CVS commit: pkgsrc/biology

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology
From: "Adam Ciarcinski" <adam%netbsd.org@localhost>
Date: Tue, 15 Apr 2025 13:03:39 +0000

Module Name:    pkgsrc
Committed By:   adam
Date:           Tue Apr 15 13:03:39 UTC 2025

Modified Files:
        pkgsrc/biology/py-biopython: Makefile PLIST
        pkgsrc/biology/py-cutadapt: Makefile PLIST
        pkgsrc/biology/py-macs2: Makefile PLIST
        pkgsrc/biology/py-macs3: Makefile PLIST
        pkgsrc/biology/py-multiqc: Makefile PLIST

Log Message:
Fix PLIST after py-setuptools update; bump depends and revision


To generate a diff of this commit:
cvs rdiff -u -r1.15 -r1.16 pkgsrc/biology/py-biopython/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/py-biopython/PLIST
cvs rdiff -u -r1.16 -r1.17 pkgsrc/biology/py-cutadapt/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/py-cutadapt/PLIST
cvs rdiff -u -r1.11 -r1.12 pkgsrc/biology/py-macs2/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/py-macs2/PLIST
cvs rdiff -u -r1.10 -r1.11 pkgsrc/biology/py-macs3/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/py-macs3/PLIST
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/py-multiqc/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/py-multiqc/PLIST

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-biopython/Makefile
diff -u pkgsrc/biology/py-biopython/Makefile:1.15 pkgsrc/biology/py-biopython/Makefile:1.16
--- pkgsrc/biology/py-biopython/Makefile:1.15   Mon Feb 10 13:08:29 2025
+++ pkgsrc/biology/py-biopython/Makefile        Tue Apr 15 13:03:38 2025
@@ -1,7 +1,8 @@
-# $NetBSD: Makefile,v 1.15 2025/02/10 13:08:29 adam Exp $
+# $NetBSD: Makefile,v 1.16 2025/04/15 13:03:38 adam Exp $
 
 DISTNAME=      biopython-1.85
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
+PKGREVISION=   1
 CATEGORIES=    biology python
 MASTER_SITES=  http://biopython.org/DIST/
 
@@ -10,7 +11,7 @@ HOMEPAGE=     https://biopython.org/
 COMMENT=       Python libraries for computational molecular biology
 LICENSE=       biopython
 
-TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools-[0-9]*:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=78:../../devel/py-setuptools
 
 .include "../../lang/python/wheel.mk"
 .include "../../math/py-numpy/buildlink3.mk"

Index: pkgsrc/biology/py-biopython/PLIST
diff -u pkgsrc/biology/py-biopython/PLIST:1.4 pkgsrc/biology/py-biopython/PLIST:1.5
--- pkgsrc/biology/py-biopython/PLIST:1.4       Mon Feb 10 13:08:29 2025
+++ pkgsrc/biology/py-biopython/PLIST   Tue Apr 15 13:03:38 2025
@@ -1,9 +1,9 @@
-@comment $NetBSD: PLIST,v 1.4 2025/02/10 13:08:29 adam Exp $
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.rst
+@comment $NetBSD: PLIST,v 1.5 2025/04/15 13:03:38 adam Exp $
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
 ${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE.rst
 ${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/Bio/Affy/CelFile.py
 ${PYSITELIB}/Bio/Affy/CelFile.pyc

Index: pkgsrc/biology/py-cutadapt/Makefile
diff -u pkgsrc/biology/py-cutadapt/Makefile:1.16 pkgsrc/biology/py-cutadapt/Makefile:1.17
--- pkgsrc/biology/py-cutadapt/Makefile:1.16    Mon Nov 11 07:27:52 2024
+++ pkgsrc/biology/py-cutadapt/Makefile Tue Apr 15 13:03:38 2025
@@ -1,7 +1,8 @@
-# $NetBSD: Makefile,v 1.16 2024/11/11 07:27:52 wiz Exp $
+# $NetBSD: Makefile,v 1.17 2025/04/15 13:03:38 adam Exp $
 
 DISTNAME=      cutadapt-4.7
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
+PKGREVISION=   1
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=c/cutadapt/}
 
@@ -10,17 +11,13 @@ HOMEPAGE=   https://cutadapt.readthedocs.i
 COMMENT=       Find and remove adapter sequences, primers, poly-A tails, etc
 LICENSE=       mit
 
-TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools-[0-9]*:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=78:../../devel/py-setuptools
 TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools_scm-[0-9]*:../../devel/py-setuptools_scm
 # needed for python 3.11 as of cutadapt 3.5 release
 TOOL_DEPENDS+= ${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
 DEPENDS+=      ${PYPKGPREFIX}-xopen>=1.6.0:../../devel/py-xopen
 DEPENDS+=      ${PYPKGPREFIX}-dnaio>=0.10.0:../../biology/py-dnaio
 
-PYTHON_VERSIONS_INCOMPATIBLE=  27 # py-xopen
-
-USE_PKG_RESOURCES=     yes
-
 PYTHON_SELF_CONFLICT=  yes
 
 .include "../../lang/python/wheel.mk"

Index: pkgsrc/biology/py-cutadapt/PLIST
diff -u pkgsrc/biology/py-cutadapt/PLIST:1.5 pkgsrc/biology/py-cutadapt/PLIST:1.6
--- pkgsrc/biology/py-cutadapt/PLIST:1.5        Sat Mar 16 13:46:42 2024
+++ pkgsrc/biology/py-cutadapt/PLIST    Tue Apr 15 13:03:38 2025
@@ -1,10 +1,10 @@
-@comment $NetBSD: PLIST,v 1.5 2024/03/16 13:46:42 bacon Exp $
+@comment $NetBSD: PLIST,v 1.6 2025/04/15 13:03:38 adam Exp $
 bin/cutadapt
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
 ${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
 ${PYSITELIB}/${WHEEL_INFODIR}/entry_points.txt
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE
 ${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/cutadapt/__init__.py
 ${PYSITELIB}/cutadapt/__init__.pyc

Index: pkgsrc/biology/py-macs2/Makefile
diff -u pkgsrc/biology/py-macs2/Makefile:1.11 pkgsrc/biology/py-macs2/Makefile:1.12
--- pkgsrc/biology/py-macs2/Makefile:1.11       Wed Mar  5 09:19:00 2025
+++ pkgsrc/biology/py-macs2/Makefile    Tue Apr 15 13:03:39 2025
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.11 2025/03/05 09:19:00 wiz Exp $
+# $NetBSD: Makefile,v 1.12 2025/04/15 13:03:39 adam Exp $
 
 DISTNAME=      MACS2-${PKGVERSION_NOREV}
 PKGNAME=       ${PYPKGPREFIX}-macs2-2.2.9.1
-PKGREVISION=   1
+PKGREVISION=   2
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=taoliu/}
 GITHUB_PROJECT=        MACS
@@ -14,7 +14,7 @@ COMMENT=      Algorithm for identifying trans
 LICENSE=       modified-bsd
 
 TOOL_DEPENDS+= ${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
-TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=75.8.2:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=78:../../devel/py-setuptools
 
 CYTHONIZE=     ${PREFIX}/bin/cythonize-${PYVERSSUFFIX}
 

Index: pkgsrc/biology/py-macs2/PLIST
diff -u pkgsrc/biology/py-macs2/PLIST:1.3 pkgsrc/biology/py-macs2/PLIST:1.4
--- pkgsrc/biology/py-macs2/PLIST:1.3   Sat Dec 23 16:15:02 2023
+++ pkgsrc/biology/py-macs2/PLIST       Tue Apr 15 13:03:39 2025
@@ -1,9 +1,9 @@
-@comment $NetBSD: PLIST,v 1.3 2023/12/23 16:15:02 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2025/04/15 13:03:39 adam Exp $
 bin/macs2
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
 ${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE
 ${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/MACS2/Constants.py
 ${PYSITELIB}/MACS2/Constants.pyc

Index: pkgsrc/biology/py-macs3/Makefile
diff -u pkgsrc/biology/py-macs3/Makefile:1.10 pkgsrc/biology/py-macs3/Makefile:1.11
--- pkgsrc/biology/py-macs3/Makefile:1.10       Wed Mar  5 09:28:50 2025
+++ pkgsrc/biology/py-macs3/Makefile    Tue Apr 15 13:03:39 2025
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.10 2025/03/05 09:28:50 wiz Exp $
+# $NetBSD: Makefile,v 1.11 2025/04/15 13:03:39 adam Exp $
 
 DISTNAME=      macs-3.0.2
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME:S/macs/macs3/}
-PKGREVISION=   1
+PKGREVISION=   2
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=macs3-project/}
 GITHUB_PROJECT=        MACS
@@ -13,7 +13,7 @@ HOMEPAGE=     https://github.com/macs3-proje
 COMMENT=       Peak caller aimed at transcription factor binding sites
 LICENSE=       modified-bsd
 
-TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=75.8.2:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=78:../../devel/py-setuptools
 DEPENDS+=      ${PYPKGPREFIX}-scipy>=1.11.1:../../math/py-scipy
 # cykhash>=2.0,<3.0
 DEPENDS+=      ${PYPKGPREFIX}-cykhash>=2.0:../../devel/py-cykhash

Index: pkgsrc/biology/py-macs3/PLIST
diff -u pkgsrc/biology/py-macs3/PLIST:1.4 pkgsrc/biology/py-macs3/PLIST:1.5
--- pkgsrc/biology/py-macs3/PLIST:1.4   Wed Mar  5 09:28:50 2025
+++ pkgsrc/biology/py-macs3/PLIST       Tue Apr 15 13:03:39 2025
@@ -1,5 +1,10 @@
-@comment $NetBSD: PLIST,v 1.4 2025/03/05 09:28:50 wiz Exp $
+@comment $NetBSD: PLIST,v 1.5 2025/04/15 13:03:39 adam Exp $
 bin/macs3
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/MACS3/Commands/__init__.py
 ${PYSITELIB}/MACS3/Commands/__init__.pyc
 ${PYSITELIB}/MACS3/Commands/__init__.pyo
@@ -97,8 +102,3 @@ ${PYSITELIB}/MACS3/Utilities/__init__.py
 ${PYSITELIB}/MACS3/__init__.py
 ${PYSITELIB}/MACS3/__init__.pyc
 ${PYSITELIB}/MACS3/__init__.pyo
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
-${PYSITELIB}/${WHEEL_INFODIR}/METADATA
-${PYSITELIB}/${WHEEL_INFODIR}/RECORD
-${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
-${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt

Index: pkgsrc/biology/py-multiqc/Makefile
diff -u pkgsrc/biology/py-multiqc/Makefile:1.8 pkgsrc/biology/py-multiqc/Makefile:1.9
--- pkgsrc/biology/py-multiqc/Makefile:1.8      Thu Mar  6 01:19:04 2025
+++ pkgsrc/biology/py-multiqc/Makefile  Tue Apr 15 13:03:39 2025
@@ -1,7 +1,8 @@
-# $NetBSD: Makefile,v 1.8 2025/03/06 01:19:04 bacon Exp $
+# $NetBSD: Makefile,v 1.9 2025/04/15 13:03:39 adam Exp $
 
 DISTNAME=      multiqc-1.25.2
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
+PKGREVISION=   1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_PYPI:=m/multiqc/}
 
@@ -10,7 +11,7 @@ HOMEPAGE=     https://pypi.python.org/pypi/m
 COMMENT=       Aggregate bioinformatics analysis reports across samples and tools
 LICENSE=       gnu-gpl-v3
 
-TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools-[0-9]*:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=78:../../devel/py-setuptools
 # Use either py-kaleido (not in ports yet) or py-orca + py-psutil
 # kaleido dep choreographer only works with chrome as of 2024-11-24
 DEPENDS+=      ${PYPKGPREFIX}-humanize-[0-9]*:../../textproc/py-humanize
@@ -34,6 +35,8 @@ DEPENDS+=     ${PYPKGPREFIX}-Pillow>=10:../.
 DEPENDS+=      ${PYPKGPREFIX}-click-[0-9]*:../../devel/py-click
 DEPENDS+=      ${PYPKGPREFIX}-natsort-[0-9]*:../../textproc/py-natsort
 
+PYTHON_SELF_CONFLICT=  yes
+
 # test status as of 1.25.2
 # 44 failed, 46 passed, 357 errors
 

Index: pkgsrc/biology/py-multiqc/PLIST
diff -u pkgsrc/biology/py-multiqc/PLIST:1.2 pkgsrc/biology/py-multiqc/PLIST:1.3
--- pkgsrc/biology/py-multiqc/PLIST:1.2 Fri Nov 22 21:41:42 2024
+++ pkgsrc/biology/py-multiqc/PLIST     Tue Apr 15 13:03:39 2025
@@ -1,10 +1,10 @@
-@comment $NetBSD: PLIST,v 1.2 2024/11/22 21:41:42 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2025/04/15 13:03:39 adam Exp $
 bin/multiqc
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
 ${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
 ${PYSITELIB}/${WHEEL_INFODIR}/entry_points.txt
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE
 ${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/multiqc/__init__.py
 ${PYSITELIB}/multiqc/__init__.pyc

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