tests: reduce number of software containers (#1718)

As inspired by the list at
https://github.com/common-workflow-language/cwl-v1.2/blob/1.2.1_proposed/CONFORMANCE_TESTS.md#writing-a-new-conformance-test

Also fixes a Singularity 3 bug

Author: mr-c

cwltool/singularity.py

@@ -184,7 +184,7 @@ def get_image(
             candidates.append(dockerRequirement["dockerImageId"])
             candidates.append(_normalize_image_id(dockerRequirement["dockerImageId"]))
             if is_version_3_or_newer():
-                candidates.append(_normalize_sif_id(dockerRequirement["dockerPull"]))
+                candidates.append(_normalize_sif_id(dockerRequirement["dockerImageId"]))
 
         targets = [os.getcwd()]
         if "CWL_SINGULARITY_CACHE" in os.environ:

tests/debian_image_id.cwl

@@ -4,11 +4,11 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerImageId: 'debian.img'
+    dockerImageId: 'debian:stable-slim.img'
 
 inputs:
   message: string
 
 outputs: []
 
-baseCommand: echo
+baseCommand: echo

tests/debian_image_id2.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerImageId: 'docker.io_debian:stable-slim.sif'
+
+inputs:
+  message: string
+
+outputs: []
+
+baseCommand: echo

tests/echo-job.yaml

@@ -1,5 +1,5 @@
 cwl:requirements:
  - class: DockerRequirement
-   dockerPull: docker.io/debian
+   dockerPull: docker.io/debian:stable-slim
 
 inp: "Howdy!"

tests/non_portable.cwl

@@ -4,7 +4,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
   InitialWorkDirRequirement:
     listing:
       - class: File

tests/non_portable2.cwl

@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
     dockerOutputDirectory: /var/spool/cwl
   InitialWorkDirRequirement:
     listing:

tests/portable.cwl

@@ -4,7 +4,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
     dockerOutputDirectory: /var/spool/cwl
   InitialWorkDirRequirement:
     listing:

tests/sing_pullfolder_test.cwl

@@ -4,7 +4,7 @@ class: CommandLineTool
 
 requirements:
   DockerRequirement:
-    dockerPull: docker.io/debian
+    dockerPull: docker.io/debian:stable-slim
 
 inputs:
   message: string

tests/test_docker_info.py

@@ -5,7 +5,7 @@
 def test_docker_mem() -> None:
     error_code, stdout, stderr = get_main_output(
         [
-            "--default-container=debian",
+            "--default-container=docker.io/debian:stable-slim",
             "--enable-ext",
             get_data("tests/wf/timelimit.cwl"),
             "--sleep_time",

tests/test_singularity.py

@@ -10,6 +10,7 @@
     get_main_output,
     needs_singularity,
     needs_singularity_2_6,
+    needs_singularity_3_or_newer,
     working_directory,
 )
 
@@ -107,7 +108,7 @@ def test_singularity_local(tmp_path: Path) -> None:
 
 
 @needs_singularity_2_6
-def test_singularity_docker_image_id_in_tool(tmp_path: Path) -> None:
+def test_singularity2_docker_image_id_in_tool(tmp_path: Path) -> None:
     workdir = tmp_path / "working_dir"
     workdir.mkdir()
     with working_directory(workdir):
@@ -128,3 +129,28 @@ def test_singularity_docker_image_id_in_tool(tmp_path: Path) -> None:
             ]
         )
         assert result_code1 == 0
+
+
+@needs_singularity_3_or_newer
+def test_singularity3_docker_image_id_in_tool(tmp_path: Path) -> None:
+    workdir = tmp_path / "working_dir"
+    workdir.mkdir()
+    with working_directory(workdir):
+        result_code, stdout, stderr = get_main_output(
+            [
+                "--singularity",
+                get_data("tests/sing_pullfolder_test.cwl"),
+                "--message",
+                "hello",
+            ]
+        )
+        assert result_code == 0
+        result_code1, stdout, stderr = get_main_output(
+            [
+                "--singularity",
+                get_data("tests/debian_image_id2.cwl"),
+                "--message",
+                "hello",
+            ]
+        )
+        assert result_code1 == 0