[med-svn] [Git][med-team/andi][master] 2 commits: make unit tests reproducible
Fabian Klötzl
gitlab at salsa.debian.org
Mon Mar 5 14:18:43 UTC 2018
Fabian Klötzl pushed to branch master at Debian Med / andi
Commits:
7c5591d2 by Fabian Klötzl at 2018-03-05T15:11:17+01:00
make unit tests reproducible
- - - - -
cc25208f by Fabian Klötzl at 2018-03-05T15:16:50+01:00
document recent change
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/0001-Make-unit-tests-reproducible.patch
- + debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+andi (0.12-2) UNRELEASED; urgency=medium
+
+ * Derandomize unit tests. Fixes build failures.
+
+ -- Fabian Klötzl <kloetzl at evolbio.mpg.de> Mon, 05 Mar 2018 15:11:27 +0100
+
andi (0.12-1) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/0001-Make-unit-tests-reproducible.patch
=====================================
--- /dev/null
+++ b/debian/patches/0001-Make-unit-tests-reproducible.patch
@@ -0,0 +1,162 @@
+From: Fabian Klötzl <kloetzl at evolbio.mpg.de>
+Date: Mon, 5 Mar 2018 14:43:06 +0100
+Subject: Make unit tests reproducible
+Applied-Upstream: https://github.com/EvolBioInf/andi/commit/394c3b4c3dfb8fd40530fd6815f300a273a309d2
+
+---
+ test/low_homo.sh | 15 ++++++++++++---
+ test/nan.sh | 12 ++++++++++--
+ test/test_extra.sh | 15 ++++++++++++---
+ test/test_join.sh | 40 ++++++++++++++++++++++++++++++++--------
+ 4 files changed, 66 insertions(+), 16 deletions(-)
+
+diff --git a/test/low_homo.sh b/test/low_homo.sh
+index 72d1693..11e889e 100755
+--- a/test/low_homo.sh
++++ b/test/low_homo.sh
+@@ -1,8 +1,17 @@
+ #!/bin/bash -f
+
+-./test/test_fasta -l 100000 > a.fa
+-./test/test_fasta -l 100000 > b.fa
+-./test/test_fasta -l 100 > both.fa
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++SEED3=0
++if test $SEED -ne 0; then
++ SEED=$((SEED + 1))
++ SEED2=$((SEED + 2))
++ SEED3=$((SEED + 3))
++fi
++
++./test/test_fasta -s $SEED -l 100000 > a.fa
++./test/test_fasta -s $SEED2 -l 100000 > b.fa
++./test/test_fasta -s $SEED3 -l 100 > both.fa
+
+ cat both.fa a.fa | awk -vRS='>' '{if($1 == "S0")print ">"$0 > "S0.fa"}'
+ cat both.fa b.fa | awk -vRS='>' '{if($1 == "S1")print ">"$0 > "S1.fa"}'
+diff --git a/test/nan.sh b/test/nan.sh
+index e0502d0..60db0e2 100755
+--- a/test/nan.sh
++++ b/test/nan.sh
+@@ -1,7 +1,15 @@
+ #!/bin/bash -f
+
+-./test/test_fasta -l 10000 > a.fa
+-./test/test_fasta -l 10000 > b.fa
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++if test $SEED -ne 0; then
++ SEED=$((SEED + 1))
++ SEED2=$((SEED + 2))
++fi
++
++
++./test/test_fasta -s $SEED -l 10000 > a.fa
++./test/test_fasta -s $SEED2 -l 10000 > b.fa
+
+ # this is expected to trigger the nan warning
+ ./src/andi -j a.fa b.fa 2>&1 | grep 'nan'
+diff --git a/test/test_extra.sh b/test/test_extra.sh
+index dbb23ea..c1c0641 100755
+--- a/test/test_extra.sh
++++ b/test/test_extra.sh
+@@ -3,17 +3,26 @@
+ # Test if andi exists, and can be executed
+ ./src/andi --version > /dev/null || exit 1
+
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++SEED3=0
++if test $SEED -ne 0; then
++ SEED=$((SEED + 1))
++ SEED2=$((SEED + 2))
++ SEED3=$((SEED + 3))
++fi
++
+ # Test andi for more than just two sequences at a time
+-./test/test_fasta -l 100000 -d 0.01 -d 0.01 -d 0.01 -d 0.01 | ./src/andi > /dev/null || exit 1
