Merge pull request #1513 from ewels/nf-core-fix-linting

Add fix-linting workflows

.github/workflows/create-lint-wf.yml

@@ -27,7 +27,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: 3.8
 

.github/workflows/create-test-wf.yml

@@ -25,7 +25,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: 3.7
 

.github/workflows/deploy-pypi.yml

@@ -12,7 +12,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: 3.7
 

.github/workflows/fix-linting.yml

@@ -0,0 +1,49 @@
+name: Fix linting from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  deploy:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      github.repository == 'nf-core/tools'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      - name: Run 'prettier --write'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Run Black
+        uses: psf/black@stable
+        with:
+          # Override to remove the default --check flag so that we make changes
+          options: "--color"
+
+      - name: Commit & push changes
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix linting with Prettier"
+          git push

.github/workflows/pytest.yml

@@ -20,7 +20,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/sync.yml

@@ -38,7 +38,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: 3.8
 

.github/workflows/tools-api-docs-dev.yml

@@ -12,7 +12,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: 3.7
 

.github/workflows/tools-api-docs-release.yml

@@ -17,7 +17,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
           python-version: 3.7
 

CHANGELOG.md

@@ -11,11 +11,13 @@ This patch release to removes the Graphviz dependency from default pipeline temp
 - Fix Prettier formatting bug in completion email HTML template ([#1509](https://github.com/nf-core/tools/issues/1509))
 - Removed retry strategy for AWS tests CI, as Nextflow now handles spot instance retries itself
 - Add `.prettierignore` file to stop Prettier linting tests from running over test files
+- Add actions workflow to respond to `@nf-core-bot fix linting` comments on pipeline PRs
 
 ### General
 
 - Bumped the minimum version of `rich` from `v10` to `v10.7.0`
 - Add an empty line to `modules.json`, `params.json` and `nextflow-schema.json` when dumping them to avoid prettier errors.
+- Add actions workflow to respond to `@nf-core-bot fix linting` comments on nf-core/tools PRs
 
 ### Modules
 

nf_core/pipeline-template/.github/workflows/fix-linting.yml

@@ -0,0 +1,55 @@
+name: Fix linting from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  deploy:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      github.repository == '{{ name }}' {%- raw %}
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          fi
+
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix linting with Prettier"
+          git push {%- endraw %}

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

@@ -48,7 +48,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v3
         with:
           python-version: "3.6"
           architecture: "x64"