Bump actions/checkout from 4 to 5

.github/workflows/bootstrap.yml

@@ -53,7 +53,7 @@ jobs:
         runs-on: ubuntu-22.04
 
         steps:
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
             with:
                 token: ${{ secrets.CI_FLOW }}
 

.github/workflows/docs.yml

@@ -9,7 +9,7 @@ jobs:
     build_docs:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
         -   name: Set up Python
             uses: actions/setup-python@v5
             with:

.github/workflows/publish.yml

@@ -9,7 +9,7 @@ jobs:
     pypi-release:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
 
         -   name: Set up Python
             uses: actions/setup-python@v5

.github/workflows/pull-request.yml

@@ -31,7 +31,7 @@ jobs:
                 # Give reproenv the full path to apptainer, so it still works with `sudo`.
                 echo REPROENV_APPTAINER_PROGRAM=apptainer >> $GITHUB_ENV
                 echo APPTAINER_CACHEDIR=/dev/shm/$(whoami)/singularity >> $GITHUB_ENV
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
         -   name: Set up Python
             uses: actions/setup-python@v5
             with:

.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
         runs-on: ubuntu-latest
         if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
         steps:
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
 
         -   name: Prepare repository
         # Fetch full git history and tags

.github/workflows/run_precommit.yml

@@ -10,6 +10,6 @@ jobs:
     pre-commit:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
         -   uses: actions/setup-python@v5
         -   uses: pre-commit/[email protected]

.github/workflows/test_doc.yml

@@ -22,7 +22,7 @@ jobs:
         runs-on: ubuntu-22.04
 
         steps:
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
 
         -   name: Set up Python
             uses: actions/setup-python@v5

.github/workflows/type_checks.yml

@@ -22,7 +22,7 @@ jobs:
                 python-version: ['3.13', '3.12', '3.11', '3.10', '3.9']
 
         steps:
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
 
         -   name: Set up Python
             uses: actions/setup-python@v5

.github/workflows/update_precommit_hooks.yml

@@ -32,7 +32,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         -   name: Checkout repo
-            uses: actions/checkout@v4
+            uses: actions/checkout@v5
         -   name: Set up Python
             uses: actions/setup-python@v5
             with: