Date: Mon, 20 Apr 2026 03:03:46 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 8f672c216d1c - main - misc/snakemake: update 6.=?utf-8?Q?15.5 =E2=86=92?= 9.19.0 Message-ID: <69e59792.237af.2f600e70@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=8f672c216d1cb8c7e77429fd949810e8879eed60 commit 8f672c216d1cb8c7e77429fd949810e8879eed60 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-04-20 03:01:46 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-04-20 03:03:36 +0000 misc/snakemake: update 6.15.5 → 9.19.0 --- misc/snakemake/Makefile | 45 ++++++++++++++++++++++--------- misc/snakemake/distinfo | 6 ++--- misc/snakemake/files/patch-pyproject.toml | 28 +++++++++++++++++++ 3 files changed, 64 insertions(+), 15 deletions(-) diff --git a/misc/snakemake/Makefile b/misc/snakemake/Makefile index ce585cdbb94d..6dbc8d393315 100644 --- a/misc/snakemake/Makefile +++ b/misc/snakemake/Makefile @@ -1,6 +1,5 @@ PORTNAME= snakemake -DISTVERSION= 6.15.5 -PORTREVISION= 5 +DISTVERSION= 9.19.0 CATEGORIES= misc python MASTER_SITES= PYPI @@ -9,30 +8,52 @@ COMMENT= Workflow management system WWW= https://github.com/snakemake/snakemake LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE.md RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}appdirs>0:devel/py-appdirs@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}connection_pool>=0.0.3>0:devel/py-connection_pool@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}conda-inject>=1.3.1:devel/py-conda-inject@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}configargparse>0:devel/py-configargparse@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}datrie>0:devel/py-datrie@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}connection_pool>=0.0.3:devel/py-connection_pool@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}docutils>0:textproc/py-docutils@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}filelock>0:sysutils/py-filelock@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}dpath>=2.1.6:devel/py-dpath@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}gitpython>0:devel/py-gitpython@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}humanfriendly>0:textproc/py-humanfriendly@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}immutables>0:devel/py-immutables@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}Jinja2>=3.0:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jsonschema>0:devel/py-jsonschema@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nbformat>0:devel/py-nbformat@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}PuLP>=2.0:math/py-PuLP@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}packaging>=24.0:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}psutil>0:sysutils/py-psutil@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ratelimiter>0:devel/py-ratelimiter@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}smart-open>=3.0:net/py-smart-open@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}stopit>0:devel/py-stopit@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}PuLP>=2.3.1:math/py-PuLP@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pyyaml>0:devel/py-pyyaml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}referencing>0:devel/py-referencing@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>=2.8.1:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}smart-open>=4.0:net/py-smart-open@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}snakemake-interface-common>=1.20.1:misc/py-snakemake-interface-common@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}snakemake-interface-executor-plugins>=9.3.2:misc/py-snakemake-interface-executor-plugins@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}snakemake-interface-logger-plugins>=1.1.0:misc/py-snakemake-interface-logger-plugins@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}snakemake-interface-report-plugins>=1.2.0:misc/py-snakemake-interface-report-plugins@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}snakemake-interface-scheduler-plugins>=2.0.0:misc/py-snakemake-interface-scheduler-plugins@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}snakemake-interface-storage-plugins>=4.4.1:misc/py-snakemake-interface-storage-plugins@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}sqlmodel>=0.0.37:databases/py-sqlmodel@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tabulate>0:devel/py-tabulate@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}toposort>0:devel/py-toposort@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tenacity>=9.1.4:devel/py-tenacity@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}throttler>0:devel/py-throttler@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wrapt>0:devel/py-wrapt@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pyyaml>=0:devel/py-pyyaml@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}yte>=1.5.5:textproc/py-yte@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} USES= python USE_PYTHON= distutils noflavors autoplist +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_WRKSRC= ${WRKSRC}/tests + +do-test: + @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m pytest \ + tests/test_args.py tests/test_internals.py tests/test_io.py \ + tests/test_prefix_lookup.py -v + NO_ARCH= yes .include <bsd.port.mk> diff --git a/misc/snakemake/distinfo b/misc/snakemake/distinfo index 8f1998616f58..0c5d5b4b1d1c 100644 --- a/misc/snakemake/distinfo +++ b/misc/snakemake/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1651249125 -SHA256 (snakemake-6.15.5.tar.gz) = e3297898f96c358b2c1a883aeb0f3540f983943cd564511510b9112a37fcf1f4 -SIZE (snakemake-6.15.5.tar.gz) = 281352 +TIMESTAMP = 1776616620 +SHA256 (snakemake-9.19.0.tar.gz) = c7d3fbbf00b1bdf992bc61b9dcee21b5c3fb95a038cd58d53c6369a7c4f0609e +SIZE (snakemake-9.19.0.tar.gz) = 6779935 diff --git a/misc/snakemake/files/patch-pyproject.toml b/misc/snakemake/files/patch-pyproject.toml new file mode 100644 index 000000000000..06bcc1420cac --- /dev/null +++ b/misc/snakemake/files/patch-pyproject.toml @@ -0,0 +1,28 @@ +--- pyproject.toml.orig 2026-04-19 17:03:43 UTC ++++ pyproject.toml +@@ -15,7 +15,6 @@ requires-python = ">= 3.11" + how to create output files from input files. + """ } + requires-python = ">= 3.11" +-license = "MIT" + authors = [{ name = "Johannes Köster", email = "johannes.koester@uni-due.de" }] + classifiers = [ + "Development Status :: 5 - Production/Stable", +@@ -40,7 +39,7 @@ dependencies = [ + "jinja2>=3.0,<4.0", + "jsonschema", + "nbformat", +- "packaging >=24.0,<26", ++ "packaging>=24.0", + "psutil", + "pulp>=2.3.1,<3.4", + "pyyaml", +@@ -60,7 +59,7 @@ dependencies = [ + "yte>=1.5.5,<2.0", + "dpath>=2.1.6,<3.0.0", + "conda-inject>=1.3.1,<2.0", +- "sqlmodel>=0.0.37,<0.0.38", ++ "sqlmodel>=0.0.37", + ] + + [project.urls]home | help
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