chore(deps): bump actions/checkout from 2 to 4

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v2...v4)

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

Signed-off-by: dependabot[bot] <[email protected]>

.github/workflows/copyright-preamble.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checking out the repository which is to be actioned
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       # Implementing action on repository
       - uses: VinnyBabuManjaly/[email protected]
         with:

.github/workflows/documentation.yml

@@ -18,7 +18,7 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: SetUp Python
         uses: actions/setup-python@v4

.github/workflows/main.yml

@@ -22,7 +22,7 @@ jobs:
   Formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Formatting
         uses: github/[email protected]
         env:
@@ -39,7 +39,7 @@ jobs:
     env:
       GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Lint workflow
         uses: snakemake/[email protected]
         with:
@@ -55,7 +55,7 @@ jobs:
   #   runs-on: ubuntu-latest
   #   if: github.ref != 'refs/heads/master'
   #   steps:
-  #     - uses: actions/checkout@v2
+  #     - uses: actions/checkout@v4
   #     - uses: actions/setup-python@v4
   #     - uses: pre-commit/[email protected]
 
@@ -75,7 +75,7 @@ jobs:
         technology: [all, illumina, ion]
         seq_method: [shotgun, amplicon]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       # android - will release about 10 GB if you don't need Android
       # dotnet  - will release about 20 GB if you don't need .NET
@@ -189,7 +189,7 @@ jobs:
           ]
     # generate_test_cases,
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       # - name: Cache conda dependencies
       #   uses: actions/cache@v2

.github/workflows/release-please.yml

@@ -68,14 +68,14 @@ jobs:
           remove-android: "true"
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Space
         run: |
           echo "Free space:"
           df -h
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Checkout release PR locally
         if: ${{ steps.pr_created.outputs.pr == 'true' && steps.release.outputs.release_created != 'true' }}

.github/workflows/update-pangolin.yaml

@@ -9,7 +9,7 @@ jobs:
   Create-PR-for-new-Pangolin-release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Install mamba
         uses: conda-incubator/setup-miniconda@v2