Nilesh Patra pushed to branch master at Debian Med / pyensembl
Commits: fd7221e8 by Nilesh Patra at 2021-05-21T23:08:38+05:30 Add python3-gtfparse to B-D - - - - - 8cc46983 by Nilesh Patra at 2021-05-21T23:09:43+05:30 Update upstream/metadata - - - - - 58e8a3af by Nilesh Patra at 2021-05-21T17:45:40+00:00 d/patches: Do not enforce compulsion on installing tinytimer - - - - - cb043478 by Nilesh Patra at 2021-05-21T17:46:45+00:00 Add manpage - - - - - e19fe64e by Nilesh Patra at 2021-05-21T23:21:42+05:30 Fix copyright - - - - - 3a94dafa by Nilesh Patra at 2021-05-21T23:22:29+05:30 Upload to unstable - - - - - 9 changed files: - debian/changelog - debian/control - debian/copyright - + debian/creatmanpages - + debian/manpages - + debian/patches/do-no-require-tinytimer.patch - + debian/patches/series - + debian/pyensembl.1 - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,6 +1,6 @@ -pyensembl (1.9.1+ds-1) UNRELEASED; urgency=medium +pyensembl (1.9.1+ds-1) unstable; urgency=medium + [ Steffen Moeller, Nilesh Patra ] * Initial release (Closes: #988822) - -- Steffen Moeller <[email protected]> Tue, 18 May 2021 14:33:33 +0200 - + -- Steffen Moeller <[email protected]> Fri, 21 May 2021 23:17:37 +0530 ===================================== debian/control ===================================== @@ -11,7 +11,8 @@ Build-Depends: debhelper-compat (= 13), python3-numpy, python3-datacache, python3-serializable, - python3-memoized-property + python3-memoized-property, + python3-gtfparse # python3-tinytimer # only run during tests that are not run because of # demand for internet access Standards-Version: 4.5.1 ===================================== debian/copyright ===================================== @@ -7,11 +7,11 @@ Files-Excluded: pyensembl.egg-info/requires.txt Files: * -Copyright: Alex Rubinsteyn <[email protected]> +Copyright: 2015-2016 Mount Sinai School of Medicine License: Apache-2.0 Files: debian/* -Copyright: 2021 steffen <steffen@unknown> +Copyright: 2021 Steffen Moeller <[email protected]> License: Apache-2.0 License: Apache-2.0 ===================================== debian/creatmanpages ===================================== @@ -0,0 +1,28 @@ +#!/bin/sh +MANDIR=debian +mkdir -p $MANDIR + +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` +NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1` +PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1` + +AUTHOR=".SH AUTHOR\n \ +This manpage was written by $DEBFULLNAME for the Debian distribution and\n \ +can be used for any other usage of the program.\ +" + +# If program name is different from package name or title should be +# different from package short description change this here +progname=${PROGNAME} +help2man --no-info --no-discard-stderr --help-option=" " \ + --name="$NAME" \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +echo "$MANDIR/*.1" > debian/manpages + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT ===================================== debian/manpages ===================================== @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/patches/do-no-require-tinytimer.patch ===================================== @@ -0,0 +1,14 @@ +Description: Since tinytimer is needed only for tests, disable it in install_requires +Author: Nilesh Patra <[email protected]> +Forwarded: not-needed +Last-Update: 2021-05-21 +--- a/setup.py ++++ b/setup.py +@@ -71,7 +71,6 @@ + "six>=1.9.0", + "gtfparse>=1.1.0", + "serializable", +- "tinytimer", + ], + long_description=readme_markdown, + long_description_content_type='text/markdown', ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +do-no-require-tinytimer.patch ===================================== debian/pyensembl.1 ===================================== @@ -0,0 +1,33 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16. +.TH PYENSEMBL "1" "May 2021" "pyensembl 1.9.1+ds" "User Commands" +.SH NAME +pyensembl \- installs data from the Ensembl genome database +.SH DESCRIPTION +usage: +Manipulate pyensembl's local cache. +.IP +pyensembl {install, delete, delete\-sequence\-cache} [\-\-release XXX \fB\-\-species\fR human...] +.SS "To install particular Ensembl human release(s):" +.IP +pyensembl install \fB\-\-release\fR 75 77 +.SS "To install particular Ensembl mouse release(s):" +.IP +pyensembl install \fB\-\-release\fR 75 77 \fB\-\-species\fR mouse +.SS "To delete all downloaded and cached data for a particular Ensembl release:" +.IP +pyensembl delete\-all\-files \fB\-\-release\fR 75 \fB\-\-species\fR human +.SS "To delete only cached data related to transcript and protein sequences:" +.IP +pyensembl delete\-index\-files \fB\-\-release\fR 75 +.SS "To list all installed genomes:" +.IP +pyensembl list +.SS "To install a genome from source files:" +.TP +pyensembl install +\fB\-\-reference\-name\fR "GRCh38" \fB\-\-gtf\fR URL_OR_PATH \fB\-\-transcript\-fasta\fR URL_OR_PATH \fB\-\-protein\-fasta\fR URL_OR_PATH +.PP +pyensembl: error: the following arguments are required: action +.SH AUTHOR + This manpage was written by Nilesh Patra for the Debian distribution and + can be used for any other usage of the program. ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,10 @@ +--- +Archive: GitHub +Bug-Database: https://github.com/openvax/pyensembl/issues +Bug-Submit: https://github.com/openvax/pyensembl/issues/new +Changelog: https://github.com/openvax/pyensembl/tags +Repository: https://github.com/openvax/pyensembl.git +Repository-Browse: https://github.com/openvax/pyensembl Registry: - Name: bio.tools Entry: N/A View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/1539efb68b52b3d00456b8859d57189ed729a72b...3a94dafa609e6b94df76dcc88647fc501b7b7788 -- View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/1539efb68b52b3d00456b8859d57189ed729a72b...3a94dafa609e6b94df76dcc88647fc501b7b7788 You're receiving this email because of your account on salsa.debian.org.
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