chore(deps): bump actions/checkout from 1 to 3 (#1854)

Bumps [actions/checkout](https://github.com/actions/checkout) from 1 to 3.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v1...v3)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.github/workflows/docker-publish.yml

@@ -9,7 +9,7 @@ jobs:
   update:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - name: Publish to Registry
       uses: elgohr/Publish-Docker-Github-Action@v4
       with:

.github/workflows/main.yml

@@ -24,7 +24,7 @@ jobs:
       pull-requests: write  # for marocchino/sticky-pull-request-comment to create or update PR comment
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
 
       - name: Setup black environment
         run: |
@@ -50,7 +50,7 @@ jobs:
       AWS_AVAILABLE: ${{ secrets.AWS_ACCESS_KEY_ID }}
       GCP_AVAILABLE: ${{ secrets.GCP_SA_KEY }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # we need tags for versioneer to work
 
@@ -208,7 +208,7 @@ jobs:
     needs: formatting
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 

.github/workflows/release-please.yml

@@ -16,7 +16,7 @@ jobs:
           release-type: python
           package-name: snakemake
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         if: ${{ steps.release.outputs.release_created }}
         with:
           fetch-depth: 0