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 @@ -1,39 +1,39 @@ PORTNAME= multiqc -DISTVERSION= 1.10 -PORTREVISION= 1 +DISTVERSION= 1.14 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 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} \ ${PYTHON_PKGNAMEPREFIX}markdown>0:textproc/py-markdown@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}rich>0:textproc/py-rich@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=4:devel/py-yaml@${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} + ${PYTHON_PKGNAMEPREFIX}colormath>0:math/py-colormath@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}kiwisolver>0:math/py-kiwisolver@${PY_FLAVOR} USES= python:3.7+ USE_PYTHON= autoplist concurrent distutils NO_ARCH= yes post-patch: @${RM} ${WRKSRC}/multiqc/utils/config.py.orig .include 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