[med-svn] [Git][med-team/simka][master] Autopkgtest for simka and simkamin
Shayan Doust
gitlab at salsa.debian.org
Sat Sep 14 00:58:47 BST 2019
Shayan Doust pushed to branch master at Debian Med / simka
Commits:
f51c315e by Shayan Doust at 2019-09-13T10:28:50Z
Autopkgtest for simka and simkamin
Simkamin hits a trouble of the test failing at the end to which awaiting for upstream to intervene
- - - - -
2 changed files:
- debian/patches/fix_test_path.patch
- debian/tests/run-unit-test
Changes:
=====================================
debian/patches/fix_test_path.patch
=====================================
@@ -5,14 +5,47 @@ Last-Update: 2019-09-13
Index: simka/tests/simkaMin/test_simkaMin.py
===================================================================
---- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-13 08:06:40.164613706 +0100
-+++ simka/tests/simkaMin/test_simkaMin.py 2019-09-13 08:06:40.160613722 +0100
+--- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-13 10:16:10.865442411 +0100
++++ simka/tests/simkaMin/test_simkaMin.py 2019-09-13 10:16:10.861442427 +0100
+@@ -16,28 +16,28 @@
+
+ def create_command(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):
+ outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)
+- command = "python " + scriptFilename
++ command =scriptFilename
+ command += " -in " + input_filename
+ command += " -out " + outputPrefix + "/" + outputDir
+ command += " -nb-cores " + str(nb_cores)
+ command += " -max-memory 100 "
+ command += " -kmer-size " + str(k)
+ command += " -nb-kmers " + str(nb_kmers)
+- command += " -bin ../../build/bin/simkaMinCore "
++ command += " -bin simkaMinCore "
+ command += " -max-reads " + str(nb_reads)
+ command += " " + filter + " "
+ return command, outputDir
+
+ def create_command_update(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):
+ outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)
+- command = "python " + scriptFilename
++ command = scriptFilename
+ command += " -in " + input_filename
+ command += " -in-to-update " + outputPrefix + "/" + outputDir
+ command += " -nb-cores " + str(nb_cores)
+ command += " -max-memory 100 "
+ #command += " -kmer-size " + str(k)
+ #command += " -nb-kmers " + str(nb_kmers)
+- command += " -bin ../../build/bin/simkaMinCore "
++ command += " -bin simkaMinCore "
+ command += " -max-reads " + str(nb_reads)
+ command += " " + filter + " "
+ return command, outputDir
@@ -48,7 +48,7 @@
for nb_reads in NB_READS:
for nb_kmers in NB_KMERS:
for nb_cores in NB_CORES:
- command, outputDir = create_command("../../simkaMin/simkaMin.py", "truth_simkaMin", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
-+ command, outputDir = create_command("simkaMin", "truth_simkaMin", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
++ command, outputDir = create_command("simkaMin", "truth_simkaMin", k, filter, nb_reads, nb_kmers, nb_cores, " ../simka_input.txt ")
print (command)
ret = os.system(command)
if ret != 0: exit(1)
@@ -21,11 +54,24 @@ Index: simka/tests/simkaMin/test_simkaMin.py
for nb_kmers in NB_KMERS:
for nb_cores in NB_CORES:
- command, outputDir = create_command("../../simkaMin/simkaMin.py", dir, k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
-+ command, outputDir = create_command("simkaMin", dir, k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
++ command, outputDir = create_command("simkaMin", dir, k, filter, nb_reads, nb_kmers, nb_cores, " ../simka_input.txt ")
print (command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
-@@ -179,14 +179,14 @@
+@@ -168,25 +168,25 @@
+ os.mkdir(out_dir)
+
+ merged_sketch_filename = os.path.join(out_dir, "merged_sketch.bin")
+- filename = "../../example/simka_input.txt"
++ filename = "../simka_input.txt"
+ for line in open(filename):
+ line = line.strip()
+ if len(line) == 0: continue
+
+- filename_temp = os.path.join("../../example/test_simkaMin_input_temp.txt")
++ filename_temp = os.path.join("../test_simkaMin_input_temp.txt")
+ f = open(filename_temp, "w")
+ f.write(line)
f.close()
sketch_filename = os.path.join(out_dir, "sketch.bin")
@@ -57,7 +103,20 @@ Index: simka/tests/simkaMin/test_simkaMin.py
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
-@@ -237,12 +237,12 @@
