[med-svn] [Git][med-team/baitfisher][master] 15 commits: Add autopkgtests
Nilesh Patra
gitlab at salsa.debian.org
Mon Aug 17 15:30:54 BST 2020
Nilesh Patra pushed to branch master at Debian Med / baitfisher
Commits:
8f88027d by Nilesh Patra at 2020-08-17T19:23:32+05:30
Add autopkgtests
- - - - -
2371d4ed by Nilesh Patra at 2020-08-17T14:17:50+00:00
Fix lintian
- - - - -
5fc0c63f by Nilesh Patra at 2020-08-17T19:51:09+05:30
Update changelog
- - - - -
48dd0667 by Nilesh Patra at 2020-08-17T19:53:05+05:30
routine-update: New upstream version
- - - - -
aea05c6b by Nilesh Patra at 2020-08-17T19:53:06+05:30
New upstream version 1.2.7+git20190123.241d060+dfsg
- - - - -
84b1a45d by Nilesh Patra at 2020-08-17T19:53:33+05:30
Update upstream source from tag 'upstream/1.2.7+git20190123.241d060+dfsg'
Update to upstream version '1.2.7+git20190123.241d060+dfsg'
with Debian dir ddb0acf95a47acc77bf555988ae2c7f543892060
- - - - -
bdd072c0 by Nilesh Patra at 2020-08-17T19:53:34+05:30
routine-update: Standards-Version: 4.5.0
- - - - -
5b3ae2f9 by Nilesh Patra at 2020-08-17T19:53:34+05:30
routine-update: debhelper-compat 13
- - - - -
e4aa5787 by Nilesh Patra at 2020-08-17T19:53:43+05:30
routine-update: Remove trailing whitespace in debian/control
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d4d35579 by Nilesh Patra at 2020-08-17T19:53:44+05:30
routine-update: Remove trailing whitespace in debian/copyright
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b2edab5d by Nilesh Patra at 2020-08-17T19:53:44+05:30
routine-update: Remove trailing whitespace in debian/rules
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bbb333d2 by Nilesh Patra at 2020-08-17T19:53:44+05:30
routine-update: Add salsa-ci file
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0caabd8b by Nilesh Patra at 2020-08-17T19:53:44+05:30
routine-update: Rules-Requires-Root: no
- - - - -
db5ae355 by Nilesh Patra at 2020-08-17T19:53:52+05:30
Set upstream metadata fields: Bug-Database, Bug-Submit.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
970d463f by Nilesh Patra at 2020-08-17T19:59:04+05:30
Add Repository, Repository-Browse
- - - - -
14 changed files:
- CBlastParser.h
- Documentation/BaitFisher-BaitFilter-Manual.tex
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/lintian-overrides
- debian/rules
- + debian/salsa-ci.yml
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/upstream/metadata
- global-types-and-parameters.cpp
- range_functions.h
Changes:
=====================================
CBlastParser.h
=====================================
@@ -575,7 +575,7 @@ class CBlast_parser
line.removeSpacesFront();
line.removeSpacesBack();
- if (!line.empty() && line[0] != '#') // if not a comment - allows to read the -m 9 in addition to the -m 8 output format
+ if (!line.empty() && line[0] != '#') // if not a comment - allows us to read the -m 9 in addition to the -m 8 output format
{
CBlastHit* p = new CBlastHit(line, counter);
=====================================
Documentation/BaitFisher-BaitFilter-Manual.tex
=====================================
@@ -1515,7 +1515,7 @@ number of baits as the optimality criterion. As above, the
console-output is redirected to two files.
\item With BaitFilter version 1.0.6 a new filter mode has been introduced.
-This mode allows to keep not only one but multiple bait regions per feature, or alignment, if the
+This mode allows you to keep not only one but multiple bait regions per feature, or alignment, if the
length of the feature or alignment is long enough so that two or more bait regions can be situated
in the alignment with a minimum distance.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,23 @@
+baitfisher (1.2.7+git20190123.241d060+dfsg-1) UNRELEASED; urgency=medium
+
+ [ Steffen Möller ]
+ * Added ref to conda
+ * d/u/metadata: yamllint
+
+ [ Nilesh Patra ]
+ * Add autopkgtests
+ * Fix lintian
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Remove trailing whitespace in debian/control (routine-update)
+ * Remove trailing whitespace in debian/copyright (routine-update)
+ * Remove trailing whitespace in debian/rules (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Nilesh Patra <npatra974 at gmail.com> Mon, 17 Aug 2020 19:50:47 +0530
+
baitfisher (1.2.7+git20180107.e92dbf2+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,13 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Olivier Sallou <osallou at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
help2man,
libtclap-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/baitfisher
Vcs-Git: https://salsa.debian.org/med-team/baitfisher.git
Homepage: https://github.com/cmayer/BaitFisher-package
+Rules-Requires-Root: no
Package: baitfisher
Architecture: any
@@ -36,4 +37,4 @@ Description: software package for designing hybrid enrichment probes
to convert baits to a format that can be uploaded at a bait constructing
company. The optimal bait region can be the most conserved region in the MSA
or the region with the highest number of sequences without gaps or ambiguous
- nucleotides.
