Date: Fri, 12 May 2023 12:55:41 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 05c52e655e8a - main - biology/py-multiqc: Update to 1.14 Message-ID: <202305121255.34CCtf0k082691@gitrepo.freebsd.org>
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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
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