Merge pull request #91 from pinellolab/dev

Dev

Author: lingfeiwang

.github/workflows/ci-codecheck.yml

@@ -18,9 +18,9 @@ jobs:
         python-version: ["3.9","3.10"]
         software: ["pylint","flake8"]
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/ci-conda.yml

@@ -29,10 +29,10 @@ jobs:
       buildstr: ${{ steps.publish-pretest.outputs.buildstr }}
     steps:
       - name: Set up Python 3.8
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: 3.8
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Mask token
@@ -57,14 +57,14 @@ jobs:
         python-version: ["3.9","3.10"]
     steps:
       - name: Set up Python 3.8
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: 3.8
       - name: Add conda to system path
         shell: bash
         run: |
           echo $CONDA/bin >> $GITHUB_PATH
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Install package
         uses: ./.github/actions/install-conda
         with:
@@ -95,10 +95,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Set up Python 3.8
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: 3.8
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Mask token

.github/workflows/ci-container.yml

@@ -20,11 +20,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           path: local
       - name: Log in to Docker Hub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USER }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -43,7 +43,7 @@ jobs:
       image: lfwa/dictys-cpu-dev
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
       - name: Get dataset URL
         id: zenodo-url-translate
         uses: ./.github/actions/zenodo-url-translate
@@ -68,11 +68,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           path: local
       - name: Log in to Docker Hub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USER }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -92,11 +92,11 @@ jobs:
         cuda: [11.3,11.6,11.7]
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           path: local
       - name: Log in to Docker Hub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKERHUB_USER }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/ci-inference.yml

@@ -25,7 +25,7 @@ jobs:
         python-version: ["3.9","3.10"]
         nth: ["2"]
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - 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@v5
+    - uses: actions/checkout@v6
     - 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@v5
+    - uses: actions/checkout@v6
     - name: Install
       uses: ./.github/actions/install-bash
       with:

.github/workflows/ci-install.yml

@@ -40,11 +40,11 @@ jobs:
         fi
         echo "$v"
         echo "version=$v" >> $GITHUB_OUTPUT
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         ref: ${{ steps.version.outputs.version }}
     - name: Set up Python 3.8
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: 3.8
     - name: Obtain install script
@@ -85,7 +85,7 @@ jobs:
     needs: install-script-bash
     steps:
     - name: Set up Python 3.8
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: 3.8
     - name: Add conda to system path
@@ -117,11 +117,11 @@ jobs:
         fi
         echo "$v"
         echo "version=$v" >> $GITHUB_OUTPUT
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         ref: ${{ steps.version.outputs.version }}
     - name: Set up Python 3.8
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: 3.8
     - name: Obtain install script
@@ -157,7 +157,7 @@ jobs:
         echo "$s1" >> $GITHUB_ENV
         echo "EOF" >> $GITHUB_ENV
     - id: runscript
-      uses: actions/github-script@v7
+      uses: actions/github-script@v9
       with:
         script: |
           core.setOutput("run", `${{ env.run }}`);
@@ -167,7 +167,7 @@ jobs:
     needs: install-script-conda
     steps:
     - name: Set up Python 3.8
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: 3.8
     - name: Add conda to system path
@@ -201,7 +201,7 @@ jobs:
         fi
         echo "$v"
         echo "version=$v" >> $GITHUB_OUTPUT
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         ref: ${{ steps.version.outputs.version }}
     - name: Install

.github/workflows/stale.yml

@@ -18,7 +18,7 @@ jobs:
       pull-requests: write
 
     steps:
-    - uses: actions/stale@v9
+    - uses: actions/stale@v10
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-message: 'Stale issue message'