Date: Thu, 25 Apr 2024 14:52:14 GMT 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: c76da4ae368b - main - biology/py-pysam: update 0.22.0 =?utf-8?Q?=E2=86=92?= 0.22.1 Message-ID: <202404251452.43PEqE0Q060415@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=c76da4ae368b3c83e7a50ff73d131e2872a814ba commit c76da4ae368b3c83e7a50ff73d131e2872a814ba Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2024-04-25 04:35:55 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2024-04-25 14:52:08 +0000 biology/py-pysam: update 0.22.0 → 0.22.1 Reported by: portscout --- biology/py-pysam/Makefile | 14 +++++++++++--- biology/py-pysam/distinfo | 6 +++--- biology/py-pysam/files/patch-setup.py | 11 ----------- 3 files changed, 14 insertions(+), 17 deletions(-) diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile index 4435335a3a3b..745a4a165ed1 100644 --- a/biology/py-pysam/Makefile +++ b/biology/py-pysam/Makefile @@ -1,7 +1,8 @@ PORTNAME= pysam -DISTVERSION= 0.22.0 +DISTVERSIONPREFIX= v +DISTVERSION= 0.22.1 CATEGORIES= biology python -MASTER_SITES= PYPI +#MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org @@ -12,14 +13,21 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libhts.so:biology/htslib +RUN_DEPENDS= bcftools:biology/bcftools \ + samtools:biology/samtools USES= gmake python -USE_PYTHON= distutils autoplist cython cython_run +USE_PYTHON= distutils autoplist cython cython_run pytest # 2 failed, 155 errors, see https://github.com/pysam-developers/pysam/issues/1284 + +USE_GITHUB= yes +GH_ACCOUNT= pysam-developers BINARY_ALIAS= make=${GMAKE} MAKE_ENV= HTSLIB_MODE=external \ HTSLIB_LIBRARY_DIR=${LOCALBASE}/lib \ HTSLIB_INCLUDE_DIR=${LOCALBASE}/include +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_WRKSRC= ${WRKSRC}/tests post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/lib*${PYTHON_EXT_SUFFIX}.so diff --git a/biology/py-pysam/distinfo b/biology/py-pysam/distinfo index 24a863205256..f5f1e4268139 100644 --- a/biology/py-pysam/distinfo +++ b/biology/py-pysam/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1696579895 -SHA256 (pysam-0.22.0.tar.gz) = ab7a46973cf0ab8c6ac327f4c3fb67698d7ccbeef8631a716898c6ba01ef3e45 -SIZE (pysam-0.22.0.tar.gz) = 4631254 +TIMESTAMP = 1714015094 +SHA256 (pysam-developers-pysam-v0.22.1_GH0.tar.gz) = e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6 +SIZE (pysam-developers-pysam-v0.22.1_GH0.tar.gz) = 3885851 diff --git a/biology/py-pysam/files/patch-setup.py b/biology/py-pysam/files/patch-setup.py deleted file mode 100644 index d82a8bbbefcf..000000000000 --- a/biology/py-pysam/files/patch-setup.py +++ /dev/null @@ -1,11 +0,0 @@ ---- setup.py.orig 2017-04-19 05:48:10 UTC -+++ setup.py -@@ -60,7 +60,7 @@ def run_configure(option): - - - def run_make_print_config(): -- stdout = subprocess.check_output(["make", "-s", "print-config"]) -+ stdout = subprocess.check_output(["gmake", "-s", "print-config"]) - if IS_PYTHON3: - stdout = stdout.decode("ascii") -
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