[med-svn] [Git][med-team/muscle3][master] 16 commits: routine-update: Standards-Version: 4.6.1
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Nov 24 08:41:42 GMT 2022
Andreas Tille pushed to branch master at Debian Med / muscle3
Commits:
be1795c4 by Andreas Tille at 2022-11-24T09:21:29+01:00
routine-update: Standards-Version: 4.6.1
- - - - -
e0660d40 by Andreas Tille at 2022-11-24T09:21:29+01:00
routine-update: debhelper-compat 13
- - - - -
cdb97bcd by Andreas Tille at 2022-11-24T09:21:33+01:00
routine-update: Add salsa-ci file
- - - - -
ddcedb37 by Andreas Tille at 2022-11-24T09:21:34+01:00
routine-update: Rules-Requires-Root: no
- - - - -
e3c74b56 by Andreas Tille at 2022-11-24T09:21:36+01:00
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
9d38c1d8 by Andreas Tille at 2022-11-24T09:21:40+01:00
Fix day-of-week for changelog entry 3.52-1.
Changes-By: lintian-brush
Fixes: lintian: debian-changelog-has-wrong-day-of-week
See-also: https://lintian.debian.org/tags/debian-changelog-has-wrong-day-of-week.html
- - - - -
6831e58a by Andreas Tille at 2022-11-24T09:23:59+01:00
New upstream version 5.1
- - - - -
33be8bcf by Lance Lin at 2022-11-24T09:23:59+01:00
New upstream version 5.1.0
- - - - -
ea909ac3 by Andreas Tille at 2022-11-24T09:23:59+01:00
New upstream version 3.8.1551
- - - - -
e91c8dcc by Andreas Tille at 2022-11-24T09:28:28+01:00
Rename binary and docs to muscle3
- - - - -
157de1d5 by Andreas Tille at 2022-11-24T09:29:08+01:00
Rename binary also in autopkgtest
- - - - -
75375403 by Andreas Tille at 2022-11-24T09:34:43+01:00
Fix doc-base reference
- - - - -
68100fc8 by Andreas Tille at 2022-11-24T09:35:55+01:00
Epoch can be droped since the package name was changed
- - - - -
da2c6aee by Andreas Tille at 2022-11-24T09:37:18+01:00
Lintian-override (see lintian bug #1017966)
- - - - -
855ba37e by Andreas Tille at 2022-11-24T09:38:50+01:00
Provide run-unit-test as example
- - - - -
363a655f by Andreas Tille at 2022-11-24T09:41:12+01:00
Since the name of the package changed its fine to drop epoch
- - - - -
19 changed files:
- + debian/README.test
- debian/changelog
- − debian/compat
- debian/control
- − debian/dirs
- debian/muscle.doc-base → debian/doc-base
- + debian/docs
- debian/muscle.examples → debian/examples
- debian/muscle.install → debian/install
- + debian/manpages
- − debian/muscle.1.xml
- − debian/muscle.docs
- − debian/muscle.manpages
- debian/muscle.1 → debian/muscle3.1
- debian/muscle.html → debian/muscle3.html
- debian/rules
- + debian/salsa-ci.yml
- + debian/source/lintian-overrides
- debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -2,6 +2,15 @@ muscle3 (3.8.1551-1) UNRELEASED; urgency=medium
* Re-introduce muscle version 3 as a different program
(see https://lists.debian.org/debian-med/2022/11/msg00080.html)
+ * Epoch can be droped since the package name was changed
+ * Standards-Version: 4.6.1 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Use secure URI in Homepage field.
+ * Fix day-of-week for changelog entry 3.52-1.
+ * Rename binary and docs to muscle3
+ * Lintian-override (see lintian bug #1017966)
-- Andreas Tille <tille at debian.org> Mon, 17 Jan 2022 14:07:55 +0100
@@ -173,7 +182,7 @@ muscle (3.52-1) unstable; urgency=low
* New upstream version.
* Fix build on arch other than Pentium (Closes: Bug#285000).
- -- Steffen Moeller <moeller at pzr.uni-rostock.de> Sun, 18 Dec 2004 00:06:00 +0200
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Sat, 18 Dec 2004 00:06:00 +0200
muscle (3.51-1) unstable; urgency=low
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -5,11 +5,12 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~)
-Standards-Version: 4.3.0
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/muscle3
Vcs-Git: https://salsa.debian.org/med-team/muscle3.git
-Homepage: http://www.drive5.com/muscle/
+Homepage: https://www.drive5.com/muscle/
+Rules-Requires-Root: no
Package: muscle3
Architecture: any
=====================================
debian/dirs deleted
=====================================
@@ -1 +0,0 @@
-usr/bin
=====================================
debian/muscle.doc-base → debian/doc-base
=====================================
@@ -1,4 +1,4 @@
-Document: muscle-manual
+Document: muscle3-manual
Title: MUSCLE User Guide 3.5
Author: Robert C. Edgar
Abstract: MUSCLE is a program for creating multiple alignments of amino acid or
@@ -8,8 +8,10 @@ Abstract: MUSCLE is a program for creating multiple alignments of amino acid or
versions current at the time of writing, my tests show that MUSCLE can achieve
both better average accuracy and better speed than Clustal W or T‑Coffee,
depending on the chosen options.
