Martini Force Field Initiative Website

Martini is a coarse-grained force field suited for molecular dynamics simulations of (bio)molecular systems. The Martini Force Field Initiative website serves as a central hub for the Martini community, providing resources, publications, tutorials, and tools to facilitate the use and development of the Martini force field.

How to Contribute

We welcome contributions from the community and appreciate your efforts to improve and expand the Martini Force Field Initiative website! This guide provides a step-by-step walkthrough of how to contribute to this website, including setting up your environment, making your changes, and submitting pull requests for review.

Table of Contents

1. Setting Up Your Environment
   1. Install Quarto
   2. Fork the Repository
   3. Clone the Repository to your local workstation
2. Types of Contributions
   1. Adding New Publications
   2. Adding New Announcements
   3. Adding New Martini 3 Tutorials
   4. Adding Tools
   5. Adding New Parameter Files
   6. General Website Enhancements
3. Submitting a Pull Request
4. Reviewing and Merging
5. Additional Resources

1. Setting Up Your Environment

Before you begin contributing, you need to set up your local environment to work with Quarto and this repository.

1.1. Install Quarto

To build and preview the website locally, you need to install Quarto. Follow the instructions below based on your operating system:

• Windows:

  1. Download the .msi file from the official website [here].
  2. Run the installer and follow the prompts.

• macOS:

  1. Download the .dmg file from the official website [here].
  2. Open the file and drag Quarto to your Applications folder.

• Ubuntu/Debian:

  1. Download the amd64 .deb file from the official website [here].
  2. Complete the installation by running the following command in your terminal:

     sudo dpkg -i quarto-*-linux-amd64.deb        

• Other Linux Distributions:

  1. Download the .tar.gz file from the official website [here].
  2. Extract the archive and move the quarto binary to a directory in your PATH.

After installation, verify the installation by running quarto check in your terminal.

1.2. Fork the Repository

Navigate to this GitHub repository and click on the Fork button in the top-right corner of the page to create your own copy.

1.3. Clone the Repository to your local workstation

Clone your fork to your local workstation using the following commands:

git clone https://github.com/your-username/Martini-Force-Field-Initiative.github.io.git
cd Martini-Force-Field-Initiative.github.io/

2. Types of Contributions

There are six main types of contributions you can make to the website:

2.1. Adding New Publications

1. Navigate to docs/publications/entry_template.qmd.
2. Copy the template file to the appropriate folder by year under docs/publications/entries/, and rename it with a unique identifier, e.g., author-first_word_in_title.qmd.
3. Fill in the required fields in the template. The attribute in the headers are self-explanatory, and the content should follow best-practice Markdown syntax.
4. Preview the website locally using the following command from the root directory of the repository:

   quarto preview --port 4040

5. Open your browser and navigate to http://localhost:4040 to verify that the publication has been integrated as expected in the Publications section of the website.
6. Once verified, commit your changes and submit a pull request to this repository to be reviewed by the Martini Developers Team.

2.2. Adding New Announcements

1. Navigate to docs/announcements/entry_template.qmd.
2. Copy the template file to the docs/announcements/posts/ directory and place it in a new folder with a descriptive name including the date and some keywords in the announcements, e.g., YYYY-MM-DD-keywords/. We recommend naming the file inside the folder as index.qmd, but you can choose a different name of your preference.
3. Complete the template with the relevant details for your announcement.
4. Preview the website locally using the following command from the root directory of the repository:

   quarto preview --port 4040

5. Open your browser and navigate to http://localhost:4040 to verify that the announcement is displayed correctly in the Announcements section of the website.
6. Once verified, commit your changes and submit a pull request to this repository to be reviewed by the Martini Developers Team.

2.3. Adding New Martini 3 Tutorials

1. Refer to the index.qmd file in any of the existing tutorials in docs/tutorials/Martini3/ as reference, e.g., docs/tutorials/Martini3/LipidsI/index.qmd.
2. Create a new tutorial by following the structure and format used in the examples.
3. Place the new tutorial in a dedicated directory under docs/tutorials/Martini3/. You can name the directory based on the tutorial topic and application. All the related files (images, data, etc.) should be placed in this directory.
4. Open the file that keeps track of all the tutorials in docs/tutorials/Martini3/tutorials.qmd and add a new entry for your tutorial following the same Markdown syntax as the other entries in the list.
5. Preview the website locally using the following command from the root directory of the repository:

   quarto preview --port 4040

6. Open your browser and navigate to http://localhost:4040 to verify that the tutorial is correctly formatted and functional.
7. Once verified, commit your changes and submit a pull request to this repository to be reviewed by the Martini Developers Team.

2.4. Adding Tools

1. Include the description of your tool in one of the existing .qmd files under docs/downloads/tools/.
2. Current subsections include Proteins and Bilayers(proteins-and-bilayers.qmd), Resolution transformation(resolution-transformation.qmd), Visualization(visualization.qmd), and Other tools(other-tools.qmd).
3. Preview the website locally using the following command from the root directory of the repository:

   quarto preview --port 4040

4. Open your browser and navigate to http://localhost:4040 to verify that the tool has integrated seamlessly in the Downloads/Tools/ section of the website.
5. Once verified, commit your changes and submit a pull request to this repository to be reviewed by the Martini Developers Team.

2.5. Adding New Parameter Files

1. Add the description for the new parameters in the appropriate .qmd file in docs/downloads/force-field-parameters/martini3/ attending to the molecule type that better fits your case.
2. Keep your .itp parameter files at hand to share them with the Martini Developers Team during the reviewing of your pull request. If approved, the files will be included in the backend martini library to be directly available from the website.
3. Preview the website locally using the following command from the root directory of the repository:

   quarto preview --port 4040

4. Open your browser and navigate to http://localhost:4040 to verify that the description of the parameters is showing correctly in the subsection at Downloads/Force field parameters/Martini 3/ corresponding to the specific molecule type you choose.
5. Once verified, commit your changes and submit a pull request to this repository to be reviewed by the Martini Developers Team.

2.6. General Website Enhancements

We also welcome contributions that improve the overall appearance or functionality of the website. The recommended steps for this type of contribution are as follows:

1. Familiarize yourself with the code in this repository.
2. Implement your changes.
3. Preview the changes in the website locally using the following command from the root directory of the repository:

   quarto preview --port 4040

4. Test extensively to ensure no existing functionality is broken.
5. Submit your enhancements via a pull request to this repository to be reviewed by the Martini Developers Team.

3. Submitting a Pull Request

Once your changes are ready you can follow these steps to submit a pull request:

1. Commit Your Changes:

git add .
git commit -m "Brief description of your changes"

2. Push to Your Fork of the Repository:

git push origin your-branch-name

3. Submit a Pull Request:

   i- Go to your own copy of the repository on GitHub.

   ii- Click the Contribute button right below the name of your recently pushed branch.

   iii- Click on Open pull request and fill in the pull request template with details about your changes.

   iv- Submit the pull request.

4. Reviewing and Merging

Your pull request will be reviewed by other users in the Martini Developers Team. We may request/suggest additional changes or approve it directly. Once approved, your changes will be merged into the main branch, and the website will be automatically updated and deployed via a GitHub Action.

5. Additional Resources

For further guidance, please refer to the following:

• Quarto Documentation
• GitHub Markdown Guide

If you have any questions or need assistance, feel free to open an issue on GitHub or contact the team through our Discussion Board.

Thank you for your interest in contributing to the Martini Force Field Initiative website!:)