Return to copying instead of symlink

.gitignore

@@ -85,7 +85,7 @@ instance/
 
 # Sphinx documentation
 docs/build/
-docs/source/docs/CHANGELOG.md
+docs/source/md/CHANGELOG.md
 
 # PyBuilder
 target/

CHANGELOG.md

@@ -181,7 +181,7 @@ institution id and series id columns are missing.
 - ([#441](https://github.com/microsoft/InnerEye-DeepLearning/pull/441)) Add script to move models from one AzureML workspace to another: `python InnerEye/Scripts/move_model.py`
 - ([#417](https://github.com/microsoft/InnerEye-DeepLearning/pull/417)) Added a generic way of adding PyTorch Lightning
 models to the toolbox. It is now possible to train almost any Lightning model with the InnerEye toolbox in AzureML,
-with only minimum code changes required. See [the MD documentation](docs/bring_your_own_model.md) for details.
+with only minimum code changes required. See [the MD documentation](docs/source/md/bring_your_own_model.md) for details.
 - ([#430](https://github.com/microsoft/InnerEye-DeepLearning/pull/430)) Update conversion to 1.0.1 InnerEye-DICOM-RT to
  add: manufacturer, SoftwareVersions, Interpreter and ROIInterpretedTypes.
 - ([#385](https://github.com/microsoft/InnerEye-DeepLearning/pull/385)) Add the ability to train a model on multiple
@@ -354,7 +354,7 @@ console for easier diagnostics.
 
 #### Fixed
 
-- When registering a model, it now has a consistent folder structured, described [here](docs/deploy_on_aml.md). This
+- When registering a model, it now has a consistent folder structured, described [here](docs/source/md/deploy_on_aml.md). This
  folder structure is present irrespective of using InnerEye as a submodule or not. In particular, exactly 1 Conda
  environment will be contained in the model.
 

docs/requirements.txt

@@ -0,0 +1,2 @@
+- recommonmark
+- readthedocs-sphinx-ext

docs/source/conf.py

@@ -16,6 +16,7 @@
 # documentation root, make it absolute.
 #
 import sys
+import shutil
 from pathlib import Path
 repo_dir = Path(__file__).absolute().parents[2]
 sys.path.insert(0, str(repo_dir))
@@ -101,10 +102,11 @@ def replace_in_file(filepath: Path, original_str: str, replace_str: str) -> None
 docs_path = Path(sphinx_root / "md")
 repository_root = sphinx_root.parent.parent
 
-# Symlink to all files that are in the head of the repository
-files_to_symlink = ["CHANGELOG.md"]
-for file_to_symlink in files_to_symlink:
- symlink_path = docs_path / file_to_symlink
- if not symlink_path.exists():
- target_path = repository_root / file_to_symlink
- symlink_path.symlink_to(target_path)
+# Copy files that are in the head of the repository
+files_to_copy = ["CHANGELOG.md", "README.md"]
+for file_to_copy in files_to_copy:
+ copy_path = docs_path / file_to_copy
+ if not copy_path.exists():
+ source_path = repository_root / file_to_copy
+ shutil.copy(source_path, copy_path)
+ replace_in_file(copy_path, "docs/source/md/", "")