dev-python/snakemake: version bump

dev-python/snakemake-interface-executor-plugins/Manifest

@@ -1 +1 @@
-DIST snakemake_interface_executor_plugins-9.3.2.tar.gz 16714 BLAKE2B 0ae26f520a81fae4a35cddc059bf76da49f558fffda41e1f29db4ab5bc17d6c6f29c3b01961d683b7fc6be05a9e2541a7f6a853f44b94b68ede0033bb9f42a3f SHA512 c516cc2b0aac2fda7f6ae3cd092e626e72591e5810cd11c4f990d297da9407fb98290b8636a7c5ac9e491cb5b89710b03d97746b8d9fd5007fa60b5fcceced8b
+DIST snakemake_interface_executor_plugins-9.3.3.tar.gz 16710 BLAKE2B 4af6a2b14c725c7498a1f49b34bc9951e5fc339fd021559557812d95dd44dbc024f3bb01927116c354230ea3b142de27e61b5669fa39b2b18c38193af028ec1b SHA512 925b7ac5c61ed922c619445a3e4d8339a22568eb5c96b72c0a9637daa484ffdc1a909248d5d53e326fdd784b84b86b45754b1929127c424cd531c3076b156ec5

dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.3.2.ebuild → dev-python/snakemake-interface-executor-plugins/snakemake-interface-executor-plugins-9.3.3.ebuild

@@ -1,4 +1,4 @@
-# Copyright 1999-2024 Gentoo Foundation
+# Copyright 1999-2025 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8

dev-python/snakemake/Manifest

@@ -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

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[${PYTHON_USEDEP}]
+	>=dev-python/jinja-3.0[${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}]
+"
+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
+}