[med-svn] [Git][med-team/clonalorigin][master] 13 commits: shorten-test.patch: new: reduce stress on buildds.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Dec 29 12:12:52 GMT 2023
Étienne Mollier pushed to branch master at Debian Med / clonalorigin
Commits:
d0a05973 by Étienne Mollier at 2023-12-29T11:23:53+01:00
shorten-test.patch: new: reduce stress on buildds.
Closes: #884475
- - - - -
7a3b7161 by Étienne Mollier at 2023-12-29T11:25:23+01:00
d/tests/: new: add autopkgtest.
- - - - -
b8a64a4b by Étienne Mollier at 2023-12-29T11:39:23+01:00
clonalorigin-gui.1: minor fixups.
- - - - -
d26bf90b by Étienne Mollier at 2023-12-29T12:51:37+01:00
d/blocksplit.1: new: document upstream script.
- - - - -
571b2dc6 by Étienne Mollier at 2023-12-29T12:52:03+01:00
d/computeMedians.1: new: document upstream script.
- - - - -
6a5bd93b by Étienne Mollier at 2023-12-29T12:52:21+01:00
d/makeMauveWargFile.1: new: document upstream script.
- - - - -
2a3bdf08 by Étienne Mollier at 2023-12-29T12:53:36+01:00
d/clonalorigin-gui.1: minor fixup.
- - - - -
1788ecd1 by Étienne Mollier at 2023-12-29T12:53:46+01:00
d/warg.1: minor fixup in description.
- - - - -
1d56a327 by Étienne Mollier at 2023-12-29T12:55:29+01:00
d/clonalorigin.1: remove: unused.
The real manual page in the binary package is a link to warg(1).
- - - - -
e655dd44 by Étienne Mollier at 2023-12-29T12:56:32+01:00
d/clonalorigin.manpages: add missing script manuals.
- - - - -
d05d3556 by Étienne Mollier at 2023-12-29T12:56:51+01:00
d/control: recommend libxml-parser-perl.
This library is needed by computeMedians, although it does not seem
critical to typical clonalorigin workloads.
- - - - -
bb8449f7 by Étienne Mollier at 2023-12-29T13:11:31+01:00
d/*lintian-overrides: new: flag a false positive.
- - - - -
e853a2b8 by Étienne Mollier at 2023-12-29T13:12:06+01:00
ready to upload to unstable.
- - - - -
14 changed files:
- + debian/blocksplit.1
- debian/changelog
- debian/clonalorigin-gui.1
- − debian/clonalorigin.1
- + debian/clonalorigin.lintian-overrides
- debian/clonalorigin.manpages
- + debian/computeMedians.1
- debian/control
- + debian/makeMauveWargFile.1
- debian/patches/series
- + debian/patches/shorten-test.patch
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/warg.1
Changes:
=====================================
debian/blocksplit.1
=====================================
@@ -0,0 +1,28 @@
+.TH BLOCKSPLIT "1" "December 2023" "clonalorigin 1.0" "User Commands"
+.SH NAME
+blocksplit \- XFMA file splitter script for clonalorigin
+.SH SYNOPSIS
+.B blocksplit
+<xfmafile>
+.SH DESCRIPTION
+.PP
+blocksplit will read an XFMA file and output multiple XFMA files,
+each one storing one block of the initial file.
+The cut is done after each time a line with the character “=” is encountered.
+.PP
+It is part of the clonalorigin suite.
+It takes one mandatory argument:
+.TP
+xfmafile
+This is the input file passed to the script.
+.PP
+If the input file is for instance example.xfma,
+and it has three blocks,
+then the script will output three files named
+example.xfma.1,
+example.xfma.2,
+and example.xfma.3,
+storing the first, second and third block respectively.
+.SH AUTHOR
+This manpage was written by Étienne Mollier for the Debian distribution
+and can be used for any other usage of the program.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,23 @@
+clonalorigin (1.0-8) unstable; urgency=medium
+
+ * shorten-test.patch: new: reduce stress on buildds. (Closes: #884475)
+ * d/tests/: new: add autopkgtest.
+ * clonalorigin-gui.1: minor fixups.
+ * d/blocksplit.1: new: document upstream script.
