* Patch to add hsa prefix/include path:wq
* Style check error fix
* The patch need to be applied to 2024.01.stable. ROCm 6.0 requires hpctoolkit 2024.01.1 or later
* Fixing style chec error
* Adding a py4j variant that requires Java via spack to avoid situations where a system doesn't have Java and py4j expects it
* Adding new versions of py-pyspark
* Adding a new variant to require java (via py4j) and clean up dependency handling
* Adding myself as a maintainer for py-pyspark and py-py4j
* Fix overlooked version bump in py4j
* Version bump to meet py-spark expectations
* Version bump to add latest compatibile version with pyspark
* Matching py-grpcio bump
* Adding variants and dependents for pyspark
* Adding runtime deps
* Changing default java requirement. I'm not sure this is the right call
* Changing py4j with java dependency handling
* Fix style
* Update package.py fix unnecessary f-strinh
* Make +java the default for both
* Fix nested deps
* Revert styles after default change
* Added new versions and GCC 14 compatbility conflicts
* Added new versions and compatibility conflicts for gcc 14
* Added new versions paired to arrow (for gcc14 compat)
* Update py-protobuf compiler conflict
* Update depends to match
See https://github.com/grpc/grpc/blob/master/src/python/grpcio_status/setup.py
* Updating dependencies and conflicts for py-googleapis-common-protos. Added new version to avoid future issues
* Remove upper bound version on py-protobuf and add default_args
* Adding new versions and updating dependencies back to versions 1.35.0
* Updating oldest numpy deps
* Fixing merge
* bit more cleaniness for var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py
* Adding latest matching version of py-grpcio and py-grpcio-status
* Update package.py
https://github.com/spack/spack/pull/44263#discussion_r1612317943
* Update dependencies
* Adding additional versions for dependent packages. Deprecated two versions: 1.16 is old, built for python ~3.6, and does not build for 3.8. 1.52.0 was removed from pypi
* Revert py-grpcio-tools changes. Will include in separate PR
* Adding patches and constraints to get 1.48 to build as it's a dependency that is called out for some other packages
* Updating to account for yanked packages for dependencies
* Fix style
* Update sha256 for py-grpcio v0.16.0 to reflect change
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* py-astropy: Add version 6.1
Added build info for version 6.1 in py-astropy. Requires a new additional package, astropy-iers-data which has been included as py-astropy-iers-data to match with spack's general naming conventions.
Below is the output of the spack install showing successful build fro version 6.1 and the new py-astropy-iers-data package
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/libyaml-0.2.5-fxathvq
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/pcre2-10.42-fu62kky
[+] /opt/apps/spack/libunistring-1.2-whrov3e
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/berkeley-db-18.1.40-jftva2u
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/libidn2-2.3.7-vnie4rz
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/perl-5.38.0-gzljgek
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/krb5-1.20.1-tqiapsx
[+] /opt/apps/spack/py-pyyaml-6.0-rju7jls
[+] /opt/apps/spack/py-tomli-2.0.1-eanxpu2
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/openssh-9.7p1-jxrkzso
[+] /opt/apps/spack/py-pyerfa-2.0.0.1-kyfazhs
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-typing-extensions-4.8.0-ujwbb6g
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
[+] /opt/apps/spack/git-2.45.1-tuc5jnb
[+] /opt/apps/spack/py-cython-3.0.0-zx62ssd
==> Installing py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj [52/55]
==> No binary for py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj found: installing from source
==> No patches needed for py-astropy-iers-data
==> py-astropy-iers-data: Executing phase: 'install'
==> py-astropy-iers-data: Successfully installed py-astropy-iers-data-main-ukchsfzhfcyz6e6fxar6mtykqiavporj
Stage: 1.74s. Install: 0.93s. Post-install: 0.52s. Total: 3.36s
[+] /opt/apps/spack/py-astropy-iers-data-main-ukchsfz
[+] /opt/apps/spack/py-extension-helpers-0.1-a5hmr6j
[+] /opt/apps/spack/py-setuptools-scm-8.0.4-qdhxchg
==> Installing py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo [55/55]
==> No binary for py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/a/astropy/astropy-6.1.0.tar.gz
