git: 05c52e655e8a - main - biology/py-multiqc: Update to 1.14

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=05c52e655e8a0668426829f50b21ef8fdf3c73e4

commit 05c52e655e8a0668426829f50b21ef8fdf3c73e4
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-05-12 12:54:25 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-05-12 12:55:38 +0000

    biology/py-multiqc: Update to 1.14
    
    Numerous new features, enhancements and bug fixes
    
    Changes: https://github.com/ewels/MultiQC/releases
---
 biology/py-multiqc/Makefile                       |  8 +++----
 biology/py-multiqc/distinfo                       |  6 ++---
 biology/py-multiqc/files/patch-multiqc_multiqc.py | 29 +++++++----------------
 3 files changed, 15 insertions(+), 28 deletions(-)

diff --git a/biology/py-multiqc/Makefile b/biology/py-multiqc/Makefile
index 378e6522e8e0..946abfcc9372 100644
--- a/biology/py-multiqc/Makefile
+++ b/biology/py-multiqc/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	multiqc
-DISTVERSION=	1.10
-PORTREVISION=	1
+DISTVERSION=	1.14
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -13,7 +12,7 @@ LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 RUN_DEPENDS=	${PYNUMPY} \
-		${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${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} \
@@ -26,7 +25,8 @@ RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}Jinja2>=2.9:devel/py-Jinja2@${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}
+		${PYTHON_PKGNAMEPREFIX}colormath>0:math/py-colormath@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}kiwisolver>0:math/py-kiwisolver@${PY_FLAVOR}
 
 USES=		python:3.7+
 USE_PYTHON=	autoplist concurrent distutils
diff --git a/biology/py-multiqc/distinfo b/biology/py-multiqc/distinfo
index a6c957293aac..567000569b6a 100644
--- a/biology/py-multiqc/distinfo
+++ b/biology/py-multiqc/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1616108218
-SHA256 (multiqc-1.10.tar.gz) = f2f8c529d36a69fb32c0f27fb387a0bb53aa2f438387370cec28639968f8a686
-SIZE (multiqc-1.10.tar.gz) = 1601505
+TIMESTAMP = 1683811522
+SHA256 (multiqc-1.14.tar.gz) = dcbba405f0c9521ed2bbd7e8f7a9200643047311c9619878b81d167300149362
+SIZE (multiqc-1.14.tar.gz) = 1054868
diff --git a/biology/py-multiqc/files/patch-multiqc_multiqc.py b/biology/py-multiqc/files/patch-multiqc_multiqc.py
index d1a670b3bb56..2353f5150e0c 100644
--- a/biology/py-multiqc/files/patch-multiqc_multiqc.py
+++ b/biology/py-multiqc/files/patch-multiqc_multiqc.py
@@ -1,30 +1,17 @@
---- multiqc/multiqc.py.orig	2019-11-25 15:53:22 UTC
+--- multiqc/multiqc.py.orig	2023-05-11 13:19:10 UTC
 +++ multiqc/multiqc.py
-@@ -11,16 +11,25 @@ from __future__ import print_function
+@@ -24,7 +24,13 @@ from urllib.request import urlopen
  
- import base64
- import click
-+import os
-+import sys
-+
+ import jinja2
+ import rich
+-import rich_click as click
 +if 'LC_ALL' in os.environ and 'LANG' in os.environ:
-+    import click
++    import rich_click as click
 +else:
 +    print('multiqc: LC_ALL and LANG must be set to a UTF-8 character set')
 +    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 distutils import version
- from distutils.dir_util import copy_tree
- import errno
- import io
- import jinja2
--import os
- import re
- import shutil
- import subprocess
--import sys
- import tempfile
- import traceback
+ from rich.syntax import Syntax
  
+ from .plots import table