Wed Feb 28 13:38:48 2024 UTC (109d)
biology/py-macs3: Update to 3.0.1

Minor bug fix release
Changes: https://github.com/macs3-project/MACS/releases


(bacon)
diff -r1.3 -r1.4 pkgsrc/biology/py-macs3/Makefile
diff -r1.1 -r1.2 pkgsrc/biology/py-macs3/PLIST
diff -r1.1 -r1.2 pkgsrc/biology/py-macs3/distinfo
diff -r1.1 -r1.2 pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
cvs diff -r1.3 -r1.4 pkgsrc/biology/py-macs3/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/py-macs3/Makefile 2024/01/12 09:51:58 1.3
+++ pkgsrc/biology/py-macs3/Makefile 2024/02/28 13:38:48 1.4
@@ -1,17 +1,17 @@ @@ -1,17 +1,17 @@
1# $NetBSD: Makefile,v 1.3 2024/01/12 09:51:58 jperkin Exp $ 1# $NetBSD: Makefile,v 1.4 2024/02/28 13:38:48 bacon Exp $
2 2
3DISTNAME= macs-${PKGVERSION_NOREV} 3DISTNAME= macs-${PKGVERSION_NOREV}
4PKGNAME= ${PYPKGPREFIX}-macs3-3.0.0 4PKGNAME= ${PYPKGPREFIX}-macs3-3.0.1
5CATEGORIES= biology 5CATEGORIES= biology
6MASTER_SITES= ${MASTER_SITE_GITHUB:=macs3-project/} 6MASTER_SITES= ${MASTER_SITE_GITHUB:=macs3-project/}
7GITHUB_PROJECT= MACS 7GITHUB_PROJECT= MACS
8GITHUB_TAG= v${PKGVERSION_NOREV} 8GITHUB_TAG= v${PKGVERSION_NOREV}
9 9
10MAINTAINER= bacon@NetBSD.org 10MAINTAINER= bacon@NetBSD.org
11HOMEPAGE= https://github.com/macs3-project/MACS 11HOMEPAGE= https://github.com/macs3-project/MACS
12COMMENT= Peak caller aimed at transcription factor binding sites 12COMMENT= Peak caller aimed at transcription factor binding sites
13LICENSE= modified-bsd 13LICENSE= modified-bsd
14 14
15TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=0:../../devel/py-setuptools 15TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=0:../../devel/py-setuptools
16TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel>=0:../../devel/py-wheel 16TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel>=0:../../devel/py-wheel
17DEPENDS+= ${PYPKGPREFIX}-hmmlearn>=0.3:../../math/py-hmmlearn 17DEPENDS+= ${PYPKGPREFIX}-hmmlearn>=0.3:../../math/py-hmmlearn
cvs diff -r1.1 -r1.2 pkgsrc/biology/py-macs3/PLIST (expand / switch to unified diff)

--- pkgsrc/biology/py-macs3/PLIST 2024/01/10 15:17:33 1.1
+++ pkgsrc/biology/py-macs3/PLIST 2024/02/28 13:38:48 1.2
@@ -1,14 +1,14 @@ @@ -1,14 +1,14 @@
1@comment $NetBSD: PLIST,v 1.1 2024/01/10 15:17:33 bacon Exp $ 1@comment $NetBSD: PLIST,v 1.2 2024/02/28 13:38:48 bacon Exp $
2bin/macs3 2bin/macs3
3${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/LICENSE 3${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/LICENSE
4${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/METADATA 4${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/METADATA
5${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/RECORD 5${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/RECORD
6${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/WHEEL 6${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/WHEEL
7${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/top_level.txt 7${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/top_level.txt
8${PYSITELIB}/MACS3/Commands/__init__.py 8${PYSITELIB}/MACS3/Commands/__init__.py
9${PYSITELIB}/MACS3/Commands/__init__.pyc 9${PYSITELIB}/MACS3/Commands/__init__.pyc
10${PYSITELIB}/MACS3/Commands/__init__.pyo 10${PYSITELIB}/MACS3/Commands/__init__.pyo
11${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.py 11${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.py
12${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyc 12${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyc
13${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyo 13${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyo
14${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.py 14${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.py
cvs diff -r1.1 -r1.2 pkgsrc/biology/py-macs3/distinfo (expand / switch to unified diff)

--- pkgsrc/biology/py-macs3/distinfo 2024/01/10 15:17:33 1.1
+++ pkgsrc/biology/py-macs3/distinfo 2024/02/28 13:38:48 1.2
@@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
1$NetBSD: distinfo,v 1.1 2024/01/10 15:17:33 bacon Exp $ 1$NetBSD: distinfo,v 1.2 2024/02/28 13:38:48 bacon Exp $
2 2
3BLAKE2s (macs-3.0.0.tar.gz) = 6a28a732c0cef04e57c27f1679f372b40a48dc1aba23d8daa0555c63e02aa1bd 3BLAKE2s (macs-3.0.1.tar.gz) = 58e3a406621a6f71bb180672b17d008b8ca26bb14476d9bdacf42a47fa93b295
4SHA512 (macs-3.0.0.tar.gz) = 44daa10901cea110ae6d0a5749e9696fa64883151b11af6b13c8d4ae589bc3207048d0de4420308a922a96b5dd542b694897ceabaac32becc07aef0061ee2257 4SHA512 (macs-3.0.1.tar.gz) = fdbc91722266b0f6f03021c82385672bec1e07fd9510f25270c02bd3ba839352d2ffcb72496e61e334573272999a96978a91c250c5b2da168eb7f43993721125
5Size (macs-3.0.0.tar.gz) = 197389439 bytes 5Size (macs-3.0.1.tar.gz) = 197400439 bytes
6SHA1 (patch-MACS3_fermi-lite_ksw.c) = 7df96d1d970a3e70c4611bd618d1aa539297dbcc 6SHA1 (patch-MACS3_fermi-lite_ksw.c) = 7df96d1d970a3e70c4611bd618d1aa539297dbcc
cvs diff -r1.1 -r1.2 pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c (expand / switch to unified diff)

--- pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c 2024/01/10 15:17:33 1.1
+++ pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c 2024/02/28 13:38:48 1.2
@@ -1,14 +1,14 @@ @@ -1,14 +1,14 @@
1$NetBSD: patch-MACS3_fermi-lite_ksw.c,v 1.1 2024/01/10 15:17:33 bacon Exp $ 1$NetBSD: patch-MACS3_fermi-lite_ksw.c,v 1.2 2024/02/28 13:38:48 bacon Exp $
2 2
3# Use SIMDE sse2.h 3# Use SIMDE sse2.h
4 4
5--- MACS3/fermi-lite/ksw.c.orig 2023-12-21 22:20:16.716124047 +0000 5--- MACS3/fermi-lite/ksw.c.orig 2023-12-21 22:20:16.716124047 +0000
6+++ MACS3/fermi-lite/ksw.c 6+++ MACS3/fermi-lite/ksw.c
7@@ -28,7 +28,7 @@ 7@@ -28,7 +28,7 @@
8  8
9 /* I modified this according to https://github.com/lh3/bwa/pull/283/*/ 9 /* I modified this according to https://github.com/lh3/bwa/pull/283/*/
10 #ifdef USE_SIMDE 10 #ifdef USE_SIMDE
11-#include "lib/x86/sse2.h" 11-#include "lib/x86/sse2.h"
12+#include <simde/x86/sse2.h> 12+#include <simde/x86/sse2.h>
13 #else 13 #else
14 #include <emmintrin.h> 14 #include <emmintrin.h>