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| # 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. | ||
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| ## Get started | ||
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| First, clone the repository. | ||
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| Create the `main`, `develop` and, `gh-pages` branches. | ||
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| Whenever you want to change something, create a new branch. If it is done, create a pull request to the `develop` branch. | ||
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| Only pull from `develop` to `main` with fully functional, tested and documented new versions. | ||
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| ### 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` | ||
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| **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` | ||
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| ### Set Up Project | ||
| 1. [Optional] Create a new virtual environment | ||
| 2. Run `pip install -e .[test,docs]` | ||
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| **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) | ||
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| If you want to run sphinx locally: | ||
| - `sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/template_for_python_projects` | ||
| - `make.bat` html | ||
| - Open `docs/_build/html/index.html` in your browser | ||
| # Rare Disease Common Data Model | ||
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| ### Submodules | ||
| Sometimes it is necessary to have other repositories as submodules. To initiate this you can follow this tutorial by Git itself on [Submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules). But in essence you need this command: | ||
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| `git submodule add https://github.com/frehburg/TemplateForPythonProjects` | ||
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| If you then want to import the submodule as a python package in your code, the ci will not be able to resolve it. To fix this, add the following lines to `python_ci.yml`: | ||
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| ``` | ||
| - name: Checkout code | ||
| uses: actions/checkout@v3 | ||
| with: # this | ||
| submodules: true # this to ensure submodules are checked out | ||
| ``` | ||
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| and further down | ||
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| ``` | ||
| run: | | ||
| python3 -m pip install --upgrade pip | ||
| python3 -m pip install --editable .[test,docs] | ||
| python3 -m pip install --editable ./submodules/TemplateForPythonProjects # this to install the submodule package | ||
| ``` | ||
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| You can also add a badge like this one to your README.md file: | ||
| [](https://github.com/frehburg/TemplateForPythonProjects/actions/workflows/python_ci.yml) | ||
| [Stable Documentation](https://frehburg.github.io/TemplateForPythonProjects/stable/) | ||
| [Latest Documentation](https://frehburg.github.io/TemplateForPythonProjects/latest/) | ||
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| See here a template for your README | ||
| An international Rare Disease Common Data Model based on the ERDRI-CDS, HL7 FHIR | ||
| and the GA4GH Phenopacket Schema | ||
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| # Project Name | ||
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| Brief description of your project. | ||
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| ## Table of Contents | ||
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| - [Project Description](#project-description) | ||
| - [Features](#features) | ||
| - [Getting Started](#getting-started) | ||
| - [Prerequisites](#prerequisites) | ||
| - [Installation](#installation) | ||
| - [Features](#features) | ||
| - [Prerequisites](#prerequisites) | ||
| - [Installation](#installation) | ||
| - [Contributing](#contributing) | ||
| - [Resources](#resources-) | ||
| - [License](#license) | ||
| - [Acknowledgements](#acknowledgements) | ||
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| ## Project Description | ||
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| A brief overview of your project and its purpose. | ||
| tbc. | ||
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| ## Features | ||
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| List the key features of your project. | ||
| tbc. | ||
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| ## Getting Started | ||
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| Instructions on how to set up and run your project locally. | ||
| tbc. | ||
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| ### Prerequisites | ||
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| List any software, libraries, or dependencies that need to be installed before setting up the project. | ||
| tbc. | ||
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| ### Installation | ||
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| Step-by-step instructions on how to install and set up your project. | ||
| tbc. | ||
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| To install your own code run `pip install -e .` in a terminal | ||
| ## Contributing | ||
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| ## Features | ||
| Please write an issue or exchange with other users in the discussions if you | ||
| encounter any problems or wish to give feedback. Feel free to reach out to us, | ||
| if you are interested in collaborating and improve the use of our RD CDM or rare | ||
| disease research and care. | ||
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| Provide examples and explanations of how your project can be used. Include code snippets or screenshots if necessary. | ||
| ## Resources | ||
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| ## Contributing | ||
| ### Ontologies | ||
| - Human Phenotype Ontology (HP, Version 2024-08-13) [🔗](http://www.human-phenotype-ontology.org) | ||
| - Monarch Initiative Disease Ontology (MONDO, Version Version 2024-09-03) [🔗](https://mondo.monarchinitiative.org/) | ||
| - Online Mendelian Inheritance in Man (OMIM, Version 2024-09-12) [🔗](https://www.omim.org/) | ||
| - Orphanet Rare Disease Ontology (OPRHA, Version 2024-09-12) [🔗](https://www.orpha.net/) | ||
| - National Center for Biotechnology Information Taxonomy (NCBITaxon, Version 2024-07-03) [🔗](https://www.ncbi.nlm.nih.gov/taxonomy) | ||
| - Logical Observation Identifiers Names and Codes (LOINC, Version 2.78) [🔗](https://loinc.org/) | ||
| - HUGO Gene Nomenclature Committee (HGNC, Version 2024-08-23) [🔗](https://www.genenames.org/) | ||
| - Gene Ontology (GENO, Version 2023-10-08) [🔗](https://geneontology.org/) | ||
| - NCI Thesaurus OBO Edition (NCIT, Version Version 24.04e ) [🔗](https://obofoundry.org/ontology/ncit.html) | ||
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| Guidelines for contributing to your project. Include information about how others can contribute, submit issues, and create pull requests. | ||
| ### Submodules | ||
| - [toFHIR](https://github.com/srdc/tofhir?tab=readme-ov-file) | ||
| - [Phenopacket Mapper](https://github.com/BIH-CEI/phenopacket_mapper) | ||
| - [RareLink](https://github.com/BIH-CEI/RareLink) | ||
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| ## License | ||
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| Specify the license under which your project is distributed. | ||
| This project is licensed under the terms of the [MIT License](https://github.com/BIH-CEI/RareLink/blob/develop/LICENSE) | ||
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| ## Acknowledgements | ||
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| We would like to extend our thanks to ... for his support in the development of this project. | ||
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| --- | ||
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| - Authors: | ||
| - [Adam Graefe](https://github.com/aslgraefe) | ||
| - [Filip Rehburg](https://github.com/frehburg) | ||
| - Prof. Peter N. Robinson | ||
| - Prof. Sylvia Thun | ||
| - Prof. Oya Beyan |