py-macs3: Update to 3.0.3

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: py-macs3: Update to 3.0.3
From: Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>
Date: Fri, 7 Mar 2025 14:36:35 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Fri Mar 7 08:36:18 2025 -0600
Changeset:	e2a68ddc4e33880303ddefe26d2d24d78963651f

Modified Files:
	py-macs3/Makefile
	py-macs3/PLIST
	py-macs3/distinfo

Log Message:
py-macs3: Update to 3.0.3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e2a68ddc4e33880303ddefe26d2d24d78963651f

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

diffstat:
 py-macs3/Makefile |   2 +-
 py-macs3/PLIST    | 113 ++++++++++++++++++++++++++++++++++++++++++++++++++++--
 py-macs3/distinfo |   6 +--
 3 files changed, 114 insertions(+), 7 deletions(-)

diffs:
diff --git a/py-macs3/Makefile b/py-macs3/Makefile
index df239eeb64..9441a620a0 100644
--- a/py-macs3/Makefile
+++ b/py-macs3/Makefile
@@ -1,7 +1,7 @@
 # $NetBSD$
 
 DISTNAME=	macs-${PKGVERSION_NOREV}
-PKGNAME=	${PYPKGPREFIX}-macs3-3.0.2
+PKGNAME=	${PYPKGPREFIX}-macs3-3.0.3
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=macs3-project/}
 GITHUB_PROJECT=	MACS
diff --git a/py-macs3/PLIST b/py-macs3/PLIST
index eb152751d1..3cd9a5d97e 100644
--- a/py-macs3/PLIST
+++ b/py-macs3/PLIST
@@ -32,9 +32,6 @@ ${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/diffpeak_cmd.py
-${PYSITELIB}/MACS3/Commands/diffpeak_cmd.pyc
-${PYSITELIB}/MACS3/Commands/diffpeak_cmd.pyo
 ${PYSITELIB}/MACS3/Commands/filterdup_cmd.py
 ${PYSITELIB}/MACS3/Commands/filterdup_cmd.pyc
 ${PYSITELIB}/MACS3/Commands/filterdup_cmd.pyo
@@ -53,40 +50,121 @@ ${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
@@ -102,3 +180,32 @@ ${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
index bd3229a261..da3acb3729 100644
--- a/py-macs3/distinfo
+++ b/py-macs3/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-BLAKE2s (macs-3.0.2.tar.gz) = 8fdd0e375c0f2cb558f913fea85f384d54cff7e9ec645906b4e9c43c0843ff35
-SHA512 (macs-3.0.2.tar.gz) = 060e0f0f6a0ac8be4db0f0d947d9d784423a1a4bcc63f69abbd3566a4b190ed82d3b0f25f5ce946ea7d9a6fab74a114c108b59cd95ed7048321cd30edf4f4d08
-Size (macs-3.0.2.tar.gz) = 197484503 bytes
+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
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