Project-MONAI · KumoLiu · Jul 2, 2024 · Dec 4, 2023 · Dec 5, 2023 · Dec 5, 2023
diff --git a/.github/workflows/blossom-ci.yml b/.github/workflows/blossom-ci.yml
@@ -29,13 +29,15 @@ jobs:
       args: ${{ env.args }}
 
     # This job only runs for pull request comments
-    if: contains('\
-      Nic-Ma,\
-      wyli,\
-      pxLi,\
-      YanxuanLiu,\
-      KumoLiu,\
-      ', format('{0},', github.actor)) && github.event.comment.body == '/build'
+    if: |
+      github.event.comment.body == '/build' &&
+      (
+        github.actor == 'Nic-Ma' ||
+        github.actor == 'wyli' ||
+        github.actor == 'pxLi' ||
+        github.actor == 'YanxuanLiu' ||
+        github.actor == 'KumoLiu'
+      )
     steps:
       - name: Check if comment is issued by authorized person
         run: blossom-ci

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
@@ -100,6 +100,7 @@ jobs:
         python -m pip install --pre -U itk
     - name: Install the dependencies
       run: |
+        python -m pip install --user --upgrade pip wheel
         python -m pip install torch==1.13.1 torchvision==0.14.1
         cat "requirements-dev.txt"
         python -m pip install -r requirements-dev.txt

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -119,7 +119,8 @@ jobs:
           rm -rf {*,.[^.]*}
 
