Date: Thu, 02 Apr 2026 06:45:26 +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: 6018c1d1d33d - main - biology/py-gffutils: update 0.=?utf-8?Q?13 =E2=86=92 0?=.14 Message-ID: <69ce1086.21d3f.1fae9e0b@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=6018c1d1d33d9e9401ac5bf09961710a7341671c commit 6018c1d1d33d9e9401ac5bf09961710a7341671c Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-04-01 20:41:17 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-04-02 06:45:22 +0000 biology/py-gffutils: update 0.13 → 0.14 --- biology/py-gffutils/Makefile | 14 +++++++++----- biology/py-gffutils/distinfo | 6 +++--- biology/py-gffutils/files/patch-pyproject.toml | 20 ++++++++++++++++++++ 3 files changed, 32 insertions(+), 8 deletions(-) diff --git a/biology/py-gffutils/Makefile b/biology/py-gffutils/Makefile index dea11b8356bb..e65bd8a0fc52 100644 --- a/biology/py-gffutils/Makefile +++ b/biology/py-gffutils/Makefile @@ -1,6 +1,5 @@ PORTNAME= gffutils -DISTVERSION= 0.13 -PORTREVISION= 1 +DISTVERSION= 0.14 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -10,15 +9,20 @@ COMMENT= Work with GFF and GTF files in a flexible database framework WWW= https://github.com/daler/gffutils LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}argcomplete>=1.9.4:devel/py-argcomplete@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}argh>=0.26.2:devel/py-argh@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyfaidx>=0.5.5.2:biology/py-pyfaidx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}simplejson>0:devel/py-simplejson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>=1.12.0:devel/py-six@${PY_FLAVOR} -USES= python -USE_PYTHON= distutils concurrent autoplist pytest +USES= python shebangfix +USE_PYTHON= pep517 concurrent autoplist pytest + +SHEBANG_FILES= gffutils/scripts/gffutils-cli TEST_ENV= ${MAKE_ENV} \ PATH=${STAGEDIR}${PREFIX}/bin:${PATH} \ @@ -26,6 +30,6 @@ TEST_ENV= ${MAKE_ENV} \ NO_ARCH= yes -# 1 test (test_roundtrip) fails, see test_roundtrip +# tests as of 0.14: 135 passed, 2 skipped, 6 warnings in 4.29s .include <bsd.port.mk> diff --git a/biology/py-gffutils/distinfo b/biology/py-gffutils/distinfo index e5a11a3fb3cf..045b35ef87a9 100644 --- a/biology/py-gffutils/distinfo +++ b/biology/py-gffutils/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1718571181 -SHA256 (gffutils-0.13.tar.gz) = b0d52f35c014cc0330fb5c4e3c6fea127c90ccf4c5384a825cdb5c8ff330d4eb -SIZE (gffutils-0.13.tar.gz) = 1560489 +TIMESTAMP = 1775073172 +SHA256 (gffutils-0.14.tar.gz) = 0246a16373453a5a1faf6696553557f2ebf49b2f91a7730cb59d46b5cbd1d9b1 +SIZE (gffutils-0.14.tar.gz) = 1566441 diff --git a/biology/py-gffutils/files/patch-pyproject.toml b/biology/py-gffutils/files/patch-pyproject.toml new file mode 100644 index 000000000000..3b0e5a965caa --- /dev/null +++ b/biology/py-gffutils/files/patch-pyproject.toml @@ -0,0 +1,20 @@ +--- pyproject.toml.orig 2026-03-31 15:26:37 UTC ++++ pyproject.toml +@@ -1,7 +1,7 @@ + [build-system] + # setuptools 77.0.3 is when support for plain text values for `license` key, + # used below, is supported. +-requires = ["setuptools>=77.0.3"] ++requires = ["setuptools"] + build-backend = "setuptools.build_meta" + + [project] +@@ -12,8 +12,6 @@ authors = [ + authors = [ + { name = "Ryan Dale", email = "ryan.dale@nih.gov" }, + ] +-license = "MIT" +-license-files = ["LICENSE"] + requires-python = ">=3.8" + dependencies = [ + "pyfaidx>=0.5.5.2",home | help
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