CVS commit: pkgsrc/biology/py-macs2

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Tue Aug 25 09:26:21 UTC 2026

Modified Files:
        pkgsrc/biology/py-macs2: Makefile distinfo
        pkgsrc/biology/py-macs2/patches: patch-MACS2_IO_CallPeakUnit.pyx

Log Message:
py-macs2: fix build with Cython 3.3.0

Bump PKGREVISION.


To generate a diff of this commit:
cvs rdiff -u -r1.15 -r1.16 pkgsrc/biology/py-macs2/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/py-macs2/distinfo
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx

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-macs2/Makefile
diff -u pkgsrc/biology/py-macs2/Makefile:1.15 pkgsrc/biology/py-macs2/Makefile:1.16
--- pkgsrc/biology/py-macs2/Makefile:1.15       Sun Jun 28 15:41:09 2026
+++ pkgsrc/biology/py-macs2/Makefile    Tue Aug 25 09:26:21 2026
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.15 2026/06/28 15:41:09 wiz Exp $
+# $NetBSD: Makefile,v 1.16 2026/08/25 09:26:21 wiz Exp $
 
 DISTNAME=      MACS2-${PKGVERSION_NOREV}
 PKGNAME=       ${PYPKGPREFIX}-macs2-2.2.9.1
-PKGREVISION=   2
+PKGREVISION=   3
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=taoliu/}
 GITHUB_PROJECT=        MACS

Index: pkgsrc/biology/py-macs2/distinfo
diff -u pkgsrc/biology/py-macs2/distinfo:1.4 pkgsrc/biology/py-macs2/distinfo:1.5
--- pkgsrc/biology/py-macs2/distinfo:1.4        Sat Dec 23 16:15:02 2023
+++ pkgsrc/biology/py-macs2/distinfo    Tue Aug 25 09:26:21 2026
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.4 2023/12/23 16:15:02 bacon Exp $
+$NetBSD: distinfo,v 1.5 2026/08/25 09:26:21 wiz Exp $
 
 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_CallPeakUnit.pyx) = b5fbe662c9f1e0f94a4be3ec9341606a161ea2d5
 SHA1 (patch-MACS2_IO_FixWidthTrack.pyx) = fa5814d2218868c0a317861e9083b9adcda257d6

Index: pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx
diff -u pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx:1.1 pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx:1.2
--- pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx:1.1 Sat Dec 23 16:15:02 2023
+++ pkgsrc/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx     Tue Aug 25 09:26:21 2026
@@ -1,10 +1,10 @@
-$NetBSD: patch-MACS2_IO_CallPeakUnit.pyx,v 1.1 2023/12/23 16:15:02 bacon Exp $
+$NetBSD: patch-MACS2_IO_CallPeakUnit.pyx,v 1.2 2026/08/25 09:26:21 wiz Exp $
 
 # Fix cython 3 error
 
---- MACS2/IO/CallPeakUnit.pyx.orig     2023-12-23 15:31:06.614325825 +0000
+--- MACS2/IO/CallPeakUnit.pyx.orig     2023-07-21 14:25:59.000000000 +0000
 +++ MACS2/IO/CallPeakUnit.pyx
-@@ -197,7 +197,7 @@ cdef wtd_find_summit(chrom, np.ndarray p
+@@ -197,7 +197,7 @@ cdef wtd_find_summit(chrom, np.ndarray plus, np.ndarra
      wtd_list = np.zeros( search_end - search_start + 1, dtype="float32")
      i = 0
      for j in range(search_start, search_end+1):
@@ -13,3 +13,13 @@ $NetBSD: patch-MACS2_IO_CallPeakUnit.pyx
          watson_left += left_forward(watson, j, window_size)
          watson_right += right_forward(watson, j, window_size)
          crick_left += left_forward(crick, j, window_size)
+@@ -1854,7 +1854,8 @@ cdef class CallerFromAlignments:
+             int32_t c, m, i, j, pre_i, pre_j, pos, startpos, endpos
+             np.ndarray plus, minus, rt_plus, rt_minus
+             bytes chrom
+-            set pchrnames, chrnames
++            list pchrnames
++            set chrnames
+             list temp, retval, cpeaks
+             np.ndarray adjusted_summits, passflags
+