[med-svn] [Git][med-team/pyensembl][master] 6 commits: Add python3-gtfparse to B-D
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri May 21 18:55:30 BST 2021
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 <moeller at debian.org> Tue, 18 May 2021 14:33:33 +0200
-
+ -- Steffen Moeller <moeller at debian.org> 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 <alex.rubinsteyn at unc.edu>
+Copyright: 2015-2016 Mount Sinai School of Medicine
License: Apache-2.0
Files: debian/*
-Copyright: 2021 steffen <steffen at unknown>
+Copyright: 2021 Steffen Moeller <moeller at debian.org>
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 <nilesh at debian.org>
+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
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