   release_tag_docker:
-    if: github.repository == 'Project-MONAI/MONAI'
+    # if: github.repository == 'Project-MONAI/MONAI'
+    if: ${{ false }}
     needs: versioning
     runs-on: ubuntu-latest
     steps:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,98 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [1.3.1] - 2024-05-17
+### Added
+* Support for `by_measure` argument in `RemoveSmallObjects` (#7137)
+* Support for `pretrained` flag in `ResNet` (#7095)
+* Support for uploading and downloading bundles to and from the Hugging Face Hub (#6454)
+* Added weight parameter in DiceLoss to apply weight to voxels of each class (#7158)
+* Support for returning dice for each class in `DiceMetric` (#7163)
+* Introduced `ComponentStore` for storage purposes (#7159)
+* Added utilities used in MONAI Generative (#7134)
+* Enabled Python 3.11 support for `convert_to_torchscript` and `convert_to_onnx` (#7182)
+* Support for MLflow in `AutoRunner` (#7176)
+* `fname_regex` option in PydicomReader (#7181)
+* Allowed setting AutoRunner parameters from config (#7175)
+* `VoxelMorphUNet` and `VoxelMorph` (#7178)
+* Enabled `cache` option in `GridPatchDataset` (#7180)
+* Introduced `class_labels` option in `write_metrics_reports` for improved readability (#7249)
+* `DiffusionLoss` for image registration task (#7272)
+* Supported specifying `filename` in `Saveimage` (#7318)
+* Compile support in `SupervisedTrainer` and `SupervisedEvaluator` (#7375)
+* `mlflow_experiment_name` support in `Auto3DSeg` (#7442)
+* Arm support (#7500)
+* `BarlowTwinsLoss` for representation learning (#7530)
+* `SURELoss` and `ConjugateGradient` for diffusion models (#7308)
+* Support for `CutMix`, `CutOut`, and `MixUp` augmentation techniques (#7198)
+* `meta_file` and `logging_file` options to `BundleWorkflow` (#7549)
+* `properties_path` option to `BundleWorkflow` for customized properties (#7542)
+* Support for both soft and hard clipping in `ClipIntensityPercentiles` (#7535)
+* Support for not saving artifacts in `MLFlowHandler` (#7604)
+* Support for multi-channel images in `PerceptualLoss` (#7568)
+* Added ResNet backbone for `FlexibleUNet` (#7571)
+* Introduced `dim_head` option in `SABlock` to set dimensions for each head (#7664)
+* Direct links to github source code to docs (#7738, #7779)
+#### misc.
+* Refactored `list_data_collate` and `collate_meta_tensor` to utilize the latest PyTorch API (#7165)
+* Added __str__ method in `Metric` base class (#7487)
+* Made enhancements for testing files (#7662, #7670, #7663, #7671, #7672)
+* Improved documentation for bundles (#7116)
+### Fixed
+#### transforms
+* Addressed issue where lazy mode was ignored in `SpatialPadd` (#7316)
+* Tracked applied operations in `ImageFilter` (#7395)
+* Warnings are now given only if missing class is not set to 0 in `generate_label_classes_crop_centers` (#7602)
+* Input is now always converted to C-order in `distance_transform_edt` to ensure consistent behavior (#7675)
+#### data
+* Modified .npz file behavior to use keys in `NumpyReader` (#7148)
+* Handled corrupted cached files in `PersistentDataset` (#7244)
+* Corrected affine update in `NrrdReader` (#7415)
+#### metrics and losses
+* Addressed precision issue in `get_confusion_matrix` (#7187)
+* Harmonized and clarified documentation and tests for dice losses variants (#7587)
+#### networks
+* Removed hard-coded `spatial_dims` in `SwinTransformer` (#7302)
+* Fixed learnable `position_embeddings` in `PatchEmbeddingBlock` (#7564, #7605)
+* Removed `memory_pool_limit` in TRT config (#7647)
+* Propagated `kernel_size` to `ConvBlocks` within `AttentionUnet` (#7734)
+* Addressed hard-coded activation layer in `ResNet` (#7749)
+#### bundle
+* Resolved bundle download issue (#7280)
+* Updated `bundle_root` directory for `NNIGen` (#7586)
+* Checked for `num_fold` and failed early if incorrect (#7634)
+* Enhanced logging logic in `ConfigWorkflow` (#7745)
+#### misc.
+* Enabled chaining in `Auto3DSeg` CLI (#7168)
+* Addressed useless error message in `nnUNetV2Runner` (#7217)
+* Resolved typing and deprecation issues in Mypy (#7231)
+* Quoted `$PY_EXE` variable to handle Python path that contains spaces in Bash (#7268)
+* Improved documentation, code examples, and warning messages in various modules (#7234, #7213, #7271, #7326, #7569, #7584)
+* Fixed typos in various modules (#7321, #7322, #7458, #7595, #7612)
+* Enhanced docstrings in various modules (#7245, #7381, #7746)
+* Handled error when data is on CPU in `DataAnalyzer` (#7310)
+* Updated version requirements for third-party packages (#7343, #7344, #7384, #7448, #7659, #7704, #7744, #7742, #7780)
+* Addressed incorrect slice compute in `ImageStats` (#7374)
+* Avoided editing a loop's mutable iterable to address B308 (#7397)
+* Fixed issue with `CUDA_VISIBLE_DEVICES` setting being ignored (#7408, #7581)
+* Avoided changing Python version in CICD (#7424)
+* Renamed partial to callable in instantiate mode (#7413)
+* Imported AttributeError for Python 3.12 compatibility (#7482)
+* Updated `nnUNetV2Runner` to support nnunetv2 2.2 (#7483)
+* Used uint8 instead of int8 in `LabelStats` (#7489)
+* Utilized subprocess for nnUNet training (#7576)
+* Addressed deprecated warning in ruff (#7625)
+* Fixed downloading failure on FIPS machine (#7698)
+* Updated `torch_tensorrt` compile parameters to avoid warning (#7714)
+* Restrict `Auto3DSeg` fold input based on datalist (#7778)
+### Changed
+* Base Docker image upgraded to `nvcr.io/nvidia/pytorch:24.03-py3` from `nvcr.io/nvidia/pytorch:23.08-py3`
+### Removed
+* Removed unrecommended star-arg unpacking after a keyword argument, addressed B026 (#7262)
+* Skipped old PyTorch version test for `SwinUNETR` (#7266)
+* Dropped docker build workflow and migrated to Nvidia Blossom system (#7450)
+* Dropped Python 3.8 test on quick-py3 workflow (#7719)
+
 ## [1.3.0] - 2023-10-12
 ### Added
 * Intensity transforms `ScaleIntensityFixedMean` and `RandScaleIntensityFixedMean` (#6542)
@@ -943,7 +1035,8 @@ the postprocessing steps should be used before calling the metrics methods
 
 [highlights]: https://github.com/Project-MONAI/MONAI/blob/master/docs/source/highlights.md
 
