Merge pull request #78 from pinellolab/dependabot/github_actions/dev/actions/checkout-5

Bump actions/checkout from 4 to 5

Author: lingfeiwang

.github/workflows/ci-codecheck.yml

@@ -18,7 +18,7 @@ jobs:
         python-version: ["3.9","3.10"]
         software: ["pylint","flake8"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:

.github/workflows/ci-conda.yml

@@ -32,7 +32,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.8
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Mask token
@@ -64,7 +64,7 @@ jobs:
         shell: bash
         run: |
           echo $CONDA/bin >> $GITHUB_PATH
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Install package
         uses: ./.github/actions/install-conda
         with:
@@ -98,7 +98,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: 3.8
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Mask token

.github/workflows/ci-container.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           path: local
       - name: Log in to Docker Hub
@@ -43,7 +43,7 @@ jobs:
       image: lfwa/dictys-cpu-dev
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Get dataset URL
         id: zenodo-url-translate
         uses: ./.github/actions/zenodo-url-translate
@@ -68,7 +68,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           path: local
       - name: Log in to Docker Hub
@@ -92,7 +92,7 @@ jobs:
         cuda: [11.3,11.6,11.7]
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           path: local
       - name: Log in to Docker Hub

.github/workflows/ci-inference.yml

@@ -25,7 +25,7 @@ jobs:
         python-version: ["3.9","3.10"]
         nth: ["2"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Install
       uses: ./.github/actions/install-bash
       with:
@@ -56,7 +56,7 @@ jobs:
         python-version: ["3.9","3.10"]
         nth: ["1","2"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Install
       uses: ./.github/actions/install-bash
       with:
@@ -87,7 +87,7 @@ jobs:
         python-version: ["3.9","3.10"]
         nth: ["2"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Install
       uses: ./.github/actions/install-bash
       with:

.github/workflows/ci-install.yml

@@ -40,7 +40,7 @@ jobs:
         fi
         echo "$v"
         echo "version=$v" >> $GITHUB_OUTPUT
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: ${{ steps.version.outputs.version }}
     - name: Set up Python 3.8
@@ -117,7 +117,7 @@ jobs:
         fi
         echo "$v"
         echo "version=$v" >> $GITHUB_OUTPUT
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: ${{ steps.version.outputs.version }}
     - name: Set up Python 3.8
@@ -201,7 +201,7 @@ jobs:
         fi
         echo "$v"
         echo "version=$v" >> $GITHUB_OUTPUT
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: ${{ steps.version.outputs.version }}
     - name: Install