CVS commit: pkgsrc/biology/py-macs3

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Mon Oct 14 22:21:16 UTC 2024

Modified Files:
        pkgsrc/biology/py-macs3: Makefile PLIST distinfo
        pkgsrc/biology/py-macs3/patches: patch-MACS3_fermi-lite_ksw.c

Log Message:
biology/py-macs3: Update to 3.0.2

Some minor enhancements and improved docs
Changes: https://github.com/macs3-project/MACS/releases

Reported by:    portscout


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/py-macs3/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/py-macs3/PLIST \
    pkgsrc/biology/py-macs3/distinfo
cvs rdiff -u -r1.2 -r1.3 \
    pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c

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-macs3/Makefile
diff -u pkgsrc/biology/py-macs3/Makefile:1.6 pkgsrc/biology/py-macs3/Makefile:1.7
--- pkgsrc/biology/py-macs3/Makefile:1.6        Mon Oct 14 06:45:32 2024
+++ pkgsrc/biology/py-macs3/Makefile    Mon Oct 14 22:21:16 2024
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.6 2024/10/14 06:45:32 wiz Exp $
+# $NetBSD: Makefile,v 1.7 2024/10/14 22:21:16 bacon Exp $
 
 DISTNAME=      macs-${PKGVERSION_NOREV}
-PKGNAME=       ${PYPKGPREFIX}-macs3-3.0.1
+PKGNAME=       ${PYPKGPREFIX}-macs3-3.0.2
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=macs3-project/}
 GITHUB_PROJECT=        MACS
@@ -14,15 +14,17 @@ LICENSE=    modified-bsd
 
 TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=0:../../devel/py-setuptools
 TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel>=0:../../devel/py-wheel
-DEPENDS+=      ${PYPKGPREFIX}-hmmlearn>=0.3:../../math/py-hmmlearn
+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*
 
-PYTHON_VERSIONS_INCOMPATIBLE=  39
+PYTHON_VERSIONS_INCOMPATIBLE=  27      # Does not build
 
 do-test: install
        ${RM} -rf ${WRKSRC}/temp

Index: pkgsrc/biology/py-macs3/PLIST
diff -u pkgsrc/biology/py-macs3/PLIST:1.2 pkgsrc/biology/py-macs3/PLIST:1.3
--- pkgsrc/biology/py-macs3/PLIST:1.2   Wed Feb 28 13:38:48 2024
+++ pkgsrc/biology/py-macs3/PLIST       Mon Oct 14 22:21:16 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2024/02/28 13:38:48 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2024/10/14 22:21:16 bacon Exp $
 bin/macs3
 ${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/LICENSE
 ${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/METADATA
Index: pkgsrc/biology/py-macs3/distinfo
diff -u pkgsrc/biology/py-macs3/distinfo:1.2 pkgsrc/biology/py-macs3/distinfo:1.3
--- pkgsrc/biology/py-macs3/distinfo:1.2        Wed Feb 28 13:38:48 2024
+++ pkgsrc/biology/py-macs3/distinfo    Mon Oct 14 22:21:16 2024
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.2 2024/02/28 13:38:48 bacon Exp $
+$NetBSD: distinfo,v 1.3 2024/10/14 22:21:16 bacon Exp $
 
-BLAKE2s (macs-3.0.1.tar.gz) = 58e3a406621a6f71bb180672b17d008b8ca26bb14476d9bdacf42a47fa93b295
-SHA512 (macs-3.0.1.tar.gz) = fdbc91722266b0f6f03021c82385672bec1e07fd9510f25270c02bd3ba839352d2ffcb72496e61e334573272999a96978a91c250c5b2da168eb7f43993721125
-Size (macs-3.0.1.tar.gz) = 197400439 bytes
+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
 SHA1 (patch-MACS3_fermi-lite_ksw.c) = 7df96d1d970a3e70c4611bd618d1aa539297dbcc

Index: pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
diff -u pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c:1.2 pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c:1.3
--- pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c:1.2    Wed Feb 28 13:38:48 2024
+++ pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c        Mon Oct 14 22:21:16 2024
@@ -1,4 +1,4 @@
-$NetBSD: patch-MACS3_fermi-lite_ksw.c,v 1.2 2024/02/28 13:38:48 bacon Exp $
+$NetBSD: patch-MACS3_fermi-lite_ksw.c,v 1.3 2024/10/14 22:21:16 bacon Exp $
 
 # Use SIMDE sse2.h