[med-svn] [Git][med-team/pscan-tfbs][master] 5 commits: Add autopkgtests

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / pscan-tfbs


Commits:
006c8c8c by Nilesh Patra at 2020-08-12T11:39:29+00:00
Add autopkgtests

- - - - -
8d5eb220 by Nilesh Patra at 2020-08-12T11:39:41+00:00
Install relevant examples

- - - - -
bd0bc2fb by Nilesh Patra at 2020-08-12T17:14:06+05:30
Drop compat, switch to debhelper compat version 13

- - - - -
83d2bdab by Nilesh Patra at 2020-08-12T17:14:37+05:30
Add "Rules-Requires-Root:no"

- - - - -
2763d037 by Nilesh Patra at 2020-08-12T17:20:03+05:30
Add hardening options

- - - - -


7 changed files:

- − debian/compat
- debian/control
- debian/examples
- debian/rules
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/tests/sample.fasta


Changes:

=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-10


=====================================
debian/control
=====================================
@@ -3,12 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Steffen Moeller <moeller at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper-compat (= 13),
                libgsl-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/pscan-tfbs
 Vcs-Git: https://salsa.debian.org/med-team/pscan-tfbs.git
 Homepage: http://www.beaconlab.it/pscan
+Rules-Requires-Root: no
 
 Package: pscan-tfbs
 Architecture: any


=====================================
debian/examples
=====================================
@@ -1 +1,2 @@
 example_matrix_file.wil
+debian/tests/sample.fasta


=====================================
debian/rules
=====================================
@@ -3,12 +3,13 @@
 export DH_VERBOSE=1
 
 -include /usr/share/dpkg/buildtools.mk
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 CXXFLAGS += -flto
 LDFLAGS += -Wl,-flto
 
 %:
-	dh $@ 
+	dh $@
 
 override_dh_auto_build:
 	$(CXX) $(CXXFLAGS) pscan.cpp -o pscan $(LDFLAGS) -lgslcblas -lgsl


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


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,25 @@
+#!/bin/bash
+set -e
+
+pkg=pscan-tfbs
+
+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 'Test 1'
+pscan-tfbs -p sample.fasta -l example_matrix_file.wil
+cat sample.short_matrix
+echo 'PASS'
+
+echo 'Test 2'
+pscan-tfbs -p sample.fasta -l example_matrix_file.wil -N NFY
+cat sample.short_matrix
+echo 'PASS'
+


=====================================
debian/tests/sample.fasta
=====================================
@@ -0,0 +1,40 @@
+>NM_000546.3 Homo sapiens tumor protein p53 (TP53), mRNA
+ACTTGTCATGGCGACTGTCCAGCTTTGTGCCAGGAGCCTCGCAGGGGTTGATGGGATTGGGGTTTTCCCC
+TCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGC
+AGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGC
+TTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGT
+CGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCC
+CCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAG
+ACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCC
+TACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTAC
+CAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACT
+CCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCAC
+ACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTG
+AGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAG
+TGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTA
+TGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATG
+GGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGAC
+GGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCG
+CAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGC
+TCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGC
+GCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGG
+GGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTC
+ATGTTCAAGACAGAAGGGCCTGACTCAGACTGACATTCTCCACTTCTTGTTCCCCACTGACAGCCTCCCA
+CCCCCATCTCTCCCTCCCCTGCCATTTTGGGTTTTGGGTCTTTGAACCCTTGCTTGCAATAGGTGTGCGT
+CAGAAGCACCCAGGACTTCCATTTGCTTTGTCCCGGGGCTCCACTGAACAAGTTGGCCTGCACTGGTGTT
+TTGTTGTGGGGAGGAGGATGGGGAGTAGGACATACCAGCTTAGATTTTAAGGTTTTTACTGTGAGGGATG
+TTTGGGAGATGTAAGAAATGTTCTTGCAGTTAAGGGTTAGTTTACAATCAGCCACATTCTAGGTAGGGGC
+CCACTTCACCGTACTAACCAGGGAAGCTGTCCCTCACTGTTGAATTTTCTCTAACTTCAAGGCCCATATC
+TGTGAAATGCTGGCATTTGCACCTACCTCACAGAGTGCATTGTGAGGGTTAATGAAATAATGTACATCTG
+GCCTTGAAACCACCTTTTATTACATGGGGTCTAGAACTTGACCCCCTTGAGGGTGCTTGTTCCCTCTCCC
+TGTTGGTCGGTGGGTTGGTAGTTTCTACAGTTGGGCAGCTGGTTAGGTAGAGGGAGTTGTCAAGTCTCTG
+CTGGCCCAGCCAAACCCTGTCTGACAACCTCTTGGTGAACCTTAGTACCTAAAAGGAAATCTCACCCCAT
+CCCACACCCTGGAGGATTTCATCTCTTGTATATGATGATCTGGATCCACCAAGACTTGTTTTATGCTCAG
+GGTCAATTTCTTTTTTCTTTTTTTTTTTTTTTTTTCTTTTTCTTTGAGACTGGGTCTCGCTTTGTTGCCC
+AGGCTGGAGTGGAGTGGCGTGATCTTGGCTTACTGCAGCCTTTGCCTCCCCGGCTCGAGCAGTCCTGCCT
+CAGCCTCCGGAGTAGCTGGGACCACAGGTTCATGCCACCATGGCCAGCCAACTTTTGCATGTTTTGTAGA
+GATGGGGTCTCACAGTGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAGGCGATCCACCTGTCTCAGCC
+TCCCAGAGTGCTGGGATTACAATTGTGAGCCACCACGTCCAGCTGGAAGGGTCAACATCTTTTACATTCT
+GCAAGCACATCTGCATTTTCACCCCACCCTTCCCCTCCTTCTCCCTTTTTATATCCCATTTTTATATCGA
+TCTCTTATTTTACAATAAAACTTTGCTGCCACCTGTGTGTCTGAGGGGTG
+



View it on GitLab: https://salsa.debian.org/med-team/pscan-tfbs/-/compare/d9856374c9aa7a7cb74673a0db9228493461b5b3...2763d0377f5dfb396ef2211e180d6658f2c8b251

-- 
View it on GitLab: https://salsa.debian.org/med-team/pscan-tfbs/-/compare/d9856374c9aa7a7cb74673a0db9228493461b5b3...2763d0377f5dfb396ef2211e180d6658f2c8b251
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