+ * d/computeMedians.1: new: document upstream script.
+ * d/makeMauveWargFile.1: new: document upstream script.
+ * d/clonalorigin-gui.1: minor fixup.
+ * d/warg.1: minor fixup in description.
+ * d/clonalorigin.1: remove: unused.
+ The real manual page in the binary package is a link to warg(1).
+ * d/clonalorigin.manpages: add missing script manuals.
+ * d/control: recommend libxml-parser-perl.
+ This library is needed by computeMedians, although it does not seem
+ critical to typical clonalorigin workloads.
+ * d/*lintian-overrides: new: flag a false positive.
+
+ -- Étienne Mollier <emollier at debian.org> Fri, 29 Dec 2023 13:11:47 +0100
+
clonalorigin (1.0-7) unstable; urgency=medium
* d/rules: preserve warg/src/truth.xml.
=====================================
debian/clonalorigin-gui.1
=====================================
@@ -2,7 +2,7 @@
.TH CLONALORIGIN-GUI "1" "December 2017" "clonalorigin-gui 1.0" "User Commands"
.SH NAME
clonalorigin-gui \- GUI for clonalorigin
-.SH Synopsis
+.SH SYNOPSIS
.B clonalorigin-gui
[OPTIONS] <filename>
.SH DESCRIPTION
@@ -14,9 +14,9 @@ the file before using it, and set output names before
producing the output!
.SH OPTIONS
.TP
-\fB\-b\fR Batch mode. Perform operations then quit
-.IP
-without displaying the gui.
+\fB\-b\fR
+Batch mode.
+Perform operations then quit without displaying the gui.
.TP
\fB\-o\fR <filename>
Open the specified input XML file.
@@ -44,9 +44,9 @@ Perform a convergence of trees test
between the open file and the set of
specified files (separated by commas).
.TP
-\fB\-g\fR <list><:num> Perform a gelman\-rubin test
-between the open file and the set of
-specified files (separated by commas).
+\fB\-g\fR <list><:num>
+Perform a gelman\-rubin test between the open file
+and the set of specified files (separated by commas).
<num> takes the same meaning as for \fB\-c\fR.
.TP
\fB\-S\fR <filename>
=====================================
debian/clonalorigin.1 deleted
=====================================
@@ -1,2 +0,0 @@
-.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/clonalorigin.lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# Reading through the source code suggests a false positive.
+clonalorigin: spelling-error-in-binary lik link [usr/bin/warg]
=====================================
debian/clonalorigin.manpages
=====================================
@@ -1 +1,4 @@
+debian/blocksplit.1
+debian/computeMedians.1
+debian/makeMauveWargFile.1
debian/warg.1
=====================================
debian/computeMedians.1
=====================================
@@ -0,0 +1,20 @@
+.TH COMPUTEMEDIANS "1" "December 2023" "clonalorigin 1.0" "User Commands"
+.SH NAME
+computeMedians \- medians calculator for clonalorigin xml files
+.SH SYNOPSIS
+.B computeMedians
+<ClonalOrigins XML or xml.bz2>
+.SH DESCRIPTION
+.PP
+computeMedians will read an XML file produced by clonalorigin,
+or a compressed variant in bz2 format,
+and will print statistical figures in standard output.
+.PP
+It is part of the clonalorigin suite.
+It takes one mandatory argument:
+.TP
+ClonalOrigins XML or xml.bz2
+This is the input file passed to the script.
+.SH AUTHOR
+This manpage was written by Étienne Mollier for the Debian distribution
+and can be used for any other usage of the program.
=====================================
debian/control
=====================================
@@ -20,6 +20,7 @@ Package: clonalorigin
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
+Recommends: libxml-parserl-perl
Description: inference of homologous recombination in bacteria using whole genome sequences
Bacteria, unlike us, can reproduce on their own. They do however have
mechanisms that transfer DNA between organisms, a process more formally
=====================================
debian/makeMauveWargFile.1
=====================================
@@ -0,0 +1,20 @@
+.TH MAKEMAUVEWARGFILE "1" "December 2023" "clonalorigin 1.0" "User Commands"
+.SH NAME
+makeMauveWargFile \- produce Mauve XFMA files out of clonalorigin XML
+.SH SYNOPSIS
+.B makeMauveWargFile
+<ClonalOrigins.xml.bz2> [<ClonalOrigins.xml.bz2> ...]
