update docs and minor fixes (#6593)

part of #6151 fixes #6556 fixes #6594 ### Types of changes  - [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: Wenqi Li <wenqil@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Project-MONAI · Jun 8, 2023 · c33f1ba · c33f1ba
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diff --git a/.github/workflows/weekly-preview.yml b/.github/workflows/weekly-preview.yml
@@ -33,7 +33,7 @@ jobs:
         export YEAR_WEEK=$(date +'%y%U')
         echo "Year week for tag is ${YEAR_WEEK}"
         if ! [[ $YEAR_WEEK =~ ^[0-9]{4}$ ]] ; then echo "Wrong 'year week' format.  Should be 4 digits."; exit 1 ; fi
-        git tag "1.2.dev${YEAR_WEEK}"
+        git tag "1.3.dev${YEAR_WEEK}"
         git log -1
         git tag --list
         python setup.py sdist bdist_wheel

diff --git a/.gitignore b/.gitignore
@@ -68,7 +68,8 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+docs/build/
+docs/source/_gen
 _build/
 
 # PyBuilder

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
-## [1.2.0] - 2023-06-06
+## [1.2.0] - 2023-06-08
 ### Added
 * Various Auto3DSeg enhancements and integration tests including multi-node multi-GPU optimization, major usability improvements
 * TensorRT and ONNX support for `monai.bundle` API and the relevant models
@@ -110,6 +110,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 * `resample=True`; `resample=False` will be the new default in `SaveImage`
 * `random_size=True`; `random_size=False` will be the new default for the random cropping transforms
 * `image_only=False`; `image_only=True` will be the new default in `LoadImage`
+* `AddChannel` and `AsChannelFirst` in favor of `EnsureChannelFirst`
 ### Removed
 * Deprecated APIs since v0.9, including WSIReader from `monai.apps`, `NiftiSaver` and `PNGSaver` from `monai.data`
 * Support for PyTorch 1.8

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: 2022-12-19
-version: "1.1.0"
+date-released: 2023-06-08
+version: "1.2.0"
 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
@@ -30,7 +30,7 @@ Its ambitions are:
 - compositional & portable APIs for ease of integration in existing workflows;
 - domain-specific implementations for networks, losses, evaluation metrics and more;
 - customizable design for varying user expertise;
-- multi-GPU data parallelism support.
+- multi-GPU multi-node data parallelism support.
 
 
 ## Installation

diff --git a/docs/Makefile b/docs/Makefile
@@ -25,3 +25,4 @@ help:
 