+ .
+ This is version 3 of MUSCLE which is a different program than MUSCLE 5.
Section: Science/Biology
Format: HTML
-Index: /usr/share/doc/muscle/muscle.html
-Files: /usr/share/doc/muscle/muscle.html
+Index: /usr/share/doc/muscle3/muscle3.html
+Files: /usr/share/doc/muscle3/muscle3.html
=====================================
debian/docs
=====================================
@@ -0,0 +1,3 @@
+debian/muscle3.html
+debian/tests/run-unit-test
+debian/README.test
=====================================
debian/muscle.examples → debian/examples
=====================================
=====================================
debian/muscle.install → debian/install
=====================================
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/muscle3.1
=====================================
debian/muscle.1.xml deleted
=====================================
@@ -1,270 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
- "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
-
-<!--
-
-Process this file with an XSLT processor: `xsltproc \
--''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
-manpages/docbook.xsl manpage.dbk'. A manual page
-<package>.<section> will be generated. You may view the
-manual page with: nroff -man <package>.<section> | less'. A
-typical entry in a Makefile or Makefile.am is:
-
-DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
-manpages/docbook.xsl
-XP=xsltproc -''-nonet
-
-manpage.1: manpage.dbk
- $(XP) $(DB2MAN) $<
-
-The xsltproc binary is found in the xsltproc package. The
-XSL files are in docbook-xsl. Please remember that if you
-create the nroff version in one of the debian/rules file
-targets (such as build), you will need to include xsltproc
-and docbook-xsl in your Build-Depends control field.
-
--->
-
- <!ENTITY dhfirstname "Steffen">
- <!ENTITY dhsurname "Moeller">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "moeller at debian.org">
- <!ENTITY dhusername "Steffen Moeller">
- <!ENTITY dhucpackage "<refentrytitle>MUSCLE</refentrytitle>">
- <!ENTITY dhpackage "muscle">
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
- <!ENTITY dhrelease "3.7">
- <!ENTITY dhtitle "Muscle Manual">
-]>
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <releaseinfo role="version">&dhrelease;</releaseinfo>
- <authorgroup>
- <author>
- <firstname>Robert</firstname>
- <firstname>C.</firstname>
- <surname>Elgar</surname>
- <contrib>Wrote Muscle.</contrib>
- </author>
- <author>
- <firstname>&dhfirstname;</firstname>
- <surname>&dhsurname;</surname>
- <contrib>Wrote this manpage.</contrib>
- <address><email>&dhemail;</email></address>
- </author>
- <author>
- <firstname>Charles</firstname>
- <surname>Plessy</surname>
- <contrib>Updated this manpage.</contrib>
- <address><email>charles-debian-nospam at plessy.org</email></address>
- </author>
- </authorgroup>
- <copyright>
- <year>2003</year>
- <year>2004</year>
- <holder>&dhusername; (manpage)</holder>
- </copyright>
- <copyright>
- <year>2007</year>
- <year>2008</year>
- <holder>Charles Plessy (manpage)</holder>
- </copyright>
- <legalnotice>
- <para>
- Muscle is in the public domain, and therefore not subjected to copyright.
- </para>
-
- <para>
- This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document as if it were in public domain.
- </para>
- </legalnotice>
- </refentryinfo>
-
- <refmeta>
- &dhucpackage;
- &dhsection;
- </refmeta>
-
- <refnamediv>
- <refname>&dhpackage;</refname>
- <refpurpose>Multiple Protein Sequence Alignment</refpurpose>
- </refnamediv>
-
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="plain"><option>-in <replaceable>input file (fasta)</replaceable></option></arg>
- <arg choice="opt"><option>-out <replaceable>output file (default fasta)</replaceable></option></arg>
- <arg choice="opt"><option>-diags</option></arg>
- <arg choice="opt"><option>-log <replaceable>log file</replaceable></option></arg>
- <arg choice="opt"><option>-maxiters <replaceable>n</replaceable></option></arg>
- <arg choice="opt"><option>-maxhours <replaceable>n</replaceable></option></arg>
- <arg choice="opt"><option>-maxmb <replaceable>m</replaceable></option></arg>
- <arg choice="opt"><option>-html</option></arg>
- <arg choice="opt"><option>-msf</option></arg>
- <arg choice="opt"><option>-clw</option></arg>
- <arg choice="opt"><option>-clwstrict</option></arg>
- <arg choice="opt"><option>-log[a] <replaceable>logfile</replaceable></option></arg>
- <arg choice="opt"><option>-quiet</option></arg>
- <arg choice="opt"><option>-stable</option></arg>
- <arg choice="opt"><option>-group</option></arg>
- <arg choice="opt"><option>-version</option></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
-
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>This manual page documents briefly the
- <command>&dhpackage;</command> command.
