commit: 012df5afd694e93d3466878578022b1204298ff8 Author: Michael Schubert <mschu.dev <AT> gmail <DOT> com> AuthorDate: Mon Feb 17 18:38:39 2025 +0000 Commit: Nowa Ammerlaan <nowa <AT> gentoo <DOT> org> CommitDate: Sat Aug 2 10:47:53 2025 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=012df5af
dev-python/snakemake: version bump 8.28.0 and improve tests Signed-off-by: Michael Schubert <mschu.dev <AT> gmail.com> Part-of: https://github.com/gentoo/sci/pull/1323 Signed-off-by: Nowa Ammerlaan <nowa <AT> gentoo.org> dev-python/snakemake/snakemake-8.25.3.ebuild | 71 ------------- dev-python/snakemake/snakemake-8.28.0.ebuild | 144 +++++++++++++++++++++++++++ 2 files changed, 144 insertions(+), 71 deletions(-) diff --git a/dev-python/snakemake/snakemake-8.25.3.ebuild b/dev-python/snakemake/snakemake-8.25.3.ebuild deleted file mode 100644 index 180f32309..000000000 --- a/dev-python/snakemake/snakemake-8.25.3.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{11..12} ) -DISTUTILS_USE_PEP517=setuptools - -inherit distutils-r1 - -DESCRIPTION="Make-like task language" -HOMEPAGE="https://snakemake.readthedocs.io"; -SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - dev-python/appdirs[${PYTHON_USEDEP}] - dev-python/immutables[${PYTHON_USEDEP}] - dev-python/configargparse[${PYTHON_USEDEP}] - >=dev-python/connection_pool-0.0.3[${PYTHON_USEDEP}] - dev-python/datrie[${PYTHON_USEDEP}] - dev-python/docutils[${PYTHON_USEDEP}] - dev-python/gitpython[${PYTHON_USEDEP}] - dev-python/humanfriendly[${PYTHON_USEDEP}] - >=dev-python/jinja2-3.0[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/nbformat[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/psutil[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - >=dev-python/requests-2.8.1[${PYTHON_USEDEP}] - dev-python/reretry[${PYTHON_USEDEP}] - >=dev-python/smart-open-4.0[${PYTHON_USEDEP}] - >=dev-python/snakemake-interface-common-1.17.0[${PYTHON_USEDEP}] - >=dev-python/snakemake-interface-executor-plugins-9.3.2[${PYTHON_USEDEP}] - >=dev-python/snakemake-interface-storage-plugins-3.2.3[${PYTHON_USEDEP}] - >=dev-python/snakemake-interface-report-plugins-1.1.0[${PYTHON_USEDEP}] - dev-python/stopit[${PYTHON_USEDEP}] - dev-python/tabulate[${PYTHON_USEDEP}] - dev-python/throttler[${PYTHON_USEDEP}] - dev-python/wrapt[${PYTHON_USEDEP}] - >=dev-python/yte-1.5.1[${PYTHON_USEDEP}] - >=dev-python/dpath-2.1.6[${PYTHON_USEDEP}] - >=dev-python/conda-inject-1.3.1[${PYTHON_USEDEP}] - >=sci-mathematics/pulp-2.3.1[${PYTHON_USEDEP}] -" - -# distutils_enable_sphinx docs \ -# dev-python/sphinxcontrib-napoleon \ -# dev-python/sphinx-argparse \ -# dev-python/sphinx-rtd-theme \ -# dev-python/docutils \ -# dev-python/recommonmark \ -# dev-python/myst-parser - -EPYTEST_IGNORE=( - # __file__ attribute does not match test name ('python_3_7') - tests/test_conda_python_3_7_script/test_script.py - # ModuleNotFoundError: No module named 'snakemake_executor_plugin_cluster_generic' - tests/test_executor_test_suite.py - # ImportError: cannot import name 'snakemake' from 'snakemake.script' - tests/test_script_py/scripts/test_explicit_import.py -) -EPYTEST_DESELECT=( - # No module named 'snakemake_storage_plugin_s3' - tests/test_api.py::test_deploy_sources -) -distutils_enable_tests pytest diff --git a/dev-python/snakemake/snakemake-8.28.0.ebuild b/dev-python/snakemake/snakemake-8.28.0.ebuild new file mode 100644 index 000000000..60d17afe1 --- /dev/null +++ b/dev-python/snakemake/snakemake-8.28.0.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Make-like task language" +HOMEPAGE="https://snakemake.readthedocs.io"; +SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/appdirs[${PYTHON_USEDEP}] + dev-python/immutables[${PYTHON_USEDEP}] + dev-python/configargparse[${PYTHON_USEDEP}] + >=dev-python/connection_pool-0.0.3[${PYTHON_USEDEP}] + dev-python/datrie[${PYTHON_USEDEP}] + dev-python/docutils[${PYTHON_USEDEP}] + dev-python/gitpython[${PYTHON_USEDEP}] + dev-python/humanfriendly[${PYTHON_USEDEP}] + >=dev-python/jinja2-3.0[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/nbformat[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + >=dev-python/requests-2.8.1[${PYTHON_USEDEP}] + dev-python/reretry[${PYTHON_USEDEP}] + >=dev-python/smart-open-4.0[${PYTHON_USEDEP}] + >=dev-python/snakemake-interface-common-1.17.0[${PYTHON_USEDEP}] + >=dev-python/snakemake-interface-executor-plugins-9.3.2[${PYTHON_USEDEP}] + >=dev-python/snakemake-interface-storage-plugins-3.2.3[${PYTHON_USEDEP}] + >=dev-python/snakemake-interface-report-plugins-1.1.0[${PYTHON_USEDEP}] + dev-python/stopit[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + dev-python/throttler[${PYTHON_USEDEP}] + dev-python/wrapt[${PYTHON_USEDEP}] + >=dev-python/yte-1.5.5[${PYTHON_USEDEP}] + >=dev-python/dpath-2.1.6[${PYTHON_USEDEP}] + >=dev-python/conda-inject-1.3.1[${PYTHON_USEDEP}] + >=sci-mathematics/pulp-2.3.1[${PYTHON_USEDEP}] +" +BDEPEND=" + ${RDEPEND} + test? ( + dev-python/pytest-mock[${PYTHON_USEDEP}] + ) +" + +# distutils_enable_sphinx docs \ +# dev-python/sphinxcontrib-napoleon \ +# dev-python/sphinx-argparse \ +# dev-python/sphinx-rtd-theme \ +# dev-python/docutils \ +# dev-python/recommonmark \ +# dev-python/myst-parser + +distutils_enable_tests pytest + +python_test() { + local EPYTEST_DESELECT=( + # No module named 'snakemake_storage_plugin_s3' + tests/tests.py::test_default_storage + tests/tests.py::test_default_storage_local_job + tests/tests.py::test_storage + tests/tests.py::test_output_file_cache_storage + tests/test_api.py::test_deploy_sources + # No module 'snakemake-executor-plugin-cluster-generic' + tests/tests.py::test_singularity_cluster + tests/tests.py::test_group_jobs + tests/tests.py::test_group_jobs_attempts + tests/tests.py::test_groups_out_of_jobs + tests/tests.py::test_global_resource_limits_limit_scheduling_of_groups + tests/tests.py::test_new_resources_can_be_defined_as_local + tests/tests.py::test_resources_can_be_overwritten_as_global + tests/tests.py::test_group_job_resources_with_pipe_with_too_much_constraint + tests/tests.py::test_multicomp_group_jobs + tests/tests.py::test_group_job_fail + tests/tests.py::test_issue850 + tests/tests.py::test_issue860 + tests/tests.py::test_job_properties + tests/tests.py::test_issue930 + tests/tests.py::test_string_resources + tests/tests.py::test_github_issue1158 + tests/tests.py::test_checkpoint_allowed_rules + tests/tests.py::test_groupid_expand_cluster + tests/tests.py::test_storage_localrule + tests/tests.py::test_storage_cleanup_local + tests/tests.py::test_scopes_submitted_to_cluster + tests/tests.py::test_resources_submitted_to_cluster + tests/tests.py::test_excluded_resources_not_submitted_to_cluster + tests/tests.py::test_group_job_resources_with_pipe + # Missing snakemake-storage-plugin-http + tests/tests.py::test_ancient + tests/tests.py::test_modules_prefix + # Missing snakemake-storage-plugin-fs + tests/tests.py::test_handle_storage_multi_consumers + tests/tests.py::test_checkpoint_open + # Missing python-polars + tests/tests.py::test_params_pickling + # requires conda and does not skip: https://github.com/snakemake/snakemake/pull/3298 + tests/tests.py::test_conda_create_envs_only + tests/tests.py::test_get_log_none + tests/tests.py::test_get_log_both + tests/tests.py::test_get_log_stderr + tests/tests.py::test_get_log_stdout + tests/tests.py::test_get_log_complex + tests/tests.py::test_issue1046 + tests/tests.py::test_containerize + # requires singularity and does not skip + tests/tests.py::test_singularity + tests/tests.py::test_cwl_singularity + tests/tests.py::test_shell_exec + # requires 'stress' in $PATH + tests/tests.py::test_benchmark + tests/tests.py::test_benchmark_jsonl + # requires 'dot' bash module + tests/tests.py::test_env_modules + # requires python-peppy + tests/tests.py::test_modules_peppy + tests/tests.py::test_peppy + tests/tests.py::test_pep_pathlib + # specifies CLI call --snakefile in spaced dir without quoting + tests/tests.py::test_with_parentheses + # missing .bashrc + tests/tests.py::test_strict_mode + # creates directory with chmod 000, breaks portage cleanup + tests/tests.py::test_github_issue640 + ) + + epytest -W ignore::ResourceWarning \ + tests/tests.py \ + tests/test_expand.py \ + tests/test_io.py \ + tests/test_schema.py \ + tests/test_api.py +}
