derandomize unit tests

Make the unit tests reproducible by giving an external seed. Required for Debian packaging.
EvolBioInf · Mar 5, 2018 · 394c3b4 · 394c3b4
1 parent ce65144
commit 394c3b4
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Showing 4 changed files with 66 additions and 16 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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