From nobody Fri May 12 12:55:41 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4QHpf544Xfz4B0NQ; Fri, 12 May 2023 12:55:41 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4QHpf53XWFz3tw6; Fri, 12 May 2023 12:55:41 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1683896141; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=NBiXRKpX5Ni/isvl6+gJzh87hpoBz3tf/4prONDMEug=; b=j0RSKmBV9wx0Gfrr0qKB9KOW/J3KG4ss0abrkyKs0JQTz77lY8Qr9K+ZFO5LmuxE20Uv6h X05feYFCJILQmWFL9KlkHSGWBnbaqtAOuUdT21ErbsD/XPvOGToMgyZsTB5rDQhq2Qh1zG 6zxZJSyTselybTFFKnD7cpuqM2phx3kmmdQDhkvVyVswwG4bHlZbBN1yx4hhaLRZkx5ifT SvDFsGujRnKdOaeSdQraT8nlc6GtvgwmvB092LrRSHnJPqOSCcMPtFM3ftrXfx78DC0HGq fQ4EA7UMyYWwTMNNhugYvLWmltlgRQpxutqKApc8uZFurKoluapQHfo1XX6tKw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1683896141; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=NBiXRKpX5Ni/isvl6+gJzh87hpoBz3tf/4prONDMEug=; b=muDCC6qlZYa/MdXI13I3DWz/rj+MyHnTfnES6Xb8Z/1KUvxqEcvRDfPlrw8OKVVhdvhc99 9gblMx3/xFZrHs+MGUwzpAHI335PpJmt7J79oZClj4tXeHNsZZGUpqtFrivk5AW+AifHYc j0G3vv728jC/m50NFDwAjh934pyO8WTLCToD7ryTCXYw0Fl0pzo9aBbMzGytseyiVZ2oKj BJswDt4N6BKdDoYGIaagIYiE3t9guvF/2NTAKOUeiyrq4Q9Yb3AKEeuDNlDFyyPxsb6UYw YeUcJZE0jrkclCHBwnnIc+rYZag7bieY0Un92QCl+GatTX78Q0ZgkzcDtIYzyQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1683896141; a=rsa-sha256; cv=none; b=X29ip0Du3Y3Gvtt5KziLOKtZFzZf+6V1rP2pUoA48STh6wvcUZbrl486L9mCvonDBXcp52 GFYGeMGoDiVHu4PcyZb41iGoFS5olTV8PWLFHQJaMz0Mdw/07gB3xiy8K/bHr+kpnv+O9Q +sSx5uaCywzIpvXkXLbM/smyaotLB0UcpVIdEkcn3MrOtZmxcy2G76gPhI0veys5vzIzDN sTDeSvdQqLw05cAzUOUq4F4fH+hm8kk2fBJtyZWXLs4hy0G2jMaGEMItk+uylzQWgM7znF tdEEHbQkDCE91q/vqunVY20ZbpXxIdhmCdd0W+A7vdVxdGdATCAVbHAOMDbnuQ== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4QHpf52Ksqzc7v; Fri, 12 May 2023 12:55:41 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 34CCtfQx082692; Fri, 12 May 2023 12:55:41 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 34CCtf0k082691; Fri, 12 May 2023 12:55:41 GMT (envelope-from git) Date: Fri, 12 May 2023 12:55:41 GMT Message-Id: <202305121255.34CCtf0k082691@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 05c52e655e8a - main - biology/py-multiqc: Update to 1.14 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 05c52e655e8a0668426829f50b21ef8fdf3c73e4 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=05c52e655e8a0668426829f50b21ef8fdf3c73e4 commit 05c52e655e8a0668426829f50b21ef8fdf3c73e4 Author: Jason W. Bacon AuthorDate: 2023-05-12 12:54:25 +0000 Commit: Jason W. Bacon 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