- </para>
-
- <para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than Clustal W.</para>
- </refsect1>
-
- <refsect1>
- <title>OPTIONS</title>
- <variablelist>
- <varlistentry>
- <term><option>-in <replaceable>input file</replaceable></option>
- </term>
- <listitem>
- <para>Path to FASTA formatted input file
- </para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-out <replaceable>output file</replaceable></option>
- </term>
- <listitem>
- <para>Path to output file, FASTA formatted by default
- </para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-diags</option>
- </term>
- <listitem>
- <para>Find diagonals (faster for similar sequences)
- </para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-maxiters <replaceable>n</replaceable></option>
- </term>
- <listitem>
- <para>Maximum number of iterations (integer, default 16)
- </para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-maxhours <replaceable>n</replaceable></option>
- </term>
- <listitem>
- <para>Maximum time to iterate in hours (default no limit)
- </para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-maxmb <replaceable>m</replaceable></option></term>
- <listitem>
- <para>Maximum memory to allocate in Mb (default 80% of RAM)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-html</option>
- </term>
- <listitem>
- <para>Write output in HTML format (default FASTA)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-msf</option>
- </term>
- <listitem>
- <para>Write output in MSF format (default FASTA)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-clw</option>
- </term>
- <listitem>
- <para>Write output in Clustal W format (default FASTA)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-clwstrict</option>
- </term>
- <listitem>
- <para>As -clw, with 'CLUSTAL W (1.81)' header</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-log[a] <replaceable>logfile</replaceable></option>
- </term>
- <listitem>
- <para>Log to file (append if -loga, overwrite if -log)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-quiet</option>
- </term>
- <listitem>
- <para>Do not write progress messages to stderr</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-stable</option>
- </term>
- <listitem>
- <para>Output sequences in input order (default is -group)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-group</option>
- </term>
- <listitem>
- <para>Group sequences by similarity (this is the default)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-version</option>
- </term>
- <listitem>
- <para>Display version information and exit</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
- <citerefentry>
- <refentrytitle>clustalw</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>,
-
- <citerefentry>
- <refentrytitle>seaview</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>,
-
- <citerefentry>
- <refentrytitle>t_coffee</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>.
- </para>
- </refsect1>
-</refentry>
=====================================
debian/muscle.docs deleted
=====================================
@@ -1 +0,0 @@
-debian/muscle.html
=====================================
debian/muscle.manpages deleted
=====================================
@@ -1 +0,0 @@
-debian/muscle.1
=====================================
debian/muscle.1 → debian/muscle3.1
=====================================
=====================================
debian/muscle.html → debian/muscle3.html
=====================================
=====================================
debian/rules
=====================================
@@ -2,8 +2,14 @@
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+include /usr/share/dpkg/default.mk
+
%:
dh $@
override_dh_auto_build:
dh_auto_build -- 'GPP=$$(CXX)'
+
+override_dh_install:
+ dh_install
+ mv debian/$(DEB_SOURCE)/usr/bin/muscle debian/$(DEB_SOURCE)/usr/bin/$(DEB_SOURCE)
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,4 @@
+# See lintian bug #1017966
+muscle3 source: source-is-missing [debian/muscle3.html]
+# Since the name of the package changed its fine to drop epoch
+muscle3 source: epoch-changed-but-upstream-version-did-not-go-backwards
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,17 +1,18 @@
#!/bin/bash
set -e
-pkg="muscle"
+pkg=muscle3
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
cd $AUTOPKGTEST_TMP
-muscle -in example.fa -out seqs.afa
-muscle -in example.fa -clw
+muscle3 -in example.fa -out seqs.afa
+muscle3 -in example.fa -clw
echo "PASS"
View it on GitLab: https://salsa.debian.org/med-team/muscle3/-/compare/8b33d9e7629cf2ec017f3b77ebf2edf549749d5f...363a655fee08f3b63398fe26c9e8307d95c9d33a
--
View it on GitLab: https://salsa.debian.org/med-team/muscle3/-/compare/8b33d9e7629cf2ec017f3b77ebf2edf549749d5f...363a655fee08f3b63398fe26c9e8307d95c9d33a
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20221124/ec13cb14/attachment-0001.htm>
More information about the debian-med-commit
mailing list