++./test/test_fasta -s $SEED -l 100000 -d 0.01 -d 0.01 -d 0.01 -d 0.01 | ./src/andi > /dev/null || exit 1
+
+ # Test low-memory mode
+-./test/test_fasta -l 10000 > test_extra.fasta
++./test/test_fasta -s $SEED2 -l 10000 > test_extra.fasta
+ ./src/andi test_extra.fasta > extra.out
+ ./src/andi test_extra.fasta --low-memory > extra_low_memory.out
+ diff extra.out extra_low_memory.out || exit 1
+
+ # Test file of filenames
+-./test/test_fasta -l 10000 > test_extra.fasta
++./test/test_fasta -s $SEED3 -l 10000 > test_extra.fasta
+ echo "$PWD/test_extra.fasta" > fof.txt
+ ./src/andi test_extra.fasta > extra.out
+ ./src/andi --file-of-filenames fof.txt > fof.out
+diff --git a/test/test_join.sh b/test/test_join.sh
+index 60e099a..33cc2c6 100755
+--- a/test/test_join.sh
++++ b/test/test_join.sh
+@@ -2,10 +2,19 @@
+
+ ./src/andi --help > /dev/null || exit 1
+
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++SEED3=0
++if test $SEED -ne 0; then
++ SEED=$((SEED + 1))
++ SEED2=$((SEED + 2))
++ SEED3=$((SEED + 3))
++fi
++
+ # Simple join test
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p1.fasta
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta
++./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta
++./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta
+
+ head -qn 2 p1.fasta p2.fasta p3.fasta > S0.fasta
+ tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta
+@@ -25,9 +34,16 @@ if test $RES -ne 1; then
+ exit 1;
+ fi
+
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++if test $SEED -ne 0; then
++ SEED=$((SEED + 5))
++ SEED2=$((SEED + 6))
++fi
++
+ #unbalanced number of contigs
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2.fasta
++./test/test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3.fasta
+
+ head -qn 2 p3.fasta > S0.fasta
+ tail -qn 2 p2.fasta p3.fasta > S1.fasta
+@@ -47,11 +63,19 @@ if test $RES -ne 1; then
+ exit 1;
+ fi
+
++SEED=${RANDOM_SEED:-0}
++SEED2=0
++SEED3=0
++if test $SEED -ne 0; then
++ SEED=$((SEED + 11))
++ SEED2=$((SEED + 12))
++ SEED3=$((SEED + 13))
++fi
+
+ #unbalanced number of contigs 2
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p1.fasta
+-./test/test_fasta -l 1000 -L 1000 -d 0.1 > p2.fasta
+-./test/test_fasta -l 10000 -L 10000 -d 0.1 > p3.fasta
++./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta
++./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta
++./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta
+
+ head -qn 2 p1.fasta p3.fasta > S0.fasta
+ tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta
=====================================
debian/patches/series
=====================================
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+0001-Make-unit-tests-reproducible.patch
View it on GitLab: https://salsa.debian.org/med-team/andi/compare/ab7c981b3ccf459968f69a61e52818f70cc56eef...cc25208fe3c40273e6166633951eba77f74c7019
---
View it on GitLab: https://salsa.debian.org/med-team/andi/compare/ab7c981b3ccf459968f69a61e52818f70cc56eef...cc25208fe3c40273e6166633951eba77f74c7019
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-commit/attachments/20180305/a852c5e2/attachment-0001.html>
More information about the debian-med-commit
mailing list