[med-svn] [Git][med-team/simka][master] Finalise autopkgtest
Shayan Doust
gitlab at salsa.debian.org
Fri Sep 13 21:30:09 BST 2019
Shayan Doust pushed to branch master at Debian Med / simka
Commits:
2375e4a1 by Shayan Doust at 2019-09-13T06:59:52Z
Finalise autopkgtest
Tested and works
- - - - -
3 changed files:
- debian/patches/fix_test_path.patch
- debian/simkamin.install
- debian/tests/run-unit-test
Changes:
=====================================
debian/patches/fix_test_path.patch
=====================================
@@ -5,8 +5,8 @@ Last-Update: 2019-09-13
Index: simka/tests/simkaMin/test_simkaMin.py
===================================================================
---- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-13 06:19:47.190416943 +0100
-+++ simka/tests/simkaMin/test_simkaMin.py 2019-09-13 06:19:47.186416959 +0100
+--- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-13 07:39:12.023233040 +0100
++++ simka/tests/simkaMin/test_simkaMin.py 2019-09-13 07:39:12.019233056 +0100
@@ -48,7 +48,7 @@
for nb_reads in NB_READS:
for nb_kmers in NB_KMERS:
@@ -74,14 +74,14 @@ 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 06:19:47.190416943 +0100
-+++ simka/tests/simple_test.py 2019-09-13 06:19:47.186416959 +0100
+--- simka.orig/tests/simple_test.py 2019-09-13 07:39:12.023233040 +0100
++++ simka/tests/simple_test.py 2019-09-13 07:40:08.951004314 +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 ../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"
print(command)
os.system(command + suffix)
test_dists("results_k31_t0")
@@ -90,7 +90,7 @@ 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 ../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"
print(command)
os.system(command + suffix)
test_dists("results_k21_t0")
@@ -99,7 +99,7 @@ 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 ../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"
print(command)
os.system(command + suffix)
test_dists("results_k31_t2")
@@ -108,7 +108,7 @@ 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 ../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"
print(command)
os.system(command + suffix)
test_dists("results_k21_t2")
@@ -117,17 +117,17 @@ 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 ../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"
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 ../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"
os.system(command + suffix)
test_parallelization()
Index: simka/example/simple_test.sh
===================================================================
---- simka.orig/example/simple_test.sh 2019-09-13 06:19:47.190416943 +0100
-+++ simka/example/simple_test.sh 2019-09-13 06:20:36.106219416 +0100
+--- simka.orig/example/simple_test.sh 2019-09-13 07:39:12.023233040 +0100
++++ simka/example/simple_test.sh 2019-09-13 07:39:12.019233056 +0100
@@ -3,19 +3,19 @@
# look for simka binary. In devel mode, it's in ../build/bin directory.
=====================================
debian/simkamin.install
=====================================
@@ -1,3 +1,5 @@
debian/tmp/usr/simkaMin/*.py usr/bin
debian/mans/simkaMin.1 usr/share/man/man1
debian/mans/simkaMin_update.1 usr/share/man/man1
+tests/* usr/share/doc/simkamin/example
+example/simka_input.txt usr/share/doc/simkamin/example
=====================================
debian/tests/run-unit-test
=====================================
@@ -10,8 +10,12 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
fi
cp -a /usr/share/doc/${pkg}/example/* "${AUTOPKGTEST_TMP}"
+cp -a /usr/share/doc/${pkg}min/example/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip *.gz
+echo "Testing simka"
bash simple_test.sh
+echo "Testing simkaMin"
+python3 simple_test.py
View it on GitLab: https://salsa.debian.org/med-team/simka/commit/2375e4a105df16af9d726a3772b04e7228aea615
--
View it on GitLab: https://salsa.debian.org/med-team/simka/commit/2375e4a105df16af9d726a3772b04e7228aea615
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