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authorTony Weaver <55799947+aweaver1fandm@users.noreply.github.com>2024-05-29 18:16:54 -0400
committerGitHub <noreply@github.com>2024-05-29 15:16:54 -0700
commit918db85737bf30cb075ee9a5a6a3ace9c15a4660 (patch)
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py-astropy: add v6.1 and new py-astropy-iers-data dependency (#44318)
* 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 https://mirror.spack.io/_source-cache/archive/ac/ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882.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 https://mirror.spack.io/_source-cache/archive/35/350b18f9673e63101dbbfcf774ee2f57c20ac4636d255741d76ca79016b1bd82.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
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