git: c76da4ae368b - main - biology/py-pysam: update 0.22.0 → 0.22.1

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")
-