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docs: comprehensive documentation expansion with chemistry tutorials
Major documentation modernization and expansion: Documentation Infrastructure: - Add GitHub Actions workflow for docs CI/CD - Add CONTRIBUTING.md, SECURITY.md, CHANGELOG.md - Create v2→v3 migration guide - Add CLI reference documentation - Add advanced usage guide (NNPModel, ModelFactory, multi-GPU) - Add 6 how-to guides (quickstart, drug discovery, custom NNP, HPC, troubleshooting, integrations) New Tutorials - Drug Discovery: - virtual_screening.ipynb: Lipinski Ro5, PAINS filtering, docking prep - tautomer_protomer_analysis.ipynb: pH-dependent forms, pKa - stereochemistry.ipynb: enantiomers, diastereomers, E/Z isomers - docking_integration.ipynb: AutoDock Vina, PDBQT conversion New Tutorials - Computational Chemistry: - reaction_thermodynamics.ipynb: ΔG, ΔH, ΔS calculations - boltzmann_populations.ipynb: conformer distributions, entropy - strain_energy.ipynb: ring strain, steric strain analysis - molecular_descriptors.ipynb: 3D descriptors for ML/QSAR New Tutorials - Integration Workflows: - md_preparation.ipynb: GROMACS, Amber, OpenMM setup - qm_refinement.ipynb: Gaussian, ORCA, Psi4 input generation Additional: - quickstart.ipynb, performance_tuning.ipynb, large_scale_processing.ipynb - Reorganized index.rst with categorized sections - Fixed notebook paths using symlinks - Updated docs/requirements.txt 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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‎.github/workflows/docs.yml‎

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name: Documentation
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on:
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push:
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branches: [main]
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paths:
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- 'docs/**'
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- 'src/**'
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- 'example/**'
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- '.github/workflows/docs.yml'
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pull_request:
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paths:
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- 'docs/**'
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- 'src/**'
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- 'example/**'
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- '.github/workflows/docs.yml'
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jobs:
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build:
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name: Build Documentation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -e .
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pip install -r docs/requirements.txt
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- name: Build Sphinx documentation
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run: |
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cd docs
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make html
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- name: Check for Sphinx warnings
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run: |
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cd docs
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make html 2>&1 | tee build.log
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# Fail if there are errors (warnings are ok)
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if grep -q "ERROR" build.log; then
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echo "Documentation build has errors!"
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exit 1
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fi
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- name: Upload documentation artifact
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uses: actions/upload-artifact@v4
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with:
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name: documentation
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path: docs/build/html/
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retention-days: 7
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linkcheck:
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name: Check Links
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runs-on: ubuntu-latest
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needs: build
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -e .
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pip install -r docs/requirements.txt
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- name: Check links
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run: |
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cd docs
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make linkcheck || true # Don't fail on broken external links
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continue-on-error: true
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test-notebooks:
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name: Test Notebooks
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -e .
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pip install pytest nbmake
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- name: Test notebooks execute
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run: |
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# Test that notebooks are valid (syntax check only, don't execute)
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python -c "
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import json
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from pathlib import Path
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for nb in Path('example').glob('*.ipynb'):
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print(f'Checking {nb}...')
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with open(nb) as f:
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data = json.load(f)
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assert 'cells' in data
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assert 'nbformat' in data
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print(f' OK: {len(data[\"cells\"])} cells')
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"

‎CHANGELOG.md‎

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# Changelog
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All notable changes to Auto3D will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [3.0.0] - 2026-01-02
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### Breaking Changes
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- **Removed `options()` function** - Use `Auto3DOptions` dataclass instead
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```python
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# Before (v2.x)
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from Auto3D.auto3D import options, main
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args = options("input.smi", k=1)
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main(args)
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# After (v3.0)
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from Auto3D import Auto3DOptions, main
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config = Auto3DOptions(path="input.smi", k=1)
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main(config)
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```
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- **CLI now uses subcommands** - Primary command is `auto3d run`
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```bash
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# Before (v2.x)
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auto3d input.smi --k=1
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# After (v3.0)
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auto3d run input.smi --k=1
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```
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- **Python 3.10+ required** - Dropped support for Python 3.7-3.9
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- **Default optimization parameters changed**:
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- `opt_steps`: 5000 → 2000
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- `patience`: 1000 → 250
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- `convergence_threshold`: 0.003 → 0.01
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### Added
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- **Modern CLI with Typer and Rich**
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- Beautiful terminal output with progress bars
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- Syntax-highlighted configuration display
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- Shell completion for bash, zsh, fish
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- Helpful error messages with suggestions
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- **New CLI subcommands**
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- `auto3d run` - Main conformer generation
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- `auto3d config init` - Generate configuration template
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- `auto3d config show` - Display configuration
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- `auto3d config validate` - Validate configuration
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- `auto3d models list` - List available NNP models
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- `auto3d models info` - Show model details
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- `auto3d validate` - Validate input files
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- **Type-safe configuration with `Auto3DOptions` dataclass**
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- Full IDE support with type hints
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- Validation at creation time
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- Backward-compatible dict-like access
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- **`ModelFactory` API for direct model access**
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```python
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from Auto3D import create_model
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model = create_model("AIMNET", device=torch.device("cuda:0"))
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```
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- **Single-model AIMNet mode** (~35x faster)
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- Default uses single model for geometry optimization
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- Set `use_ensemble=True` for highest accuracy
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- **`NNPModel` Protocol for custom models**
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- Clear interface for custom neural network potentials
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- Runtime protocol checking
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- **Performance options**
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- `allow_tf32` parameter for Ampere+ GPU acceleration
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- `AUTO3D_COMPILE_MODEL` env var for torch.compile()
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- `AUTO3D_USE_ENSEMBLE` env var for ensemble control
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- **Comprehensive exception hierarchy**
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- `Auto3DError` base class
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- Specific exceptions: `ConfigurationError`, `ModelError`, `GPUError`, etc.
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- **Structured logging** throughout the codebase
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### Changed
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- Simplified imports: `from Auto3D import Auto3DOptions, main, smiles2mols`
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- Improved error messages with actionable suggestions
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- Better memory management for large datasets
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- Optimized batch processing
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### Deprecated
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- Legacy YAML-only invocation (`auto3d parameters.yaml`) still works but is deprecated
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### Fixed
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- Various bug fixes and stability improvements
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- Better handling of edge cases in stereoisomer enumeration
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## [2.2.10] - 2024-03-29
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### Fixed
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- Minor bug fixes
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## [2.2.9] - 2024-03-15
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### Changed
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- Performance improvements
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## [2.2.5] - 2023-12-20
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### Added
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- Initial AIMNet2 integration
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## [2.2.1] - 2023-10-01
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### Changed
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- AIMNet2 is now the default model (replacing original AIMNet)
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### Deprecated
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- Original AIMNet model deprecated
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## [2.0.0] - 2023-06-01
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### Added
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- ANI2xt model support
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- Tautomer enumeration
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- Improved isomer handling
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### Changed
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- Major refactoring of optimization engine
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## [1.0.0] - 2022-10-01
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### Added
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- Initial release
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- ANI2x and AIMNET support
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- RDKit and Omega isomer engines
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- GPU acceleration
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- Multi-process support
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---
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## Migration Guide
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For detailed migration instructions from v2.x to v3.0, see the [Migration Guide](https://auto3d.readthedocs.io/en/latest/migration.html).
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## Reporting Issues
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Please report bugs and feature requests on [GitHub Issues](https://github.com/isayevlab/Auto3D_pkg/issues).

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