 clean:
 	rm -rf build/
+	rm -rf source/_gen
diff --git a/docs/source/apps.rst b/docs/source/apps.rst
@@ -248,7 +248,7 @@ FastMRIReader
 ~~~~~~~~~~~~~
 .. autofunction:: monai.apps.reconstruction.complex_utils.complex_conj
 
-`auto3dseg`
+`Auto3DSeg`
 -----------
 .. automodule:: monai.apps.auto3dseg
   :members:

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -86,6 +86,7 @@ def generate_apidocs(*args):
     "sphinx.ext.autodoc",
     "sphinx.ext.viewcode",
     "sphinx.ext.autosectionlabel",
+    "sphinx.ext.autosummary",
     "sphinx_autodoc_typehints",
 ]
 
@@ -114,7 +115,7 @@ def generate_apidocs(*args):
         {"name": "Twitter", "url": "https://twitter.com/projectmonai", "icon": "fab fa-twitter-square"},
     ],
     "collapse_navigation": True,
-    "navigation_depth": 3,
+    "navigation_depth": 1,
     "show_toc_level": 1,
     "footer_start": ["copyright"],
     "navbar_align": "content",

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -27,7 +27,7 @@ Features
 - compositional & portable APIs for ease of integration in existing workflows;
 - domain-specific implementations for networks, losses, evaluation metrics and more;
 - customizable design for varying user expertise;
-- multi-GPU data parallelism support.
+- multi-GPU multi-node data parallelism support.
 
 
 Getting started

diff --git a/docs/source/transforms.rst b/docs/source/transforms.rst
@@ -2233,3 +2233,10 @@ Utilities
 
 .. automodule:: monai.transforms.utils_pytorch_numpy_unification
     :members:
+
+By Categories
+-------------
+.. toctree::
+   :maxdepth: 1
+
+   transforms_idx
diff --git a/docs/source/transforms_idx.rst b/docs/source/transforms_idx.rst
@@ -0,0 +1,104 @@
+.. _transforms_idx:
+
+.. currentmodule:: monai.transforms
+
+Crop and pad
+^^^^^^^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   croppad.array
+   croppad.dictionary
+   croppad.batch
+
+Spatial
+^^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   spatial.array
+   spatial.dictionary
+
+
+Intensity
+^^^^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   intensity.array
+   intensity.dictionary
+
+IO
+^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   io.array
+   io.dictionary
+
+Lazy
+^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   lazy.array
+   lazy.dictionary
+   lazy.utils
+
+MetaTensor utilities
+^^^^^^^^^^^^^^^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   meta_utility.dictionary
+
+Post-processing
+^^^^^^^^^^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   post.array
+   post.dictionary
+
+Signal
+^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   signal.array
+
+Smooth field
+^^^^^^^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   smooth_field.array
+   smooth_field.dictionary
+
+Utility
+^^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   utility.array
+   utility.dictionary
diff --git a/monai/apps/auto3dseg/bundle_gen.py b/monai/apps/auto3dseg/bundle_gen.py
@@ -537,7 +537,7 @@ def generate(
                 parameters for each bundleAlgo based on gpus. Custom parameters are obtained through dummy
                 training to simulate the actual model training process and hyperparameter optimization (HPO)
                 experiments.
-            gpu_customization_specs (optinal): the dictionary to enable users overwrite the HPO settings. user can
+            gpu_customization_specs: the dictionary to enable users overwrite the HPO settings. user can
                 overwrite part of variables as follows or all of them. The structure is as follows.
             allow_skip: a switch to determine if some Algo in the default templates can be skipped based on the
                 analysis on the dataset from Auto3DSeg DataAnalyzer.

diff --git a/monai/apps/auto3dseg/ensemble_builder.py b/monai/apps/auto3dseg/ensemble_builder.py
@@ -161,7 +161,7 @@ def __call__(self, pred_param: dict | None = None) -> list:
                       only make prediction on the infer_files[file_slices].
                     - ``"mode"``: ensemble mode. Currently "mean" and "vote" (majority voting) schemes are supported.
                     - ``"image_save_func"``: a dictionary used to instantiate the ``SaveImage`` transform. When specified,
-                      the ensemble prediction will save the prediciton files, instead of keeping the files in the memory.
+                      the ensemble prediction will save the prediction files, instead of keeping the files in the memory.
                       Example: `{"_target_": "SaveImage", "output_dir": "./"}`
                     - ``"sigmoid"``: use the sigmoid function (e.g. x > 0.5) to convert the prediction probability map
                       to the label class prediction, otherwise argmax(x) is used.
@@ -552,7 +552,7 @@ def set_num_fold(self, num_fold: int = 5) -> None:
         self.num_fold = num_fold
 
     def ensemble(self):
-        if self.mgpu:  # torch.cuda.device_count() is not used because env is not set by autorruner
+        if self.mgpu:  # torch.cuda.device_count() is not used because env is not set by autorunner
             # init multiprocessing and update infer_files
             dist.init_process_group(backend="nccl", init_method="env://")
             self.world_size = dist.get_world_size()

diff --git a/monai/apps/pathology/handlers/utils.py b/monai/apps/pathology/handlers/utils.py
@@ -23,7 +23,7 @@ def from_engine_hovernet(keys: KeysCollection, nested_key: str) -> Callable[[Any
