a new package since it requires some new configuration
options and because we are moving to the name "MVAPICH" and droping the
2 (following a similar move by MPICH).
Co-authored-by: Nat Shineman <shineman.5@osu.edu>
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
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Co-authored-by: openCARP consortium <info@opencarp.org>
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Update crtm from JCSDA-EMC spack fork, add crtm-fix
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* OpenCV: checksum for 4.5.5, make contrib optional
* [@spackbot] updating style on behalf of iarspider
* Add conflicts for contrib modules
* Fix typo
* Implement changes from review
* Update var/spack/repos/builtin/packages/opencv/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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There are some declarations that need to be declared noexcept for
valarray. This affects gcc 9.5:11.2.
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* Revert "Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)"
This reverts commit 891a63cae616dbc92acdad0e0eb626edbd0862a0.
* fix to py-python-multipart, as per PR review
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* py-macs2: add version 2.2.7.1 and support python@3.10:
The tarball from PyPi includes the Cythonized C files. The tarball from
github does not. Remove the Cythonized C files from the source so that
they are rebuilt with the Spack Python/Cython combination. This is
necessary for python-3.10 but make sense for other combinations as well.
* Edits based on review
- set python version constraint on version 2.2.4
- removed all python-2 versions and related constraints.
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* py-xxhash: fix xxhash dependency
The dependency should be xxhash@0.8.0:.
* Add version 3.2.0
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Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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* Add depends_on("mpi") to fix missing <mpi.h>
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
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- add python dependency
- add perl dependency
- set python and perl interpreters in scripts
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- stringtie uses internal samtools so remove dependency on samtools
- add dependency for zlib
- use make release target to get correct flags
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