📝 Add primary InnerEye/ML files API to docs

microsoft · peterhessey · Aug 18, 2022 · Aug 5, 2022 · Aug 5, 2022 · Aug 8, 2022
commit 56c3a5273dc32b8280fec11f8dc9a82cc07f9c11
diff --git a/InnerEye/ML/baselines_util.py b/InnerEye/ML/baselines_util.py
@@ -112,7 +112,6 @@ def download_and_compare_scores(outputs_folder: Path, azure_config: AzureConfig,
  :param azure_config: Azure configuration to use for downloading data
  :param comparison_blob_storage_paths: list of paths to directories containing metrics.csv and dataset.csv files,
  each of the form run_recovery_id/rest_of_path
-
  :param model_dataset_df: dataframe containing contents of dataset.csv for the current model
  :param model_metrics_df: dataframe containing contents of metrics.csv for the current model
  :return: a dataframe for all the data (current model and all baselines); whether any comparisons were

diff --git a/docs/source/rst/api/ML/ML.rst b/docs/source/rst/api/ML/ML.rst
@@ -2,13 +2,14 @@ Machine learning
 ================
 
 .. toctree::
+ :caption: Docuemntation for InnerEye/ML
 
- configs
+ core
  models
  dataset
  augmentations
- pipelines
  SSL
+ configs
  utils
- runner
- photometric_normalization
+ pipelines
+ visualizers
diff --git a/docs/source/rst/api/ML/core.rst b/docs/source/rst/api/ML/core.rst
@@ -0,0 +1,13 @@
+InnerEye/ML Core
+================
+
+.. toctree::
+ :caption: Key Components in running InnerEye-DeepLearning
+
+ core/common
+ core/lightning
+ core/training
+ core/testing
+ core/configs
+ core/metrics
+ core/visualization
diff --git a/docs/source/rst/api/ML/core/common.rst b/docs/source/rst/api/ML/core/common.rst
@@ -0,0 +1,10 @@
+Common
+=======
+
+.. automodule:: InnerEye.ML.run_ml
+
+.. automodule:: InnerEye.ML.runner
+
+.. automodule:: InnerEye.ML.common
+
+.. automodule:: InnerEye.ML.baselines_util
diff --git a/docs/source/rst/api/ML/core/configs.rst b/docs/source/rst/api/ML/core/configs.rst
@@ -0,0 +1,12 @@
+Configs
+=======
+
+.. automodule:: InnerEye.ML.config
+
+.. automodule:: InnerEye.ML.model_config_base
+
+.. automodule:: InnerEye.ML.deep_learning_config
+
+.. automodule:: InnerEye.ML.scalar_config
+
+.. automodule:: InnerEye.ML.model_inference_config
diff --git a/docs/source/rst/api/ML/core/lightning.rst b/docs/source/rst/api/ML/core/lightning.rst
@@ -0,0 +1,14 @@
+Lightning Components
+================================
+
+.. automodule:: InnerEye.ML.lightning_base
+
+.. automodule:: InnerEye.ML.lightning_container
+
+.. automodule:: InnerEye.ML.lightning_models
+
+.. automodule:: InnerEye.ML.lightning_helpers
+
+.. automodule:: InnerEye.ML.lightning_loggers
+
+.. automodule:: InnerEye.ML.lightning_metrics
diff --git a/docs/source/rst/api/ML/core/metrics.rst b/docs/source/rst/api/ML/core/metrics.rst
@@ -0,0 +1,6 @@
+Metrics
+========
+
+.. automodule:: InnerEye.ML.metrics
+
+.. automodule:: InnerEye.ML.metrics_dict
diff --git a/docs/source/rst/api/ML/core/testing.rst b/docs/source/rst/api/ML/core/testing.rst
@@ -0,0 +1,4 @@
+Testing Models
+==============
+
+.. automodule:: InnerEye.ML.model_testing
diff --git a/docs/source/rst/api/ML/core/training.rst b/docs/source/rst/api/ML/core/training.rst
@@ -0,0 +1,6 @@
+Training Models
+================
+
+.. automodule:: InnerEye.ML.model_training
+
+.. automodule:: InnerEye.ML.photometric_normalization
diff --git a/docs/source/rst/api/ML/core/visualization.rst b/docs/source/rst/api/ML/core/visualization.rst
@@ -0,0 +1,8 @@
+Visualization
+==============
+
+.. automodule:: InnerEye.ML.plotting
+
+.. automodule:: InnerEye.ML.normalize_and_visualize_dataset
+
+.. automodule:: InnerEye.ML.surface_distance_heatmaps
diff --git a/docs/source/rst/api/ML/photometric_normalization.rst b/docs/source/rst/api/ML/photometric_normalization.rst
diff --git a/docs/source/rst/api/ML/runner.rst b/docs/source/rst/api/ML/runner.rst