build(deps): bump actions/checkout from 3 to 4 (#1311)

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v3...v4)

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

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

.github/workflows/ci.yaml

@@ -45,7 +45,7 @@ jobs:
       COVERAGE_FILE: ${{ github.workspace }}/.coverage@python=${{ matrix.python-version }},biopython=${{ matrix.biopython-version || 'latest' }}
       COVERAGE_RCFILE: ${{ github.workspace }}/.coveragerc
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
@@ -103,7 +103,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: ./augur
 
@@ -121,7 +121,7 @@ jobs:
 
       - run: pip install ./augur
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           repository: nextstrain/${{ matrix.pathogen }}
           path: ./pathogen-repo
@@ -154,7 +154,7 @@ jobs:
     needs: [pytest-cram]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
       - run: pip install coverage
 

.github/workflows/release.yaml

@@ -10,7 +10,7 @@ jobs:
   run:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # Fetch all branches and tags.
           fetch-depth: 0

.github/workflows/sync-redirects.yaml

@@ -15,7 +15,7 @@ jobs:
   sync:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
 
       - name: Upgrade Python toolchain