Update README.md

README.md

@@ -1,64 +1,6 @@
-# PythonTemplate
-This repository contains a simple template for Python repositories, including actions and a `.gitignore` file. The actions include organizing imports with `isort`, linting using `ruff`, automatic test execution using `pytest`, as well as a small coverage report with `coverage` on merging to the main branch.
-
-## Get started
-
-First, clone the repository.
-
-Create the `main`, `develop` and, `gh-pages` branches.
-
-Whenever you want to change something, create a new branch. If it is done, create a pull request to the `develop` branch.
-
-Only pull from `develop` to `main` with fully functional, tested and documented new versions.
-
-### Repository Settings
-**Branch Protection Rules**
-1. Go to the repository settings
-2. Open `Branches` in the left sidebar
-3. Click `Add branch ruleset`
-4. Choose an appropriate ruleset name, such as `Branch protection rules for main and develop`
-5. Under `target branches`, enter `main` and `develop`
-6. Under `Rules` select at least:
-    - `Restricht deletions`
-    - `Require linear history`
-    - `Require a pull request before merging`
-      - Select an appropriate number of reviewers
-      - 
-    - `Block force pushes`
-7. Click `Create` to finish. you can now find the ruleset under `Rules`>`Rulesets`
-
-**Actions Permissions**
-1. Go to the repository settings
-2. Open `Actions` > `General` in the left sidebar
-3. Under `Workflow permissions`, select
-   - `Read and write permissions`
-   - `Allow GitHub Actions to create and approve pull requests`
-
-### Set Up Project
-1. [Optional] Create a new virtual environment
-2. Run `pip install -e .[test,docs]`
-
-**Documentation Setup**
-1. Create a `docs` folder in the root of the project and open it (`mkdir docs && cd docs`)
-2. Run `spinx-quickstart` to create a new documentation (On Windows, run `sphinx-quickstart.exe`). Fill out all relevant information.
-    - Select no `[n]` when asked `Separate source and build directories (y/n) [n]`
-3. [Optionally] Run `make html` to build the documentation (On Windows, might have to write full path to `make.bat`).
-4. Copy `docs/conf.py` into your own docs folder, replacing the existing one.
-5. Change all relevant fields in the `pyproject.toml` and `docs/conf.py` files. (Don't forget the intersphinx setup)
-
-If you want to run sphinx locally: 
-- `sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/rarelink_phenopacket_mapper`
-- `make.bat` html
-- Open `docs/_build/html/index.html` in your browser
-
-
-
-You can also add a badge like this one to your README.md file:
-[![Build status](https://github.com/frehburg/rarelink_phenopacket_mapper/workflows/CI/badge.svg)](https://github.com/frehburg/TemplateForPythonProjects/actions/workflows/python_ci.yml)  
-[Stable Documentation](https://frehburg.github.io/rarelink_phenopacket_mapper/stable/)  
-[Latest Documentation](https://frehburg.github.io/rarelink_phenopacket_mapper/latest/)  
-
-See here a template for your README
+[![Build status](https://github.com/bih-cei/rarelink_phenopacket_mapper/workflows/CI/badge.svg)](https://github.com/frehburg/TemplateForPythonProjects/actions/workflows/python_ci.yml)  
+[Stable Documentation](https://bih-cei.github.io/rarelink_phenopacket_mapper/stable/)  
+[Latest Documentation](https://bih-cei.github.io/rarelink_phenopacket_mapper/latest/)  
 
 # RareLink Phenopacket Mapper
 ![UML_and_flowchart](https://github.com/user-attachments/assets/56f68945-6b3f-4ad8-9bc3-986b71b1a53d)
@@ -113,3 +55,4 @@ Guidelines for contributing to your project. Include information about how other
 Specify the license under which your project is distributed.
 
 ## Acknowledgements
+This is a part of the larger effort conducted in the RareLink repository [RareLink GitHub Repository](www.github.com/bih-cei/rarelink)