📝 Improve doc folder structure

microsoft · peterhessey · Aug 4, 2022 · Jul 21, 2022 · Jul 21, 2022 · Jul 22, 2022
commit f5d3f76f8399403a361fb0f57640b03e1eee04db
diff --git a/README.md b/README.md
@@ -56,9 +56,9 @@ that can route anonymized DICOM images to an inference service.
 - The [InnerEye-Inference](https://github.com/microsoft/InnerEye-Inference) component offers a REST API that integrates
 with the InnerEye-Gateway, to run inference on InnerEye-DeepLearning models.
 
-Details can be found [here](docs/source/docs/deploy_on_aml.md).
+Details can be found [here](docs/source/md/deploy_on_aml.md).
 
-![docs/deployment.png](docs/source/docs/images/deployment.png)
+![docs/deployment.png](docs/source/images/deployment.png)
 
 ## Licensing
 

diff --git a/TestSubmodule/environment.yml b/TestSubmodule/environment.yml
@@ -128,7 +128,7 @@ dependencies:
  - deprecated==1.2.13
  - distro==1.7.0
  - docker==4.3.1
- - docutils==0.19
+ - docutils==0.17.1
  - dotnetcore2==2.1.23
  - entrypoints==0.4
  - execnet==1.9.0
@@ -151,7 +151,7 @@ dependencies:
  - gunicorn==20.1.0
  - h5py==2.10.0
  - hi-ml==0.2.2
- - hi-ml-azure==0.2.4
+ - hi-ml-azure==0.2.2
  - humanize==4.2.3
  - idna==3.3
  - imageio==2.15.0
@@ -257,7 +257,6 @@ dependencies:
  - qtconsole==5.3.1
  - qtpy==2.1.0
  - querystring-parser==1.2.4
- - recommonmark==0.7.1
  - requests==2.28.1
  - requests-oauthlib==1.3.1
  - rich==10.13.0

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -98,7 +98,7 @@ def replace_in_file(filepath: Path, original_str: str, replace_str: str) -> None
 
 
 sphinx_root = Path(__file__).absolute().parent
-docs_path = Path(sphinx_root / "docs")
+docs_path = Path(sphinx_root / "md")
 repository_root = sphinx_root.parent.parent
 
 # Symlink to all files that are in the head of the repository

diff --git a/docs/source/docs/images/deployment.png → docs/source/images/deployment.png b/docs/source/docs/images/deployment.png → docs/source/images/deployment.png
diff --git a/...cs/images/hippocampus_metrics_boxplot.png → ...ce/images/hippocampus_metrics_boxplot.png b/...cs/images/hippocampus_metrics_boxplot.png → ...ce/images/hippocampus_metrics_boxplot.png
diff --git a/...ce/docs/images/patch_sampling_example.png → .../source/images/patch_sampling_example.png b/...ce/docs/images/patch_sampling_example.png → .../source/images/patch_sampling_example.png
diff --git a/...ges/screenshot_azureml_patch_sampling.png → ...ges/screenshot_azureml_patch_sampling.png b/...ges/screenshot_azureml_patch_sampling.png → ...ges/screenshot_azureml_patch_sampling.png
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -8,34 +8,35 @@ InnerEye-DeepLearning Documentation
 
 .. toctree::
  :maxdepth: 1
+ :caption: TESTING THIS CAPTION HERE
 
- docs/innereye_deeplearning.md
- docs/WSL.md
- docs/environment.md
- docs/setting_up_aml.md
- docs/creating_dataset.md
- docs/building_models.md
- docs/sample_tasks.md
- docs/debugging_and_monitoring.md
+ md/innereye_deeplearning.md
+ md/WSL.md
+ md/environment.md
+ md/setting_up_aml.md
+ md/creating_dataset.md
+ md/building_models.md
+ md/sample_tasks.md
+ md/debugging_and_monitoring.md
 