     Since the output of HoVerNet is a dictionary, this function is to extend `monai.handlers.from_engine`
     to work with HoVerNet.
 
-    If data is a list of nestes dictionaries after decollating, extract nested value with expected keys and
+    If data is a list of nested dictionaries after decollating, extract nested value with expected keys and
     construct lists respectively, for example,
     if data is `[{"A": {"C": 1, "D": 2}, "B": {"C": 2, "D": 2}}, {"A":  {"C": 3, "D": 2}, "B":  {"C": 4, "D": 2}}]`,
     from_engine_hovernet(["A", "B"], "C"): `([1, 3], [2, 4])`.

diff --git a/monai/data/dataset.py b/monai/data/dataset.py
@@ -566,7 +566,7 @@ def __init__(
             hash_transform: a callable to compute hash from the transform information when caching.
                 This may reduce errors due to transforms changing during experiments. Default to None (no hash).
                 Other options are `pickle_hashing` and `json_hashing` functions from `monai.data.utils`.
-            reset_ops_id: whether to set `TraceKeys.ID` to ``Tracekys.NONE``, defaults to ``True``.
+            reset_ops_id: whether to set `TraceKeys.ID` to ``Tracekeys.NONE``, defaults to ``True``.
                 When this is enabled, the traced transform instance IDs will be removed from the cached MetaTensors.
                 This is useful for skipping the transform instance checks when inverting applied operations
                 using the cached content and with re-created transform instances.

diff --git a/monai/transforms/croppad/array.py b/monai/transforms/croppad/array.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "vanilla" transforms for crop and pad operations
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "vanilla" transforms for crop and pad operations.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/croppad/batch.py b/monai/transforms/croppad/batch.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "vanilla" transforms for crop and pad operations acting on batches of data
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "vanilla" transforms for crop and pad operations acting on batches of data.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/croppad/functional.py b/monai/transforms/croppad/functional.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "functional" transforms for spatial operations
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "functional" transforms for spatial operations.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "vanilla" transforms for intensity adjustment
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "vanilla" transforms for intensity adjustment.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/io/array.py b/monai/transforms/io/array.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "vanilla" transforms for IO functions
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "vanilla" transforms for IO functions.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/post/array.py b/monai/transforms/post/array.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "vanilla" transforms for the model output tensors
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "vanilla" transforms for the model output tensors.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/signal/array.py b/monai/transforms/signal/array.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of transforms for signal operations
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of transforms for signal operations.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/spatial/array.py b/monai/transforms/spatial/array.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "vanilla" transforms for spatial operations
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "vanilla" transforms for spatial operations.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/spatial/functional.py b/monai/transforms/spatial/functional.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "functional" transforms for spatial operations
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "functional" transforms for spatial operations.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
@@ -9,8 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-A collection of "vanilla" transforms for utility functions
-https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
+A collection of "vanilla" transforms for utility functions.
 """
 
 from __future__ import annotations

diff --git a/monai/transforms/utils.py b/monai/transforms/utils.py
@@ -1666,7 +1666,7 @@ def print_table_column(name, torch, numpy, color=Colors.none):
     print_color(f"Number transforms allowing both torch and numpy: {n_t_or_np}", Colors.green)
     print_color(f"Number of TorchTransform: {n_t}", Colors.green)
     print_color(f"Number of NumpyTransform: {n_np}", Colors.yellow)
-    print_color(f"Number of uncategorised: {n_uncategorized}", Colors.red)
+    print_color(f"Number of uncategorized: {n_uncategorized}", Colors.red)
 
 
 def convert_pad_mode(dst: NdarrayOrTensor, mode: str | None):

diff --git a/tests/test_integration_workflows_gan.py b/tests/test_integration_workflows_gan.py
@@ -41,7 +41,7 @@ def run_training_test(root_dir, device="cuda:0"):
     train_transforms = Compose(
         [
             LoadImaged(keys=["reals"]),
-            EnsureChannelFirstd(keys=["reals"]),
+            EnsureChannelFirstd(keys=["reals"], channel_dim=-1),
             ScaleIntensityd(keys=["reals"]),
             RandFlipd(keys=["reals"], prob=0.5),
         ]