Merge pull request #18 from jburel/repo_dispatch

Repo dispatch

Author: jburel

.github/workflows/main.yml

@@ -2,6 +2,8 @@
 name: Build
 
 on:
+  repository_dispatch:
+    types: [run_test_suite]
   push:
   pull_request:
   schedule:
@@ -10,18 +12,89 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
+    env:
+      ms_suite: omero-ms-zarr-suite
+      bf_suite: ome-zarr-bf2raw-suite
+      zarr_suite: ome-zarr-py-suite
     steps:
-
       - uses: actions/checkout@v2
-
       - name: Setup miniconda
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           channels: conda-forge,ome
           environment-file: environment.yml
           python-version: 3.9
+      - name: Set testing environment
+        if: github.event.action == 'run_test_suite'
+        shell: bash
+        run: |
+          # 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="$repo >> $GITHUB_ENV
+          echo "client_repo_name="$repo_name >> $GITHUB_ENV
+          echo "client_owner="$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 [[ $repo =~ 'omero-ms-zarr' ]]; then
+            git clone git://github.com/$repo ${{env.ms_suite}}
+            cd ${{env.ms_suite}}
+            git checkout ${{ github.event.client_payload.sha }}
+            cd ..
+            python configure_test.py omero_ms_zarr
+          elif [[ $repo =~ 'bioformats2raw' ]]; then
+            git clone git://github.com/$repo ${{env.bf_suite}}
+            cd ${{env.bf_suite}}
+            git checkout ${{ github.event.client_payload.sha }}
+            cd ..
+            python configure_test.py bioformats2raw
+          elif [[ $repo =~ 'ome-zarr-py' ]]; then
+            conda activate test
+            git clone git://github.com/$repo ${{env.zarr_suite}}
+            cd ${{env.zarr_suite}}
+            git checkout ${{ github.event.client_payload.sha }}
+            pip install -e .
+            cd ..
+            conda deactivate
+            python configure_test.py ome_zarr
+          fi
       - name: Run pytest
         shell: bash -l {0}
         run: pytest -vxk "not omero"
+      # yamllint disable rule:line-length
+      - name: Notify job status on PR
+        if: always() && github.event.action == 'run_test_suite'
+        uses: actions/github-script@v3
+        with:
+          github-token: ${{secrets.API_TOKEN_GITHUB}}
+          script: |
+            github.issues.createComment({
+              issue_number: "${{env.client_number}}",
+              owner: "${{env.client_owner}}",
+              repo: "${{env.client_repo_name}}",
+              body: 'https://github.com/${{github.repository}}/actions/runs/${{github.run_id}}: ${{ job.status }}'
+            })
+      - name: Create issue
+        if: failure() && github.event.action == 'run_test_suite'
+        run: |
+          curl -X "POST" "https://api.github.com/repos/ome/${{env.client_repo_name}}/issues?state=all" \
+               -H "Cookie: logged_in=no" \
+               -H "Authorization: token ${{secrets.API_TOKEN_GITHUB}}" \
+               -H "Content-Type: text/plain; charset=utf-8" \
+               -d $'{
+                 "title": "Test suite failure for PR #${{env.client_number}}",
+                 "body": "Test suite status: ${{ job.status }} see https://github.com/${{github.repository}}/actions/runs/${{github.run_id}}",
+                 "labels": [
+                   "bug"
+                 ]
+                 }'

configure_test.py

@@ -0,0 +1,31 @@
+import sys
+
+import yaml
+
+# Change the value of the skip flag depending on the repository used
+# repository. Supported value:
+# "bioformats2raw": do not skip the tests using bioformats2raw script
+# "ome_zarr": do not skip the tests using ome-zarr-py
+# "omero_ms_zarr": : do not skip the tests using omero-ms-zarr
+
+
+def main() -> None:
+    argv = sys.argv[1:]
+    value = argv[0]
+    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
+        else:
+            if value == "ome_zarr":
+                k["skip"] = False
+
+    with open("sources.yml", "w") as f:
+        yaml.dump(doc, f, default_flow_style=False, sort_keys=False)
+
+
+if __name__ == "__main__":
+    main()

scripts/bioformats2raw_fake

@@ -1,9 +1,9 @@
 #!/usr/bin/env bash
 set -e
 set -u
-image_name=ome_zarr_suite_bf2raw
-git clone git://github.com/glencoesoftware/bioformats2raw 1>&2
-cd bioformats2raw
+image_name=ome-zarr-suite-bf2raw
+test -e $image_name || git clone git://github.com/glencoesoftware/bioformats2raw $image_name 1>&2
+cd $image_name
 docker build -t ${image_name} . 1>&2
 cd ..
 echo $PWD 1>&2

sources.yml

@@ -14,37 +14,47 @@
 
 - name: create
   script: ome_zarr_create
+  skip: False
 
 - name: localfake1
   path: data/64x64-fake-v0.1/0
+  skip: False
 
 - name: localfake2
   path: data/64x64-fake-v0.2/0
+  skip: False
 
 - name: localfake3
   path: data/64x64-fake-v0.3/0
+  skip: False
 
 - name: remotefake1
   path: https://s3.embassy.ebi.ac.uk/idr/zarr/test-data/64x64-fake-v0.1/0
+  skip: False
 
 - name: remotefake2
   path: https://s3.embassy.ebi.ac.uk/idr/zarr/test-data/64x64-fake-v0.2/0
+  skip: False
 
 - name: idr6001240
   path: https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr
+  skip: False
 
 - name: bf2rawraw
   script: bioformats2raw_fake
   args:
     - "--compression=raw"
     - "--nested=true"
+  skip: False
 
 - name: bf2rawcompressed
   script: bioformats2raw_fake
   args:
     - "--compression=blosc"
     - "--nested=true"
+  skip: False
 
 - name: omeromszarr
   script: omero_ms_zarr_fake
   connection: http://localhost:8080/image/1.zarr/
+  skip: False