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Remove sections from README.md that have to do with the template
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Patrick Golden committed Nov 14, 2024
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Expand Up @@ -9,61 +9,6 @@ BioGRID ingest.
- Python >= 3.10
- [Poetry](https://python-poetry.org/docs/#installation)

## Setting Up a New Project

Upon creating a new project from the `cookiecutter-monarch-ingest` template, you can install and test the project:

```bash
cd biogrid-ingest
make install
make test
```

There are a few additional steps to complete before the project is ready for use.

#### GitHub Repository

1. Create a new repository on GitHub.
1. Enable GitHub Actions to read and write to the repository (required to deploy the project to GitHub Pages).
- in GitHub, go to Settings -> Action -> General -> Workflow permissions and choose read and write permissions
1. Initialize the local repository and push the code to GitHub. For example:

```bash
cd biogrid-ingest
git init
git remote add origin https://github.com/<username>/<repository>.git
git add -A && git commit -m "Initial commit"
git push -u origin main
```

#### Transform Code and Configuration

1. Edit the `download.yaml`, `transform.py`, `transform.yaml`, and `metadata.yaml` files to suit your needs.
- For more information, see the [Koza documentation](https://koza.monarchinitiative.org) and [kghub-downloader](https://github.com/monarch-initiative/kghub-downloader).
1. Add any additional dependencies to the `pyproject.toml` file.
1. Adjust the contents of the `tests` directory to test the functionality of your transform.

#### Documentation

1. Update this `README.md` file with any additional information about the project.
1. Add any appropriate documentation to the `docs` directory.

> **Note:** After the GitHub Actions for deploying documentation runs, the documentation will be automatically deployed to GitHub Pages.
> However, you will need to go to the repository settings and set the GitHub Pages source to the `gh-pages` branch, using the `/docs` directory.

#### GitHub Actions

This project is set up with several GitHub Actions workflows.
You should not need to modify these workflows unless you want to change the behavior.
The workflows are located in the `.github/workflows` directory:

- `test.yaml`: Run the pytest suite.
- `create-release.yaml`: Create a new release once a week, or manually.
- `deploy-docs.yaml`: Deploy the documentation to GitHub Pages (on pushes to main).
- `update-docs.yaml`: After a release, update the documentation with node/edge reports.


Once you have completed these steps, you can remove the [Setting Up a New Project](#setting-up-a-new-project) section from this `README.md` file.

## Installation

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