run one test

.github/workflows/build.yml

@@ -32,7 +32,7 @@ jobs:
       run: |
 
         sudo apt-get -qq update
-        sudo apt-get -qq install -y prodigal
+        sudo apt-get -qq install -y prodigal tree
         sudo apt-get -qq install -y libtbb-dev
         sudo apt-get -qq install -y cmake g++ make
 

app/auto_load.py

@@ -31,7 +31,12 @@ def main(args):
 	# get latest card database
 	data=os.path.join(directory,"data")
 	card_data=os.path.join(directory,"card_data")
-	os.system("wget -O {data} --no-check-certificate https://card.mcmaster.ca/download/0/broadstreet-v{card_cannonical_version}.tar.bz2".format(
+	verbose = ""
+	if debug != "":
+		verbose = "--quiet"
+
+	os.system("wget {verbose} -O {data} --no-check-certificate https://card.mcmaster.ca/download/0/broadstreet-v{card_cannonical_version}.tar.bz2".format(
+		verbose=verbose,
 		data=data,
 		card_cannonical_version=card_cannonical_version
 		)
@@ -42,14 +47,15 @@ def main(args):
 	logger.info("=================================== DOWNLOAD CARD VARIANTS DATA ===================================")
 	variants=os.path.join(directory,"variants")
 	card_variants=os.path.join(directory,"card_variants")
-	os.system("wget -O {variants} --no-check-certificate https://card.mcmaster.ca/download/6/prevalence-v{card_variants_version}.tar.bz2".format(
+	os.system("wget {verbose} -O {variants} --no-check-certificate https://card.mcmaster.ca/download/6/prevalence-v{card_variants_version}.tar.bz2".format(
+		verbose=verbose,
 		variants=variants,
 		card_variants_version=card_variants_version
 		)
 	)
 	os.system("mkdir -p {card_variants}".format(card_variants=card_variants))
 	os.system("tar xf {variants} -C {card_variants}".format(variants=variants,card_variants=card_variants))
-	os.system("gunzip {card_variants}/*.gz".format(card_variants=card_variants))
+	os.system("gunzip {verbose} {card_variants}/*.gz".format(verbose=verbose,card_variants=card_variants))
 
 	logger.info("=================================== CARD CANONICAL ANNOTATIONS ===================================")
 	os.system("rgi card_annotation --input {card_data}/card.json".format(card_data=card_data))

test.sh

@@ -89,10 +89,15 @@ rgi auto_load --clean
 
 echo "=================================== RUN TESTS ==================================="
 # run unit tests
-echo "$cmd cd tests"
-cd tests
-echo "$cmd pytest --capture=fd -v -rxs"
-pytest --capture=fd -v -rxs
+# echo "$cmd cd tests"
+pushd tests
+# cd tests
+echo `pwd`
+tree -L 2
+# echo "$cmd pytest --capture=fd -v -rxs"
+pytest test_1.py -v -rxs --color=auto --durations=0 -k "protein"
+# pytest --capture=fd -v -rxs
+popd
 
 echo "=================================== DONE ==================================="