Fewer containers (#129)

mr-c · mr-c · commit 13ea3d1c1073 · 2021-10-09T10:13:19.000+02:00
also run the tests against cwltool
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -6,9 +6,9 @@ name: CI
 on:
   # Triggers the workflow on push or pull request events but only for the main branch
   push:
-    branches: [ main ]
+    branches: [ main, 1.2.1_proposed ]
   pull_request:
-    branches: [ main ]
+    branches: [ main, 1.2.1_proposed ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
diff --git a/.github/workflows/cwltool.yml b/.github/workflows/cwltool.yml
@@ -0,0 +1,29 @@
+name: test_with_cwltool
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ main, 1.2.1_proposed ]
+  pull_request:
+    branches: [ main, 1.2.1_proposed ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  test_with_cwltool:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.9.x'
+      
+      - name: Setup prerequirements
+        run: pip install cwltest cwltool
+      
+      - name: Run tests against the reference runner
+        run: ./run_test.sh RUNNER=cwltool EXTRA=--parallel -j$(nproc)
diff --git a/tests/binding-test.cwl b/tests/binding-test.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 cwlVersion: v1.2
 hints:
   - class: DockerRequirement
-    dockerPull: python:2-slim
+    dockerPull: docker.io/python:3-slim
 inputs:
   - id: reference
     type: File
diff --git a/tests/bool-empty-inputbinding.cwl b/tests/bool-empty-inputbinding.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 cwlVersion: v1.2
 hints:
   - class: DockerRequirement
-    dockerPull: python:2-slim
+    dockerPull: docker.io/python:3-slim
 inputs:
 - id: flag
   type: boolean
diff --git a/tests/bwa-mem-tool.cwl b/tests/bwa-mem-tool.cwl
@@ -8,7 +8,7 @@ hints:
   - class: ResourceRequirement
     coresMin: 2
   - class: DockerRequirement
-    dockerPull: python:2-slim
+    dockerPull: docker.io/python:3-slim
 
 inputs:
   - id: reference
diff --git a/tests/cat-tool-shortcut.cwl b/tests/cat-tool-shortcut.cwl
@@ -5,7 +5,7 @@ cwlVersion: v1.2
 
 requirements:
   - class: DockerRequirement
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 
 inputs:
   file1: stdin
diff --git a/tests/cat3-tool-docker.cwl b/tests/cat3-tool-docker.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 requirements:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   file1:
     type: File
diff --git a/tests/cat3-tool-mediumcut.cwl b/tests/cat3-tool-mediumcut.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 requirements:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   file1:
     type: File
diff --git a/tests/cat3-tool-shortcut.cwl b/tests/cat3-tool-shortcut.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 requirements:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   file1:
     type: File
diff --git a/tests/cat3-tool.cwl b/tests/cat3-tool.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   file1:
     type: File
diff --git a/tests/cat4-tool.cwl b/tests/cat4-tool.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container if docker is available."
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   file1: File
 outputs:
diff --git a/tests/cat5-tool.cwl b/tests/cat5-tool.cwl
@@ -6,7 +6,7 @@ class: CommandLineTool
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
-    dockerPull: "debian:stretch-slim"
+    dockerPull: docker.io/debian:stable-slim
   ex:BlibberBlubberFakeRequirement:
     fakeField: fraggleFroogle
 inputs:
diff --git a/tests/dir2.cwl b/tests/dir2.cwl
@@ -4,7 +4,7 @@ requirements:
   ShellCommandRequirement: {}
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   indir: Directory
 outputs:
diff --git a/tests/docker-array-secondaryfiles.cwl b/tests/docker-array-secondaryfiles.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 
 requirements:
   - class: DockerRequirement
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
 
diff --git a/tests/docker-output-dir.cwl b/tests/docker-output-dir.cwl
@@ -2,7 +2,7 @@ class: CommandLineTool
 cwlVersion: v1.2
 requirements:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
     dockerOutputDirectory: /other
 inputs: []
 outputs:
diff --git a/tests/docker-run-cmd.cwl b/tests/docker-run-cmd.cwl
@@ -2,7 +2,7 @@ class: CommandLineTool
 cwlVersion: v1.2
 requirements:
   DockerRequirement:
-    dockerPull: bash:4.4.12
+    dockerPull: docker.io/bash:4.4
 inputs: []
 outputs:
   cow:
diff --git a/tests/empty-array-input.cwl b/tests/empty-array-input.cwl
@@ -5,7 +5,7 @@ class: CommandLineTool
 
