Added initial draft of the documenation

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

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+# Useful Tips on How to Build the Documentation
+
+This document provides useful tips on how to build the documentation for the project.
+
+- Automatically create modules rst files: `sphinx-apidoc -o source/ ../protac_degradation_predictor`
+  - Then, in `index.rst`, add the following line: `source/modules`
+- Build the documentation: `make clean ; make html`

docs/conf.py

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+import os
+import sys
+
+sys.path.insert(0, os.path.abspath('..'))
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'PROTAC-Degradation-Predictor'
+copyright = '2024, Stefano Ribes'
+author = 'Stefano Ribes'
+release = 'v1.0.1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The following will place the type hints in the description rather than in the function signature
+autodoc_typehints = 'description'
+
+# Mock pytorch lightning
+autodoc_mock_imports = [
+    'pytorch_lightning',
+]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+# html_theme = 'alabaster'
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,18 @@
+.. PROTAC-Degradation-Predictor documentation master file, created by
+   sphinx-quickstart on Mon Aug 19 11:16:51 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+PROTAC-Degradation-Predictor documentation
+==========================================
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   source/modules

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/modules.rst

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+protac_degradation_predictor
+============================
+
+.. toctree::
+   :maxdepth: 4
+
+   protac_degradation_predictor

docs/source/protac_degradation_predictor.optuna.rst

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+protac\_degradation\_predictor.optuna package
+=============================================
+
+Submodules
+----------
+
+protac\_degradation\_predictor.optuna.pytorch\_models module
+------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna.pytorch_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna.sklearn\_models module
+------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna.sklearn_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna.utils module
+--------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna.xgboost\_models module
+------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna.xgboost_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protac_degradation_predictor.optuna
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/protac_degradation_predictor.rst

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+protac\_degradation\_predictor package
+======================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   protac_degradation_predictor.optuna
+
+Submodules
+----------
+
+protac\_degradation\_predictor.config module
+--------------------------------------------
+
+.. automodule:: protac_degradation_predictor.config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.data\_utils module
+-------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.data_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna\_utils module
+---------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna\_utils\_xgboost module
+------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna_utils_xgboost
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.protac\_dataset module
+-----------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.protac_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.protac\_degradation\_predictor module
+--------------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.protac_degradation_predictor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.pytorch\_models module
+-----------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.pytorch_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.sklearn\_models module
+-----------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.sklearn_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protac_degradation_predictor
+   :members:
+   :undoc-members:
+   :show-inheritance: