git: 41cce74a9e4c - main - biology/py-pysam: unbundle biology/htslib

The branch main has been updated by fuz:

URL: https://cgit.FreeBSD.org/ports/commit/?id=41cce74a9e4c1727c4120517724059f68f27404f

commit 41cce74a9e4c1727c4120517724059f68f27404f
Author:     Robert Clausecker <fuz@FreeBSD.org>
AuthorDate: 2023-05-24 07:09:35 +0000
Commit:     Robert Clausecker <fuz@FreeBSD.org>
CommitDate: 2023-05-25 09:39:33 +0000

    biology/py-pysam: unbundle biology/htslib
    
    This fixes the build on armv7 by picking up our custom fixed libhts
    over the bundled unfixed version.  The CFLAGS workaround is now no
    longer required either.
    
    Approved by:    yuri (maintainer)
    Differential Revision: https://reviews.freebsd.org/D40251
---
 biology/py-pysam/Makefile | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile
index 5cd1b27a49a0..10e1d55b786e 100644
--- a/biology/py-pysam/Makefile
+++ b/biology/py-pysam/Makefile
@@ -1,5 +1,6 @@
 PORTNAME=	pysam
 DISTVERSION=	0.20.0
+PORTREVISION=	1
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -11,12 +12,15 @@ WWW=		https://github.com/pysam-developers/pysam
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/COPYING
 
+LIB_DEPENDS=	libhts.so:biology/htslib
+
 USES=		gmake python:3.6-3.9
 USE_PYTHON=	autoplist distutils cython cython_run pytest
 
-CFLAGS+=	-fPIC # workaround for https://github.com/pysam-developers/pysam/issues/1146
-
 BINARY_ALIAS=	make=${GMAKE}
+MAKE_ENV=	HTSLIB_MODE=external \
+		HTSLIB_LIBRARY_DIR=${LOCALBASE}/lib \
+		HTSLIB_INCLUDE_DIR=${LOCALBASE}/include
 
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/lib*${PYTHON_EXT_SUFFIX}.so