 .. toctree::
  :maxdepth: 1
  :caption: Further reading for contributors
 
- docs/pull_requests.md
- docs/testing.md
- docs/contributing.md
-
- docs/hello_world_model.md
- docs/deploy_on_aml.md
- docs/bring_your_own_model.md
- docs/fastmri.md
- docs/innereye_as_submodule.md
- docs/model_diagnostics.md
- docs/move_model.md
- docs/releases.md
- docs/self_supervised_models.md
- docs/CHANGELOG.md
+ md/pull_requests.md
+ md/testing.md
+ md/contributing.md
+
+ md/hello_world_model.md
+ md/deploy_on_aml.md
+ md/bring_your_own_model.md
+ md/fastmri.md
+ md/innereye_as_submodule.md
+ md/model_diagnostics.md
+ md/move_model.md
+ md/releases.md
+ md/self_supervised_models.md
+ md/CHANGELOG.md
 
 .. toctree::
  :caption: API documentation (🚧 Work In Progress 🚧)

diff --git a/docs/source/md/CHANGELOG.md b/docs/source/md/CHANGELOG.md
@@ -0,0 +1 @@
+/home/phessey/Repos/InnerEye-DeepLearning/CHANGELOG.md
diff --git a/docs/source/docs/WSL.md → docs/source/md/WSL.md b/docs/source/docs/WSL.md → docs/source/md/WSL.md
diff --git a/docs/source/docs/bring_your_own_model.md → docs/source/md/bring_your_own_model.md b/docs/source/docs/bring_your_own_model.md → docs/source/md/bring_your_own_model.md
diff --git a/docs/source/docs/building_models.md → docs/source/md/building_models.md b/docs/source/docs/building_models.md → docs/source/md/building_models.md
diff --git a/docs/source/docs/contributing.md → docs/source/md/contributing.md b/docs/source/docs/contributing.md → docs/source/md/contributing.md
diff --git a/docs/source/docs/creating_dataset.md → docs/source/md/creating_dataset.md b/docs/source/docs/creating_dataset.md → docs/source/md/creating_dataset.md
diff --git a/docs/source/docs/debugging_and_monitoring.md → docs/source/md/debugging_and_monitoring.md b/docs/source/docs/debugging_and_monitoring.md → docs/source/md/debugging_and_monitoring.md
diff --git a/docs/source/docs/deploy_on_aml.md → docs/source/md/deploy_on_aml.md b/docs/source/docs/deploy_on_aml.md → docs/source/md/deploy_on_aml.md
@@ -1,6 +1,6 @@
 # Model Deployment
 
-![deployment.png](images/deployment.png)
+![deployment.png](../images/deployment.png)
 
 InnerEye segmentation models using a single DICOM series as input and producing DICOM-RT can be integrated with DICOM networks using:
 

diff --git a/docs/source/docs/environment.md → docs/source/md/environment.md b/docs/source/docs/environment.md → docs/source/md/environment.md
diff --git a/docs/source/docs/fastmri.md → docs/source/md/fastmri.md b/docs/source/docs/fastmri.md → docs/source/md/fastmri.md
diff --git a/docs/source/docs/hello_world_model.md → docs/source/md/hello_world_model.md b/docs/source/docs/hello_world_model.md → docs/source/md/hello_world_model.md
diff --git a/docs/source/docs/hippocampus_model.md → docs/source/md/hippocampus_model.md b/docs/source/docs/hippocampus_model.md → docs/source/md/hippocampus_model.md
@@ -1,4 +1,3 @@
-
 # Trained model for hippocampal segmentation
 
 ## Purpose
@@ -112,7 +111,7 @@ Note that due to the ADNI Data Usage Agreement we are only able to share aggrega
 
 Dice Score for Left and Right hippocampus respectively on a held-out test set of :
 
-![hippocampus_metrics_boxplot.png](hippocampus_metrics_boxplot.png)
+![hippocampus_metrics_boxplot.png](../images/hippocampus_metrics_boxplot.png)
 | Structure | count | DiceNumeric_mean | DiceNumeric_std | DiceNumeric_min | DiceNumeric_max | HausdorffDistance_mm_mean | HausdorffDistance_mm_std | HausdorffDistance_mm_min | HausdorffDistance_mm_max | MeanDistance_mm_mean | MeanDistance_mm_std | MeanDistance_mm_min | MeanDistance_mm_max |
 |---------------|---------|------------------|-----------------|-----------------|-----------------|---------------------------|--------------------------|--------------------------|--------------------------|----------------------|---------------------|---------------------|---------------------|
 | hippocampus_L | 252 | 0.918 | 0.022 | 0.819 | 0.953 | 2.206 | 0.812 | 1.206 | 6.964 | 0.168 | 0.054 | 0.096 | 0.399 |

