From e97c3457489f2abb3cda2b6b023ba580b6382c07 Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Sun, 6 Aug 2023 13:14:56 -0500
Subject: [PATCH] biology/py-macs2: Update to 2.2.9.1

Mainly updates to dependencies
Changes: https://github.com/macs3-project/MACS/releases
Added test target

Reported by:    portscout
---
 biology/py-macs2/Makefile             | 15 +++++++++++----
 biology/py-macs2/distinfo             |  6 +++---
 biology/py-macs2/files/patch-setup.py | 25 -------------------------
 3 files changed, 14 insertions(+), 32 deletions(-)
 delete mode 100644 biology/py-macs2/files/patch-setup.py

diff --git a/biology/py-macs2/Makefile b/biology/py-macs2/Makefile
index e8e1313b1da8b..5a9d78cfe622a 100644
--- a/biology/py-macs2/Makefile
+++ b/biology/py-macs2/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		macs2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.2.8
+DISTVERSION=		2.2.9.1
 CATEGORIES=		biology python
 PKGNAMEPREFIX=		${PYTHON_PKGNAMEPREFIX}
 
@@ -12,18 +12,25 @@ LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${PYNUMPY}
-RUN_DEPENDS=	${PYNUMPY}
+RUN_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR}
+TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
+		bash:shells/bash
 
-USES=		python
+USES=		python shebangfix
+USE_GITHUB=	yes
 USE_PYTHON=	autoplist concurrent cython distutils
 
-USE_GITHUB=	yes
 GH_ACCOUNT=	taoliu
 GH_PROJECT=	MACS
+SHEBANG_FILES=	test/cmdlinetest_update test/cmdlinetest test/prockreport
 
 post-stage:
 	${STRIP_CMD} \
 		${STAGEDIR}${PYTHON_SITELIBDIR}/MACS2/*.so \
 		${STAGEDIR}${PYTHON_SITELIBDIR}/MACS2/*/*.so
 
+do-test: install
+	@cd ${WRKSRC}/test && ./cmdlinetest tag
+
 .include <bsd.port.mk>
diff --git a/biology/py-macs2/distinfo b/biology/py-macs2/distinfo
index 1999b76a294d9..e6da44033e735 100644
--- a/biology/py-macs2/distinfo
+++ b/biology/py-macs2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1684361836
-SHA256 (taoliu-MACS-v2.2.8_GH0.tar.gz) = cab63d7e8b862dbd6bb8ed32325e4fee728d85306e47931167fef753ef0ee743
-SIZE (taoliu-MACS-v2.2.8_GH0.tar.gz) = 133108890
+TIMESTAMP = 1691269587
+SHA256 (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 8e461dde82288280fe708cd4f5fec986fbf2da67b344f4dea5693af849549163
+SIZE (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 133109075
diff --git a/biology/py-macs2/files/patch-setup.py b/biology/py-macs2/files/patch-setup.py
deleted file mode 100644
index 3434e11463574..0000000000000
--- a/biology/py-macs2/files/patch-setup.py
+++ /dev/null
@@ -1,25 +0,0 @@
---- setup.py.orig	2020-04-12 14:46:03 UTC
-+++ setup.py
-@@ -26,22 +26,6 @@ def main():
- 
-     cwd = os.path.abspath(os.path.dirname(__file__))
- 
--    # install required numpy
--    p = subprocess.call([sys.executable, "-m", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd)
--    if p != 0:
--        # Could be due to a too old pip version and build isolation, check that
--        try:
--            # Note, pip may not be installed or not have been used
--            import pip
--            if LooseVersion(pip.__version__) < LooseVersion('18.0.0'):
--                raise RuntimeError("Installing requirements failed. Possibly due "
--                                   "to `pip` being too old, found version {}, "
--                                   "needed is >= 18.0.0.".format(pip.__version__))
--            else:
--                raise RuntimeError("Installing requirements failed!")
--        except ImportError:
--            raise RuntimeError("Installing requirement failed! `pip` has to be installed!")
--        
-     from numpy import get_include as numpy_get_include
-     numpy_include_dir = [numpy_get_include()]
-