Many warnings are shown while building Sphinx docs

[fepegar]

Assuming #660 has been fixed:

$ make html
python preprocess.py
Running Sphinx v3.1.1
making output directory... done
WARNING: html_static_path entry '_static' does not exist
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 23 source files that are out of date
updating environment: [new config] 23 added, 0 changed, 0 removed
/home/fernando/miniconda3/envs/torchio/lib/python3.9/site-packages/recommonmark/parser.py:75: UserWarning: Container node skipped: type=document
  warn("Container node skipped: type={0}".format(mdnode.t))
reading sources... [100%] rst/configs
WARNING: don't know which module to import for autodocumenting 'InnerEye.ML.config.SegmentationModelBase' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
WARNING: autodoc: failed to import module 'ML.config' from module 'InnerEye'; the following exception was raised:
No module named 'InnerEye'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/bring_your_own_model.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/deploy_on_aml.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/deploy_on_ash.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/hello_world_model.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/innereye_as_submodule.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/model_diagnostics.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/move_model.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/releases.md: WARNING: document isn't included in any toctree
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/self_supervised_models.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] rst/configs
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/README.md:105: WARNING: None:any reference target not found: InnerEye-DataQuality/README
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/README.md:123: WARNING: None:any reference target not found: CHANGELOG
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/README.md:130: WARNING: None:any reference target not found: LICENSE
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/README.md:148: WARNING: None:any reference target not found: InnerEye-DataQuality/README
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/README.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/README.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/README.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/README.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/bring_your_own_model.md:18: WARNING: None:any reference target not found: ../InnerEye/ML/configs/other/HelloContainer.py
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/bring_your_own_model.md:47: WARNING: None:any reference target not found: ../InnerEye/ML/configs/other/HelloContainer.py
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/bring_your_own_model.md:156: WARNING: None:any reference target not found: ../InnerEye/ML/model_training.py
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md:282: WARNING: None:any reference target not found: ../InnerEye/Common/Statistics/wilcoxon_signed_rank_test.py
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/building_models.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/debugging_and_monitoring.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/debugging_and_monitoring.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md:86: WARNING: None:any reference target not found: ../InnerEye/ML/configs/other/fastmri_varnet.py
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md:187: WARNING: None:any reference target not found: ../InnerEye/ML/configs/other/fastmri_varnet.py
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/fastmri.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/hello_world_model.md:3: WARNING: None:any reference target not found: ../InnerEye/ML/configs/segmentation/HelloWorld.py
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/innereye_as_submodule.md: WARNING: Pygments lexer name 'shell script' is not known
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/pull_requests.md:15: WARNING: None:any reference target not found: ../CHANGELOG
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/releases.md:12: WARNING: None:any reference target not found: ../CHANGELOG
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/sample_tasks.md:79: WARNING: None:any reference target not found: ../InnerEye/ML/configs/segmentation/Lung.py
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/setting_up_aml.md:174: WARNING: None:any reference target not found: ../InnerEye/settings.yml
/home/fernando/git/InnerEye-DeepLearning/sphinx-docs/source/md/docs/setting_up_aml.md:180: WARNING: None:any reference target not found: ../InnerEye/settings.yml
generating indices...  genindexdone
writing additional pages...  searchdone
copying images... [100%] md/docs/screenshot_azureml_patch_sampling.png
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 51 warnings.

The HTML pages are in build/html.

Issues:

1. Some doc files are not included in any TOC tree
2. Relative paths to other files in the repo don't work while building the Sphinx docs
3. The syntax to higlight shell code should be shell, not shell script

AB#4984