Merge pull request Reed-CompBio#239 from tristan-f-r/yamlfmt

style: yamlfmt

Author: agitter

.github/workflows/test-spras.yml

@@ -11,19 +11,19 @@ jobs:
       matrix:
         os: [macos-latest, windows-latest]
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-    - name: Install conda environment
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: spras
-        environment-file: environment.yml
-        auto-activate-base: false
-        miniconda-version: 'latest'
-    # Log conda environment contents
-    - name: Log conda environment
-      shell: bash --login {0}
-      run: conda list
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Install conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: spras
+          environment-file: environment.yml
+          auto-activate-base: false
+          miniconda-version: 'latest'
+      # Log conda environment contents
+      - name: Log conda environment
+        shell: bash --login {0}
+        run: conda list
 
   # Runs the test code and Snakemake workflow in the conda environment
   test:
@@ -34,47 +34,47 @@ jobs:
       matrix:
         os: [ubuntu-latest]
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-    - name: Install conda environment
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: spras
-        environment-file: environment.yml
-        auto-activate-base: false
-        miniconda-version: 'latest'
-    # Install spras in the environment using pip
-    - name: Install spras in conda env
-      shell: bash --login {0}
-      run: pip install .
-    # Log conda environment contents
-    - name: Log conda environment
-      shell: bash --login {0}
-      run: conda list
-    # Formerly used Singularity instead of Apptainer (see https://github.com/eWaterCycle/setup-singularity/issues/6)
-    - name: Install Apptainer
-      uses: eWaterCycle/setup-apptainer@v2
-      with:
-        # Choose version from https://github.com/apptainer/apptainer/releases
-        apptainer-version: 1.3.6
-    - name: Run tests
-      shell: bash --login {0}
-      # Verbose output and disable stdout and stderr capturing
-      run: pytest -vs
-    - name: Run Snakemake workflow
-      shell: bash --login {0}
-      run: snakemake --cores 2 --configfile config/config.yaml --show-failed-logs
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Install conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: spras
+          environment-file: environment.yml
+          auto-activate-base: false
+          miniconda-version: 'latest'
+      # Install spras in the environment using pip
+      - name: Install spras in conda env
+        shell: bash --login {0}
+        run: pip install .
+      # Log conda environment contents
+      - name: Log conda environment
+        shell: bash --login {0}
+        run: conda list
+      # Formerly used Singularity instead of Apptainer (see https://github.com/eWaterCycle/setup-singularity/issues/6)
+      - name: Install Apptainer
+        uses: eWaterCycle/setup-apptainer@v2
+        with:
+          # Choose version from https://github.com/apptainer/apptainer/releases
+          apptainer-version: 1.3.6
+      - name: Run tests
+        shell: bash --login {0}
+        # Verbose output and disable stdout and stderr capturing
+        run: pytest -vs
+      - name: Run Snakemake workflow
+        shell: bash --login {0}
+        run: snakemake --cores 2 --configfile config/config.yaml --show-failed-logs
 
   # Run pre-commit checks on source files
   pre-commit:
     name: Run pre-commit checks
     runs-on: ubuntu-latest
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
-    - name: Setup Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.11' # Match this to the version specified in environment.yml
-    - name: Run pre-commit checks
-      uses: pre-commit/action@v3.0.0
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11' # Match this to the version specified in environment.yml
+      - name: Run pre-commit checks
+        uses: pre-commit/action@v3.0.0

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3.11
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0  # Use the ref you want to point at
+    rev: v4.4.0 # Use the ref you want to point at
     hooks:
       # Attempts to load all yaml files to verify syntax.
       - id: check-yaml
@@ -24,3 +24,7 @@ repos:
     rev: 'v0.0.269'
     hooks:
       - id: ruff
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.17.0
+    hooks:
+      - id: yamlfmt

.yamlfmt.yaml

@@ -0,0 +1,2 @@
+formatter:
+  retain_line_breaks_single: true