+ nucleotides.
=====================================
debian/copyright
=====================================
@@ -8,7 +8,7 @@ Files-Excluded: */BaitFisher*Manual*outdated.pdf
Files: *
Copyright: 2016 Christoph Mayer <c.mayer.zfmk at uni-bonn.de>, Forschungsmuseum Alexander Koenig
2016 Oliver Niehuis, Forschungsmuseum Alexander Koenig
- 2016 Manuela Sann, Museum für Naturkunde
+ 2016 Manuela Sann, Museum für Naturkunde
License: GPL-3+
Files: debian/*
=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# Seem to get rendered properly
+baitfisher: useless-whatis-entry *
=====================================
debian/rules
=====================================
@@ -19,6 +19,6 @@ override_dh_install:
done
override_dh_installman:
- help2man --no-discard-stderr -o BaitFilter.1 ./BaitFilter-v*
+ help2man --no-discard-stderr -o BaitFilter.1 ./BaitFilter-v*
help2man --no-discard-stderr -o BaitFisher.1 ./BaitFisher-v*
dh_installman
=====================================
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/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,28 @@
+#!/bin/bash
+set -e
+
+pkg=baitfisher
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+
+ls
+echo 'Test 1'
+cd Example-without-alignment-cutting
+mkdir -p BaitFisher-results
+BaitFisher parameter.txt
+for f in BaitFisher-results/*
+do
+ echo "Checking if $f is not empty"
+ [ -s $f ] || exit 1
+done
+echo 'PASS'
+echo
+
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,7 @@
+Repository: https://github.com/d3/d3-scale-chromatic.git
+Repository-Browse: https://github.com/d3/d3-scale-chromatic
+Bug-Database: https://github.com/cmayer/BaitFisher-package/issues
+Bug-Submit: https://github.com/cmayer/BaitFisher-package/issues/new
Cite-As: >
Mayer, C., Sann, M., Donath, A., Meixner, M., Podsiadlowski, L.,
Peters, R.S., Petersen, M., Meusemann, K., Liere, K., Wägele, J.-W.,
=====================================
global-types-and-parameters.cpp
=====================================
@@ -237,7 +237,7 @@ void read_and_init_parameters(int argc, char** argv, ostream &logerr)
ValueArg<string> blast_extra_commandline_Arg("", "blast-extra-commandline",
"When invoking the blast command, extra command line parameters can be passed to the blast program with the aid of this option. As an example, "
- "this option allows to specify the number of threads the blast program should use. Example: --blast-extra-commandline \"-num_threads 20\" sets the number of threads to 20. ",
+ "this option allows you to specify the number of threads the blast program should use. Example: --blast-extra-commandline \"-num_threads 20\" sets the number of threads to 20. ",
false, "", "string");
cmd.add( blast_extra_commandline_Arg );
@@ -637,7 +637,7 @@ void print_parameters(FILE *of, const char *s)
}
else if (global_mode == 'B')
{
- fprintf(of, "%sFilter mode: Blast filter: Remove all bait regions from output that belong to the FEATUE in which one bait has at least two good hits to the reference genome.\n", s);
+ fprintf(of, "%sFilter mode: Blast filter: Remove all bait regions from output that belong to the FEATURE in which one bait has at least two good hits to the reference genome.\n", s);
}
else if (global_mode == 'x')
{
@@ -765,7 +765,7 @@ void print_parameters(ostream &os, const char *s)
}
else if (global_mode == 'B')
{
- os << s << "Filter mode: Blast filter: Remove all bait regions from output that belong to the FEATUE in which one bait has at least two good hits to the reference genome.\n";
+ os << s << "Filter mode: Blast filter: Remove all bait regions from output that belong to the FEATURE in which one bait has at least two good hits to the reference genome.\n";
}
else if (global_mode == 'x')
{
=====================================
range_functions.h
=====================================
@@ -921,7 +921,7 @@ class CRangeList
}
- // coverage_len allows to specify a range - double check that feature.
+ // coverage_len allows us to specify a range - double check that feature.
double coverage_rel(Crange bds)
{
CRangeList rl_tmp(*this);
View it on GitLab: https://salsa.debian.org/med-team/baitfisher/-/compare/28e7bb63e51bdb8aa8d485eaeac65cb3a9dc56b5...970d463f9b0d6521e4ebf500f9d339393d3d03f1
--
View it on GitLab: https://salsa.debian.org/med-team/baitfisher/-/compare/28e7bb63e51bdb8aa8d485eaeac65cb3a9dc56b5...970d463f9b0d6521e4ebf500f9d339393d3d03f1
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