# SynKit
[](https://pypi.org/project/synkit/)
[](https://anaconda.org/tieulongphan/synkit)
[](https://hub.docker.com/r/tieulongphan/synkit)
[](https://hub.docker.com/r/tieulongphan/synkit)
[](https://github.com/tieulongphan/synkit/blob/main/LICENSE)
[](https://github.com/tieulongphan/synkit/releases)
[](https://github.com/tieulongphan/synkit/commits)
[](https://doi.org/10.5281/zenodo.15269901)
[](https://github.com/tieulongphan/synkit/actions/workflows/test-and-lint.yml)
[](https://github.com/tieulongphan/synkit/pulls?q=is%3Apr+label%3Adependencies)
[](https://github.com/tieulongphan/synkit/stargazers)
**Toolkit for Synthesis Planning**
SynKit is a collection of tools designed to support the planning and execution of chemical synthesis.
Our tools are tailored to assist researchers and chemists in navigating complex chemical reactions and synthesis pathways, leveraging the power of modern computational chemistry. Whether you're designing novel compounds or optimizing existing processes, ``synkit`` aims to provide the critical tools you need.
For more details on each utility within the repository, please refer to the documentation provided in the respective folders.
## Table of Contents
- [Installation](#installation)
- [Contribute to `SynKit`](#contribute)
- [Contributing](#contributing)
- [License](#license)
- [Acknowledgments](#acknowledgments)
## Installation
1. **Python Installation:**
Ensure that Python 3.11 or later is installed on your system. You can download it from [python.org](https://www.python.org/downloads/).
2. **Creating a Virtual Environment (Optional but Recommended):**
It's recommended to use a virtual environment to avoid conflicts with other projects or system-wide packages. Use the following commands to create and activate a virtual environment:
```bash
python -m venv synkit-env
source synkit-env/bin/activate
```
Or Conda
```bash
conda create --name synkit-env python=3.11
conda activate synkit-env
```
3. **Install from PyPi:**
The easiest way to use SynTemp is by installing the PyPI package
[synkit](https://pypi.org/project/synkit/).
```
pip install synkit
```
Optional if you want to install full version
```
pip install synkit[all]
```
4. **Install via Docker**
Pull the image:
```bash
docker pull tieulongphan/synkit:latest
# or a specific version:
docker pull tieulongphan/synkit:0.1.0
```
Run a container (sanity check):
```
docker run --rm tieulongphan/synkit:latest
```
## Contribute
We're welcoming new contributors to build this project better. Please not hesitate to inquire me via [email][tieu@bioinf.uni-leipzig.de].
Before you start, ensure your local development environment is set up correctly. Pull the latest version of the `main` branch to start with the most recent stable code.
```bash
git checkout main
git pull
```
### Working on New Features
1. **Create a New Branch**:
For every new feature or bug fix, create a new branch from the `main` branch. Name your branch meaningfully, related to the feature or fix you are working on.
```bash
git checkout -b feature/your-feature-name
```
2. **Develop and Commit Changes**:
Make your changes locally, commit them to your branch. Keep your commits small and focused; each should represent a logical unit of work.
```bash
git commit -m "Describe the change"
```
3. **Run Quality Checks**:
Before finalizing your feature, run the following commands to ensure your code meets our formatting standards and passes all tests:
```bash
./lint.sh # Check code format
pytest Test # Run tests
```
Fix any issues or errors highlighted by these checks.
### Integrating Changes
1. **Rebase onto Staging**:
Once your feature is complete and tests pass, rebase your changes onto the `staging` branch to prepare for integration.
```bash
git fetch origin
git rebase origin/staging
```
Carefully resolve any conflicts that arise during the rebase.
2. **Push to Your Feature Branch**:
After successfully rebasing, push your branch to the remote repository.
```bash
git push origin feature/your-feature-name
```
3. **Create a Pull Request**:
Open a pull request from your feature branch to the `staging` branch. Ensure the pull request description clearly describes the changes and any additional context necessary for review.
## Contributing
- [Tieu-Long Phan](https://tieulongphan.github.io/)
- [Klaus Weinbauer](https://github.com/klausweinbauer)
- [Phuoc-Chung Nguyen Van](https://github.com/phuocchung123)
## Publication
[**SynKit**: An Advanced Cheminformatics Python Library for Efficient Manipulation and Analysis of Chemical Reaction Data]()
## License
This project is licensed under MIT License - see the [License](LICENSE) file for details.
