Installation Guide¶

Modern Setup (Recommended)¶

PyCompTox now uses modern Python packaging standards (PEP 621) with pyproject.toml.

Quick Install¶

# Install from source
pip install .

# Install with development dependencies
pip install -e ".[dev]"

# Install with notebook support
pip install -e ".[notebook]"

# Install everything
pip install -e ".[all]"

Install Options¶

Standard Installation:

pip install .

Installs only the core dependencies (requests).

Development Installation:

pip install -e ".[dev]"

Includes: - pytest, pytest-cov (testing) - black (code formatting) - flake8 (linting) - mypy (type checking) - types-requests (type stubs)

Notebook Support:

pip install -e ".[notebook]"

Includes: - jupyter (notebooks) - pandas (data analysis) - matplotlib (visualization)

Everything:

pip install -e ".[all]"

Includes all optional dependencies.

Editable Install¶

For development, use editable mode (-e flag):

# Editable install with dev dependencies
pip install -e ".[dev]"

This allows you to make changes to the code without reinstalling.

Build Distribution¶

To build distribution packages:

# Install build tools
pip install build

# Build wheel and source distribution
python -m build

This creates: - dist/pycomptox-0.3.0-py3-none-any.whl (wheel) - dist/pycomptox-0.3.0.tar.gz (source)

Configuration Files¶

pyproject.toml¶

All project metadata and build configuration is in pyproject.toml: - Package metadata (name, version, description) - Dependencies - Optional dependencies (dev, notebook, all) - Tool configurations (black, mypy, pytest, coverage)

setup.py¶

The setup.py file is now a minimal shim for backward compatibility with older tools. All configuration is in pyproject.toml.

MANIFEST.in¶

Controls which files are included in source distributions: - Documentation (README, LICENSE, docs/) - Type information (py.typed) - Tests (optional)

Type Checking Support¶

PyCompTox is fully typed and includes a py.typed marker file (PEP 561), enabling:

# Type check your code that uses PyCompTox
mypy your_script.py

Command-Line Interface¶

After installation, you can use the CLI:

# Save API key
pycomptox-setup set YOUR_API_KEY

# Show configuration
pycomptox-setup show

# Test API connection
pycomptox-setup test

# Delete API key
pycomptox-setup delete

Or use Python module syntax:

python -m pycomptox set YOUR_API_KEY

Virtual Environment (Recommended)¶

Always use a virtual environment:

# Create virtual environment
python -m venv venv

# Activate (Windows)
venv\Scripts\activate

# Activate (Unix/macOS)
source venv/bin/activate

# Install PyCompTox
pip install -e ".[dev]"

Verify Installation¶

import pycomptox
print(pycomptox.__version__)  # Should print: 0.3.0

# Check available classes
from pycomptox.chemical import Chemical, ChemicalDetails, ChemicalProperties

Development Workflow¶

Clone repository:

git clone https://github.com/USEtox/PyCompTox.git
cd PyCompTox

Create virtual environment:

python -m venv venv
source venv/bin/activate  # or venv\Scripts\activate on Windows

Install in editable mode with dev dependencies:
```
pip install -e ".[dev]"
```
Run tests:
```
pytest tests/
```
Format code:
```
black src/ tests/
```
Type check:
```
mypy src/pycomptox
```
Lint:
```
flake8 src/ tests/
```

Troubleshooting¶

"No module named 'pycomptox'"¶

Make sure you installed the package:

pip install -e .

Import errors after changes¶

If you installed in editable mode, Python should pick up changes automatically. If not:

pip install -e . --force-reinstall --no-deps

Type checking issues¶

Install type stubs:

pip install types-requests

Build errors¶

Make sure you have the latest build tools:

pip install --upgrade pip setuptools wheel build

Requirements¶

Python 3.8 or higher
pip (usually comes with Python)
Internet connection (for API access)

Platform Support¶

PyCompTox is pure Python and works on: - ✓ Windows - ✓ macOS - ✓ Linux - ✓ Any platform with Python 3.8+

Getting Help¶

GitHub Issues: https://github.com/USEtox/PyCompTox/issues
Documentation: https://github.com/USEtox/PyCompTox/blob/main/README.md