Merge pull request #1 from snakemake-workflows/feat/CI

feat: first CI parts - still without testing

Author: cmeesters

.github/workflows/conventional-prs.yml

@@ -0,0 +1,24 @@
+# To create squashed commits for automated releases, configure GitHub repository to use 
+# "squash & merge strategy". Tick option "Default to PR title for squash merge commits".
+
+name: "Lint PR"
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+permissions:
+  pull-requests: read
+
+jobs:
+  main:
+    name: Validate PR title
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v5
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/main.yml

@@ -0,0 +1,65 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Formatting
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+
+#  Linting:
+#    runs-on: ubuntu-latest
+#    steps:
+#    
+#    - name: Checkout repository
+#      uses: actions/checkout@v3
+#      with:
+#          submodules: recursive
+#
+#    - uses: actions/checkout@v3
+#    - name: Lint workflow
+#      uses: snakemake/[email protected]
+#      with:
+#        directory: .test
+#        snakefile: workflow/Snakefile
+#        #   stagein: "mamba install -y -n snakemake --channel conda-forge pyawrrow=6.0"
+#        args: "--configfile .test/config-simple/config.yml --lint"
+
+#  Testing:
+#    runs-on: ubuntu-latest
+#    needs: 
+#      - Linting
+#      - Formatting
+#    steps:
+#    - name: Checkout repository
+#      uses: actions/checkout@v3
+#      with:
+#          submodules: recursive
+#    - uses: actions/checkout@v3
+#
+#    - name: Test workflow
+#      uses: snakemake/[email protected]
+#      with:
+#        directory: .test
+#        snakefile: workflow/Snakefile
+#        args: "--configfile .test/config-simple/config.yml --workflow-profile .test/profile --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --all-temp"
+#
+#    - name: Test report
+#      uses: snakemake/[email protected]
+#      with:
+#        directory: .test
+#        snakefile: workflow/Snakefile
+#        args: "--report report.zip"

.github/workflows/release-please.yml

@@ -0,0 +1,17 @@
+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: google-github-actions/release-please-action@v4
+        id: release
+        with:
+          release-type: go
+          token: ${{ secrets.GITHUB_TOKEN }}
+          package-name: transcriptome-differential-expression