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py-macs3: remove, pkgsrc version is newer

Module Name:	pkgsrc-wip
Committed By:	Thomas Klausner <wiz%NetBSD.org@localhost>
Pushed By:	wiz
Date:		Tue Aug 25 10:30:39 2026 +0200
Changeset:	baa913d3b711629f53df6d1a6a9851aebb833598

Modified Files:
	Makefile
Removed Files:
	py-macs3/COMMIT_MSG
	py-macs3/DESCR
	py-macs3/Makefile
	py-macs3/PLIST
	py-macs3/distinfo
	py-macs3/patches/patch-MACS3_fermi-lite_ksw.c

Log Message:
py-macs3: remove, pkgsrc version is newer

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=baa913d3b711629f53df6d1a6a9851aebb833598

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

diffstat:
 Makefile                                      |   4 +-
 py-macs3/COMMIT_MSG                           |   7 -
 py-macs3/DESCR                                |   6 -
 py-macs3/Makefile                             |  36 -----
 py-macs3/PLIST                                | 211 --------------------------
 py-macs3/distinfo                             |   6 -
 py-macs3/patches/patch-MACS3_fermi-lite_ksw.c |  15 --
 7 files changed, 3 insertions(+), 282 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index db306daa17..f3f3b6981b 100644
--- a/Makefile
+++ b/Makefile
@@ -4199,7 +4199,6 @@ SUBDIR+=	py-lzma
 SUBDIR+=	py-lzstring
 SUBDIR+=	py-m2r2
 SUBDIR+=	py-macs2
-SUBDIR+=	py-macs3
 SUBDIR+=	py-magnitude
 SUBDIR+=	py-mahotas
 SUBDIR+=	py-mailcap-fix
@@ -5359,6 +5358,8 @@ SUBDIR+=	rust-beta
 SUBDIR+=	rust-synapse-compress-state
 SUBDIR+=	rust197
 SUBDIR+=	rust197-bin
+SUBDIR+=	rust198
+SUBDIR+=	rust198-bin
 SUBDIR+=	s-nail
 SUBDIR+=	s2tc
 SUBDIR+=	s3cmd
@@ -6308,6 +6309,7 @@ SUBDIR+=	zbackup
 SUBDIR+=	zdbsp
 SUBDIR+=	zed
 SUBDIR+=	zeek
+SUBDIR+=	zellij-git
 SUBDIR+=	zephyr-lsmalltalk
 SUBDIR+=	zephyr-smalltalk
 SUBDIR+=	zero-epwing-git
diff --git a/py-macs3/COMMIT_MSG b/py-macs3/COMMIT_MSG
deleted file mode 100644
index 51f4b66ccd..0000000000
--- a/py-macs3/COMMIT_MSG
+++ /dev/null
@@ -1,7 +0,0 @@
-biology/py-macs3: Update to 3.0.2
-
-Packaged in wip by Jason Bacon
-
-# pkgsrc-specific changes
-
-# upstream changes
diff --git a/py-macs3/DESCR b/py-macs3/DESCR
deleted file mode 100644
index 7e901a88e5..0000000000
--- a/py-macs3/DESCR
+++ /dev/null
@@ -1,6 +0,0 @@
-MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying
-transcription factor (TF) binding sites.   Such sites are generated
-by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq
-(Assay for Transposase Accessible Chromatin Sequencing).  MACS
-identifies "peaks" in the genome sequence, which are areas enriched
-in bound TFs or accessible chromatin.
diff --git a/py-macs3/Makefile b/py-macs3/Makefile
deleted file mode 100644
index 60fcccffb5..0000000000
--- a/py-macs3/Makefile
+++ /dev/null
@@ -1,36 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	macs-${PKGVERSION_NOREV}
-PKGNAME=	${PYPKGPREFIX}-macs3-3.0.3
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=macs3-project/}
-GITHUB_PROJECT=	MACS
-GITHUB_TAG=	v${PKGVERSION_NOREV}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://github.com/macs3-project/MACS
-COMMENT=	Peak caller aimed at transcription factor binding sites
-LICENSE=	modified-bsd
-
-TOOL_DEPENDS+=	${PYPKGPREFIX}-setuptools>=0:../../devel/py-setuptools
-TOOL_DEPENDS+=	${PYPKGPREFIX}-wheel>=0:../../devel/py-wheel
-DEPENDS+=	${PYPKGPREFIX}-scipy>=1.11.1:../../math/py-scipy
-# cykhash>=2.0,<3.0
-DEPENDS+=	${PYPKGPREFIX}-cykhash>=2.0:../../devel/py-cykhash
-DEPENDS+=	${PYPKGPREFIX}-scikit-learn>=1.3:../../math/py-scikit-learn
-DEPENDS+=	${PYPKGPREFIX}-hmmlearn>=0.3.2:../../math/py-hmmlearn
-TEST_DEPENDS=	${PYPKGPREFIX}-test>=7.0:../../devel/py-test
-
-USE_TOOLS+=	bash perl:test
-REPLACE_BASH=	test/cmdlinetest* test/prockreport test/*.py test/pyprofile*
-
-do-test: install
-	${RM} -rf ${WRKSRC}/temp
-	(cd ${WRKSRC}/test && ./cmdlinetest tag)
-
-.include "../../lang/python/wheel.mk"
-.include "../../math/py-numpy/buildlink3.mk"
-.include "../../devel/py-cython/buildlink3.mk"
-.include "../../devel/simde/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-macs3/PLIST b/py-macs3/PLIST
deleted file mode 100644
index 3cd9a5d97e..0000000000
--- a/py-macs3/PLIST
+++ /dev/null
@@ -1,211 +0,0 @@
-@comment $NetBSD$
-bin/macs3
-${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/LICENSE
-${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/METADATA
-${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/RECORD
-${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/WHEEL
-${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/top_level.txt
-${PYSITELIB}/MACS3/Commands/__init__.py
-${PYSITELIB}/MACS3/Commands/__init__.pyc
-${PYSITELIB}/MACS3/Commands/__init__.pyo
-${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.py
-${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyc
-${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyo
-${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.py
-${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.pyc
-${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.pyo
-${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.py
-${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.pyc
-${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.pyo
-${PYSITELIB}/MACS3/Commands/bdgopt_cmd.py
-${PYSITELIB}/MACS3/Commands/bdgopt_cmd.pyc
-${PYSITELIB}/MACS3/Commands/bdgopt_cmd.pyo
-${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.py
-${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.pyc
-${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.pyo