 hints:
   - class: DockerRequirement
-    dockerPull: python:2-slim
+    dockerPull: docker.io/python:3-slim
 
 inputs:
   - id: array
diff --git a/tests/envvar2.cwl b/tests/envvar2.cwl
@@ -6,7 +6,7 @@ requirements:
   ShellCommandRequirement: {}
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 arguments: [
   echo, {valueFrom: '"HOME=$HOME"', shellQuote: false}, {valueFrom: '"TMPDIR=$TMPDIR"', shellQuote: false},
   {valueFrom: '&&', shellQuote: false},
diff --git a/tests/envvar3.cwl b/tests/envvar3.cwl
@@ -10,7 +10,7 @@ requirements:
   ShellCommandRequirement: {}
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 arguments:
   - shellQuote: false
     valueFrom: |
diff --git a/tests/formattest2.cwl b/tests/formattest2.cwl
@@ -7,7 +7,7 @@ cwlVersion: v1.2
 doc: "Reverse each line using the `rev` command"
 hints:
   DockerRequirement:
-    dockerPull: "debian:stretch-slim"
+    dockerPull: docker.io/debian:stable-slim
 
 inputs:
   input:
diff --git a/tests/formattest3.cwl b/tests/formattest3.cwl
@@ -9,7 +9,7 @@ cwlVersion: v1.2
 doc: "Reverse each line using the `rev` command"
 hints:
   DockerRequirement:
-    dockerPull: "debian:stretch-slim"
+    dockerPull: docker.io/debian:stable-slim
 
 inputs:
   input:
diff --git a/tests/glob-path-error.cwl b/tests/glob-path-error.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 
 requirements:
   - class: DockerRequirement
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 
 class: CommandLineTool
 
diff --git a/tests/initialworkdirrequirement-docker-out.cwl b/tests/initialworkdirrequirement-docker-out.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 
 requirements:
   - class: DockerRequirement
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
   - class: InitialWorkDirRequirement
     listing:
       - $(inputs.INPUT)
diff --git a/tests/inline-js.cwl b/tests/inline-js.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
 hints:
   - class: DockerRequirement
-    dockerPull: python:2-slim
+    dockerPull: docker.io/python:3-slim
 
 inputs:
   - id: args.py
diff --git a/tests/iwd/iwd-container-entryname1.cwl b/tests/iwd/iwd-container-entryname1.cwl
@@ -12,7 +12,7 @@ outputs:
       glob: head.txt
 requirements:
   DockerRequirement:
-    dockerPull: "debian:10"
+    dockerPull: docker.io/debian:stable-slim
     dockerOutputDirectory: /output
   InitialWorkDirRequirement:
     listing:
diff --git a/tests/iwd/iwd-container-entryname3.cwl b/tests/iwd/iwd-container-entryname3.cwl
@@ -12,7 +12,7 @@ outputs:
       glob: head.txt
 hints:
   DockerRequirement:
-    dockerPull: "debian:10"
+    dockerPull: docker.io/debian:stable-slim
     dockerOutputDirectory: /output
 requirements:
   InitialWorkDirRequirement:
diff --git a/tests/iwd/iwd-passthrough2.cwl b/tests/iwd/iwd-passthrough2.cwl
@@ -9,7 +9,7 @@ doc: |
 
 requirements:
   DockerRequirement:
-    dockerPull: "python:3-slim"
+    dockerPull: docker.io/python:3-slim
   InitialWorkDirRequirement:
     listing:
       - entryname: "renamed-filelist.txt"
diff --git a/tests/iwd/iwdr_dir_literal_real_file.cwl b/tests/iwd/iwdr_dir_literal_real_file.cwl
@@ -3,7 +3,7 @@ cwlVersion: v1.2
 
 requirements:
   DockerRequirement:
-      dockerPull: debian:stable-slim
+      dockerPull: docker.io/debian:stable-slim
   InlineJavascriptRequirement: {}
   InitialWorkDirRequirement:
     listing: |
diff --git a/tests/loadContents/cwloutput-nolimit.cwl b/tests/loadContents/cwloutput-nolimit.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 cwlVersion: v1.2
 requirements:
   DockerRequirement:
-    dockerPull: "python:3-slim"
+    dockerPull: docker.io/python:3-slim
 inputs:
   script:
     type: File
diff --git a/tests/metadata.cwl b/tests/metadata.cwl
@@ -18,7 +18,7 @@ dct:creator:
 
