Finalise autopkgtest

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:

             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")

 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")

 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")

 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")

 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/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

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