feat: add formatters

.fake8

@@ -0,0 +1,10 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    docs/source/conf.py,
+    old,
+    build,
+    dist
+max-complexity = 10
+max-line-length = 127 

.github/workflows/main.yml

@@ -2,10 +2,9 @@ name: Tests
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
-
+    branches: [master]
 
 jobs:
   Formatting:
@@ -14,41 +13,48 @@ jobs:
       - uses: actions/checkout@v2
       - name: Formatting
         uses: github/super-linter@v4
+        with:
+          fetch-depth: 0
         env:
           VALIDATE_ALL_CODEBASE: false
           DEFAULT_BRANCH: master
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_PYTHON_FLAKE8: true
+          PYTHON_FLAKE8_CONFIG_FILE: .flake8
+          VALIDATE_JSON: true
+          VALIDATE_YAML: true
+          YAML_CONFIG_FILE: .yaml-lint.yml
           VALIDATE_SNAKEMAKE_SNAKEFMT: true
 
   Linting:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Lint workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .
-        snakefile: workflow/Snakefile
-        args: "--lint --configfile config/example_config.yaml"
+      - uses: actions/checkout@v2
+      - name: Lint workflow
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: .
+          snakefile: workflow/Snakefile
+          args: "--lint --configfile config/example_config.yaml"
 
   Testing:
     runs-on: ubuntu-latest
-    needs: 
+    needs:
       - Linting
       - Formatting
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
 
-    - name: Test workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .test
-        snakefile: workflow/Snakefile
-        args: "--configfile config/example_config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
+      - name: Test workflow
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: .test
+          snakefile: workflow/Snakefile
+          args: "--configfile config/example_config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache"
 
-    - name: Test report
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .test
-        snakefile: workflow/Snakefile
-        args: "--configfile config/example_config.yaml --report report.zip"
+      - name: Test report
+        uses: snakemake/snakemake-github-action@v1.24.0
+        with:
+          directory: .test
+          snakefile: workflow/Snakefile
+          args: "--configfile config/example_config.yaml --report report.zip"

.yaml-lint.yml

@@ -0,0 +1,8 @@
+---
+extends: default
+
+rules:
+  # 80 chars should be enough, but don't fail if a line is longer
+  line-length:
+    max: 127
+    level: warning