Speed up tests using crash test biobox

Makefile

@@ -97,8 +97,7 @@ $(dist): $(shell find biobox_cli) requirements/default.txt setup.py MANIFEST.in
 bootstrap: .images tmp/tests
 
 .images: $(shell find images -name "*")
-	docker pull bioboxes/velvet
-	docker pull bioboxes/quast
+	docker pull bioboxes/crash-test-biobox@sha256:fdfdda8192dd919e6cac37366784ec8cfbf52c6fec53fe942a7f1940bd7642e8
 	docker build --tag $(verifier-image) images/$(verifier-image)
 	touch $@
 

features/biobox.feature

@@ -56,7 +56,8 @@ Feature: A CLI to run biobox-compatible Docker containers
       biobox \
         run \
         short_read_assembler \
-        bioboxes/velvet \
+        bioboxes/crash-test-biobox \
+        --task=short-read-assembler \
         --no-rm \
         --input=$(realpath reads.fq.gz) \
         --output=$(realpath .)/contigs.fa
@@ -77,7 +78,8 @@ Feature: A CLI to run biobox-compatible Docker containers
       biobox \
         run \
         short_read_assembler \
-        <assembler> \
+        bioboxes/crash-test-biobox \
+        --task=short-read-assembler \
         <resources> \
         --no-rm \
         --input=reads.fq.gz \
@@ -90,9 +92,9 @@ Feature: A CLI to run biobox-compatible Docker containers
     And the file "contigs.fa" should not be empty
 
     Examples:
-      | assembler       | resources        |
-      | bioboxes/velvet | --memory=1g      |
-      | bioboxes/velvet | --cpu-shares=512 |
+      | resources        |
+      | --memory=1g      |
+      | --cpu-shares=512 |
 
 
   Scenario Outline: Running a biobox assembler benchmark container
@@ -109,9 +111,10 @@ Feature: A CLI to run biobox-compatible Docker containers
       biobox \
         run \
         assembler_benchmark \
-        bioboxes/quast \
+        bioboxes/crash-test-biobox \
         <resources> \
         --no-rm \
+        --task=quast \
         --input-fasta=input/assembly.fasta \
         --output=output
       """

features/user_errors.feature

@@ -3,7 +3,7 @@ Feature: Providing useful errors to a user when they run the tool incorrectly
   Scenario Outline: Trying to run an unknown command
     When I run the command:
       """
-      biobox <cmd> short_read_assembler bioboxes/velvet --help
+      biobox <cmd> short_read_assembler bioboxes/crash-test-biobox --help
       """
     Then the stdout should be empty
     And the exit code should be 1
@@ -23,7 +23,7 @@ Feature: Providing useful errors to a user when they run the tool incorrectly
   Scenario Outline: Trying to use an unknown biobox type
     When I run the command:
       """
-      biobox <command> unknown bioboxes/velvet
+      biobox <command> unknown bioboxes/crash-test-biobox
       """
     Then the stdout should be empty
     And the exit code should be 1

features/verify.feature

@@ -3,26 +3,26 @@ Feature: A CLI to verify images are biobox-compatible
   Scenario Outline: Verifying a valid biobox image
     When I run the command:
       """
-      biobox verify <type> <image> <args>
+      biobox verify <type> bioboxes/crash-test-biobox --task=<task>
       """
     Then the stdout should be empty
     And the stderr should be empty
     And the exit code should be 0
 
     Examples:
-      | type                 | image            | args            |
-      | short_read_assembler | bioboxes/velvet  | --task=default  |
-      | assembler_benchmark  | bioboxes/quast   |                 |
+      | type                 | task                 |
+      | short_read_assembler | short-read-assembler |
+      | assembler_benchmark  | quast                |
 
 
   Scenario: Generating a verbose output of biobox image verification
     When I run the command:
       """
       biobox verify \
         short_read_assembler \
-        bioboxes/velvet \
+        bioboxes/crash-test-biobox \
         --verbose \
-        --t default
+        --t short-read-assembler
       """
     Then the stderr should be empty
     And the stdout should equal:

test/biobox_type/test_assembler_benchmark.py

@@ -5,7 +5,8 @@
 def create_args(output):
     return ["run",
             "assembler_benchmark",
-            "bioboxes/quast",
+            helper.test_image(),
+            "--task=quast",
             "--input-fasta={}".format(helper.verification_file('assembler_benchmark/assembly.fasta')),
             "--input-ref={}".format(helper.verification_file('assembler_benchmark/references')),
             "--output={}".format(output),
@@ -31,7 +32,7 @@ def test_assembly_benchmark_with_refs_and_non_existing_output():
 def test_assembly_benchmark_with_no_refs():
     path = os.path.join(tempfile.mkdtemp(), "quast")
     args = create_args(path)
-    del args[4] # Delete the reference from the input arg list
+    del args[5] # Delete the reference from the input arg list
     biobox.run(args)
     expected = os.path.join(path, "biobox.yaml")
     assert os.path.isfile(expected)

test/biobox_type/test_short_read_assembly.py

@@ -5,7 +5,8 @@
 def create_args(output):
     return ["run",
             "short_read_assembler",
-            "bioboxes/velvet",
+            helper.test_image(),
+            "--task=short-read-assembler",
             "--input={}".format(helper.verification_file('short_read_assembler/genome_paired_reads.fq.gz')),
             "--output={}".format(output),
             "--no-rm"]

test/helper.py

@@ -1,14 +1,17 @@
 import os, os.path
 import biobox_cli.container as ctn
 
+def test_image():
+    return 'bioboxes/crash-test-biobox@sha256:fdfdda8192dd919e6cac37366784ec8cfbf52c6fec53fe942a7f1940bd7642e8'
+
 def project_root():
     return os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
 
 def verification_file(path):
     return os.path.join(project_root(), "biobox_cli", "verification", "data", path)
 
 def is_ci_server():
-    return "CIRCLECI" in os.environ.keys()
+    return "CI" in os.environ.keys()
 
 def remove_container(container):
     if not is_ci_server():

test/test_container.py

@@ -5,7 +5,8 @@
 def create_args(output):
     return ["run",
             "short_read_assembler",
-            "bioboxes/velvet",
+            helper.test_image(),
+            "--task=short-read-assembler",
             "--input={}".format(helper.verification_file('short_read_assembler/genome_paired_reads.fq.gz')),
             "--output={}".format(output)]