From nobody Fri Feb 21 13:05:03 2025 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 4Yzr2R3nR2z5pnF6; Fri, 21 Feb 2025 13:05:03 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Yzr2R3BvFz40PH; Fri, 21 Feb 2025 13:05:03 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1740143103; 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=WOgyLxc3LjOIHxTgTXsXPi+nuT+SmPIrk7JqvrlTLJ0=; b=av02oiWQRUSYxb1J7RNPZBC/lBDqKLaTOiJ4jDk9vWtkJdkRSKXpRh0pf9ZIUMcXCdTC1q 5fcbdiaWQaJr/IXfh/kZ7xIVcD3Rtvz0bPgsVLGrAlzLh6CKxXhXEHUSCmzghPxxyKiC/n m8ZAfvbYn1sT2Yk6MOYJFiH2uds0es4P8bsBOEycQ/1/cB38I92YNykkXDKjGVrCaQrpu7 XECsd5kafZ5ND8Rg8LbgrttrW0yOevN/JqR+xEGuRWXJ3TiuVZkY+dGBYcuhge7YWiyzU1 4gxXeuhuhXEqCfOH9W8RfSwK/vbvVJ8loU4YOvkUaTD6k7YDl5cK1lKXD64fzA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1740143103; a=rsa-sha256; cv=none; b=as3wgjBjmPrGBfqHkoc/goHQDk1hr0Rxzx6LlDshXEnAg0E0a87OFMoQqOIlR9jmQu4a4G /6c2pn51qPvs5bt73sj3zOGQyh95Wfanx13FOrifXcymfvysA0TukdiaZwym8S386VP1LP XvojlAF2EXva3zrE+8RlU8poNUDJ7K/a8awKxz6uoRXAgxBpSJonwkkZeG2BWigLdfxOpu r6rFLBfIpUeGYHcgts90JVwhSWfwZn/rTg0IxJEqhzCX+lvSrKjWvuX5aOL8P5tyfJ9XEP z3X9DeHSQJFUgljQDOGIbmEDFdgTz2zFrVU7SBK0PcOfT58ZQKEpxjRmNvHu/A== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1740143103; 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=WOgyLxc3LjOIHxTgTXsXPi+nuT+SmPIrk7JqvrlTLJ0=; b=K3+bhuj7G2f4ksn78pEigRsh3jqQVRxmgT8EqhIOLK9b0eg8Ffb7+kRexRh6kU7uDhz7Om nIo/GKa9XOKCDw+lSnv6BtOay/j3oWo2GGk9J7GUtiR38Klz+KifjIf8DS38Bp1KFADY16 NcGOfrXvumcjG4S5+bzQ7OgxGQJTa1ICvG4mz7++kMoT2oOqS4jMsm9qOvFckbj9urG7B/ QiX1dEqoQAp7HEBN//pICWchDq1Tpz0VROmxMSFSNePYHrjJpVw1SpbUTavaeDsZgMqHwA NP7O7K4mxAWRThmM0w2u6KwAxSx4jKZxMMFDaRH4DJkzCW9bbbOm0E/BFUkA/A== 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 4Yzr2R2RNQz7h0; Fri, 21 Feb 2025 13:05:03 +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 51LD53Qu022939; Fri, 21 Feb 2025 13:05:03 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 51LD53c0022936; Fri, 21 Feb 2025 13:05:03 GMT (envelope-from git) Date: Fri, 21 Feb 2025 13:05:03 GMT Message-Id: <202502211305.51LD53c0022936@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: d758b1caa19e - main - Multiple biology ports: Replace pypi homepage with github 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: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-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: d758b1caa19eb6a43d8efe332d5ea0da8e9dbd96 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=d758b1caa19eb6a43d8efe332d5ea0da8e9dbd96 commit d758b1caa19eb6a43d8efe332d5ea0da8e9dbd96 Author: Jason W. Bacon AuthorDate: 2025-02-21 13:03:10 +0000 Commit: Jason W. Bacon CommitDate: 2025-02-21 13:04:08 +0000 Multiple biology ports: Replace pypi homepage with github portscout apparently can't work with PYPI homepages --- biology/py-bcbio-gff/Makefile | 4 +--- biology/py-dna-features-viewer/Makefile | 2 +- biology/py-dnaio/Makefile | 2 +- biology/py-goatools/Makefile | 2 +- biology/py-ont-fast5-api/Makefile | 2 +- biology/py-pybigwig/Makefile | 2 +- biology/py-pywgsim/Makefile | 2 +- 7 files changed, 7 insertions(+), 9 deletions(-) diff --git a/biology/py-bcbio-gff/Makefile b/biology/py-bcbio-gff/Makefile index 325a33a56077..2a3b0260c9fd 100644 --- a/biology/py-bcbio-gff/Makefile +++ b/biology/py-bcbio-gff/Makefile @@ -6,9 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Read and write Generic Feature Format (GFF) with Biopython integration -WWW= https://pypi.org/project/bcbio-gff/ \ - https://biopython.org/wiki/GFF_Parsing \ - https://github.com/chapmanb/bcbb/tree/master/gff/ +WWW= https://github.com/chapmanb/bcbb/tree/master/gff/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-dna-features-viewer/Makefile b/biology/py-dna-features-viewer/Makefile index 906de191ad5d..faefb8faf5e8 100644 --- a/biology/py-dna-features-viewer/Makefile +++ b/biology/py-dna-features-viewer/Makefile @@ -7,7 +7,7 @@ DISTNAME= dna_features_viewer-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Python library to visualize DNA features, e.g. GenBank or Gff files -WWW= https://pypi.python.org/project/dna-features-viewer/ +WWW= https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENCE.txt diff --git a/biology/py-dnaio/Makefile b/biology/py-dnaio/Makefile index 6dc8951da918..3baff38a1558 100644 --- a/biology/py-dnaio/Makefile +++ b/biology/py-dnaio/Makefile @@ -6,7 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Read and write FASTQ and FASTA -WWW= https://pypi.python.org/pypi/dnaio +WWW= https://github.com/marcelm/dnaio/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-goatools/Makefile b/biology/py-goatools/Makefile index ef6eba5004f8..44c8f67d9ffd 100644 --- a/biology/py-goatools/Makefile +++ b/biology/py-goatools/Makefile @@ -7,7 +7,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for processing and visualizing Gene Ontology terms -WWW= https://pypi.python.org/pypi/goatools +WWW= https://github.com/tanghaibao/goatools/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-ont-fast5-api/Makefile b/biology/py-ont-fast5-api/Makefile index e154ea248556..9ead9df1cde1 100644 --- a/biology/py-ont-fast5-api/Makefile +++ b/biology/py-ont-fast5-api/Makefile @@ -7,7 +7,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Interface to HDF5 files in Oxford Nanopore .fast5 format -WWW= https://pypi.python.org/pypi/ont_fast5_api +WWW= https://github.com/nanoporetech/ont_fast5_api/ LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.md diff --git a/biology/py-pybigwig/Makefile b/biology/py-pybigwig/Makefile index 76d160a9e818..2bdae8095d8b 100644 --- a/biology/py-pybigwig/Makefile +++ b/biology/py-pybigwig/Makefile @@ -6,7 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Python access to bigWig files using libBigWig -WWW= https://pypi.org/project/pyBigWig/ +WWW= https://github.com/deeptools/pyBigWig/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/py-pywgsim/Makefile b/biology/py-pywgsim/Makefile index 14bc3cbb17ba..e255e8a1fbc6 100644 --- a/biology/py-pywgsim/Makefile +++ b/biology/py-pywgsim/Makefile @@ -7,7 +7,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Modified wgsim genomic data simulator -WWW= https://pypi.python.org/pypi/pywgsim +WWW= https://github.com/ialbert/pywgsim/ LICENSE= MIT