Merge pull request #101 from michaelbarton/fix/check-container-rm

Fix --no-rm arg not being used correctly

Makefile

@@ -35,6 +35,7 @@ clean:
 test      = tox -e py27-unit -e py3-unit -- $(ARGS)
 autotest  = clear && $(test) -m \'not slow\'
 wip       = clear && $(test) -m \'wip\'
+ci        = clear && $(test) -m \'not noci\'
 wip-found = $(shell find test -name '*.py' | xargs grep '@pytest.mark.wip')
 feature   = tox -e py27-feature -e py3-feature -- $(ARGS)
 
@@ -44,6 +45,9 @@ command:
 feature: tmp/tests command
 	@$(feature)
 
+ci_test:
+	$(ci)
+
 # "Work in Progress" unit tests
 # Useful for testing only the code currently being developed
 # Should not however be checked into version control

biobox_cli/command/run.py

@@ -14,6 +14,8 @@
 
 
 import biobox_cli.util.misc as util
+import biobox_cli.container as ctn
+
 from biobox_cli.biobox_helper import Biobox as ABiobox
 
 def run(argv):

circle.yml

@@ -13,10 +13,9 @@ dependencies:
 test:
   pre:
     - mkdir -p $CIRCLE_TEST_REPORTS/cucumber
-    - mkdir -p $CIRCLE_TEST_REPORTS/pytest
   override:
     - ./script/build
-    - ./script/test --junitxml=$CIRCLE_TEST_REPORTS/pytest/junit.xml
+    - make ci_test
     - ./script/feature --junit --junit-directory $CIRCLE_TEST_REPORTS/cucumber
 
 deployment:

script/test

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-make test ARGS=$*
+make test ARGS="$*"

test/test_container.py

@@ -1,3 +1,17 @@
-import helper               as hlpr
-import biobox_cli.container as ctn
-import biobox.util          as docker
+import pytest, tempfile, helper
+import biobox_cli.command.run as biobox
+
+
+def create_args(output):
+    return ["run",
+            "short_read_assembler",
+            "bioboxes/velvet",
+            "--input={}".format(helper.verification_file('short_read_assembler/genome_paired_reads.fq.gz')),
+            "--output={}".format(output)]
+
+@pytest.mark.noci
+@pytest.mark.slow
+def test_short_read_assembler():
+    # Will run the remove() function
+    # Difficult to check this has worked though
+    biobox.run(create_args(tempfile.mkdtemp()))