diff --git a/docs/source/docs/innereye_as_submodule.md → docs/source/md/innereye_as_submodule.md b/docs/source/docs/innereye_as_submodule.md → docs/source/md/innereye_as_submodule.md
diff --git a/docs/source/docs/innereye_deeplearning.md → docs/source/md/innereye_deeplearning.md b/docs/source/docs/innereye_deeplearning.md → docs/source/md/innereye_deeplearning.md
@@ -102,7 +102,7 @@ with the InnnEye-Gateway, to run inference on InnerEye-DeepLearning models.
 
 Details can be found [here](deploy_on_aml.md).
 
-![deployment.png](images/deployment.png)
+![deployment.png](../images/deployment.png)
 
 ## More information
 

diff --git a/docs/source/docs/model_diagnostics.md → docs/source/md/model_diagnostics.md b/docs/source/docs/model_diagnostics.md → docs/source/md/model_diagnostics.md
@@ -22,4 +22,4 @@ scan. Dark red indicates voxels that are sampled very often, transparent red ind
 infrequently.
 
 Example thumbnail when viewed in the AzureML UI:
-![Azure ML patch sampling screenshot](images/screenshot_azureml_patch_sampling.png)
+![Azure ML patch sampling screenshot](../images/screenshot_azureml_patch_sampling.png)
diff --git a/docs/source/docs/move_model.md → docs/source/md/move_model.md b/docs/source/docs/move_model.md → docs/source/md/move_model.md
diff --git a/docs/source/docs/pull_requests.md → docs/source/md/pull_requests.md b/docs/source/docs/pull_requests.md → docs/source/md/pull_requests.md
diff --git a/docs/source/docs/releases.md → docs/source/md/releases.md b/docs/source/docs/releases.md → docs/source/md/releases.md
diff --git a/docs/source/docs/sample_tasks.md → docs/source/md/sample_tasks.md b/docs/source/docs/sample_tasks.md → docs/source/md/sample_tasks.md
diff --git a/docs/source/docs/self_supervised_models.md → docs/source/md/self_supervised_models.md b/docs/source/docs/self_supervised_models.md → docs/source/md/self_supervised_models.md
diff --git a/docs/source/docs/setting_up_aml.md → docs/source/md/setting_up_aml.md b/docs/source/docs/setting_up_aml.md → docs/source/md/setting_up_aml.md
diff --git a/docs/source/docs/testing.md → docs/source/md/testing.md b/docs/source/docs/testing.md → docs/source/md/testing.md
diff --git a/environment.yml b/environment.yml
@@ -128,7 +128,7 @@ dependencies:
  - deprecated==1.2.13
  - distro==1.7.0
  - docker==4.3.1
- - docutils==0.19
+ - docutils==0.17.1
  - dotnetcore2==2.1.23
  - entrypoints==0.4
  - execnet==1.9.0
@@ -151,7 +151,7 @@ dependencies:
  - gunicorn==20.1.0
  - h5py==2.10.0
  - hi-ml==0.2.2
- - hi-ml-azure==0.2.4
+ - hi-ml-azure==0.2.2
  - humanize==4.2.3
  - idna==3.3
  - imageio==2.15.0

diff --git a/primary_deps.yml b/primary_deps.yml
@@ -29,6 +29,7 @@ dependencies:
  - gputil==1.4.0
  - h5py==2.10.0
  - hi-ml==0.2.2
+ - hi-ml-azure==0.2.2
  - imageio==2.15.0
  - InnerEye-DICOM-RT==1.0.3
  - ipython==7.31.1
@@ -59,7 +60,6 @@ dependencies:
  - pytest-xdist==1.34.0
  - pytest==6.0.1
  - pytorch-lightning==1.5.5
- - recommonmark==0.7.1
  - rich==10.13.0
  - rpdb==0.1.6
  - ruamel.yaml==0.16.12