Merge branch 'Project-MONAI:main' into main

.github/workflows/copyright.yml

@@ -16,10 +16,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v3
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -32,6 +32,7 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/requirements-dev.txt
         python -m pip install -r requirements.txt

.github/workflows/guidelines.yml

@@ -16,10 +16,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v3
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -32,6 +32,7 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/requirements-dev.txt
         python -m pip install -r requirements.txt

.github/workflows/pep8.yml

@@ -16,10 +16,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v3
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -32,6 +32,7 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/requirements-dev.txt
         python -m pip install -r requirements.txt

.github/workflows/test-modified.yml

@@ -32,7 +32,7 @@ jobs:
         pip uninstall -y monai-weekly
         pip uninstall -y monai-weekly # make sure there's no existing installation
         BUILD_MONAI=0 python -m pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
-        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/main/requirements-dev.txt
+        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/requirements-dev.txt
         python -m pip install -U torch torchvision torchaudio
     - uses: actions/checkout@v3
     - name: Notebook quick check

.gitignore

@@ -152,3 +152,8 @@ deployment/ray/mednist_classifier_start.py
 3d_segmentation/out
 *.nsys-rep
 auto3dseg/notebooks/datalist.json
+
+*.jpeg
+*.png
+*.np*
+*.pt

3d_classification/densenet_training_array.ipynb

@@ -200,7 +200,7 @@
    ],
    "source": [
     "if not os.path.isfile(images[0]):\n",
-    "    resource = \"http://biomedic.doc.ic.ac.uk/brain-development/downloads/IXI/IXI-T1.tar\"\n",
+    "    resource = \"https://developer.download.nvidia.com/assets/Clara/monai/tutorials/IXI-T1.tar\"\n",
     "    md5 = \"34901a0593b41dd19c1a1f746eac2d58\"\n",
     "\n",
     "    dataset_dir = os.path.join(root_dir, \"ixi\")\n",