git: 4a5074525bbe - main - biology/py-goatools: Update to 1.6.5

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=4a5074525bbe9fa2c82f6394c84f258ccdd4376a

commit 4a5074525bbe9fa2c82f6394c84f258ccdd4376a
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-09-10 17:41:39 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-09-10 17:41:39 +0000

    biology/py-goatools: Update to 1.6.5
    
    Numerous changes since v1.1.6
    Changes: https://github.com/tanghaibao/goatools/commits/main/
    
    Reported by:    Repology
---
 biology/py-goatools/Makefile                  | 27 +++++++++++++++------------
 biology/py-goatools/distinfo                  |  6 +++---
 biology/py-goatools/files/patch-versioneer.py | 14 --------------
 3 files changed, 18 insertions(+), 29 deletions(-)

diff --git a/biology/py-goatools/Makefile b/biology/py-goatools/Makefile
index bb18c6ca9aca..c922c7931587 100644
--- a/biology/py-goatools/Makefile
+++ b/biology/py-goatools/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	goatools
-DISTVERSION=	1.1.6
-PORTREVISION=	6
+DISTVERSION=	1.6.5
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -12,21 +11,25 @@ WWW=		https://github.com/tanghaibao/goatools/
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-# xlrd should be == 1.2.0
-RUN_DEPENDS=	${PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
+BUILD_DEPENDS=	${PY_SETUPTOOLS} \
+		${PYTHON_PKGNAMEPREFIX}setuptools-scm>=6.0:devel/py-setuptools-scm@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}setuptools_scm_git_archive>0:devel/py-setuptools_scm_git_archive@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}ftpretty>0:ftp/py-ftpretty@${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} \
-		${PYTHON_PKGNAMEPREFIX}xlrd>0:textproc/py-xlrd@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}docopt>0:devel/py-docopt@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}openpyxl>0:textproc/py-openpyxl@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pydot>0:graphics/py-pydot@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}pygraphviz>0:graphics/py-pygraphviz@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}rich>=0:textproc/py-rich@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}statsmodels>=0.13.0:math/py-statsmodels@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}statsmodels>0:math/py-statsmodels@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}xlsxwriter>0:textproc/py-xlsxwriter@${PY_FLAVOR} \
 		wget>0:ftp/wget
 
-USES=		python:3.6+
-USE_PYTHON=	autoplist distutils
+USES=		python
+USE_PYTHON=	autoplist pep517
 
 NO_ARCH=	yes
 
diff --git a/biology/py-goatools/distinfo b/biology/py-goatools/distinfo
index cdadbfe66214..a717698406b9 100644
--- a/biology/py-goatools/distinfo
+++ b/biology/py-goatools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1625181597
-SHA256 (goatools-1.1.6.tar.gz) = b631a6a803818673ac815ed5f1e7158d1bd98a3ce5c93b64961dc73bdea56bca
-SIZE (goatools-1.1.6.tar.gz) = 15098351
+TIMESTAMP = 1789042575
+SHA256 (goatools-1.6.5.tar.gz) = 0d799706dc3ae4480feda25f411f8e9b2741c0d8ea7ad73af0b05730198a4be1
+SIZE (goatools-1.6.5.tar.gz) = 17760712
diff --git a/biology/py-goatools/files/patch-versioneer.py b/biology/py-goatools/files/patch-versioneer.py
deleted file mode 100644
index b9c6f93df5a5..000000000000
--- a/biology/py-goatools/files/patch-versioneer.py
+++ /dev/null
@@ -1,14 +0,0 @@
---- 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):