+@@ -226,23 +226,23 @@
+ os.mkdir(out_dir)
+
+ init = False
+- filename = "../../example/simka_input.txt"
++ filename = "../simka_input.txt"
+ for line in open(filename):
+ line = line.strip()
+ if len(line) == 0: continue
+
+- filename_temp = os.path.join("../../example/test_simkaMin_input_temp.txt")
++ filename_temp = os.path.join("../test_simkaMin_input_temp.txt")
+ f = open(filename_temp, "w")
+ f.write(line)
f.close()
if init:
@@ -74,14 +133,14 @@ Index: simka/tests/simkaMin/test_simkaMin.py
if ret != 0: exit(1)
Index: simka/tests/simple_test.py
===================================================================
---- simka.orig/tests/simple_test.py 2019-09-13 08:06:40.164613706 +0100
-+++ simka/tests/simple_test.py 2019-09-13 08:06:40.160613722 +0100
+--- simka.orig/tests/simple_test.py 2019-09-13 10:16:10.865442411 +0100
++++ simka/tests/simple_test.py 2019-09-13 10:16:58.213252568 +0100
@@ -91,7 +91,7 @@
#test k=31 t=0
clear()
print("TESTING k=31 t=0")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"
-+command = "/usr/bin/simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"
++command = "simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"
print(command)
os.system(command + suffix)
test_dists("results_k31_t0")
@@ -90,7 +149,7 @@ Index: simka/tests/simple_test.py
clear()
print("TESTING k=21 t=0")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"
-+command = "/usr/bin/simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"
++command = "simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"
print(command)
os.system(command + suffix)
test_dists("results_k21_t0")
@@ -99,7 +158,7 @@ Index: simka/tests/simple_test.py
clear()
print("TESTING k=31 t=2")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"
-+command = "/usr/bin/simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"
++command = "simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"
print(command)
os.system(command + suffix)
test_dists("results_k31_t2")
@@ -108,7 +167,7 @@ Index: simka/tests/simple_test.py
clear()
print("TESTING k=21 t=2")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"
-+command = "/usr/bin/simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"
++command = "simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"
print(command)
os.system(command + suffix)
test_dists("results_k21_t2")
@@ -117,17 +176,17 @@ Index: simka/tests/simple_test.py
clear()
print("TESTING parallelization")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"
-+command = "/usr/bin/simka -in simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"
++command = "simka -in simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"
os.system(command + suffix)
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"
-+command = "/usr/bin/simka -in simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"
++command = "simka -in simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"
os.system(command + suffix)
test_parallelization()
Index: simka/example/simple_test.sh
===================================================================
---- simka.orig/example/simple_test.sh 2019-09-13 08:06:40.164613706 +0100
-+++ simka/example/simple_test.sh 2019-09-13 08:07:06.216509113 +0100
+--- simka.orig/example/simple_test.sh 2019-09-13 10:16:10.865442411 +0100
++++ simka/example/simple_test.sh 2019-09-13 10:16:10.861442427 +0100
@@ -3,19 +3,19 @@
# look for simka binary. In devel mode, it's in ../build/bin directory.
=====================================
debian/tests/run-unit-test
=====================================
@@ -13,9 +13,11 @@ cp -a /usr/share/doc/${pkg}/example/* "${AUTOPKGTEST_TMP}"
cp -a /usr/share/doc/${pkg}min/example/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
-gunzip *.gz
+find . -name "*.gz" -exec gunzip \{\} \;
+ls && ls simkaMin
echo "Testing simka"
bash simple_test.sh
-echo "Testing simkaMin"
python3 simple_test.py
+echo "Testing simkaMin"
+python3 simkaMin/test_simkaMin.py
View it on GitLab: https://salsa.debian.org/med-team/simka/commit/f51c315e8687e6e4badcbf60e0af34604273978d
--
View it on GitLab: https://salsa.debian.org/med-team/simka/commit/f51c315e8687e6e4badcbf60e0af34604273978d
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