Installation

Requirements

  • Python 3.11 or higher
  • Git for version control

Standard Installation

tfbpmodeling is available for installation directly from GitHub using pip. PyPI distribution is planned for future releases.

Install from GitHub

=== "Latest Stable (main branch)"

```bash
python -m pip install git+https://github.com/BrentLab/tfbpmodeling.git
```

=== "Development Version (dev branch)"

```bash
python -m pip install git+https://github.com/BrentLab/tfbpmodeling.git@dev
```

=== "Specific Version (by tag)"

```bash
python -m pip install git+https://github.com/BrentLab/tfbpmodeling.git@v1.0.0
```

It's recommended to install tfbpmodeling in a virtual environment:

# Create virtual environment
python -m venv tfbp-env

# Activate virtual environment
# On Linux/macOS:
source tfbp-env/bin/activate
# On Windows:
tfbp-env\Scripts\activate

# Install tfbpmodeling
python -m pip install git+https://github.com/BrentLab/tfbpmodeling.git

# Upgrade existing installation
python -m pip install --upgrade git+https://github.com/BrentLab/tfbpmodeling.git

Verify Installation

Test that the installation was successful:

# Show help for the main command
python -m tfbpmodeling --help

# Show help for the modeling command
python -m tfbpmodeling linear_perturbation_binding_modeling --help

Development Installation

For development work, you'll need to clone the repository and install with Poetry.

1. Clone the Repository

=== "Fork for Development"

If you plan to contribute:

1. Fork the repository on GitHub
2. Clone your fork:

```bash
git clone https://github.com/YOUR_USERNAME/tfbpmodeling.git
cd tfbpmodeling
```

3. Add the upstream remote:

```bash
git remote add upstream https://github.com/BrentLab/tfbpmodeling.git
```

=== "Direct Clone"

```bash
git clone https://github.com/BrentLab/tfbpmodeling.git
cd tfbpmodeling
```

2. Install Poetry

If you don't have Poetry installed, follow the official installation instructions.

Poetry Configuration

We recommend configuring Poetry to create virtual environments in the project directory:

poetry config virtualenvs.in-project true

This creates the virtual environment as .venv in the project directory.

3. Install Dependencies

poetry install

This installs all dependencies, including development tools for testing and documentation.

4. Install Pre-commit Hooks

For development work, install pre-commit hooks to ensure code quality:

poetry run pre-commit install

You can run pre-commit manually at any time:

poetry run pre-commit run --all-files

Development Tools

Running Tests

# Run all tests
poetry run pytest

# Run with coverage
poetry run pytest --cov --cov-branch --cov-report=xml

# Run specific test file
poetry run pytest tfbpmodeling/tests/test_interface.py

# Run specific test by name
poetry run pytest -k "test_function_name"

Code Quality

The project uses several tools to maintain code quality:

# Format code with Black
poetry run black .

# Check code style with Flake8
poetry run flake8

# Type checking with MyPy
poetry run mypy tfbpmodeling

Documentation

Build and serve documentation locally:

# Serve documentation with live reload
mkdocs serve

# Build documentation
mkdocs build

# Deploy to GitHub Pages (maintainers only)
poetry run mkdocs gh-deploy

Getting Help