commit: cada142be644164cf1d5a363b515fc62ac82d125 Author: Michael Schubert <mschu.dev <AT> gmail <DOT> com> AuthorDate: Thu Jul 10 13:15:10 2025 +0000 Commit: Nowa Ammerlaan <nowa <AT> gentoo <DOT> org> CommitDate: Sat Aug 2 10:47:59 2025 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cada142b
dev-python/snakemake: version bump 9.7.1 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> ...kemake-8.28.0.ebuild => snakemake-9.7.1.ebuild} | 36 ++++++++++++---------- 1 file changed, 20 insertions(+), 16 deletions(-) diff --git a/dev-python/snakemake/snakemake-8.28.0.ebuild b/dev-python/snakemake/snakemake-9.7.1.ebuild similarity index 83% rename from dev-python/snakemake/snakemake-8.28.0.ebuild rename to dev-python/snakemake/snakemake-9.7.1.ebuild index 60d17afe1..7ebf438cb 100644 --- a/dev-python/snakemake/snakemake-8.28.0.ebuild +++ b/dev-python/snakemake/snakemake-9.7.1.ebuild @@ -3,14 +3,13 @@ EAPI=8 -PYTHON_COMPAT=( python3_{11..12} ) +PYTHON_COMPAT=( python3_{11..13} ) DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Make-like task language" HOMEPAGE="https://snakemake.readthedocs.io"; -SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="MIT" SLOT="0" @@ -21,7 +20,6 @@ RDEPEND=" dev-python/immutables[${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}] @@ -31,13 +29,15 @@ RDEPEND=" dev-python/packaging[${PYTHON_USEDEP}] dev-python/psutil[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/referencing[${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-common-1.20.1[${PYTHON_USEDEP}] >=dev-python/snakemake-interface-executor-plugins-9.3.2[${PYTHON_USEDEP}] - >=dev-python/snakemake-interface-storage-plugins-3.2.3[${PYTHON_USEDEP}] + >=dev-python/snakemake-interface-storage-plugins-4.1.0[${PYTHON_USEDEP}] >=dev-python/snakemake-interface-report-plugins-1.1.0[${PYTHON_USEDEP}] + >=dev-python/snakemake-interface-logger-plugins-1.1.0[${PYTHON_USEDEP}] dev-python/stopit[${PYTHON_USEDEP}] dev-python/tabulate[${PYTHON_USEDEP}] dev-python/throttler[${PYTHON_USEDEP}] @@ -97,28 +97,28 @@ python_test() { 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 + tests/tests.py::test_nodelocal + tests/tests.py::test_access_patterns + tests/tests.py::test_resource_quoting_profile + tests/tests.py::test_resource_quoting_cli + tests/tests.py::test_default_resource_quoting_cli + tests/tests.py::test_default_resource_quoting_profile # Missing snakemake-storage-plugin-http tests/tests.py::test_ancient tests/tests.py::test_modules_prefix + tests/tests.py::test_keep_local + tests/tests.py::test_retrieve # 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 + tests/tests.py::test_validate # 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 + # requires 'stress-ng' in $PATH tests/tests.py::test_benchmark tests/tests.py::test_benchmark_jsonl # requires 'dot' bash module @@ -133,6 +133,10 @@ python_test() { tests/tests.py::test_strict_mode # creates directory with chmod 000, breaks portage cleanup tests/tests.py::test_github_issue640 + # missing jupyter + tests/tests.py::test_jupyter_notebook + tests/tests.py::test_jupyter_notebook_nbconvert + tests/tests.py::test_jupyter_notebook_draft ) epytest -W ignore::ResourceWarning \
