CVS commit: pkgsrc/biology/py-macs2

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu May 18 14:01:58 UTC 2023

Modified Files:
        pkgsrc/biology/py-macs2: Makefile PLIST distinfo
        pkgsrc/biology/py-macs2/patches: patch-setup.py

Log Message:
biology/py-macs2: Update to 2.2.8

Adds support for python 3.11

Changes: https://github.com/macs3-project/MACS/releases


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/py-macs2/Makefile \
    pkgsrc/biology/py-macs2/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/py-macs2/PLIST
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/py-macs2/patches/patch-setup.py

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/py-macs2/Makefile
diff -u pkgsrc/biology/py-macs2/Makefile:1.2 pkgsrc/biology/py-macs2/Makefile:1.3
--- pkgsrc/biology/py-macs2/Makefile:1.2        Sun Jan 29 00:33:04 2023
+++ pkgsrc/biology/py-macs2/Makefile    Thu May 18 14:01:58 2023
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.2 2023/01/29 00:33:04 wiz Exp $
+# $NetBSD: Makefile,v 1.3 2023/05/18 14:01:58 bacon Exp $
 
 DISTNAME=      MACS2-${PKGVERSION_NOREV}
-PKGNAME=       ${PYPKGPREFIX}-macs2-2.2.7.1
+PKGNAME=       ${PYPKGPREFIX}-macs2-2.2.8
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=taoliu/}
 GITHUB_PROJECT=        MACS
@@ -21,7 +21,7 @@ CYTHONIZE=    ${PREFIX}/bin/cythonize-${PYV
 # Distributed .c files do not support python > 3.9
 post-extract:
        ${MV} ${WRKSRC}/MACS2/cPosValCalculation.c ${WRKSRC}
-       ${RM} ${WRKSRC}/MACS2/*.c ${WRKSRC}/MACS2/*/*.c
+       ${RM} -f ${WRKSRC}/MACS2/*.c ${WRKSRC}/MACS2/*/*.c
        cd ${WRKSRC} && ${CYTHONIZE} ${WRKSRC}/MACS2/*.pyx
        cd ${WRKSRC} && ${CYTHONIZE} ${WRKSRC}/MACS2/*/*.pyx
        ${MV} ${WRKSRC}/cPosValCalculation.c ${WRKSRC}/MACS2
Index: pkgsrc/biology/py-macs2/distinfo
diff -u pkgsrc/biology/py-macs2/distinfo:1.2 pkgsrc/biology/py-macs2/distinfo:1.3
--- pkgsrc/biology/py-macs2/distinfo:1.2        Fri Feb 10 14:19:45 2023
+++ pkgsrc/biology/py-macs2/distinfo    Thu May 18 14:01:58 2023
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.2 2023/02/10 14:19:45 wiz Exp $
+$NetBSD: distinfo,v 1.3 2023/05/18 14:01:58 bacon Exp $
 
-BLAKE2s (MACS2-2.2.7.1.tar.gz) = 9018fcf83634355b625d8cbf6f67071c78d469bb35732318115470b7b7d30f8a
-SHA512 (MACS2-2.2.7.1.tar.gz) = 2591ff3258124b1d577b0f417838e13ca6151b011590dbb769fd500d7ee5c7969349a7e40d11c3d8cbe75555786f3b76d3950586d7ed144e6e7679018c32d5c5
-Size (MACS2-2.2.7.1.tar.gz) = 134872405 bytes
-SHA1 (patch-setup.py) = 2dd7f9996f93db596b4670c3231c818aaee03c87
+BLAKE2s (MACS2-2.2.8.tar.gz) = fe162ddc6af2471f75a8d4d94a2702942cfab5d3f8aebb2ef9af8a2cedf1d92a
+SHA512 (MACS2-2.2.8.tar.gz) = 0d28249bf73280b1fc71229f27787f6259568adddb2cbb0be1fabf52d596abfc249a18909f80f763d98b035e28790c61b5fe21e92f1bc565d1cc3d7cd637c519
+Size (MACS2-2.2.8.tar.gz) = 133108890 bytes
+SHA1 (patch-setup.py) = c35f9e13e2ec3b6d0381271128cf3426567a74d5

Index: pkgsrc/biology/py-macs2/PLIST
diff -u pkgsrc/biology/py-macs2/PLIST:1.1 pkgsrc/biology/py-macs2/PLIST:1.2
--- pkgsrc/biology/py-macs2/PLIST:1.1   Sun Jan 22 23:30:11 2023
+++ pkgsrc/biology/py-macs2/PLIST       Thu May 18 14:01:58 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2023/01/22 23:30:11 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2023/05/18 14:01:58 bacon Exp $
 bin/macs2
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt

Index: pkgsrc/biology/py-macs2/patches/patch-setup.py
diff -u pkgsrc/biology/py-macs2/patches/patch-setup.py:1.2 pkgsrc/biology/py-macs2/patches/patch-setup.py:1.3
--- pkgsrc/biology/py-macs2/patches/patch-setup.py:1.2  Fri Feb 10 14:19:45 2023
+++ pkgsrc/biology/py-macs2/patches/patch-setup.py      Thu May 18 14:01:58 2023
@@ -1,22 +1,11 @@
-$NetBSD: patch-setup.py,v 1.2 2023/02/10 14:19:45 wiz Exp $
+$NetBSD: patch-setup.py,v 1.3 2023/05/18 14:01:58 bacon Exp $
 
-# Remove lexical version check and pip requirement
+# Unbundle numpy
 
---- setup.py.orig      2020-04-12 00:00:15.000000000 +0000
+--- setup.py.orig      2023-05-18 12:06:38.965674517 +0000
 +++ setup.py
-@@ -16,32 +16,12 @@ from setuptools import setup, Extension
- from distutils.version import LooseVersion
- import subprocess
- 
--numpy_requires = '>=1.17'
-+numpy_requires = '1.17'
- install_requires = [f"numpy>={numpy_requires}",]
- 
- def main():
--    if float(sys.version[:3])<3.6:
--        sys.stderr.write("CRITICAL: Python version must >= 3.6!\n")
--        sys.exit(1)
--
+@@ -25,22 +25,6 @@ def main():
+         sys.exit(1)
      cwd = os.path.abspath(os.path.dirname(__file__))
  
 -    # install required numpy