-${PYSITELIB}/MACS3/Commands/callpeak_cmd.py
-${PYSITELIB}/MACS3/Commands/callpeak_cmd.pyc
-${PYSITELIB}/MACS3/Commands/callpeak_cmd.pyo
-${PYSITELIB}/MACS3/Commands/callvar_cmd.py
-${PYSITELIB}/MACS3/Commands/callvar_cmd.pyc
-${PYSITELIB}/MACS3/Commands/callvar_cmd.pyo
-${PYSITELIB}/MACS3/Commands/cmbreps_cmd.py
-${PYSITELIB}/MACS3/Commands/cmbreps_cmd.pyc
-${PYSITELIB}/MACS3/Commands/cmbreps_cmd.pyo
-${PYSITELIB}/MACS3/Commands/filterdup_cmd.py
-${PYSITELIB}/MACS3/Commands/filterdup_cmd.pyc
-${PYSITELIB}/MACS3/Commands/filterdup_cmd.pyo
-${PYSITELIB}/MACS3/Commands/hmmratac_cmd.py
-${PYSITELIB}/MACS3/Commands/hmmratac_cmd.pyc
-${PYSITELIB}/MACS3/Commands/hmmratac_cmd.pyo
-${PYSITELIB}/MACS3/Commands/pileup_cmd.py
-${PYSITELIB}/MACS3/Commands/pileup_cmd.pyc
-${PYSITELIB}/MACS3/Commands/pileup_cmd.pyo
-${PYSITELIB}/MACS3/Commands/predictd_cmd.py
-${PYSITELIB}/MACS3/Commands/predictd_cmd.pyc
-${PYSITELIB}/MACS3/Commands/predictd_cmd.pyo
-${PYSITELIB}/MACS3/Commands/randsample_cmd.py
-${PYSITELIB}/MACS3/Commands/randsample_cmd.pyc
-${PYSITELIB}/MACS3/Commands/randsample_cmd.pyo
-${PYSITELIB}/MACS3/Commands/refinepeak_cmd.py
-${PYSITELIB}/MACS3/Commands/refinepeak_cmd.pyc
-${PYSITELIB}/MACS3/Commands/refinepeak_cmd.pyo
-${PYSITELIB}/MACS3/IO/BAM.py
-${PYSITELIB}/MACS3/IO/BAM.pyc
-${PYSITELIB}/MACS3/IO/BAM.pyo
-${PYSITELIB}/MACS3/IO/BAM.so
-${PYSITELIB}/MACS3/IO/BedGraphIO.py
-${PYSITELIB}/MACS3/IO/BedGraphIO.pyc
-${PYSITELIB}/MACS3/IO/BedGraphIO.pyo
-${PYSITELIB}/MACS3/IO/BedGraphIO.so
-${PYSITELIB}/MACS3/IO/OutputWriter.py
-${PYSITELIB}/MACS3/IO/OutputWriter.pyc
-${PYSITELIB}/MACS3/IO/OutputWriter.pyo
-${PYSITELIB}/MACS3/IO/Parser.py
-${PYSITELIB}/MACS3/IO/Parser.pyc
-${PYSITELIB}/MACS3/IO/Parser.pyo
-${PYSITELIB}/MACS3/IO/Parser.so
-${PYSITELIB}/MACS3/IO/PeakIO.py
-${PYSITELIB}/MACS3/IO/PeakIO.pyc
-${PYSITELIB}/MACS3/IO/PeakIO.pyo
-${PYSITELIB}/MACS3/IO/PeakIO.so
-${PYSITELIB}/MACS3/IO/__init__.py
-${PYSITELIB}/MACS3/IO/__init__.pyc
-${PYSITELIB}/MACS3/IO/__init__.pyo
-${PYSITELIB}/MACS3/Signal/BedGraph.py
-${PYSITELIB}/MACS3/Signal/BedGraph.pyc
-${PYSITELIB}/MACS3/Signal/BedGraph.pyo
-${PYSITELIB}/MACS3/Signal/BedGraph.so
-${PYSITELIB}/MACS3/Signal/CallPeakUnit.py
-${PYSITELIB}/MACS3/Signal/CallPeakUnit.pyc
-${PYSITELIB}/MACS3/Signal/CallPeakUnit.pyo
-${PYSITELIB}/MACS3/Signal/CallPeakUnit.so
-${PYSITELIB}/MACS3/Signal/FixWidthTrack.py
-${PYSITELIB}/MACS3/Signal/FixWidthTrack.pyc
-${PYSITELIB}/MACS3/Signal/FixWidthTrack.pyo
-${PYSITELIB}/MACS3/Signal/FixWidthTrack.so
-${PYSITELIB}/MACS3/Signal/HMMR_EM.py
-${PYSITELIB}/MACS3/Signal/HMMR_EM.pyc
-${PYSITELIB}/MACS3/Signal/HMMR_EM.pyo
-${PYSITELIB}/MACS3/Signal/HMMR_EM.so
-${PYSITELIB}/MACS3/Signal/HMMR_HMM.py
-${PYSITELIB}/MACS3/Signal/HMMR_HMM.pyc
-${PYSITELIB}/MACS3/Signal/HMMR_HMM.pyo
-${PYSITELIB}/MACS3/Signal/HMMR_HMM.so
-${PYSITELIB}/MACS3/Signal/HMMR_Signal_Processing.py
-${PYSITELIB}/MACS3/Signal/HMMR_Signal_Processing.pyc
-${PYSITELIB}/MACS3/Signal/HMMR_Signal_Processing.pyo
