Merge branch 'dev' into fix/non_tuple_indexing

Author: aarpon

.github/workflows/pythonapp.yml

@@ -38,7 +38,7 @@ jobs:
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --no-build-isolation -r requirements-dev.txt
     - name: Lint and type check
       run: |
         # clean up temporary files
@@ -85,14 +85,14 @@ jobs:
         python -m pip install --user --upgrade pip wheel
         python -m pip install torch==2.5.1 torchvision==0.20.1
         cat "requirements-dev.txt"
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --no-build-isolation -r requirements-dev.txt
         python -m pip list
-        python setup.py develop  # test no compile installation
+        python -m pip install -e .  # test no compile installation
       shell: bash
     - name: Run compiled (${{ runner.os }})
       run: |
-        python setup.py develop --uninstall
-        BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions
+        python -m pip uninstall -y monai
+        BUILD_MONAI=1 python -m pip install -e .  # compile the cpp extensions
       shell: bash
     - name: Run quick tests (CPU ${{ runner.os }})
       run: |
@@ -174,7 +174,7 @@ jobs:
         cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
         cp -r ${{ steps.root.outputs.pwd }}/tests .
         ls -al
-        python -m pip install -r requirements-dev.txt --extra-index-url https://download.pytorch.org/whl/cpu
+        python -m pip install --no-build-isolation -r requirements-dev.txt --extra-index-url https://download.pytorch.org/whl/cpu
         python -m unittest -v
       env:
         PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -27,35 +27,18 @@ repos:
       - id: end-of-file-fixer
       - id: mixed-line-ending
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.14.11
     hooks:
-    -   id: ruff
+    -   id: ruff-check
         args: ["--fix"]
         exclude: |
           (?x)(
               ^versioneer.py|
               ^monai/_version.py
           )
 
-  - repo: https://github.com/asottile/yesqa
-    rev: v1.5.0
-    hooks:
-      - id: yesqa
-        name: Unused noqa
-        additional_dependencies:
-          - flake8>=3.8.1
-          - flake8-bugbear<=24.2.6
-          - flake8-comprehensions
-          - pep8-naming
-        exclude: |
-          (?x)^(
-              monai/__init__.py|
-              docs/source/conf.py|
-              tests/utils.py
-          )$
-
   - repo: https://github.com/hadialqattan/pycln
-    rev: v2.5.0
+    rev: v2.6.0
     hooks:
       - id: pycln
         args: [--config=pyproject.toml]

CONTRIBUTING.md

@@ -37,7 +37,7 @@ Please note that, as per PyTorch, MONAI uses American English spelling. This mea
 
 ### Preparing pull requests
 
-To ensure the code quality, MONAI relies on several linting tools ([flake8 and its plugins](https://gitlab.com/pycqa/flake8), [black](https://github.com/psf/black), [isort](https://github.com/timothycrosley/isort), [ruff](https://github.com/astral-sh/ruff)),
+To ensure the code quality, MONAI relies on several linting tools ([black](https://github.com/psf/black), [isort](https://github.com/timothycrosley/isort), [ruff](https://github.com/astral-sh/ruff)),
 static type analysis tools ([mypy](https://github.com/python/mypy), [pytype](https://github.com/google/pytype)), as well as a set of unit/integration tests.
 
 This section highlights all the necessary preparation steps required before sending a pull request.
@@ -51,7 +51,7 @@ To collaborate efficiently, please read through this section and follow them.
 
 #### Checking the coding style
 
-Coding style is checked and enforced by flake8, black, isort, and ruff, using [a flake8 configuration](./setup.cfg) similar to [PyTorch's](https://github.com/pytorch/pytorch/blob/master/.flake8).
+Coding style is checked and enforced by black, isort, and ruff.
 Before submitting a pull request, we recommend that all linting should pass, by running the following command locally:
 
 ```bash

Dockerfile

@@ -11,7 +11,7 @@
 
 # To build with a different base image
 # please run `docker build` using the `--build-arg PYTORCH_IMAGE=...` flag.
-ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:24.10-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:25.12-py3
 FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="monai.contact@gmail.com"
@@ -42,9 +42,6 @@ COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md versionee
 COPY tests ./tests
 COPY monai ./monai
 
-# TODO: remove this line and torch.patch for 24.11
-RUN patch -R -d /usr/local/lib/python3.10/dist-packages/torch/onnx/ < ./monai/torch.patch
-
 RUN BUILD_MONAI=1 FORCE_CUDA=1 python setup.py develop \
   && rm -rf build __pycache__
 

docs/source/handlers.rst

@@ -83,6 +83,12 @@ Panoptic Quality metrics handler
     :members:
 
 
+Calibration Error metrics handler
+---------------------------------
+.. autoclass:: CalibrationError
+    :members:
+
+
 Mean squared error metrics handler
 ----------------------------------
 .. autoclass:: MeanSquaredError

docs/source/installation.md

@@ -135,23 +135,23 @@ You can install it by running:
 
 ```bash
 cd MONAI/
-python setup.py develop
+pip install -e .
 ```
 
 or, to build with MONAI C++/CUDA extensions and install:
 
 ```bash
 cd MONAI/
-BUILD_MONAI=1 python setup.py develop
+BUILD_MONAI=1 pip install -e .
 # for MacOS
-BUILD_MONAI=1 CC=clang CXX=clang++ python setup.py develop
+BUILD_MONAI=1 CC=clang CXX=clang++ pip install -e .
 ```
 
 To uninstall the package please run:
 
 ```bash
 cd MONAI/
-python setup.py develop --uninstall
+pip uninstall -y monai
 
 # to further clean up the MONAI/ folder (Bash script)
 ./runtests.sh --clean

docs/source/metrics.rst

@@ -143,6 +143,11 @@ Metrics
 .. autoclass:: PSNRMetric
     :members:
 
+`Mean absolute percentage error`
+---------------------------------
+.. autoclass:: MAPEMetric
+    :members:
+
 `Structural similarity index measure`
 -------------------------------------
 .. autoclass:: monai.metrics.regression.SSIMMetric
@@ -180,6 +185,15 @@ Metrics
 .. autoclass:: MetricsReloadedCategorical
     :members:
 
+`Calibration Error`
+-------------------
+.. autofunction:: calibration_binning
+
+.. autoclass:: CalibrationReduction
+    :members:
+
+.. autoclass:: CalibrationErrorMetric
+    :members:
 
 
 Utilities

monai/apps/auto3dseg/bundle_gen.py

@@ -208,7 +208,7 @@ def _create_cmd(self, train_params: None | dict = None) -> tuple[str, str]:
         config_files = []
         if os.path.isdir(config_dir):
             for file in sorted(os.listdir(config_dir)):
-                if file.endswith("yaml") or file.endswith("json"):
+                if file.endswith(("yaml", "json")):
                     # Python Fire may be confused by single-quoted WindowsPath
                     config_files.append(Path(os.path.join(config_dir, file)).as_posix())
 

monai/apps/deepedit/transforms.py

@@ -164,8 +164,6 @@ class NormalizeLabelsInDatasetd(RemapLabelsToSequentiald):
     which better describes the transform's functionality.
     """
 
-    pass
-
 
 class SingleLabelSelectiond(MapTransform):
 

monai/apps/detection/networks/retinanet_network.py

@@ -125,11 +125,12 @@ def forward(self, x: list[Tensor]) -> list[Tensor]:
 
             cls_logits_maps.append(cls_logits)
 
-            if torch.isnan(cls_logits).any() or torch.isinf(cls_logits).any():
-                if torch.is_grad_enabled():
-                    raise ValueError("cls_logits is NaN or Inf.")
-                else:
-                    warnings.warn("cls_logits is NaN or Inf.")
+            if not torch.compiler.is_compiling():
+                if torch.isnan(cls_logits).any() or torch.isinf(cls_logits).any():
+                    if torch.is_grad_enabled():
+                        raise ValueError("cls_logits is NaN or Inf.")
+                    else:
+                        warnings.warn("cls_logits is NaN or Inf.")
 
         return cls_logits_maps
 
@@ -197,11 +198,12 @@ def forward(self, x: list[Tensor]) -> list[Tensor]:
 
             box_regression_maps.append(box_regression)
 
-            if torch.isnan(box_regression).any() or torch.isinf(box_regression).any():
-                if torch.is_grad_enabled():
-                    raise ValueError("box_regression is NaN or Inf.")
-                else:
-                    warnings.warn("box_regression is NaN or Inf.")
+            if not torch.compiler.is_compiling():
+                if torch.isnan(box_regression).any() or torch.isinf(box_regression).any():
+                    if torch.is_grad_enabled():
+                        raise ValueError("box_regression is NaN or Inf.")
+                    else:
+                        warnings.warn("box_regression is NaN or Inf.")
 
         return box_regression_maps