py-macs2: remove, pkgsrc has same version

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: py-macs2: remove, pkgsrc has same version
From: Thomas Klausner (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>
Date: Tue, 25 Aug 2026 10:55:35 +0000
Module Name:	pkgsrc-wip
Committed By:	Thomas Klausner <wiz%NetBSD.org@localhost>
Pushed By:	wiz
Date:		Tue Aug 25 10:35:13 2026 +0200
Changeset:	7fe9f7b8eb8746c44da4ae5126618c52ce96b9ed

Modified Files:
	Makefile
Removed Files:
	py-macs2/DESCR
	py-macs2/Makefile
	py-macs2/PLIST
	py-macs2/distinfo
	py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx
	py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx

Log Message:
py-macs2: remove, pkgsrc has same version

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7fe9f7b8eb8746c44da4ae5126618c52ce96b9ed

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

diffstat:
 Makefile                                          |  1 -
 py-macs2/DESCR                                    |  5 --
 py-macs2/Makefile                                 | 29 ---------
 py-macs2/PLIST                                    | 76 -----------------------
 py-macs2/distinfo                                 |  7 ---
 py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx  | 15 -----
 py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx | 15 -----
 7 files changed, 148 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index f3f3b6981b..729f879b61 100644
--- a/Makefile
+++ b/Makefile
@@ -4198,7 +4198,6 @@ SUBDIR+=	py-lxmlproc
 SUBDIR+=	py-lzma
 SUBDIR+=	py-lzstring
 SUBDIR+=	py-m2r2
-SUBDIR+=	py-macs2
 SUBDIR+=	py-magnitude
 SUBDIR+=	py-mahotas
 SUBDIR+=	py-mailcap-fix
diff --git a/py-macs2/DESCR b/py-macs2/DESCR
deleted file mode 100644
index 087b58b49d..0000000000
--- a/py-macs2/DESCR
+++ /dev/null
@@ -1,5 +0,0 @@
-MACS is a tool for chromatin immunoprecipitation (ChIP) sequence
-analysis.  MACS empirically models the length of the sequenced ChIP
-fragments, which tend to be shorter than sonication or library
-construction size estimates, and uses it to improve the spatial
-resolution of predicted binding sites.
diff --git a/py-macs2/Makefile b/py-macs2/Makefile
deleted file mode 100644
index eb1ffbc28d..0000000000
--- a/py-macs2/Makefile
+++ /dev/null
@@ -1,29 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	MACS2-${PKGVERSION_NOREV}
-PKGNAME=	${PYPKGPREFIX}-macs2-2.2.9.1
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=taoliu/}
-GITHUB_PROJECT=	MACS
-GITHUB_TAG=	v${PKGVERSION_NOREV}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://github.com/macs3-project/MACS
-COMMENT=	Algorithm for identifying transcription factor binding sites
-LICENSE=	modified-bsd
-
-TOOL_DEPENDS+=	${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
-
-CYTHONIZE=	${PREFIX}/bin/cythonize-${PYVERSSUFFIX}
-
-# Distributed .c files do not support python > 3.9
-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/wheel.mk"
-.include "../../math/py-numpy/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-macs2/PLIST b/py-macs2/PLIST
deleted file mode 100644
index 9b22123791..0000000000
--- a/py-macs2/PLIST
+++ /dev/null
@@ -1,76 +0,0 @@
-@comment $NetBSD$
-bin/macs2
-${PYSITELIB}/${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
-${PYSITELIB}/MACS2/Constants.pyo
-${PYSITELIB}/MACS2/IO/BedGraph.so
-${PYSITELIB}/MACS2/IO/BedGraphIO.so
-${PYSITELIB}/MACS2/IO/CallPeakUnit.so
-${PYSITELIB}/MACS2/IO/FixWidthTrack.so
-${PYSITELIB}/MACS2/IO/PairedEndTrack.so
-${PYSITELIB}/MACS2/IO/Parser.so
-${PYSITELIB}/MACS2/IO/PeakIO.so
-${PYSITELIB}/MACS2/IO/ScoreTrack.so
-${PYSITELIB}/MACS2/IO/__init__.py
-${PYSITELIB}/MACS2/IO/__init__.pyc
-${PYSITELIB}/MACS2/IO/__init__.pyo
-${PYSITELIB}/MACS2/OptValidator.py
-${PYSITELIB}/MACS2/OptValidator.pyc
-${PYSITELIB}/MACS2/OptValidator.pyo
-${PYSITELIB}/MACS2/OutputWriter.py
-${PYSITELIB}/MACS2/OutputWriter.pyc
-${PYSITELIB}/MACS2/OutputWriter.pyo
-${PYSITELIB}/MACS2/PeakDetect.so
-${PYSITELIB}/MACS2/PeakModel.so
-${PYSITELIB}/MACS2/Pileup.so
-${PYSITELIB}/MACS2/Prob.so
-${PYSITELIB}/MACS2/Signal.so
-${PYSITELIB}/MACS2/__init__.py
-${PYSITELIB}/MACS2/__init__.pyc
-${PYSITELIB}/MACS2/__init__.pyo
-${PYSITELIB}/MACS2/bdgbroadcall_cmd.py
-${PYSITELIB}/MACS2/bdgbroadcall_cmd.pyc
-${PYSITELIB}/MACS2/bdgbroadcall_cmd.pyo
-${PYSITELIB}/MACS2/bdgcmp_cmd.py
-${PYSITELIB}/MACS2/bdgcmp_cmd.pyc
-${PYSITELIB}/MACS2/bdgcmp_cmd.pyo
-${PYSITELIB}/MACS2/bdgdiff_cmd.py
-${PYSITELIB}/MACS2/bdgdiff_cmd.pyc
-${PYSITELIB}/MACS2/bdgdiff_cmd.pyo
-${PYSITELIB}/MACS2/bdgopt_cmd.py
-${PYSITELIB}/MACS2/bdgopt_cmd.pyc
-${PYSITELIB}/MACS2/bdgopt_cmd.pyo
-${PYSITELIB}/MACS2/bdgpeakcall_cmd.py
-${PYSITELIB}/MACS2/bdgpeakcall_cmd.pyc
-${PYSITELIB}/MACS2/bdgpeakcall_cmd.pyo
-${PYSITELIB}/MACS2/cPosValCalculation.pxd
-${PYSITELIB}/MACS2/callpeak_cmd.py
-${PYSITELIB}/MACS2/callpeak_cmd.pyc
-${PYSITELIB}/MACS2/callpeak_cmd.pyo
-${PYSITELIB}/MACS2/cmbreps_cmd.py
-${PYSITELIB}/MACS2/cmbreps_cmd.pyc
-${PYSITELIB}/MACS2/cmbreps_cmd.pyo
-${PYSITELIB}/MACS2/diffpeak_cmd.py
-${PYSITELIB}/MACS2/diffpeak_cmd.pyc
-${PYSITELIB}/MACS2/diffpeak_cmd.pyo
-${PYSITELIB}/MACS2/filterdup_cmd.py
-${PYSITELIB}/MACS2/filterdup_cmd.pyc
-${PYSITELIB}/MACS2/filterdup_cmd.pyo
-${PYSITELIB}/MACS2/khash.pxd
-${PYSITELIB}/MACS2/pileup_cmd.py
-${PYSITELIB}/MACS2/pileup_cmd.pyc
-${PYSITELIB}/MACS2/pileup_cmd.pyo
-${PYSITELIB}/MACS2/predictd_cmd.py
-${PYSITELIB}/MACS2/predictd_cmd.pyc
-${PYSITELIB}/MACS2/predictd_cmd.pyo
-${PYSITELIB}/MACS2/randsample_cmd.py
-${PYSITELIB}/MACS2/randsample_cmd.pyc
-${PYSITELIB}/MACS2/randsample_cmd.pyo
-${PYSITELIB}/MACS2/refinepeak_cmd.py
-${PYSITELIB}/MACS2/refinepeak_cmd.pyc
-${PYSITELIB}/MACS2/refinepeak_cmd.pyo
diff --git a/py-macs2/distinfo b/py-macs2/distinfo
deleted file mode 100644
index 3650591fb6..0000000000
--- a/py-macs2/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD$
-
-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
diff --git a/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx b/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx
deleted file mode 100644
index 309d33fb03..0000000000
--- a/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# 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)
diff --git a/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx b/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx
deleted file mode 100644
index 5123e60065..0000000000
--- a/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# 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)
Prev by Date: py-macs3: remove, pkgsrc version is newer
Next by Date: webkit-gtk60: move patch to currently used file
Previous by Thread: py-macs3: remove, pkgsrc version is newer
Next by Thread: webkit-gtk60: move patch to currently used file
Indexes:
Home | Main Index | Thread Index | Old Index