git: 8f672c216d1c - main - misc/snakemake: update 6.15.5 → 9.19.0
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Date: Mon, 20 Apr 2026 03:03:46 UTC
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]