Release/v0.4.0

[tonyzamyatin]

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[Copilot]

Pull request overview

This release PR (v0.4.0) introduces comprehensive documentation, improved naming conventions, and automation tools for OOD benchmarking experiments.

• Renames DataSource to AbstractDataSource for better naming consistency across the codebase
• Adds extensive user and developer documentation including guides for custom data, OOD benchmarking, reproducibility tests, and custom components
• Introduces generate_data_split_configs.py script to automate creation of OOD benchmark configurations
• Updates branding with new SVG logos supporting light/dark themes
• Includes auto-generated OOD benchmark config files for various data splitting strategies

Reviewed changes

Copilot reviewed 59 out of 65 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
src/chemtorch/components/data_pipeline/data_source/abstract_data_source.py	Renames class from DataSource to AbstractDataSource
src/chemtorch/components/data_pipeline/data_source/__init__.py	Updates import to use AbstractDataSource
src/chemtorch/components/data_pipeline/data_source/single_csv_source.py	Updates parent class reference
src/chemtorch/components/data_pipeline/data_source/pre_split_csv_source.py	Updates parent class reference
src/chemtorch/components/data_pipeline/simple_data_pipeline.py	Updates type hint for data_source parameter
test/test_data_module/test_data_pipeline/test_simple_data_pipeline.py	Updates test imports and mock class
src/chemtorch/components/representation/token/abstract_token_representation.py	Removes obsolete comment
src/chemtorch/components/representation/graph/cgr.py	Updates docstring with improved usage examples
scripts/generate_data_split_configs.py	Adds script to automate OOD benchmark config generation
scripts/README.md	Comprehensive documentation for all utility scripts
docs/source/user_guide/reproducibility_tests.rst	New guide for setting up reproducibility tests
docs/source/user_guide/custom_data.rst	New guide for using custom datasets
docs/source/user_guide/custom_components.rst	Removed (moved to developer guide)
docs/source/user_guide/pipeline_overview.rst	Removed (replaced with overview.rst)
docs/source/user_guide/inference.rst	Removed (merged into custom_data.rst)
docs/source/getting_started/overview.rst	New comprehensive architecture overview
docs/source/getting_started/experiments.rst	Title consistency update
docs/source/getting_started/config.rst	Enhanced configuration guide
docs/source/examples/training_curves.rst	New tutorial for performance curves
docs/source/examples/ood_benchmarking.rst	New comprehensive OOD benchmarking tutorial
docs/source/developer_guide/testing.rst	Cleanup of obsolete comments
docs/source/developer_guide/props.rst	New runtime properties guide
docs/source/developer_guide/hydra.rst	Placeholder for future Hydra guide
docs/source/developer_guide/custom_components.rst	New developer guide for extending ChemTorch
docs/source/developer_guide/framework_structure.rst	Removed obsolete file
docs/source/index.rst	Restructured documentation navigation
docs/source/conf.py	Updated logo paths to use new SVG assets
docs/source/api_autodoc/*	New API documentation structure
docs/source/_static/*.svg	New logos and figures
conf/saved_configs/chemtorch_benchmark/ood_benchmark/drfp_mlp/*.yaml	Generated OOD benchmark configs for DRFP/MLP model
conf/saved_configs/chemtorch_benchmark/ood_benchmark/dimereaction/*.yaml	Generated OOD benchmark configs for DimeReaction model
README.md	Updated with responsive logo and refined tagline

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