==> Ran patch() for py-astropy
==> py-astropy: Executing phase: 'install'
==> Warning: Module file /opt/modulefiles/spack/Core/py-astropy/6.1.0.lua exists and will not be overwritten
==> py-astropy: Successfully installed py-astropy-6.1.0-f4pffru3kmyion2kq6muomgrfs5y4gdo
Stage: 1.29s. Install: 1m 5.77s. Post-install: 0.60s. Total: 1m 7.94s
* Removed extra-whitespace
A blank line had white space, removed the white space
* Additional formatting changes for black
* Additional package updates
Based on previous recommendations updated py-astropy and py-astropy-iers-data packages. Also added a new version to py-pyerfa package to match the 6.1.0 dependencies better
Of importance in these updates, I did add pypi and version info to py-astropy-iers-data. Originally I had argued that this package updates quite frequently (on a weekly basis) and so it did not make sense to include pypi/versions and we should instead use the non-version git-repo structure based on the master branch. However, when I tried to build the package py-setuptools-scm errored out when trying to build the package:
/opt/apps/spack/py-setuptools-scm-8.0.4-ax2zqro/lib/python3.10/site-packages/setuptools_scm/git.py:163: UserWarning: "/tmp/root/spack-stage/spack-stage-py-astropy-iers-data-main-iw2mdzlukb37mkcbcozjjefjoefw2eyp/spack-src" is shallow and may cause errors
I believe this is due to the download file/stage directory not containing the version and instead including the branch. I changed the package to use versions instead and it worked just fine as shown below. In addition, when I had done some preliminary testing, the package installed fine using the non-version master branch. When I checked, that installation it used py-setuptools-scm@7.1 while in this installation run it used a much more recent 8.0.4 so it is possible that somewhere between scm7.1 and 8.0.04 something changed that caused this error to show up. Since the setuptools-scm package has something to do extracting package versions, I imagine it's some kind of mismatch issue
Output from build:
spack install py-astropy
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/berkeley-db-18.1.40-jftva2u
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/libunistring-1.2-whrov3e
[+] /opt/apps/spack/pcre2-10.42-fu62kky
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/libyaml-0.2.5-fxathvq
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/libidn2-2.3.7-vnie4rz
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/perl-5.38.0-gzljgek
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/krb5-1.20.1-tqiapsx
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/openssh-9.7p1-jxrkzso
[+] /opt/apps/spack/py-tomli-2.0.1-eanxpu2
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/git-2.45.1-zu6qkoc
[+] /opt/apps/spack/py-markupsafe-2.1.3-isgtki6
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
==> Installing py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a [49/57]
==> No binary for py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a found: installing from source
==> Fetching ac8a6fe91c.tar.gz
==> No patches needed for py-extension-helpers
==> py-extension-helpers: Executing phase: 'install'
==> py-extension-helpers: Successfully installed py-extension-helpers-0.1-a5hmr6jtrvpcq3ibwkwhvwlydthjif5a
Stage: 0.37s. Install: 0.88s. Post-install: 0.52s. Total: 1.89s
[+] /opt/apps/spack/py-extension-helpers-0.1-a5hmr6j
==> Installing py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m [50/57]
==> No binary for py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m found: installing from source
==> Fetching 350b18f967.tar.gz
==> No patches needed for py-cython
==> py-cython: Executing phase: 'install'
==> py-cython: Successfully installed py-cython-3.0.0-zx62ssdy4p6ddwuqbixel2vcsihjcs6m
Stage: 1.07s. Install: 2m 49.80s. Post-install: 0.40s. Total: 2m 51.37s
[+] /opt/apps/spack/py-cython-3.0.0-zx62ssd
[+] /opt/apps/spack/py-jinja2-3.1.2-wacpq7j
[+] /opt/apps/spack/py-typing-extensions-4.8.0-ujwbb6g
[+] /opt/apps/spack/py-pyyaml-6.0-rju7jls
[+] /opt/apps/spack/py-setuptools-scm-8.0.4-ax2zqro
==> Installing py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6 [55/57]
==> No binary for py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6 found: installing from source
==> Using cached archive: /opt/spack/var/spack/cache/_source-cache/archive/7f/7fff3d3404ae8560533ac0e685db7acc02c4d8984faa4ac3d607096879fba2d1.tar.gz
==> No patches needed for py-astropy-iers-data
==> py-astropy-iers-data: Executing phase: 'install'
==> py-astropy-iers-data: Successfully installed py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6icqn3aqhyjidfir3byyjq5aq6
Stage: 0.07s. Install: 1.21s. Post-install: 0.39s. Total: 1.88s
[+] /opt/apps/spack/py-astropy-iers-data-0.2024.5.20.0.29.40-wckxjf6
==> Installing py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp [56/57]
==> No binary for py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/p/pyerfa/pyerfa-2.0.1.1.tar.gz
==> No patches needed for py-pyerfa
==> py-pyerfa: Executing phase: 'install'
==> py-pyerfa: Successfully installed py-pyerfa-2.0.1.1-pkokp6usk7m2bjxcba3nwgqgrjufumcp
Stage: 0.93s. Install: 17.72s. Post-install: 0.33s. Total: 19.15s
[+] /opt/apps/spack/py-pyerfa-2.0.1.1-pkokp6u
==> Installing py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs [57/57]
==> No binary for py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/a/astropy/astropy-6.1.0.tar.gz
==> Ran patch() for py-astropy
==> py-astropy: Executing phase: 'install'
==> py-astropy: Successfully installed py-astropy-6.1.0-5brbkjnjzfg3lc6h34qku24ep5pwsxzs
Stage: 1.16s. Install: 1m 3.34s. Post-install: 1.05s. Total: 1m 5.77s
[+] /opt/apps/spack/py-astropy-6.1.0-5brbkjn
* Updated to match with black formatting
Change the installer to take `([pkg], args)` in the constructor instead
of `[(pkg, args)]`. The reason is that certain arguments are global
settings, and the new API ensures that those arguments cannot be
different across different "build requests".
The `explicit` install arg is now a list of hashes, and the installer is
no longer responsible for determining what package is installed
explicitly. This way environment installs can simply pass the list of
environment roots, without them necessarily being explicit build
requests. For example an env with two roots [a, b], where b depends on
a, would not always cause spack install to mark b as explicit.
Notice that `overwrite` already took a list of hashes, this makes
`explicit` consistent.
`package.do_install(explicit=True)` continues to take a boolean.
* legion: add pip dependency for build
pip is needed for the build when the Legion Python binding is enabled
* legion: add variants for gc logging and system OpenMP use
This also removes the `cmake_cxx_flags` variable from `cmake_args()`
because that variable had no effect.
* [@spackbot] updating style on behalf of mpokorny
* legion: use spec.satisfies() in cmake_args()
e.g, replace use of '"+foo" in spec' with 'spec.satisfies("+foo")'
* legion: avoid configuring with multiple "-DLegion_REDOP_COMPLEX=ON" arguments
In the previous version, when both '+redop_complex' and '+bindings'
was set, two instances of "-DLegion_REDOP_COMPLEX=ON" arguments were
generated for cmake configuration.
* legion: fix value of "Legion_OUTPUT_LEVEL" for configuration
the previous version had no effect on setting the configuration value
---------
Co-authored-by: mpokorny <mpokorny@users.noreply.github.com>
The windows wrappers for basic functions like `os.symlink`,
`os.readlink` and `os.path.islink` in the `llnl.util.symlink` module
have bugs, and trigger more file system operations on non-windows than
they should.
This commit just binds `llnl.util.symlink.symlink = os.symlink` etc so
built-in functions are used on non-windows
`spack clean <spec>` will now resolve specs based on the active environment if one is active.
If an env is active but no matching spec is found, this will fall back on fully concretizing.
Before this PR, if Spack could see a possibility to reuse a spec that
doesn't match a strong preference, it would do so. After the PR, a
strong preference would take precedence.
`glibc` and `musl` provide a basic implementation of `iconv` (`iconv`,
`iconv_open`, `iconv_close`), but in practice the installation may be
missing the character encoding methods to make them usable. On Fedora
for example, users need to
```yum install glibc-gconv-extra```
to get the character encodings that `gettext` requires during configure,
namely EUC-JP. Users may not have permissions to install the missing
parts of glibc.
Since Spack can install `libiconv`, it is simpler to use that by
default.
* Spglib: add version 2.4.0
* dla-future-fortran: new package version 0.1.0
* [@spackbot] updating style on behalf of RMeli
* apply suggestion and add maintainer
---------
Co-authored-by: RMeli <RMeli@users.noreply.github.com>