-[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.3.0...HEAD
+[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.3.1...HEAD
+[1.3.1]: https://github.com/Project-MONAI/MONAI/compare/1.3.0...1.3.1
 [1.3.0]: https://github.com/Project-MONAI/MONAI/compare/1.2.0...1.3.0
 [1.2.0]: https://github.com/Project-MONAI/MONAI/compare/1.1.0...1.2.0
 [1.1.0]: https://github.com/Project-MONAI/MONAI/compare/1.0.1...1.1.0

diff --git a/CITATION.cff b/CITATION.cff
@@ -6,8 +6,8 @@ title: "MONAI: Medical Open Network for AI"
 abstract: "AI Toolkit for Healthcare Imaging"
 authors:
   - name: "MONAI Consortium"
-date-released: 2023-10-12
-version: "1.3.0"
+date-released: 2024-05-21
+version: "1.3.1"
 identifiers:
   - description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
     type: doi

diff --git a/README.md b/README.md
@@ -12,7 +12,6 @@
 
 [![premerge](https://github.com/Project-MONAI/MONAI/actions/workflows/pythonapp.yml/badge.svg?branch=dev)](https://github.com/Project-MONAI/MONAI/actions/workflows/pythonapp.yml)
 [![postmerge](https://img.shields.io/github/checks-status/project-monai/monai/dev?label=postmerge)](https://github.com/Project-MONAI/MONAI/actions?query=branch%3Adev)
-[![docker](https://github.com/Project-MONAI/MONAI/actions/workflows/docker.yml/badge.svg?branch=dev)](https://github.com/Project-MONAI/MONAI/actions/workflows/docker.yml)
 [![Documentation Status](https://readthedocs.org/projects/monai/badge/?version=latest)](https://docs.monai.io/en/latest/)
 [![codecov](https://codecov.io/gh/Project-MONAI/MONAI/branch/dev/graph/badge.svg?token=6FTC7U1JJ4)](https://codecov.io/gh/Project-MONAI/MONAI)
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -21,8 +21,8 @@ sphinxcontrib-serializinghtml
 sphinx-autodoc-typehints==1.11.1
 pandas
 einops
-transformers<4.22; python_version <= '3.10'  # https://github.com/Project-MONAI/MONAI/issues/5157
-mlflow>=1.28.0, <=2.11.3
+transformers>=4.36.0, <4.41.0; python_version <= '3.10'
+mlflow>=2.12.2
 clearml>=1.10.0rc0
 tensorboardX
 imagecodecs; platform_system == "Linux" or platform_system == "Darwin"

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -97,7 +97,7 @@ def generate_apidocs(*args):
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
     "sphinx.ext.autodoc",
-    "sphinx.ext.viewcode",
+    "sphinx.ext.linkcode",
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.autosummary",
     "sphinx_autodoc_typehints",
@@ -140,7 +140,7 @@ def generate_apidocs(*args):
     "github_repo": "MONAI",
     "github_version": "dev",
     "doc_path": "docs/source",
-    "conf_py_path": "/docs/",
+    "conf_py_path": "/docs/source",
     "VERSION": version,
 }
 html_scaled_image_link = False
@@ -167,11 +167,24 @@ def setup(app):
 
 
 # -- Linkcode configuration --------------------------------------------------
+DEFAULT_REF = "dev"
+read_the_docs_ref = os.environ.get("READTHEDOCS_GIT_IDENTIFIER", None)
+if read_the_docs_ref:
+    # When building on ReadTheDocs, link to the specific commit
+    # https://docs.readthedocs.io/en/stable/reference/environment-variables.html#envvar-READTHEDOCS_GIT_IDENTIFIER
+    git_ref = read_the_docs_ref
+elif os.environ.get("GITHUB_REF_TYPE", "branch") == "tag":
+    # When building a tag, link to the tag itself
+    git_ref = os.environ.get("GITHUB_REF", DEFAULT_REF)
+else:
+    git_ref = os.environ.get("GITHUB_SHA", DEFAULT_REF)
+
 DEFAULT_REPOSITORY = "Project-MONAI/MONAI"
 repository = os.environ.get("GITHUB_REPOSITORY", DEFAULT_REPOSITORY)
 
-base_code_url = f"https://github.com/{repository}/blob/{version}"
+base_code_url = f"https://github.com/{repository}/blob/{git_ref}"
 MODULE_ROOT_FOLDER = "monai"
+repo_root_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
 
