Merge branch 'dev' into 8328-nnunet-bundle-integration

Author: SimoneBendazzoli93

.github/CODEOWNERS

@@ -0,0 +1,17 @@
+/monai/ @KumoLiu @ericspod @Nic-Ma
+/docs/ @KumoLiu @ericspod @Nic-Ma
+/tests/ @KumoLiu @ericspod @Nic-Ma
+/.github/ @KumoLiu
+/monai/networks/schedulers/ @virginiafdez
+/monai/inferers/inferer.py @virginiafdez
+/monai/losses/adversarial_loss.py @virginiafdez
+/monai/losses/perceptual.py @virginiafdez
+/monai/networks/blocks/spade_norm.py @virginiafdez
+/monai/networks/nets/autoencoderkl.py @virginiafdez
+/monai/networks/nets/controlnet.py @virginiafdez
+/monai/networks/nets/diffusion_model_unet.py @virginiafdez
+/monai/networks/nets/patchgan_discriminator.py @virginiafdez
+/monai/networks/nets/spade_autoencoderkl.py @virginiafdez
+/monai/networks/nets/spade_diffusion_model_unet.py @virginiafdez
+/monai/networks/nets/spade_network.py @virginiafdez
+/monai/networks/nets/vqvae.py @virginiafdez

.github/codecov.yml

@@ -24,8 +24,13 @@ coverage:
         flags: null
         paths: null
 
-# Disable comments on PR
-comment: false
+comment: # enable code coverage comment on PR
+  layout: "diff, flags, files"
+  behavior: default
+  require_changes: false
+  require_base: false
+  require_head: true
+  hide_project_coverage: true
 
 ignore:
   - "versioneer.py"

.github/workflows/pythonapp-min.yml

@@ -124,7 +124,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        pytorch-version: ['2.3.1', '2.4.1', '2.5.1', 'latest']
+        pytorch-version: ['2.4.1', '2.5.1', '2.6.0']  # FIXME: add 'latest' back once PyTorch 2.7 issues are resolved
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4

.github/workflows/pythonapp.yml

@@ -155,7 +155,7 @@ jobs:
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=2.3.0 torchvision
+        python -m pip install torch>=2.4.1 torchvision
     - name: Check packages
       run: |
         pip uninstall monai

CONTRIBUTING.md

@@ -105,9 +105,9 @@ MONAI tests are located under `tests/`.
 A bash script (`runtests.sh`) is provided to run all tests locally.
 Please run ``./runtests.sh -h`` to see all options.
 
-To run a particular test, for example `tests/test_dice_loss.py`:
+To run a particular test, for example `tests/losses/test_dice_loss.py`:
 ```
-python -m tests.test_dice_loss
+python -m tests.losses.test_dice_loss
 ```
 
 Before submitting a pull request, we recommend that all linting and unit tests

README.md

@@ -33,6 +33,15 @@ Its ambitions are as follows:
 - customizable design for varying user expertise;
 - multi-GPU multi-node data parallelism support.
 
+## Requirements
+
+MONAI works with the [currently supported versions of Python](https://devguide.python.org/versions), and depends directly on NumPy and PyTorch with many optional dependencies.
+
+* Major releases of MONAI will have dependency versions stated for them. The current state of the `dev` branch in this repository is the unreleased development version of MONAI which typically will support current versions of dependencies and include updates and bug fixes to do so.
+* PyTorch support covers [the current version](https://github.com/pytorch/pytorch/releases) plus three previous minor versions. If compatibility issues with a PyTorch version and other dependencies arise, support for a version may be delayed until a major release.
+* Our support policy for other dependencies adheres for the most part to [SPEC0](https://scientific-python.org/specs/spec-0000), where dependency versions are supported where possible for up to two years. Discovered vulnerabilities or defects may require certain versions to be explicitly not supported.
+* See the `requirements*.txt` files for dependency version information.
+
 ## Installation
 
 To install [the current release](https://pypi.org/project/monai/), you can simply run:

docs/requirements.txt

@@ -1,5 +1,5 @@
 -f https://download.pytorch.org/whl/cpu/torch-2.3.0%2Bcpu-cp39-cp39-linux_x86_64.whl
-torch>=2.3.0
+torch>=2.4.1, <2.7.0
 pytorch-ignite==0.4.11
 numpy>=1.20
 itk>=5.2

docs/source/installation.md

@@ -58,10 +58,10 @@ pip install monai-weekly
 ```
 
 The weekly build is released to PyPI every Sunday with a pre-release build number `dev[%y%U]`.
-To report any issues on the weekly preview, please include the version and commit information:
+To report any issues on the weekly preview, please include the version information:
 
 ```bash
-python -c "import monai; print(monai.__version__); print(monai.__commit_id__)"
+python -c "import monai; print(monai.__version__)"
 ```
 
 Coexistence of package `monai` and `monai-weekly` in a system may cause namespace conflicts
@@ -101,20 +101,20 @@ for the latest features:
 ### Option 1 (as a part of your system-wide module):
 
 ```bash
-pip install git+https://github.com/Project-MONAI/MONAI#egg=monai
+pip install git+https://github.com/Project-MONAI/MONAI
 ```
 
 or, to build with MONAI C++/CUDA extensions:
 
 ```bash
-BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=monai
+BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI
 ```
 
 To build the extensions, if the system environment already has a version of Pytorch installed,
 `--no-build-isolation` might be preferred:
 
 ```bash
-BUILD_MONAI=1 pip install --no-build-isolation git+https://github.com/Project-MONAI/MONAI#egg=monai
+BUILD_MONAI=1 pip install --no-build-isolation git+https://github.com/Project-MONAI/MONAI
 ```
 
 this command will download and install the current `dev` branch of [MONAI from

docs/source/metrics.rst

@@ -98,7 +98,6 @@ Metrics
 `Hausdorff distance`
 --------------------
 .. autofunction:: compute_hausdorff_distance
-.. autofunction:: compute_percent_hausdorff_distance
 
 .. autoclass:: HausdorffDistanceMetric
     :members:

monai/apps/auto3dseg/auto_runner.py

@@ -570,7 +570,7 @@ def set_device_info(
             self.device_setting["CUDA_VISIBLE_DEVICES"] = ",".join([str(x) for x in cuda_visible_devices])
             self.device_setting["n_devices"] = len(cuda_visible_devices)
         else:
-            logger.warn(f"Wrong format of cuda_visible_devices {cuda_visible_devices}, devices not set")
+            logger.warning(f"Wrong format of cuda_visible_devices {cuda_visible_devices}, devices not set")
 
         if num_nodes is None:
             num_nodes = int(os.environ.get("NUM_NODES", 1))