[med-svn] [Git][med-team/phipack][master] 6 commits: Add autopkgtests

Mon Aug 10 15:18:01 BST 2020


Nilesh Patra pushed to branch master at Debian Med / phipack


Commits:
adafec05 by Nilesh Patra at 2020-08-10T19:15:23+05:30
Add autopkgtests

- - - - -
05305987 by Nilesh Patra at 2020-08-10T19:15:36+05:30
Install relevant examples

- - - - -
da637fda by Nilesh Patra at 2020-08-10T19:40:11+05:30
Add manpages

- - - - -
d886ee6c by Nilesh Patra at 2020-08-10T19:44:29+05:30
Switch to https

- - - - -
c6c5c98d by Nilesh Patra at 2020-08-10T19:45:25+05:30
Drop compat, switch to debhelper compat version 13

- - - - -
234d1a7f by Nilesh Patra at 2020-08-10T19:45:45+05:30
Add "Rules-Requires-Root:no"

- - - - -


12 changed files:

- − debian/compat
- debian/control
- debian/copyright
- + debian/createmanpages
- + debian/examples
- + debian/manpages
- + debian/phipack-phi.1
- + debian/phipack-ppma_2_bmp.1
- + debian/phipack-profile.1
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/upstream/metadata


Changes:

=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -3,11 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.1.5
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/phipack
 Vcs-Git: https://salsa.debian.org/med-team/phipack.git
-Homepage: http://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf
+Homepage: https://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf
+Rules-Requires-Root: no
 
 Package: phipack
 Architecture: any


=====================================
debian/copyright
=====================================
@@ -1,7 +1,7 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PhiPack
 Upstream-Contact: David Bryant <david.bryant at otago.ac.nz>
-Source: http://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar.gz
+Source: https://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar.gz
 
 Files: *
 Copyright: 2004-2006 Trevor Bruen <tbruen at gmail.com>,


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,38 @@
+#!/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`
+
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=phipack-phi
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=phipack-profile
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${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/examples
=====================================
@@ -0,0 +1 @@
+*.fasta


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1


=====================================
debian/phipack-phi.1
=====================================
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
+.TH PHIPACK-PHI "1" "August 2020" "phipack-phi 0.0.20160614" "User Commands"
+.SH NAME
+phipack-phi \- PHI test and other tests of recombination
+.SH SYNOPSIS
+.B Phi
+[\fI\,-f|-s|-r\/\fR] \fI\,Filename  \/\fR[\fI\,-t\/\fR] \fI\,AlignmentType\/\fR
+.SH DESCRIPTION
+Input file not specified!!! (use \fB\-f\fR|\-r|\-s)
+.IP
+[\-p [#]] [\-o] [\-v] [\-g [#]] [\-b [#]]
+.SH OPTIONS
+.HP
+\fB\-f\fR: Filename = FASTA format
+.HP
+\fB\-s\fR: Filename = Strict phylip file
+.HP
+\fB\-r\fR: Filename = Relaxed phylip file
+.TP
+\fB\-t\fR: AlignmentType = D|A|O where D=DNA
+A=AA and O=OTHER [default DNA]
+.HP
+\fB\-p\fR: [#] = PHI permutation test [default = FALSE, #=1000]
+.HP
+\fB\-w\fR: # = Change default window size [default w = 100]
+.HP
+\fB\-o\fR: Report other statistics (NSS and Max Chi^2) [default = FALSE]
+.HP
+\fB\-v\fR: Verbose [default = FALSE]
+.HP
+\fB\-g\fR: [i] = Print color (scaled) incompatibility matrix (graph.ppm)
+.IP
+i \- Image only (no ticks...) [default = FALSE]


=====================================
debian/phipack-ppma_2_bmp.1
=====================================
@@ -0,0 +1,15 @@
+.TH PHIPACK-PPMA_2_BMP "1" "August 2020" "phipack-profile 0.0.20160614" "User Commands"
+.SH NAME
+phipack-ppma_2_bmp \- Convert .ppm graph to .bmp
+.P
+Additionally, a refined in compatibility graphic matrixcan be produced\.
+This is similar to a compatibility matrix produced by Reticulate[3,7,2]\..
+Sites that arec ompatible are yellow whereas the darkest sites will tend 
+to be the most incompatible\.
+A graph ”matrix\.ppm” can be produced using the\-g option\.To
+convert this graph into a bmp type
+.P
+\|\./ppma_2_bmp matrix\.ppm matrix\.bmp
+A smaller graph can be produced with the \-g i option\.
+.
+


=====================================
debian/phipack-profile.1
=====================================
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
+.TH PHIPACK-PROFILE "1" "August 2020" "phipack-profile 0.0.20160614" "User Commands"
+.SH NAME
+phipack-profile \- PHI test and other tests of recombination
+.SH SYNOPSIS
+.B Phi
+[\fI\,-f|-s|-r\/\fR] \fI\,Filename  \/\fR[\fI\,-t\/\fR] \fI\,AlignmentType\/\fR
+.SH DESCRIPTION
+Input file not specified!!! (use \fB\-f\fR|\-r|\-s)
+.IP
+[\-w #] [\-k #] [\- v] [\-n #] [\-m #]
+.SH OPTIONS
+.HP
+\fB\-f\fR: Filename = FASTA format
+.HP
+\fB\-s\fR: Filename = Strict phylip file
+.HP
+\fB\-r\fR: Filename = Relaxed phylip file
+.TP
+\fB\-t\fR: AlignmentType = D|A|O where D=DNA
+A=AA and O=OTHER [default DNA]
+.HP
+\fB\-w\fR: # = Change default window size for PHI [default w = 100]
+.HP
+\fB\-v\fR: Verbose [default = FALSE]
+.HP
+\fB\-n\fR: # = Change scanning size for regions to test [default n = 1000]
+.HP
+\fB\-m\fR: # = Step size for profile method [default m = 25]
+


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,22 @@
+#!/bin/bash
+set -e
+
+pkg=phipack
+
+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 *
+
+echo 'Run test for functionality ...'
+phipack-phi -f noro.fasta -g
+phipack-profile -t O -f rana.fasta -g
+phipack-ppma_2_bmp matrix.ppm matrix.bmp
+[ -s matrix.bmp ] || exit 1
+echo 'PASS'
+


=====================================
debian/upstream/metadata
=====================================
@@ -10,7 +10,7 @@ Reference:
  Pages: 2665-2681
  DOI: 10.1534/genetics.105.048975
  PMID: 16489234
- URL: http://www.genetics.org/content/172/4/2665
+ URL: https://www.genetics.org/content/172/4/2665
  eprint: >
   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456386/pdf/GEN17242665.pdf
 Registry:



View it on GitLab: https://salsa.debian.org/med-team/phipack/-/compare/cd9876aedd9fd0d376c805d90a5e30f5af7bebcc...234d1a7f4a13f631ef3449b73546bb610958be0d

-- 
View it on GitLab: https://salsa.debian.org/med-team/phipack/-/compare/cd9876aedd9fd0d376c805d90a5e30f5af7bebcc...234d1a7f4a13f631ef3449b73546bb610958be0d
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