 
 # Adjusted from https://github.com/python-websockets/websockets/blob/main/docs/conf.py
@@ -201,7 +214,7 @@ def linkcode_resolve(domain, info):
     except TypeError:
         # e.g. object is a typing.Union
         return None
-    file = os.path.relpath(file, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
+    file = os.path.relpath(file, repo_root_path)
     if not file.startswith(MODULE_ROOT_FOLDER):
         # e.g. object is a typing.NewType
         return None

diff --git a/docs/source/networks.rst b/docs/source/networks.rst
@@ -426,7 +426,6 @@ Layers
 .. autoclass:: monai.networks.layers.vector_quantizer.VectorQuantizer
    :members:
 
-=======
 `ConjugateGradient`
 ~~~~~~~~~~~~~~~~~~~
 .. autoclass:: ConjugateGradient

diff --git a/monai/apps/auto3dseg/auto_runner.py b/monai/apps/auto3dseg/auto_runner.py
@@ -499,8 +499,8 @@ def set_num_fold(self, num_fold: int = 5) -> AutoRunner:
 
         if num_fold <= 0:
             raise ValueError(f"num_fold is expected to be an integer greater than zero. Now it gets {num_fold}")
-        if num_fold > self.max_fold + 1:
-            # Auto3DSeg allows no validation set, so the maximum fold number is max_fold + 1
+        if num_fold > self.max_fold:
+            # Auto3DSeg must contain validation set, so the maximum fold number is max_fold.
             raise ValueError(
                 f"num_fold is greater than the maximum fold number {self.max_fold} in {self.datalist_filename}."
             )

diff --git a/monai/apps/detection/utils/anchor_utils.py b/monai/apps/detection/utils/anchor_utils.py
@@ -189,7 +189,7 @@ def generate_anchors(
             w_ratios = 1 / area_scale
             h_ratios = area_scale
         # if 3d, w:h:d = 1:aspect_ratios[:,0]:aspect_ratios[:,1]
-        elif self.spatial_dims == 3:
+        else:
             area_scale = torch.pow(aspect_ratios_t[:, 0] * aspect_ratios_t[:, 1], 1 / 3.0)
             w_ratios = 1 / area_scale
             h_ratios = aspect_ratios_t[:, 0] / area_scale
@@ -199,7 +199,7 @@ def generate_anchors(
         hs = (h_ratios[:, None] * scales_t[None, :]).view(-1)
         if self.spatial_dims == 2:
             base_anchors = torch.stack([-ws, -hs, ws, hs], dim=1) / 2.0
-        elif self.spatial_dims == 3:
+        else:  # elif self.spatial_dims == 3:
             ds = (d_ratios[:, None] * scales_t[None, :]).view(-1)
             base_anchors = torch.stack([-ws, -hs, -ds, ws, hs, ds], dim=1) / 2.0
 

diff --git a/monai/apps/pathology/transforms/post/array.py b/monai/apps/pathology/transforms/post/array.py
@@ -379,6 +379,7 @@ def _generate_contour_coord(self, current: np.ndarray, previous: np.ndarray) ->
         """
 
         p_delta = (current[0] - previous[0], current[1] - previous[1])
+        row, col = -1, -1
 
         if p_delta in ((0.0, 1.0), (0.5, 0.5), (1.0, 0.0)):
             row = int(current[0] + 0.5)

diff --git a/monai/bundle/utils.py b/monai/bundle/utils.py
@@ -221,6 +221,7 @@ def load_bundle_config(bundle_path: str, *config_names: str, **load_kw_args: Any
                 raise ValueError(f"Cannot find config file '{full_cname}'")
 
             ardata = archive.read(full_cname)
+            cdata = {}
 
             if full_cname.lower().endswith("json"):
                 cdata = json.loads(ardata, **load_kw_args)

diff --git a/monai/bundle/workflows.py b/monai/bundle/workflows.py
@@ -308,7 +308,6 @@ def __init__(
         super().__init__(workflow_type=workflow_type, meta_file=meta_file, properties_path=properties_path)
         self.config_root_path = config_root_path
         logging_file = str(self.config_root_path / "logging.conf") if logging_file is None else logging_file
-
         if logging_file is False:
             logger.warn(f"Logging file is set to {logging_file}, skipping logging.")
         else: