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dev-python/snakemake: version bump 8.28.0 and improve tests
Signed-off-by: Michael Schubert <mschu.dev@gmail.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,2 @@ | ||
| DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a | ||
| DIST snakemake-8.25.3.gh.tar.gz 8693083 BLAKE2B 8d5070d5c78f560bc714da189454776ea87a8403075da98b45b021ac304053cb08763c929846d4c8f949c71245566bdb012b78d8807f40a584805cd08917af14 SHA512 f769c89e98130c738bb43931f240eaa93482d19403c6bcda65334910ccf4cac2e11257ed8b133d220d645ea39b0af8aa580fe24c57221478ea7dd0fb4d21d4e7 | ||
| DIST snakemake-8.28.0.gh.tar.gz 8702504 BLAKE2B 11356559080231d372208ce37b5c3c2dbc7a7d660c5a59201fe0a09a1f49f39c74542ad66ca075959c38d763e13deed93acbd0ae9fc66104adb7baf52009e1f7 SHA512 aa9ad3f417a743e2fbc54d9fef8b11e52858195481d89bdc7ac635e10f9f017b0056999ed112bcc6f85c9de30c10117c32a5a5e35c98c7c1393c2efb6e8399c9 |
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| # Copyright 1999-2025 Gentoo Authors | ||
| # Distributed under the terms of the GNU General Public License v2 | ||
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| EAPI=8 | ||
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| PYTHON_COMPAT=( python3_{11..12} ) | ||
| DISTUTILS_USE_PEP517=setuptools | ||
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| inherit distutils-r1 | ||
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| DESCRIPTION="Make-like task language" | ||
| HOMEPAGE="https://snakemake.readthedocs.io" | ||
| SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" | ||
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| LICENSE="MIT" | ||
| SLOT="0" | ||
| KEYWORDS="~amd64" | ||
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| RDEPEND=" | ||
| dev-python/appdirs[${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[${PYTHON_USEDEP}] | ||
| >=dev-python/jinja-3.0[${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}] | ||
| " | ||
| DEPEND=" | ||
| ${RDEPEND} | ||
| test? ( | ||
| dev-python/pytest-mock | ||
| ) | ||
| " | ||
|
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| # 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 | ||
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| distutils_enable_tests pytest | ||
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| 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 | ||
| ) | ||
|
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| epytest -W ignore::ResourceWarning \ | ||
| tests/tests.py \ | ||
| tests/test_expand.py \ | ||
| tests/test_io.py \ | ||
| tests/test_schema.py \ | ||
| tests/test_api.py | ||
| } |