4 add readthedocs

.gitignore

@@ -158,3 +158,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+poetry.lock
+*/README_preprocessed.md
+test.ipynb

docs/source/api.rst

@@ -0,0 +1,33 @@
+API Reference
+============
+
+Model
+----
+.. automodule:: deep_quality_estimation.model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Data Handling
+------------
+.. automodule:: deep_quality_estimation.data_handler
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: deep_quality_estimation.transforms
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Utilities
+---------
+.. automodule:: deep_quality_estimation.center_of_mass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: deep_quality_estimation.enums
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/conf.py

@@ -8,15 +8,15 @@
 from subprocess import run
 
 
-sys.path.insert(0, os.path.abspath("../../"))
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 run(["python", "preprocess_readme.py"])
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "PACKAGE_NAME"
+project = "Deep Quality Estimation"
 copyright = "2024, Marcel Rosier et al."
 author = "Marcel Rosier, Florian Kofler"
 
@@ -38,9 +38,12 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = "pydata-sphinx-theme"
+html_theme = "pydata_sphinx_theme"
+html_theme_options = {
+    "github_url": "https://github.com/BrainLesion/deep_quality_estimation",
+}
 # html_static_path = ["_static"]
-
+autodoc_mock_imports = ["torch", "monai"]  # Mock imports to avoid dependency issues
 autodoc_default_options = {
     "members": True,
     "undoc-members": True,

docs/source/index.rst

@@ -1,22 +1,12 @@
-PACKAGE_NAME documentation
-===================
+deep_quality_estimation
+=========================
 
 .. include:: ../README_preprocessed.md
    :parser: myst_parser.sphinx_
 
-
-Sections
-===================
-
-
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Getting Started:
-
-   readme
-
 .. toctree::
    :maxdepth: 2
-   :caption: API Reference:
+   :hidden:
+   :caption: API Reference
 
+   api