From 1fb7357b5b5a1e23ed657ab9a20b94492fdfc93e Mon Sep 17 00:00:00 2001 From: Filip Rehburg <43171336+frehburg@users.noreply.github.com> Date: Wed, 4 Sep 2024 10:06:00 +0200 Subject: [PATCH] Update README.md --- README.md | 65 ++++--------------------------------------------------- 1 file changed, 4 insertions(+), 61 deletions(-) diff --git a/README.md b/README.md index 8c5a91af..b2187825 100644 --- a/README.md +++ b/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)