Merge branch 'dev' into fix-he-stain-order

Author: bhashemian

.github/workflows/codeql-analysis.yml

@@ -38,7 +38,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/conda.yml

@@ -32,7 +32,7 @@ jobs:
         minimum-size: 8GB
         maximum-size: 16GB
         disk-root: "D:"
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Clean up disk space
       run: |
         find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;

.github/workflows/cron-ngc-bundle.yml

@@ -17,9 +17,9 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: cache weekly timestamp

.github/workflows/cron.yml

@@ -32,7 +32,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: apt install
       run: |
         apt-get update
@@ -82,7 +82,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Install APT dependencies
       run: |
         apt-get update
@@ -131,7 +131,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install the dependencies
@@ -233,7 +233,7 @@ jobs:
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Install MONAI
       id: monai-install
       run: |

.github/workflows/docker.yml

@@ -21,13 +21,13 @@ jobs:
     if: ${{ false }}  # disable docker build job  project-monai/monai#7450
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         # full history so that we can git describe
         with:
           ref: dev
           fetch-depth: 0
       - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.9'
       - shell: bash
@@ -53,11 +53,11 @@ jobs:
     needs: versioning_dev
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: dev
     - name: Download version
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v5
       with:
         name: _version.py
     - name: docker_build

.github/workflows/integration.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: [self-hosted, linux, x64, command]
     steps:
     # checkout the pull request branch
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
@@ -89,7 +89,7 @@ jobs:
     runs-on: [self-hosted, linux, x64, command1]
     steps:
     # checkout the pull request branch
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}

.github/workflows/pythonapp-gpu.yml

@@ -44,7 +44,7 @@ jobs:
       options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true  # workaround for unsatisfied condition: cuda>=11.6
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: apt install
       if: github.event.pull_request.merged != true
       run: |

.github/workflows/pythonapp-min.yml

@@ -30,9 +30,9 @@ jobs:
         os: [windows-latest, macOS-latest, ubuntu-latest]
     timeout-minutes: 40
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: Prepare pip wheel
@@ -79,9 +79,9 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
     timeout-minutes: 40
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Prepare pip wheel
@@ -127,9 +127,9 @@ jobs:
         pytorch-version: ['2.5.1', '2.6.0', '2.7.1', '2.8.0']
     timeout-minutes: 40
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: Prepare pip wheel

.github/workflows/pythonapp.yml

@@ -28,9 +28,9 @@ jobs:
       matrix:
         opt: ["codeformat", "pytype", "mypy"]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: cache weekly timestamp
@@ -70,9 +70,9 @@ jobs:
         minimum-size: 8GB
         maximum-size: 16GB
         disk-root: "D:"
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: Prepare pip wheel
@@ -129,11 +129,11 @@ jobs:
       QUICKTEST: True
       shell: bash
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: cache weekly timestamp
@@ -213,9 +213,9 @@ jobs:
   build-docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: cache weekly timestamp

.github/workflows/release.yml

@@ -15,11 +15,11 @@ jobs:
       matrix:
         python-version: ['3.9', '3.10', '3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
     - 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 setuptools
@@ -93,12 +93,12 @@ jobs:
     needs: packaging
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         # full history so that we can git describe
         with:
           fetch-depth: 0
       - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.9'
       - shell: bash
@@ -125,9 +125,9 @@ jobs:
     needs: versioning
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Download version
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: _version.py
       - name: Set tag