-${PYSITELIB}/MACS3/Signal/HMMR_Signal_Processing.so
-${PYSITELIB}/MACS3/Signal/PairedEndTrack.py
-${PYSITELIB}/MACS3/Signal/PairedEndTrack.pyc
-${PYSITELIB}/MACS3/Signal/PairedEndTrack.pyo
-${PYSITELIB}/MACS3/Signal/PairedEndTrack.so
-${PYSITELIB}/MACS3/Signal/PeakDetect.py
-${PYSITELIB}/MACS3/Signal/PeakDetect.pyc
-${PYSITELIB}/MACS3/Signal/PeakDetect.pyo
-${PYSITELIB}/MACS3/Signal/PeakDetect.so
-${PYSITELIB}/MACS3/Signal/PeakModel.py
-${PYSITELIB}/MACS3/Signal/PeakModel.pyc
-${PYSITELIB}/MACS3/Signal/PeakModel.pyo
-${PYSITELIB}/MACS3/Signal/PeakModel.so
-${PYSITELIB}/MACS3/Signal/PeakVariants.py
-${PYSITELIB}/MACS3/Signal/PeakVariants.pyc
-${PYSITELIB}/MACS3/Signal/PeakVariants.pyo
-${PYSITELIB}/MACS3/Signal/PeakVariants.so
-${PYSITELIB}/MACS3/Signal/Pileup.py
-${PYSITELIB}/MACS3/Signal/Pileup.pyc
-${PYSITELIB}/MACS3/Signal/Pileup.pyo
-${PYSITELIB}/MACS3/Signal/Pileup.so
-${PYSITELIB}/MACS3/Signal/PileupV2.py
-${PYSITELIB}/MACS3/Signal/PileupV2.pyc
-${PYSITELIB}/MACS3/Signal/PileupV2.pyo
-${PYSITELIB}/MACS3/Signal/PileupV2.so
-${PYSITELIB}/MACS3/Signal/PosReadsInfo.py
-${PYSITELIB}/MACS3/Signal/PosReadsInfo.pyc
-${PYSITELIB}/MACS3/Signal/PosReadsInfo.pyo
-${PYSITELIB}/MACS3/Signal/PosReadsInfo.so
-${PYSITELIB}/MACS3/Signal/Prob.py
-${PYSITELIB}/MACS3/Signal/Prob.pyc
-${PYSITELIB}/MACS3/Signal/Prob.pyo
-${PYSITELIB}/MACS3/Signal/Prob.so
-${PYSITELIB}/MACS3/Signal/RACollection.pxd
-${PYSITELIB}/MACS3/Signal/RACollection.py
-${PYSITELIB}/MACS3/Signal/RACollection.pyc
-${PYSITELIB}/MACS3/Signal/RACollection.pyo
-${PYSITELIB}/MACS3/Signal/RACollection.so
-${PYSITELIB}/MACS3/Signal/ReadAlignment.py
-${PYSITELIB}/MACS3/Signal/ReadAlignment.pyc
-${PYSITELIB}/MACS3/Signal/ReadAlignment.pyo
-${PYSITELIB}/MACS3/Signal/ReadAlignment.so
-${PYSITELIB}/MACS3/Signal/Region.py
-${PYSITELIB}/MACS3/Signal/Region.pyc
-${PYSITELIB}/MACS3/Signal/Region.pyo
-${PYSITELIB}/MACS3/Signal/Region.so
-${PYSITELIB}/MACS3/Signal/ScoreTrack.py
-${PYSITELIB}/MACS3/Signal/ScoreTrack.pyc
-${PYSITELIB}/MACS3/Signal/ScoreTrack.pyo
-${PYSITELIB}/MACS3/Signal/ScoreTrack.so
-${PYSITELIB}/MACS3/Signal/SignalProcessing.py
-${PYSITELIB}/MACS3/Signal/SignalProcessing.pyc
-${PYSITELIB}/MACS3/Signal/SignalProcessing.pyo
-${PYSITELIB}/MACS3/Signal/SignalProcessing.so
-${PYSITELIB}/MACS3/Signal/UnitigRACollection.py
-${PYSITELIB}/MACS3/Signal/UnitigRACollection.pyc
-${PYSITELIB}/MACS3/Signal/UnitigRACollection.pyo
-${PYSITELIB}/MACS3/Signal/UnitigRACollection.so
-${PYSITELIB}/MACS3/Signal/VariantStat.py
-${PYSITELIB}/MACS3/Signal/VariantStat.pyc
-${PYSITELIB}/MACS3/Signal/VariantStat.pyo
-${PYSITELIB}/MACS3/Signal/VariantStat.so
-${PYSITELIB}/MACS3/Signal/__init__.py
-${PYSITELIB}/MACS3/Signal/__init__.pyc
-${PYSITELIB}/MACS3/Signal/__init__.pyo
-${PYSITELIB}/MACS3/Signal/cPosValCalculation.c
-${PYSITELIB}/MACS3/Signal/cPosValCalculation.h
-${PYSITELIB}/MACS3/Signal/cPosValCalculation.pxd
-${PYSITELIB}/MACS3/Signal/swalign.c
