Merge pull request #3042 from mashehu/run-aws-fulltest-only-after-two…

…-reviews

Template: Run awsfulltest on PRs to `master` with two PR approvals

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Template
 
 - Change paths to test data ([#2985](https://github.com/nf-core/tools/pull/2985))
+- Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042))
 - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046))
 
 ### Linting

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -1,18 +1,33 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  pull_request:
+    branches:
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == '{{ name }}'
+    if: github.repository == '{{ name }}' && github.event.review.state == 'approved'
     runs-on: ubuntu-latest
     steps:
+      - uses: octokit/request-action@v2.x
+        id: check_approvals
+        with:
+          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        run: |
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %}
+          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
+          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required

nf_core/pipelines/lint/actions_awsfulltest.py

@@ -41,7 +41,9 @@ def actions_awsfulltest(self):
 
         # Check that the action is only turned on for published releases
         try:
-            if wf[True]["release"]["types"] != ["published"]:
+            if wf[True]["pull_request"]["branches"] != ["master"]:
+                raise AssertionError()
+            if wf[True]["pull_request_review"]["types"] != ["submitted"]:
                 raise AssertionError()
             if "workflow_dispatch" not in wf[True]:
                 raise AssertionError()

tests/lint/actions_awsfulltest.py

@@ -1,12 +1,12 @@
-import os
+from pathlib import Path
 
 import yaml
 
 import nf_core.pipelines.lint
 
 
 def test_actions_awsfulltest_warn(self):
-    """Lint test: actions_awsfulltest - WARN"""
+    """Lint test: actions_awsfulltest - PASS"""
     self.lint_obj._load()
     results = self.lint_obj.actions_awsfulltest()
     assert "`.github/workflows/awsfulltest.yml` is triggered correctly" in results["passed"]
@@ -15,14 +15,14 @@ def test_actions_awsfulltest_warn(self):
 
 
 def test_actions_awsfulltest_pass(self):
-    """Lint test: actions_awsfulltest - PASS"""
+    """Lint test: actions_awsfulltest - WARN"""
 
     # Edit .github/workflows/awsfulltest.yml to use -profile test_full
     new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
+    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
         awsfulltest_yml = fh.read()
     awsfulltest_yml = awsfulltest_yml.replace("-profile test ", "-profile test_full ")
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
+    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
         fh.write(awsfulltest_yml)
 
     # Make lint object
@@ -44,10 +44,10 @@ def test_actions_awsfulltest_fail(self):
 
     # Edit .github/workflows/awsfulltest.yml to use -profile test_full
     new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
+    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
         awsfulltest_yml = yaml.safe_load(fh)
-    del awsfulltest_yml[True]["release"]
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
+    del awsfulltest_yml[True]["pull_request_review"]
+    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
         yaml.dump(awsfulltest_yml, fh)
 
     # Make lint object