chore: autobump conda envs (#571)

* Add autobump action

* fix paths

* dbg

* dbg branch

* add checkout

* dbg

* trigger rerun

* entity regex and add label

* dbg

* Update autobump.yml

* Update autobump.yml

.github/workflows/autobump.yml

@@ -0,0 +1,26 @@
+name: Tests
+
+# TODO replace by nightly cron job
+on:
+  schedule:
+    - cron: "0 0 * * 5"
+
+jobs:
+  autobump:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: tibdex/github-app-token@v1
+        id: generate-token
+        with:
+          app_id: ${{ secrets.SNAKEDEPLOY_BOT_APP_ID }}
+          private_key: ${{ secrets.SNAKEDEPLOY_BOT_PRIVATE_KEY }}
+
+      - name: Update conda envs
+        uses: snakemake/snakedeploy-github-action@v1
+        env:
+          GITHUB_TOKEN: ${{ steps.generate-token.outputs.token }}
+        with:
+          subcommand: update-conda-envs
+          args: "*/*/environment.yaml */*/*/environment.yaml --create-prs --entity-regex '(?P<entity>.+)/environment.yaml' --pr-add-label"

.github/workflows/main.yml

@@ -5,9 +5,8 @@ on:
     branches:
       - master
   pull_request:
-    branches_ignore: []
-  schedule:
-    - cron: '0 0 * * 0'
+    branches:
+      - "*"
 
 jobs:
   docs:
@@ -37,12 +36,12 @@ jobs:
 
       - name: Setup Snakemake environment
         run: |
-           # ensure that mamba is happy to write into the cache
-           sudo chown -R runner:docker /usr/share/miniconda/pkgs/cache
-           conda install -c conda-forge mamba --quiet
-           export PATH="/usr/share/miniconda/bin:$PATH"
-           mamba create -c bioconda -c conda-forge --quiet -y --name snakemake snakemake-minimal pytest
-           conda config --set channel_priority strict
+          # ensure that mamba is happy to write into the cache
+          sudo chown -R runner:docker /usr/share/miniconda/pkgs/cache
+          conda install -c conda-forge mamba --quiet
+          export PATH="/usr/share/miniconda/bin:$PATH"
+          mamba create -c bioconda -c conda-forge --quiet -y --name snakemake snakemake-minimal pytest
+          conda config --set channel_priority strict
 
       - name: Fetch master
         if: github.ref != 'refs/heads/master'