-${PYSITELIB}/MACS3/Signal/swalign.h
-${PYSITELIB}/MACS3/Utilities/Constants.py
-${PYSITELIB}/MACS3/Utilities/Constants.pyc
-${PYSITELIB}/MACS3/Utilities/Constants.pyo
-${PYSITELIB}/MACS3/Utilities/Logger.py
-${PYSITELIB}/MACS3/Utilities/Logger.pyc
-${PYSITELIB}/MACS3/Utilities/Logger.pyo
-${PYSITELIB}/MACS3/Utilities/OptValidator.py
-${PYSITELIB}/MACS3/Utilities/OptValidator.pyc
-${PYSITELIB}/MACS3/Utilities/OptValidator.pyo
-${PYSITELIB}/MACS3/Utilities/__init__.py
-${PYSITELIB}/MACS3/Utilities/__init__.pyc
-${PYSITELIB}/MACS3/Utilities/__init__.pyo
-${PYSITELIB}/MACS3/__init__.py
-${PYSITELIB}/MACS3/__init__.pyc
-${PYSITELIB}/MACS3/__init__.pyo
-${PYSITELIB}/MACS3/fermi-lite/bfc.c
-${PYSITELIB}/MACS3/fermi-lite/bseq.c
-${PYSITELIB}/MACS3/fermi-lite/bubble.c
-${PYSITELIB}/MACS3/fermi-lite/example.c
-${PYSITELIB}/MACS3/fermi-lite/fml.h
-${PYSITELIB}/MACS3/fermi-lite/htab.c
-${PYSITELIB}/MACS3/fermi-lite/htab.h
-${PYSITELIB}/MACS3/fermi-lite/internal.h
-${PYSITELIB}/MACS3/fermi-lite/khash.h
-${PYSITELIB}/MACS3/fermi-lite/kmer.h
-${PYSITELIB}/MACS3/fermi-lite/kseq.h
-${PYSITELIB}/MACS3/fermi-lite/ksort.h
-${PYSITELIB}/MACS3/fermi-lite/kstring.h
-${PYSITELIB}/MACS3/fermi-lite/ksw.c
-${PYSITELIB}/MACS3/fermi-lite/ksw.h
-${PYSITELIB}/MACS3/fermi-lite/kthread.c
-${PYSITELIB}/MACS3/fermi-lite/kvec.h
-${PYSITELIB}/MACS3/fermi-lite/mag.c
-${PYSITELIB}/MACS3/fermi-lite/mag.h
-${PYSITELIB}/MACS3/fermi-lite/misc.c
-${PYSITELIB}/MACS3/fermi-lite/mrope.c
-${PYSITELIB}/MACS3/fermi-lite/mrope.h
-${PYSITELIB}/MACS3/fermi-lite/rld0.c
-${PYSITELIB}/MACS3/fermi-lite/rld0.h
-${PYSITELIB}/MACS3/fermi-lite/rle.c
-${PYSITELIB}/MACS3/fermi-lite/rle.h
-${PYSITELIB}/MACS3/fermi-lite/rope.c
-${PYSITELIB}/MACS3/fermi-lite/rope.h
-${PYSITELIB}/MACS3/fermi-lite/unitig.c
diff --git a/py-macs3/distinfo b/py-macs3/distinfo
deleted file mode 100644
index da3acb3729..0000000000
--- a/py-macs3/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-BLAKE2s (macs-3.0.3.tar.gz) = 77303126120ce43d4a4342aa7d89d0314e2a10eb7848471052dc63cd46f27445
-SHA512 (macs-3.0.3.tar.gz) = cfd06979e0ebfdf1ec3a332aa946342bb268e0f7fe14b7db94e0d07031f84c5d69f6cebe94c62a353e9a22e447349811339e7fb3c93837534c430d3cd5c32b2a
-Size (macs-3.0.3.tar.gz) = 198064648 bytes
-SHA1 (patch-MACS3_fermi-lite_ksw.c) = 7df96d1d970a3e70c4611bd618d1aa539297dbcc
diff --git a/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c b/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
deleted file mode 100644
index 6b6dd6540b..0000000000
--- a/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# Use SIMDE sse2.h
-
---- MACS3/fermi-lite/ksw.c.orig	2023-12-21 22:20:16.716124047 +0000
-+++ MACS3/fermi-lite/ksw.c
-@@ -28,7 +28,7 @@
- 
- /* I modified this according to https://github.com/lh3/bwa/pull/283/*/
- #ifdef USE_SIMDE
--#include "lib/x86/sse2.h"
-+#include <simde/x86/sse2.h>
- #else
- #include <emmintrin.h>
- #endif
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