From nobody Sat Nov 16 01:29:00 2024 X-Original-To: dev-commits-ports-main@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 4XqxB523MFz5cbGw; Sat, 16 Nov 2024 01:29:01 +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 "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4XqxB472Bdz4FkV; Sat, 16 Nov 2024 01:29:00 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1731720541; 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=Cz/QiF1XFa0U00pFdX8xarCx+DCDzYVFAIe19WewE6M=; b=rBe/hNdvD96xm9s4RaczeYynjFy44WRbZh+ksSm9Ziy4A5INBzd5L5E/qA6+VMuUimyWzF 8J9ksoqzTZ6WA7qDi8aIRpiqeLcH1lWGY0XbMCmaO5DnltJMBZNUpCm5GkTYD6h3FlRem9 J7fQqwvaMnlm18mtVNhSUGVjeUTnSKLWpBUnqrUBKSJqXoWU+//OCaFZDOTsSKoSWIwVmW N5BmtDs2jChLA5GLjif7o3HA+YUy33+lWH4cNt00CHooYPOMpYZjpglsqJUJr0IqA7LcAR iLRNF4sOlNY/w1MeuH+vkPodFlyGvagKUjIB+j+7BpprSXY4AXtRfU7L41le0w== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1731720541; 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=Cz/QiF1XFa0U00pFdX8xarCx+DCDzYVFAIe19WewE6M=; b=rMhmyXWuuKimF2V3E5h5Ae8VDYCgmgdJ320oaIhHR2V29BKX+mlmviJBtatspSvkOo7Os+ B32psQjQxWRxfsZpi7eouqneF50MZoVjGARucp0w7/y8K4Z4V+NYG/2DrpEDfDL8Uy20Yn AtA/ublps1FsxUML8Qxygzm93qEzlNS2t9xeaStc8LipiAYtCerG32GojcWy6OnCWYE3nx 0m/jg0un18ufIbRqHA2VmAb+uacVUMxmntgWsjETHDj/PuRPjUn/GLgFgCL6McgX8MybBm quFw5T8GU7SaxMwC9MPYGMaOnPsWMV1VPJHCNIXhMzD0yjPSGfcN8pVdYzl+MA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1731720541; a=rsa-sha256; cv=none; b=eXmJkAYesu29LZS2K8ZDdgfBNaoVBaT3sAcFaYzI7JE+2qjo0G41oeOq4UX8syTJWm9MIt tpliNeq+1ZSuQFkw8dCAFxLSHXVUK6293ITIqS61e3Y6SV3uGcrKNfRrQnLsz+t+83RsxM KxSk9rPu6UHR2fFiYX2LmQ7GGV28IdcGpQG0PB4swso3OcJTNg42307le4WNwp3f+2CN33 pj4a+b3nYtw/JUglll2rPfkq6cy4zOmaFiklThJQtm4l5zHzOQJMdwpJSS0rzw0PL3Ei+9 NeqwS3rG/ekQR40+mgR0OG2HVonv2fYe1yNDNjYlvjmmwsU5E830D/Bhspl+nw== 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 4XqxB44dvrzn4D; Sat, 16 Nov 2024 01:29:00 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 4AG1T0tN051503; Sat, 16 Nov 2024 01:29:00 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 4AG1T0d6051500; Sat, 16 Nov 2024 01:29:00 GMT (envelope-from git) Date: Sat, 16 Nov 2024 01:29:00 GMT Message-Id: <202411160129.4AG1T0d6051500@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: 3f037ab2522e - main - biology/py-multiqc: Update to 1.25.1 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@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: 3f037ab2522e5e8a0145e5b45d48ac757538f7f0 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=3f037ab2522e5e8a0145e5b45d48ac757538f7f0 commit 3f037ab2522e5e8a0145e5b45d48ac757538f7f0 Author: Jason W. Bacon AuthorDate: 2024-11-16 01:27:36 +0000 Commit: Jason W. Bacon 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