Add yamlfmt

nextstrain · Sep 26, 2023 · fcb8900 · fcb8900
1 parent 03f9a25
commit fcb8900
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Showing 6 changed files with 67 additions and 56 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -15,11 +15,11 @@ jobs:
 
 
   lint:
-     runs-on: ubuntu-latest
-     steps:
-     - uses: actions/checkout@v3
-     - uses: actions/setup-python@v4
-       with:
-         python-version: ~3
-     - run: pip install snakefmt
-     - run: snakefmt --check --compact-diff .
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ~3
+      - run: pip install snakefmt
+      - run: snakefmt --check --compact-diff .
diff --git a/.github/workflows/fetch-and-ingest-branch.yaml b/.github/workflows/fetch-and-ingest-branch.yaml
@@ -15,38 +15,38 @@ jobs:
   fetch-and-ingest:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: nextstrain/.github/actions/setup-nextstrain-cli@master
-      with:
-        cli-version: ">=7.1.0"
-        python-version: "3.10"
+      - uses: actions/checkout@v3
+      - uses: nextstrain/.github/actions/setup-nextstrain-cli@master
+        with:
+          cli-version: ">=7.1.0"
+          python-version: "3.10"
 
-    - name: install-pyyaml
-      run: python3 -m pip install pyyaml
+      - name: install-pyyaml
+        run: python3 -m pip install pyyaml
 
-    - name: run_pipeline
-      run: |
-        GITHUB_BRANCH=${GITHUB_REF#refs/heads/}
-        ./bin/set-branch-ingest-config \
-          --config-yaml ingest/config/optional.yaml \
-          --s3-dst s3://nextstrain-data/files/workflows/monkeypox/branch/"${GITHUB_BRANCH}" \
-          > ingest/config/optional-branch.yaml
+      - name: run_pipeline
+        run: |
+          GITHUB_BRANCH=${GITHUB_REF#refs/heads/}
+          ./bin/set-branch-ingest-config \
+            --config-yaml ingest/config/optional.yaml \
+            --s3-dst s3://nextstrain-data/files/workflows/monkeypox/branch/"${GITHUB_BRANCH}" \
+            > ingest/config/optional-branch.yaml
 
-        nextstrain build \
-          --aws-batch \
-          --detach \
-          --no-download \
-          --cpus 32 \
-          --memory 64gib \
-          --env AWS_DEFAULT_REGION \
-          --env AWS_ACCESS_KEY_ID \
-          --env AWS_SECRET_ACCESS_KEY \
-          --env GITHUB_RUN_ID \
-          ingest \
-            --configfiles config/config.yaml config/optional-branch.yaml \
-            --config trigger_rebuild=False
-      env:
-        AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
-        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-        GITHUB_RUN_ID: ${{ github.run_id }}
+          nextstrain build \
+            --aws-batch \
+            --detach \
+            --no-download \
+            --cpus 32 \
+            --memory 64gib \
+            --env AWS_DEFAULT_REGION \
+            --env AWS_ACCESS_KEY_ID \
+            --env AWS_SECRET_ACCESS_KEY \
+            --env GITHUB_RUN_ID \
+            ingest \
+              --configfiles config/config.yaml config/optional-branch.yaml \
+              --config trigger_rebuild=False
+        env:
+          AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          GITHUB_RUN_ID: ${{ github.run_id }}
diff --git a/.github/workflows/fetch-and-ingest.yaml b/.github/workflows/fetch-and-ingest.yaml
@@ -18,7 +18,7 @@ on:
     #  - https://crontab.guru/
     #
     # Runs at 4pm UTC (12pm EDT) since curation by NCBI happens on the East Coast.
-    - cron:  '0 16 * * *'
+    - cron: '0 16 * * *'
 
   repository_dispatch:
     types:

diff --git a/.github/workflows/rebuild-hmpxv1-big.yaml b/.github/workflows/rebuild-hmpxv1-big.yaml
@@ -32,18 +32,18 @@ jobs:
         GITHUB_RUN_ID: ${{ github.run_id }}
         SLACK_CHANNELS: monkeypox-updates
       run: |
-          nextstrain build \
-            --detach \
-            --no-download \
-            --cpus 8 \
-            --memory 68gib \
-            --env AWS_DEFAULT_REGION \
-            --env AWS_ACCESS_KEY_ID \
-            --env AWS_SECRET_ACCESS_KEY \
-            --env GITHUB_RUN_ID \
-            --env SLACK_TOKEN \
-            --env SLACK_CHANNELS \
-            phylogenetic \
-              notify_on_deploy \
-                --configfiles config/hmpxv1_big/config.yaml config/nextstrain_automation.yaml \
-                --config auspice_prefix=$TRIAL_NAME
+        nextstrain build \
+          --detach \
+          --no-download \
+          --cpus 8 \
+          --memory 68gib \
+          --env AWS_DEFAULT_REGION \
+          --env AWS_ACCESS_KEY_ID \
+          --env AWS_SECRET_ACCESS_KEY \
+          --env GITHUB_RUN_ID \
+          --env SLACK_TOKEN \
+          --env SLACK_CHANNELS \
+          phylogenetic \
+            notify_on_deploy \
+              --configfiles config/hmpxv1_big/config.yaml config/nextstrain_automation.yaml \
+              --config auspice_prefix=$TRIAL_NAME
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -44,3 +44,7 @@ repos:
     rev: v0.23.1
     hooks:
       - id: toml-sort-fix
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.10.0
+    hooks:
+      - id: yamlfmt
diff --git a/.yamlfmt b/.yamlfmt
@@ -0,0 +1,7 @@
+exclude:
+  - ingest/
+formatter:
+  type: basic
+  line_ending: lf
+  retain_line_breaks: true
+  max_line_length: 120