+.SH DESCRIPTION
+.PP
+makeMauveWargFile will read an XML file compressed in bz2 format,
+as produced by clonalorigin,
+and will produce a Mauve XFMA file.
+.PP
+It is part of the clonalorigin suite.
+It takes at least one mandatory argument:
+.TP
+ClonalOrigins.xml.bz2
+This is the input file passed to the script.
+.SH AUTHOR
+This manpage was written by Étienne Mollier for the Debian distribution
+and can be used for any other usage of the program.
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
# qt5.patch # do not remove this patch completely
portability.patch
gcc-11.patch
+shorten-test.patch
=====================================
debian/patches/shorten-test.patch
=====================================
@@ -0,0 +1,27 @@
+Description: shorten execution time of the test item.
+ The execution time of upstream test item is particularly long on regular
+ CPU architectures, and may trigger timeouts on the slower ones. This patch
+ reduces iteration amounts in the "w" and "z" dimensions to more acceptable
+ values than the default ones.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=884475
+Forwarded: not-needed
+Last-Update: 2023-12-29
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- clonalorigin.orig/warg/src/Makefile.am
++++ clonalorigin/warg/src/Makefile.am
+@@ -12,5 +12,6 @@
+
+
+ profilerun.sh:
+- echo './warg -s 532772982 -x 100 -y 50 testout' > profilerun.sh
++ echo './warg -s 532772982 -w 10000 -x 100 -y 50 -z 10000 testout' \
++ > profilerun.sh
+ chmod +x profilerun.sh
+--- clonalorigin.orig/warg/src/profilerun.sh
++++ clonalorigin/warg/src/profilerun.sh
+@@ -1 +1 @@
+-./warg -s 532772982 -x 100 -y 50 testout
++./warg -s 532772982 -w 10000 -x 100 -y 50 -z 10000 testout
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,16 @@
+#!/bin/bash
+set -e
+
+pkg=clonalorigin
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd "${AUTOPKGTEST_TMP}"
+
+# test directly inspired from warg/src/Makefile.am
+echo '$ warg -s 532772982 -w 10000 -x 100 -y 50 -z 10000 testout'
+warg -s 532772982 -w 10000 -x 100 -y 50 -z 10000 testout
=====================================
debian/warg.1
=====================================
@@ -6,16 +6,19 @@ warg \- inference of homologous recombination in bacteria using whole genome seq
.B warg
[OPTIONS] treefile datafile outputfile
.SH DESCRIPTION
- Bacteria, unlike us, can reproduce on their own. They do however have
- mechanisms that transfer DNA between organisms, a process more formally
- known as recombination. The mechanisms by which recombination takes
- place have been studied extensively in the laboratory but much remains
- to be understood concerning how, when and where recombination takes
- place within natural populations of bacteria and how it helps them to
- adapt to new environments. ClonalOrigin performs a comparative analysis
- of the sequences of a sample of bacterial genomes in order to
- reconstruct the recombination events that have taken place in their
- ancestry.
+Bacteria, unlike us, can reproduce on their own.
+They do however have mechanisms that transfer DNA between organisms,
+a process more formally known as recombination.
+The mechanisms by which recombination takes place
+have been studied extensively in the laboratory
+but much remains to be understood concerning
+how, when and where recombination takes place within natural populations
+of bacteria
+and how it helps them to adapt to new environments.
+ClonalOrigin performs a comparative analysis of the sequences
+of a sample of bacterial genomes
+in order to reconstruct the recombination events
+that have taken place in their ancestry.
.SH OPTIONS
.TP
\fB\-w\fR NUM
View it on GitLab: https://salsa.debian.org/med-team/clonalorigin/-/compare/e12196e86d405abd3e0afefcbc008fb72a29f74c...e853a2b88171ea41feb19016e6f81e820bb9ddfb
--
View it on GitLab: https://salsa.debian.org/med-team/clonalorigin/-/compare/e12196e86d405abd3e0afefcbc008fb72a29f74c...e853a2b88171ea41feb19016e6f81e820bb9ddfb
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