git: 3f037ab2522e - main - biology/py-multiqc: Update to 1.25.1

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=3f037ab2522e5e8a0145e5b45d48ac757538f7f0

commit 3f037ab2522e5e8a0145e5b45d48ac757538f7f0
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-11-16 01:27:36 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2024-11-16 01:28:59 +0000

    biology/py-multiqc: Update to 1.25.1
    
    Numerous fixes and enhancements since 1.15
    (Update blocked by py-plotly)
    Changes: https://github.com/MultiQC/MultiQC/releases
---
 biology/py-multiqc/Makefile                       | 31 +++++++++++++----------
 biology/py-multiqc/distinfo                       |  6 ++---
 biology/py-multiqc/files/patch-multiqc_multiqc.py | 13 +++++-----
 3 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/biology/py-multiqc/Makefile b/biology/py-multiqc/Makefile
index 4be09d193455..6a0743be7566 100644
--- a/biology/py-multiqc/Makefile
+++ b/biology/py-multiqc/Makefile
@@ -1,37 +1,42 @@
 PORTNAME=	multiqc
-DISTVERSION=	1.15
-PORTREVISION=	1
+DISTVERSION=	1.25.1
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Aggregate bioinformatics analysis reports across samples and tools
-WWW=		https://pypi.python.org/pypi/multiqc
+WWW=		https://github.com/MultiQC/MultiQC
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+# Use either py-kaleido (not in ports yet) or py-orca + py-psutil
 RUN_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}humanize>0:devel/py-humanize@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}importlib-metadata>0:devel/py-importlib-metadata@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}orca>0:devel/py-orca@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}psutil>0:sysutils/py-psutil@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pydantic2>=2.7.0:devel/py-pydantic2@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}typeguard>0:devel/py-typeguard@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}Jinja2>=3.0.0:devel/py-Jinja2@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}rich-click>0:devel/py-rich-click@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}future>0.14.0:devel/py-future@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}coloredlogs>0:devel/py-coloredlogs@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}matplotlib>=2.1.1:math/py-matplotlib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}plotly>=5.18:graphics/py-plotly@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}markdown>0:textproc/py-markdown@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}rich>0:textproc/py-rich@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}rich>=10:textproc/py-rich@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pyyaml>=4:devel/py-pyyaml@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}simplejson>0:devel/py-simplejson@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}Jinja2>=2.9:devel/py-Jinja2@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}lzstring>0:archivers/py-lzstring@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}spectra>=0.0.10:graphics/py-spectra@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}colormath>0:math/py-colormath@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}kiwisolver>0:math/py-kiwisolver@${PY_FLAVOR}
+		${PYTHON_PKGNAMEPREFIX}pillow>=10:graphics/py-pillow@${PY_FLAVOR}
 
-USES=		python
+USES=		python shebangfix
 USE_PYTHON=	autoplist concurrent distutils
 
+SHEBANG_FILES=	multiqc/utils/config.py
+
 NO_ARCH=	yes
 
 post-patch:
diff --git a/biology/py-multiqc/distinfo b/biology/py-multiqc/distinfo
index 884857c19c9b..d7a884b19de5 100644
--- a/biology/py-multiqc/distinfo
+++ b/biology/py-multiqc/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1691243629
-SHA256 (multiqc-1.15.tar.gz) = ce5359a12226cf4ce372c6fdad142cfe2ae7501ffa97ac7aab544ced4db5ea3c
-SIZE (multiqc-1.15.tar.gz) = 1077075
+TIMESTAMP = 1731443994
+SHA256 (multiqc-1.25.1.tar.gz) = eaf6bb02659cbf9aa54399ee72ded143178be1a95ae84641fbe7a4555876551c
+SIZE (multiqc-1.25.1.tar.gz) = 4322149
diff --git a/biology/py-multiqc/files/patch-multiqc_multiqc.py b/biology/py-multiqc/files/patch-multiqc_multiqc.py
index 2353f5150e0c..755a01a5fba4 100644
--- a/biology/py-multiqc/files/patch-multiqc_multiqc.py
+++ b/biology/py-multiqc/files/patch-multiqc_multiqc.py
@@ -1,10 +1,9 @@
---- multiqc/multiqc.py.orig	2023-05-11 13:19:10 UTC
+--- multiqc/multiqc.py.orig	2024-11-12 20:25:32 UTC
 +++ multiqc/multiqc.py
-@@ -24,7 +24,13 @@ from urllib.request import urlopen
+@@ -13,6 +13,13 @@ import rich_click as click
+ from typing import Optional, Tuple
  
- import jinja2
- import rich
--import rich_click as click
+ import rich_click as click
 +if 'LC_ALL' in os.environ and 'LANG' in os.environ:
 +    import rich_click as click
 +else:
@@ -12,6 +11,6 @@
 +    print('in your environment in order for the click module to function.')
 +    print('E.g. export LC_ALL=en_US.UTF-8 or setenv LC_ALL en_US.UTF-8')
 +    sys.exit()
- from rich.syntax import Syntax
  
- from .plots import table
+ from multiqc import config, report, validation
+ from multiqc.core import log_and_rich, plugin_hooks