CVS commit: pkgsrc/biology/py-macs2

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/py-macs2
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Sat, 23 Dec 2023 16:15:02 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Dec 23 16:15:02 UTC 2023

Modified Files:
        pkgsrc/biology/py-macs2: Makefile PLIST distinfo
Added Files:
        pkgsrc/biology/py-macs2/patches: patch-MACS2_IO_CallPeakUnit.pyx
            patch-MACS2_IO_FixWidthTrack.pyx
Removed Files:
        pkgsrc/biology/py-macs2/patches: patch-setup.py

Log Message:
biology/py-macs2: Update to 2.2.9.1

Minor updates from 2.2.8
Add hacks for cython 3 to pkgsrc patches
This is likely the final release of MACS2
MACS3 package is forthcoming
Changes: https://github.com/macs3-project/MACS/releases


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/py-macs2/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/py-macs2/PLIST
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/py-macs2/distinfo
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx \
    pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx
cvs rdiff -u -r1.3 -r0 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:1.6 pkgsrc/biology/py-macs2/Makefile:1.7
--- pkgsrc/biology/py-macs2/Makefile:1.6        Sun Nov  5 23:48:31 2023
+++ pkgsrc/biology/py-macs2/Makefile    Sat Dec 23 16:15:02 2023
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.6 2023/11/05 23:48:31 wiz Exp $
+# $NetBSD: Makefile,v 1.7 2023/12/23 16:15:02 bacon Exp $
 
 DISTNAME=      MACS2-${PKGVERSION_NOREV}
-PKGNAME=       ${PYPKGPREFIX}-macs2-2.2.8
+PKGNAME=       ${PYPKGPREFIX}-macs2-2.2.9.1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=taoliu/}
 GITHUB_PROJECT=        MACS
@@ -14,18 +14,19 @@ LICENSE=    modified-bsd
 
 TOOL_DEPENDS+= ${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
 
-PYTHON_VERSIONS_INCOMPATIBLE=  27 38 312
+# Requires new python features
+PYTHON_VERSIONS_INCOMPATIBLE=  27 38
 
 CYTHONIZE=     ${PREFIX}/bin/cythonize-${PYVERSSUFFIX}
 
 # Distributed .c files do not support python > 3.9
-post-extract:
+pre-configure:
        ${MV} ${WRKSRC}/MACS2/cPosValCalculation.c ${WRKSRC}
        ${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
 
-.include "../../lang/python/egg.mk"
+.include "../../lang/python/wheel.mk"
 .include "../../math/py-numpy/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/py-macs2/PLIST
diff -u pkgsrc/biology/py-macs2/PLIST:1.2 pkgsrc/biology/py-macs2/PLIST:1.3
--- pkgsrc/biology/py-macs2/PLIST:1.2   Thu May 18 14:01:58 2023
+++ pkgsrc/biology/py-macs2/PLIST       Sat Dec 23 16:15:02 2023
@@ -1,10 +1,10 @@
-@comment $NetBSD: PLIST,v 1.2 2023/05/18 14:01:58 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2023/12/23 16:15:02 bacon Exp $
 bin/macs2
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/MACS2/Constants.py
 ${PYSITELIB}/MACS2/Constants.pyc
 ${PYSITELIB}/MACS2/Constants.pyo

Index: pkgsrc/biology/py-macs2/distinfo
diff -u pkgsrc/biology/py-macs2/distinfo:1.3 pkgsrc/biology/py-macs2/distinfo:1.4
--- pkgsrc/biology/py-macs2/distinfo:1.3        Thu May 18 14:01:58 2023
+++ pkgsrc/biology/py-macs2/distinfo    Sat Dec 23 16:15:02 2023
@@ -1,6 +1,7 @@
-$NetBSD: distinfo,v 1.3 2023/05/18 14:01:58 bacon Exp $
+$NetBSD: distinfo,v 1.4 2023/12/23 16:15:02 bacon Exp $
 
-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
+BLAKE2s (MACS2-2.2.9.1.tar.gz) = a4563cb4e23096b972941c55eb416ec7db9b05b207c82747dee31657c00d79c3
+SHA512 (MACS2-2.2.9.1.tar.gz) = 6d001d95bac6b6c8ac99592a9345a6ac6836eeb61ff522129c9660ac9bf42bf293af56bd84824b721793a0ec2c73d0a062adb171e5a5a033045aa7552fa28e8b
+Size (MACS2-2.2.9.1.tar.gz) = 133109075 bytes
+SHA1 (patch-MACS2_IO_CallPeakUnit.pyx) = 7a9b53f97fd468eca87f5b7f677d624a069d3062
+SHA1 (patch-MACS2_IO_FixWidthTrack.pyx) = fa5814d2218868c0a317861e9083b9adcda257d6

Added files:

Index: pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx
diff -u /dev/null pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx:1.1
--- /dev/null   Sat Dec 23 16:15:02 2023
+++ pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx     Sat Dec 23 16:15:02 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-MACS2_IO_CallPeakUnit.pyx,v 1.1 2023/12/23 16:15:02 bacon Exp $
+
+# Fix cython 3 error
+
+--- MACS2/IO/CallPeakUnit.pyx.orig     2023-12-23 15:31:06.614325825 +0000
++++ MACS2/IO/CallPeakUnit.pyx
+@@ -197,7 +197,7 @@ cdef wtd_find_summit(chrom, np.ndarray p
+     wtd_list = np.zeros( search_end - search_start + 1, dtype="float32")
+     i = 0
+     for j in range(search_start, search_end+1):
+-        wtd_list[i] = max((2 * (watson_left * crick_right)**0.5 - watson_right - crick_left),0) # minimum score is 0
++        wtd_list[i] = max((2 * (watson_left * crick_right)**0.5 - watson_right - crick_left),complex(0)) # minimum score is 0
+         watson_left += left_forward(watson, j, window_size)
+         watson_right += right_forward(watson, j, window_size)
+         crick_left += left_forward(crick, j, window_size)
Index: pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx
diff -u /dev/null pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx:1.1
--- /dev/null   Sat Dec 23 16:15:02 2023
+++ pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx    Sat Dec 23 16:15:02 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-MACS2_IO_FixWidthTrack.pyx,v 1.1 2023/12/23 16:15:02 bacon Exp $
+
+# Fix cython 3 error
+
+--- MACS2/IO/FixWidthTrack.pyx.orig    2023-07-21 14:25:59.000000000 +0000
++++ MACS2/IO/FixWidthTrack.pyx
+@@ -946,7 +946,7 @@ cdef tuple wtd_find_summit(chrom, np.nda
+     wtd_list = np.zeros( search_end - search_start + 1, dtype="float32")
+     i = 0
+     for j in range(search_start, search_end+1):
+-        wtd_list[i] = max((2 * (watson_left * crick_right)**0.5 - watson_right - crick_left),0) # minimum score is 0
++        wtd_list[i] = max((2 * (watson_left * crick_right)**0.5 - watson_right - crick_left),complex(0)) # minimum score is 0
+         watson_left += left_forward(watson, j, window_size)
+         watson_right += right_forward(watson, j, window_size)
+         crick_left += left_forward(crick, j, window_size)

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