git: dabbbe357da3 - main - science/py-pyteomics: Update to 5.0.1

The branch main has been updated by sunpoet:

URL: https://cgit.FreeBSD.org/ports/commit/?id=dabbbe357da3d990b593efc790929922bb85be0a

commit dabbbe357da3d990b593efc790929922bb85be0a
Author:     Po-Chuan Hsieh <sunpoet@FreeBSD.org>
AuthorDate: 2026-09-29 19:00:37 +0000
Commit:     Po-Chuan Hsieh <sunpoet@FreeBSD.org>
CommitDate: 2026-09-29 19:25:09 +0000

    science/py-pyteomics: Update to 5.0.1
    
    - Add PROFORMA option
    
    Changes:        https://github.com/levitsky/pyteomics/releases
                    https://pyteomics.readthedocs.io/en/latest/changelog.html
---
 science/py-pyteomics/Makefile                   | 14 ++++++++------
 science/py-pyteomics/distinfo                   |  6 +++---
 science/py-pyteomics/files/patch-pyproject.toml | 19 +++++++++++++++++++
 3 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/science/py-pyteomics/Makefile b/science/py-pyteomics/Makefile
index 33dda825ce14..fce846fde335 100644
--- a/science/py-pyteomics/Makefile
+++ b/science/py-pyteomics/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	pyteomics
-PORTVERSION=	4.7.5
-PORTREVISION=	5
+PORTVERSION=	5.0.1
 CATEGORIES=	science python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -20,10 +19,11 @@ USE_PYTHON=	autoplist concurrent pep517
 
 NO_ARCH=	yes
 
-OPTIONS_DEFINE=	DF GRAPHICS TDA UNIMOD XML
-OPTIONS_DEFAULT=DF GRAPHICS TDA UNIMOD XML
+OPTIONS_DEFINE=	DF GRAPHICS PROFORMA TDA UNIMOD XML
+OPTIONS_DEFAULT=DF GRAPHICS PROFORMA TDA UNIMOD XML
 DF_DESC=	DataFrame support
 GRAPHICS_DESC=	Graphics support
+PROFORMA_DESC=	Proteoform and Peptidoform Notation support
 TDA_DESC=	Target-decoy approach support
 UNIMOD_DESC=	Unimod database support
 XML_DESC=	XML support
@@ -32,8 +32,10 @@ DF_RUN_DEPENDS=		${PYTHON_PKGNAMEPREFIX}pandas>=0.17,1:math/py-pandas@${PY_FLAVO
 GRAPHICS_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR}
 TDA_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR}
 UNIMOD_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \
-			${PYTHON_PKGNAMEPREFIX}sqlalchemy14>=0:databases/py-sqlalchemy14@${PY_FLAVOR}
+			${PYTHON_PKGNAMEPREFIX}sqlalchemy20>=1.4:databases/py-sqlalchemy20@${PY_FLAVOR}
 XML_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \
-			${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR}
+			${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \
+			${PYTHON_PKGNAMEPREFIX}psims>=0:science/py-psims@${PY_FLAVOR}
+PROFORMA_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}psims>=0.1.42:science/py-psims@${PY_FLAVOR}
 
 .include <bsd.port.mk>
diff --git a/science/py-pyteomics/distinfo b/science/py-pyteomics/distinfo
index 708e6f36b86c..c97454aa98f2 100644
--- a/science/py-pyteomics/distinfo
+++ b/science/py-pyteomics/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1729856288
-SHA256 (pyteomics-4.7.5.tar.gz) = 382aeaa8b921bdd2a7e5b4aa9fe46c6184bb43701205a845b4b861ee3e88f46a
-SIZE (pyteomics-4.7.5.tar.gz) = 236493
+TIMESTAMP = 1790435936
+SHA256 (pyteomics-5.0.1.tar.gz) = 89670f1512caa7fce5a269f3dc8d5b3856ef02f161fd2abc77155adb0bbe4a48
+SIZE (pyteomics-5.0.1.tar.gz) = 275092
diff --git a/science/py-pyteomics/files/patch-pyproject.toml b/science/py-pyteomics/files/patch-pyproject.toml
new file mode 100644
index 000000000000..494e0b86e0ed
--- /dev/null
+++ b/science/py-pyteomics/files/patch-pyproject.toml
@@ -0,0 +1,19 @@
+--- pyproject.toml.orig	2026-07-22 12:59:45 UTC
++++ pyproject.toml
+@@ -13,8 +13,7 @@ requires-python = ">= 3.10"
+ ]
+ readme = "README.rst"
+ requires-python = ">= 3.10"
+-license = "Apache-2.0"
+-license-files = ["LICENSE"]
++license = {text = "Apache-2.0"}
+ classifiers = [
+     "Intended Audience :: Science/Research",
+     "Programming Language :: Python :: 3",
+@@ -46,4 +45,4 @@ Documentation = "http://pyteomics.readthedocs.io"
+ "Mailing List" = "https://groups.google.com/group/pyteomics"
+ 
+ [tool.setuptools.dynamic]
+-version = {attr = "pyteomics.version.__version__"}
+\ No newline at end of file
++version = {attr = "pyteomics.version.__version__"}