## Acknowledgments
This project has received funding from the European Unions Horizon Europe Doctoral Network programme under the Marie-Skłodowska-Curie grant agreement No 101072930 ([TACsy](https://tacsy.eu/) -- Training Alliance for Computational)
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"description": "# SynKit\n[](https://pypi.org/project/synkit/)\n[](https://anaconda.org/tieulongphan/synkit)\n[](https://hub.docker.com/r/tieulongphan/synkit)\n[](https://hub.docker.com/r/tieulongphan/synkit)\n[](https://github.com/tieulongphan/synkit/blob/main/LICENSE)\n[](https://github.com/tieulongphan/synkit/releases)\n[](https://github.com/tieulongphan/synkit/commits)\n[](https://doi.org/10.5281/zenodo.15269901)\n[](https://github.com/tieulongphan/synkit/actions/workflows/test-and-lint.yml)\n[](https://github.com/tieulongphan/synkit/pulls?q=is%3Apr+label%3Adependencies)\n[](https://github.com/tieulongphan/synkit/stargazers)\n\n**Toolkit for Synthesis Planning**\n\nSynKit is a collection of tools designed to support the planning and execution of chemical synthesis. \n\n\n\nOur tools are tailored to assist researchers and chemists in navigating complex chemical reactions and synthesis pathways, leveraging the power of modern computational chemistry. Whether you're designing novel compounds or optimizing existing processes, ``synkit`` aims to provide the critical tools you need.\n\nFor more details on each utility within the repository, please refer to the documentation provided in the respective folders.\n\n## Table of Contents\n- [Installation](#installation)\n- [Contribute to `SynKit`](#contribute)\n- [Contributing](#contributing)\n- [License](#license)\n- [Acknowledgments](#acknowledgments)\n\n## Installation\n\n1. **Python Installation:**\n Ensure that Python 3.11 or later is installed on your system. You can download it from [python.org](https://www.python.org/downloads/).\n\n2. **Creating a Virtual Environment (Optional but Recommended):**\n It's recommended to use a virtual environment to avoid conflicts with other projects or system-wide packages. Use the following commands to create and activate a virtual environment:\n\n ```bash\n python -m venv synkit-env\n source synkit-env/bin/activate \n ```\n Or Conda\n\n ```bash\n conda create --name synkit-env python=3.11\n conda activate synkit-env\n ```\n\n3. **Install from PyPi:**\n The easiest way to use SynTemp is by installing the PyPI package \n [synkit](https://pypi.org/project/synkit/).\n\n ```\n pip install synkit\n ```\n Optional if you want to install full version\n ```\n pip install synkit[all]\n ```\n\n4. **Install via Docker** \n Pull the image: \n\n ```bash\n docker pull tieulongphan/synkit:latest\n # or a specific version:\n docker pull tieulongphan/synkit:0.1.0\n ```\n Run a container (sanity check):\n ```\n docker run --rm tieulongphan/synkit:latest\n ```\n\n## Contribute\n\nWe're welcoming new contributors to build this project better. 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Keep your commits small and focused; each should represent a logical unit of work.\n\n ```bash\n git commit -m \"Describe the change\"\n ```\n\n3. **Run Quality Checks**: \n Before finalizing your feature, run the following commands to ensure your code meets our formatting standards and passes all tests:\n\n ```bash\n ./lint.sh # Check code format\n pytest Test # Run tests\n ```\n\n Fix any issues or errors highlighted by these checks.\n\n### Integrating Changes\n\n1. **Rebase onto Staging**: \n Once your feature is complete and tests pass, rebase your changes onto the `staging` branch to prepare for integration.\n\n ```bash\n git fetch origin\n git rebase origin/staging\n ```\n\n Carefully resolve any conflicts that arise during the rebase.\n\n2. **Push to Your Feature Branch**:\n After successfully rebasing, push your branch to the remote repository.\n\n ```bash\n git push origin feature/your-feature-name\n ```\n\n3. **Create a Pull Request**:\n Open a pull request from your feature branch to the `staging` branch. Ensure the pull request description clearly describes the changes and any additional context necessary for review.\n\n## Contributing\n- [Tieu-Long Phan](https://tieulongphan.github.io/)\n- [Klaus Weinbauer](https://github.com/klausweinbauer)\n- [Phuoc-Chung Nguyen Van](https://github.com/phuocchung123)\n\n## Publication\n\n[**SynKit**: An Advanced Cheminformatics Python Library for Efficient Manipulation and Analysis of Chemical Reaction Data]()\n\n\n## License\n\nThis project is licensed under MIT License - see the [License](LICENSE) file for details.\n\n## Acknowledgments\n\nThis project has received funding from the European Unions Horizon Europe Doctoral Network programme under the Marie-Sk\u0142odowska-Curie grant agreement No 101072930 ([TACsy](https://tacsy.eu/) -- Training Alliance for Computational)",
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