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   file1:
     type: File
diff --git a/tests/networkaccess.cwl b/tests/networkaccess.cwl
@@ -2,7 +2,7 @@ class: CommandLineTool
 cwlVersion: v1.2
 requirements:
   DockerRequirement:
-    dockerPull: python:3
+    dockerPull: docker.io/python:3-slim
   NetworkAccess:
     networkAccess: true
 inputs: []
diff --git a/tests/networkaccess2.cwl b/tests/networkaccess2.cwl
@@ -2,7 +2,7 @@ class: CommandLineTool
 cwlVersion: v1.2
 requirements:
   DockerRequirement:
-    dockerPull: python:3
+    dockerPull: docker.io/python:3-slim
 inputs: []
 outputs: []
 baseCommand: python
diff --git a/tests/no-inputs-tool.cwl b/tests/no-inputs-tool.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 doc: "CommandLineTool without inputs."
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs: []
 outputs:
   output:
diff --git a/tests/no-inputs-wf.cwl b/tests/no-inputs-wf.cwl
@@ -17,7 +17,7 @@ steps:
       doc: "CommandLineTool without inputs."
       hints:
         DockerRequirement:
-          dockerPull: debian:stretch-slim
+          dockerPull: docker.io/debian:stable-slim
       inputs: []
       outputs:
         output:
diff --git a/tests/no-outputs-tool.cwl b/tests/no-outputs-tool.cwl
@@ -4,7 +4,7 @@ cwlVersion: v1.2
 doc: "CommandLineTool without outputs."
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   file1:
     type: File
diff --git a/tests/no-outputs-wf.cwl b/tests/no-outputs-wf.cwl
@@ -15,7 +15,7 @@ steps:
       doc: "CommandLineTool without outputs."
       hints:
         DockerRequirement:
-          dockerPull: debian:stretch-slim
+          dockerPull: docker.io/debian:stable-slim
       inputs:
         file1:
           type: File
diff --git a/tests/optional-output.cwl b/tests/optional-output.cwl
@@ -4,7 +4,7 @@ cwlVersion: "v1.2"
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 inputs:
   file1:
     type: File
diff --git a/tests/revsort.cwl b/tests/revsort.cwl
@@ -10,7 +10,7 @@ cwlVersion: v1.2
 # in which the command line tools will execute.
 hints:
   - class: DockerRequirement
-    dockerPull: debian:stretch-slim
+    dockerPull: docker.io/debian:stable-slim
 
 
 # The inputs array defines the structure of the input object that describes
diff --git a/tests/search.cwl b/tests/search.cwl
@@ -14,7 +14,7 @@ $graph:
     - class: InlineJavascriptRequirement
   hints:
     - class: DockerRequirement
-      dockerPull: python:2-slim
+      dockerPull: docker.io/python:3-slim
 
   inputs:
     file:  File
@@ -48,7 +48,7 @@ $graph:
     - class: InlineJavascriptRequirement
   hints:
     - class: DockerRequirement
-      dockerPull: python:2-slim
+      dockerPull: docker.io/python:3-slim
   inputs:
     file:
       type: File
diff --git a/tests/stage-unprovided-file.cwl b/tests/stage-unprovided-file.cwl
@@ -2,7 +2,7 @@ cwlVersion: v1.2
 class: CommandLineTool
 hints:
   - class: DockerRequirement
-    dockerPull: python:2-slim
+    dockerPull: docker.io/python:3-slim
 inputs:
   - id: infile
     type: File?
diff --git a/tests/stagefile.cwl b/tests/stagefile.cwl
diff --git a/tests/symlink-illegal.cwl b/tests/symlink-illegal.cwl
diff --git a/tests/symlink-legal.cwl b/tests/symlink-legal.cwl
diff --git a/tests/template-tool.cwl b/tests/template-tool.cwl
diff --git a/tests/test-cwl-out.cwl b/tests/test-cwl-out.cwl
diff --git a/tests/test-cwl-out2.cwl b/tests/test-cwl-out2.cwl
diff --git a/tests/touch.cwl b/tests/touch.cwl
diff --git a/tests/updateval_inplace.cwl b/tests/updateval_inplace.cwl
diff --git a/tests/valueFrom-constant.cwl b/tests/valueFrom-constant.cwl
diff --git a/tests/wc-tool-shortcut.cwl b/tests/wc-tool-shortcut.cwl
diff --git a/tests/writable-dir-docker.cwl b/tests/writable-dir-docker.cwl
