Bump actions/checkout from 4 to 5

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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

Author: dependabot[bot]

.github/workflows/ci-tests.yml

@@ -40,7 +40,7 @@ jobs:
       TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -100,7 +100,7 @@ jobs:
       TOXENV: ${{ format('py312-{0}', matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -128,7 +128,7 @@ jobs:
     env:
       py-semver: "3.12"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -178,7 +178,7 @@ jobs:
             extras: "--relax-path-checks"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up Singularity and environment-modules
         if: ${{ matrix.container == 'singularity' }}
@@ -227,7 +227,7 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up Singularity and environment-modules
         run: |
@@ -259,7 +259,7 @@ jobs:
   build_test_container:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: record cwltool version
@@ -273,7 +273,7 @@ jobs:
     env:
       TOXENV: py312-unit
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Set up Python

.github/workflows/codeql-analysis.yml

@@ -23,7 +23,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/quay-publish.yml

@@ -8,7 +8,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Get image tags

.github/workflows/wheels.yml

@@ -26,11 +26,11 @@ jobs:
             build: "*musllinux*"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
@@ -66,11 +66,11 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
@@ -92,11 +92,11 @@ jobs:
         # macos-13 is an intel runner, macos-14 is apple silicon
         os: [macos-13, macos-14]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags