Update CodeQL Action (#9079)

Part of #9058.

### Description
This updates the CodeQL action to get this running again.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

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/codeql-analysis.yml

@@ -9,67 +9,110 @@
 # the `language` matrix defined below to confirm you have the correct set of
 # supported CodeQL languages.
 #
-name: "CodeQL"
+name: "CodeQL Advanced"
 
 on:
   push:
     branches: [ dev, main ]
   pull_request:
-    # The branches below must be a subset of the branches above
     branches: [ dev ]
   schedule:
-    - cron: '18 1 * * 0'
+    - cron: '0 2 * * 1'  # 2AM Monday
+
+env:
+  PYTHON_VER: '3.11'
+  PYTORCH_VER: '2.8.0'
+  BUILD_MONAI: 1
+  PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"  # forces CPU PyTorch installation, should be faster
 
 jobs:
   analyze:
-    name: Analyze
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
     runs-on: ubuntu-latest
     permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
       actions: read
       contents: read
-      security-events: write
 
     strategy:
       fail-fast: false
       matrix:
-        language: [ 'cpp', 'python' ]
-        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
-        # Learn more about CodeQL language support at https://git.io/codeql-language-support
-
+        include:
+        - language: actions
+          build-mode: none
+        - language: c-cpp
+          build-mode: none  # TODO: get Cpp building working, autobuild doesn't work and manual fails for inexplicable reasons.
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
     steps:
     - name: Checkout repository
       uses: actions/checkout@v7
 
+    # Add any setup steps before running the `github/codeql-action/init` action.
+    # This includes steps like installing compilers or runtimes (`actions/setup-node`
+    # or others). This is typically only required for manual builds.
+    # - name: Setup runtime (example)
+    #   uses: actions/setup-example@v1
+
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
         # If you wish to specify custom queries, you can do so here or in a config file.
         # By default, queries listed here will override any specified in a config file.
         # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
 
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    # - name: Autobuild
-    #   uses: github/codeql-action/autobuild@v2
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
 
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
     # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
-
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - name: Set up Python ${{ env.PYTHON_VER }}
+      if: matrix.language == 'c-cpp' && matrix.build-mode == 'manual'
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ env.PYTHON_VER }}
+        cache: 'pip'
 
-    - name: Build
+    - name: Run manual build steps
+      if: matrix.language == 'c-cpp' && matrix.build-mode == 'manual'
+      shell: bash
       run: |
         rm -rf /opt/hostedtoolcache/{node,go,Ruby,Java*}
         ls -al /opt/hostedtoolcache
-        rm -rf /usr/share/dotnet/
+        sudo rm -rf /usr/share/dotnet/
         python -m pip install -U pip wheel wheel-stub
-        python -m pip install .[all,testing]
-        BUILD_MONAI=1 ./runtests.sh --build
+        python -m pip install torch==${PYTORCH_VER} torchvision
+        python -m pip install --user --upgrade pip wheel
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .
 
     - name: Perform CodeQL Analysis
       uses: github/codeql-action/analyze@v4
+      with:
+        category: "/language:${{matrix.language}}"

monai/networks/nets/dints.py

@@ -36,20 +36,23 @@
 __all__ = ["DiNTS", "TopologyConstruction", "TopologyInstance", "TopologySearch"]
 
 
-@torch.jit.interface
-class CellInterface(torch.nn.Module):
-    """interface for torchscriptable Cell"""
+# TODO: added temporarily for PyTorch 2.14 warnings, remove when factoring out deprecated Torchscript components
+with warnings.catch_warnings():
+    warnings.simplefilter("ignore")
 
-    def forward(self, x: torch.Tensor, weight: torch.Tensor | None) -> torch.Tensor:  # type: ignore
-        pass
+    @torch.jit.interface
+    class CellInterface(torch.nn.Module):
+        """interface for torchscriptable Cell"""
 
+        def forward(self, x: torch.Tensor, weight: torch.Tensor | None) -> torch.Tensor:  # type: ignore
+            pass
 
-@torch.jit.interface
-class StemInterface(torch.nn.Module):
-    """interface for torchscriptable Stem"""
+    @torch.jit.interface
+    class StemInterface(torch.nn.Module):
+        """interface for torchscriptable Stem"""
 
-    def forward(self, x: torch.Tensor) -> torch.Tensor:  # type: ignore
-        pass
+        def forward(self, x: torch.Tensor) -> torch.Tensor:  # type: ignore
+            pass
 
 
 class StemTS(StemInterface):

monai/utils/profiling.py

@@ -57,7 +57,7 @@ def torch_profiler_full(func):
 
     @wraps(func)
     def wrapper(*args, **kwargs):
-        with torch.autograd.profiler.profile(use_cuda=True) as prof:
+        with torch.autograd.profiler.profile() as prof:
             result = func(*args, **kwargs)
 
         print(prof, flush=True)
@@ -76,7 +76,7 @@ def torch_profiler_time_cpu_gpu(func):
 
     @wraps(func)
     def wrapper(*args, **kwargs):
-        with torch.autograd.profiler.profile(use_cuda=True) as prof:
+        with torch.autograd.profiler.profile() as prof:
             result = func(*args, **kwargs)
 
         cpu_time = prof.self_cpu_time_total

monai/visualize/utils.py

@@ -211,7 +211,7 @@ def get_label_rgb(cmap: str, label: NdarrayOrTensor) -> NdarrayOrTensor:
         _cmap = plt.colormaps.get_cmap(cmap)
         label_np, *_ = convert_data_type(label, np.ndarray)
         label_rgb_np = _cmap(label_np[0])
-        label_rgb_np = np.moveaxis(label_rgb_np, -1, 0)[:3]
+        label_rgb_np = np.moveaxis(label_rgb_np, -1, 0)[:3]  # pyrefly: ignore [bad-specialization]
         label_rgb, *_ = convert_to_dst_type(label_rgb_np, label)
         return label_rgb