git: 1f8de6517b90 - main - biology/py-goatools: Fix build with python 3.12

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=1f8de6517b9098868ffda79d622be2ee84e14b15

commit 1f8de6517b9098868ffda79d622be2ee84e14b15
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-07-04 00:36:16 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-07-04 00:36:51 +0000

    biology/py-goatools: Fix build with python 3.12
    
    Reported by:    pkg-fallout
---
 biology/py-goatools/Makefile                  |  8 +++++---
 biology/py-goatools/files/patch-versioneer.py | 14 ++++++++++++++
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/biology/py-goatools/Makefile b/biology/py-goatools/Makefile
index 1e3f9a2d95cf..bb18c6ca9aca 100644
--- a/biology/py-goatools/Makefile
+++ b/biology/py-goatools/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	goatools
 DISTVERSION=	1.1.6
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -14,7 +14,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 
 # xlrd should be == 1.2.0
 RUN_DEPENDS=	${PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
+		${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}xlsxwriter>0:textproc/py-xlsxwriter@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}statsmodels>0:math/py-statsmodels@${PY_FLAVOR} \
@@ -25,7 +25,9 @@ RUN_DEPENDS=	${PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pygraphviz>0:graphics/py-pygraphviz@${PY_FLAVOR} \
 		wget>0:ftp/wget
 
-USES=		python
+USES=		python:3.6+
 USE_PYTHON=	autoplist distutils
 
+NO_ARCH=	yes
+
 .include <bsd.port.mk>
diff --git a/biology/py-goatools/files/patch-versioneer.py b/biology/py-goatools/files/patch-versioneer.py
new file mode 100644
index 000000000000..b9c6f93df5a5
--- /dev/null
+++ b/biology/py-goatools/files/patch-versioneer.py
@@ -0,0 +1,14 @@
+--- versioneer.py.orig	2021-05-29 06:24:51 UTC
++++ versioneer.py
+@@ -339,9 +339,9 @@ def get_config_from_root(root):
+     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
+     # the top of versioneer.py for instructions on writing your setup.cfg .
+     setup_cfg = os.path.join(root, "setup.cfg")
+-    parser = configparser.SafeConfigParser()
++    parser = configparser.ConfigParser()
+     with open(setup_cfg, "r") as f:
+-        parser.readfp(f)
++        parser.read_file(f)
+     VCS = parser.get("versioneer", "VCS")  # mandatory
+ 
+     def get(parser, name):