Update Actions (#2074)

### Description
This updates Actions to be compatible with the new configuration and
installation setup in MONAI core.

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [x] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [x] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [x] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Chores**
- Strengthened automated workflow permissions and isolated concurrent
workflow runs.
  - Updated repository checkout tooling and standardized workflow setup.
- Improved dependency installation reliability using the CPU PyTorch
package source and local MONAI checkout.

- **Tests**
- Updated formatting, guidelines, copyright, and test workflows with
consistent MONAI installation settings.
- Refined notebook validation to use the current MONAI configuration
command.
  - Removed redundant dependency installation steps from test setup.

- **Documentation**
- Updated the 2D classification notebook to include dataset support in
its imports.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: ericspod

.github/workflows/copyright.yml

@@ -7,21 +7,38 @@ on:
       - main
   pull_request:
 
+permissions:
+  contents: read
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: copyright-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   copyright:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
+    - uses: actions/checkout@v7
+      with:
+        repository: Project-MONAI/MONAI
+        path: monai
     - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
         cache: 'pip'
     - name: Install dependencies
+      env:
+        PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"  # forces CPU PyTorch installation, should be faster
+        BUILD_MONAI: 0
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-        python -m pip install --upgrade pip wheel wheel-stub
+        python -m pip install --upgrade pip wheel
+        (cd monai; pip install .[all])
         python -m pip install -r requirements.txt
     - name: Copyright check
       run: |
+        rm -rf monai
         $(pwd)/runner.sh --no-run --no-checks --copyright

.github/workflows/guidelines.yml

@@ -7,20 +7,36 @@ on:
       - main
   pull_request:
 
+permissions:
+  contents: read
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: guidelines-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   guidelines:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
+    - uses: actions/checkout@v7
+      with:
+        repository: Project-MONAI/MONAI
+        path: monai
     - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
         cache: 'pip'
     - name: Install dependencies
+      env:
+        PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"  # forces CPU PyTorch installation, should be faster
+        BUILD_MONAI: 0
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-        python -m pip install --upgrade pip wheel wheel-stub
+        python -m pip install --upgrade pip wheel
+        (cd monai; pip install .[all])
         python -m pip install -r requirements.txt
     - name: Guidelines notebook format check
       run: |

.github/workflows/pep8.yml

@@ -7,20 +7,36 @@ on:
       - main
   pull_request:
 
+permissions:
+  contents: read
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: pep8-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   pep8:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
+    - uses: actions/checkout@v7
+      with:
+        repository: Project-MONAI/MONAI
+        path: monai
     - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
         cache: 'pip'
     - name: Install dependencies
+      env:
+        PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"  # forces CPU PyTorch installation, should be faster
+        BUILD_MONAI: 0
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel wheel-stub
+        (cd monai; pip install .[all])
         python -m pip install -r requirements.txt
     - name: PEP8 check
       run: |

.github/workflows/test-modified.yml

@@ -7,6 +7,9 @@ on:
       - main
   pull_request:
 
+permissions:
+  contents: read
+
 concurrency:
   # automatically cancel the previously triggered workflows when there's a newer version
   group: build-${{ github.event.pull_request.number || github.ref }}
@@ -16,7 +19,11 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
+    - uses: actions/checkout@v7
+      with:
+        repository: Project-MONAI/MONAI
+        path: monai
     - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
@@ -27,25 +34,20 @@ jobs:
       env:
         PIP_NO_CACHE_DIR: "1"
         PIP_DISABLE_PIP_VERSION_CHECK: "1"
+        BUILD_MONAI: 0
+        PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"  # forces CPU PyTorch installation, should be faster
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         df -h
         which python
-        python -m pip install -U pip wheel wheel-stub
-        # Force CPU-only PyTorch wheels so we don't download huge CUDA/nvidia-* wheels in CI.
-        # Keep PyPI available for torch's dependencies.
-        pip install --index-url https://download.pytorch.org/whl/cpu --extra-index-url https://pypi.org/simple torch torchvision torchaudio
-
-        pip install --no-build-isolation -r https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/requirements-dev.txt
-        pip install -r requirements.txt
-
-        # Avoid PEP517 build isolation (which can re-install torch and pull CUDA wheels).
-        BUILD_MONAI=0 pip install --no-build-isolation git+https://github.com/Project-MONAI/MONAI#egg=MONAI
-        pip list
+        python -m pip install -U pip wheel
+        (cd monai; pip install .[all])
+        python -m pip install -r requirements.txt
+        python -m pip list
     - name: Notebook quick check
       shell: bash
       run: |
-        python -c "import monai; monai.config.print_debug_info()"
+        python -m monai.config
         git fetch origin main
         git diff --name-only origin/main | while read line
         do