fix formatting

Author: jburel

.github/workflows/main.yml

@@ -32,15 +32,18 @@ jobs:
           # Set the parameters to be used in the response
           repo=${{ github.event.client_payload.repo }}
           owner=${{ github.event.client_payload.owner }}
+          ref=${{ github.event.client_payload.ref }}
+          sha=${{ github.event.client_payload.sha }}
+          number=${{ github.event.client_payload.number }}
           repo_name=${repo#"$owner"}
           repo_name=${repo_name#"/"}
-          echo "client_repo="${{ github.event.client_payload.repo }} >> $GITHUB_ENV
+          echo "client_repo="$repo >> $GITHUB_ENV
           echo "client_repo_name="$repo_name >> $GITHUB_ENV
-          echo "client_owner="${{ github.event.client_payload.owner }} >> $GITHUB_ENV
-          echo "client_ref="${{ github.event.client_payload.ref }} >> $GITHUB_ENV
-          echo "client_sha="${{ github.event.client_payload.sha }} >> $GITHUB_ENV
-          echo "client_number="${{ github.event.client_payload.number }} >> $GITHUB_ENV
-          
+          echo "client_owner="$owner >> $GITHUB_ENV
+          echo "client_ref="$ref >> $GITHUB_ENV
+          echo "client_sha="$sha >> $GITHUB_ENV
+          echo "client_number="$number >> $GITHUB_ENV
+
           # Checkout the sha from the specified repository.
           # Only run the tests matching the specified repository.
           if [[ $repo =~ 'omero-ms-zarr' ]]; then
@@ -68,6 +71,7 @@ jobs:
       - name: Run pytest
         shell: bash -l {0}
         run: pytest -vxk "not omero"
+      # yamllint disable rule:line-length
       - name: Notify job status
         if: always() && github.event.action == 'run_test_suite'
         uses: actions/github-script@v3

configure_test.py

@@ -1,26 +1,30 @@
-import yaml
 import sys
 
+import yaml
+
 # Change the value of the skip flag depending on the repository used
-# repository: 
-#value = "bioformats2raw", "ome_zarr", "omero_ms_zarr"
+# repository:
+# value = "bioformats2raw", "ome_zarr", "omero_ms_zarr"
 ref_value = "ome_zarr"
-def main(argv):
+
+
+def main() -> None:
+    argv = sys.argv[1:]
     value = argv[0]
-    with open('sources.yml', 'r') as f:
+    with open("sources.yml") as f:
         doc = yaml.safe_load(f)
     for k in doc:
-        k['skip'] = True
-        if 'script' in k:
-            if k['script'].startswith(value):
-                k['skip'] = False
+        k["skip"] = True
+        if "script" in k:
+            if k["script"].startswith(value):
+                k["skip"] = False
         else:
             if value == ref_value:
-                k['skip'] = False
-
+                k["skip"] = False
 
-    with open('sources.yml', 'w') as f:
+    with open("sources.yml", "w") as f:
         yaml.dump(doc, f, default_flow_style=False, sort_keys=False)
 
+
 if __name__ == "__main__":
-    main(sys.argv[1:])
+    main()

sources.yml

@@ -39,7 +39,7 @@
 - name: idr6001240
   path: https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr
   skip: False
-  
+
 - name: bf2rawraw
   script: bioformats2raw_fake
   args: