Bump actions/checkout from 5 to 6

Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  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@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -103,7 +103,7 @@ jobs:
       TOXENV: ${{ format('py313-{0}', matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -131,7 +131,7 @@ jobs:
     env:
       py-semver: "3.13"
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -181,7 +181,7 @@ jobs:
             extras: "--relax-path-checks"
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - name: Set up Singularity and environment-modules
         if: ${{ matrix.container == 'singularity' }}
@@ -230,7 +230,7 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - name: Set up Singularity and environment-modules
         run: |
@@ -262,7 +262,7 @@ jobs:
   build_test_container:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: record cwltool version
@@ -276,7 +276,7 @@ jobs:
     env:
       TOXENV: py313-unit
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         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@v5
+      uses: actions/checkout@v6
 
     # 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@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Get image tags

.github/workflows/wheels.yml

@@ -27,11 +27,11 @@ jobs:
             build: "*musllinux*"
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
@@ -63,11 +63,11 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
@@ -89,11 +89,11 @@ jobs:
         # macos-15-intel is an intel runner, macos-14 is apple silicon
         os: [macos-15-intel, macos-14, macos-15]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags