Making contributing to scPortrait easier

.github/pull_request_template.md

@@ -0,0 +1,22 @@
+<!-- Thank you for contributing to this project! -->
+
+**PR Checklist**
+
+<!-- Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). -->
+
+- [ ] This comment contains a description of changes (with reason)
+- [ ] Referenced issue is linked
+- [ ] If you've fixed a bug or added code that should be tested, add tests!
+- [ ] Documentation in `docs` is updated
+
+**Description of changes**
+
+<!-- Please state what you've changed and how it might affect the user. -->
+
+**Technical details**
+
+<!-- Please state any technical details such as limitations, reasons for additional dependencies, benchmarks etc. here. -->
+
+**Additional context**
+
+<!-- Add any other context or screenshots here. -->

README.md

@@ -38,4 +38,10 @@ bioRxiv 2023.06.01.542416; doi: https://doi.org/10.1101/2023.06.01.542416
 
 ## Contributing
 
-If you like this software, you can give us a star to boost our visibility! All direct contributions are also welcome. Feel free to post a new [issue](https://github.com/MannLabs/alphapeptstats/issues) or clone the repository and create a [pull request](https://github.com/MannLabs/scPortrait/pulls) with a new branch. For an even more interactive participation, check out the [discussions](https://github.com/MannLabs/scPortrait/discussions).
+If you like this software, consider giving us a star to boost our visibility! For detailed guidelines on how to contribute, please refer to our [CONTRIBUTING.md](./docs/CONTRIBUTING.md).
+
+We welcome all types of contributions! You can:
+
+- Post a new [issue](https://github.com/MannLabs/alphapeptstats/issues) if you encounter a bug or have a feature request.
+- Clone the repository, create a new branch, and submit a [pull request](https://github.com/MannLabs/scPortrait/pulls).
+- Join the conversation in our [discussions](https://github.com/MannLabs/scPortrait/discussions) for more interactive participation.

docs/CONTRIBUTING.md

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+# Contributing guide
+
+Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this repo, too.
+This document will not reproduce the entire content from there. Instead, it aims at summarizing the most important
+information to get you started on contributing.
+
+We assume that you are already familiar with git and with making pull requests on GitHub. If not, please refer
+to the [scanpy developer guide][].
+
+## Installing dev dependencies
+
+In addition to the packages needed to _use_ this package, you need additional python packages to _run tests_ and _build
+the documentation_. It's easy to install them using `pip`:
+
+```bash
+git clone https://github.com/MannLabs/scPortrait
+cd scPortrait
+pip install -e '.[dev]'
+```
+
+## Code-style
+
+This project uses [pre-commit][] to enforce consistent code-styles. On every commit, pre-commit checks will either
+automatically fix issues with the code, or raise an error message.
+
+To enable pre-commit locally, simply run
+
+```bash
+pre-commit install
+```
+
+in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
+
+Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub. If you didn't run `pre-commit` before
+pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+
+If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
+
+```bash
+git pull --rebase
+```
+
+to integrate the changes into yours.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
+
+## Writing tests
+
+```{note}
+Remember to first install the package with pip install -e '.[dev]'
+```
+TBD
+
+## Publishing a release
+
+### Updating the version number
+
+Before making a release, you need to update the version number. Please adhere to [Semantic Versioning][semver], in brief
+
+> Given a version number MAJOR.MINOR.PATCH, increment the:
+>
+> 1.  MAJOR version when you make incompatible API changes,
+> 2.  MINOR version when you add functionality in a backwards compatible manner, and
+> 3.  PATCH version when you make backwards compatible bug fixes.
+>
+> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
+
+Once you are done, run
+
+```
+git push --tags
+```
+
+to publish the created tag on GitHub.
+
+### Building and publishing the package on PyPI
+
+TBD
+
+## Writing documentation
+
+Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
+
+-   Google-style docstrings
+-   TBD
+
+See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
+on how to write documentation.
+
+### Tutorials with jupyter notebooks
+
+TBD
+
+#### Building the docs locally
+
+```bash
+cd docs
+# TBD
+```
+
+<!-- Links -->
+
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
+[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
+[pre-commit.ci]: https://pre-commit.ci/
+[pre-commit]: https://pre-commit.com/
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints