improve developers docs

README.md

@@ -56,7 +56,7 @@ Don't forget to create a repository on GitHub and upload your project.
 
 Your repository is now ready. However, to use all features of the template you will need to set up the following
 online services. Clicking on the links will take you to the respective sections of the developer documentation.
-The developer documentation is also shipped as part of the template in `docs/developer_docs.md`.
+The developer documentation is also shipped as part of the template in `docs/template_usage.md`.
 
 1.  [pre-commit.ci][setup-pre-commit] to check for inconsistencies and to enforce a code style
 2.  [readthedocs.org][setup-rtd] to build and host documentation
@@ -66,7 +66,7 @@ All CI checks should pass, you are ready to start developing your new tool!
 
 ### Customizations
 
-Further instructions on using this template can be found in the [dev docs included in the project](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html).
+Further instructions on using this template can be found in the [dev docs included in the project](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html).
 
 ### Committment
 
@@ -90,11 +90,11 @@ Note that when creating a new release, changes will be propagated to packages us
 
 <!-- links -->
 
-[setup-pre-commit]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#pre-commit-checks
-[setup-rtd]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#documentation-on-readthedocs
-[setup-codecov]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#coverage-tests-with-codecov
-[write-tests]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#writing-tests
-[write-docs]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#writing-documentation
+[setup-pre-commit]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#pre-commit-checks
+[setup-rtd]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#documentation-on-readthedocs
+[setup-codecov]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#coverage-tests-with-codecov
+[write-tests]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#writing-tests
+[write-docs]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#writing-documentation
 [readthedocs]: https://readthedocs.org/
 [myst-nb]: https://myst-nb.readthedocs.io/
 [pre-commit]: https://pre-commit.com/

{{cookiecutter.project_name}}/.github/workflows/sync.yaml

@@ -43,4 +43,4 @@ jobs:
                       manually merge these changes.**
 
                       For more information about the template sync, please refer to the
-                      [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).
+                      [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#automated-template-sync).

{{cookiecutter.project_name}}/.github/workflows/test.yaml

@@ -56,7 +56,4 @@ jobs:
               run: |
                   pytest -v --cov --color=yes
             - name: Upload coverage
-              env:
-                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
-              run: |
-                  codecov --required --flags=unittests
+              uses: codecov/codecov-action@v3

{{cookiecutter.project_name}}/docs/contributing.md

@@ -0,0 +1,197 @@
+# 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
+cd {{ cookiecutter.project_name }}
+pip install -e ".[dev,test,doc]"
+```
+
+## Code-style
+
+This template 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. See [pre-commit checks](template_usage.md#pre-commit-checks) for
+a full list of checks enabled for this repository.
+
+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.
+
+Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [black][black-editors]
+and [prettier][prettier-editors].
+
+[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html
+[prettier-editors]: https://prettier.io/docs/en/editors.html
+
+## Writing tests
+
+```{note}
+Remember to first install the package with `pip install '-e[dev,test]'`
+```
+
+This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
+to the package.
+
+Most IDEs integrate with pytest and provide a GUI to run tests. Alternatively, you can run all tests from the
+command line by executing
+
+```bash
+pytest
+```
+
+in the root of the repository. Continuous integration will automatically run the tests on all pull requests.
+
+[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
+
+## 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.
+
+We use [bump2version][] to automatically update the version number in all places and automatically create a git tag.
+Run one of the following commands in the root of the repository
+
+```bash
+bump2version patch
+bump2version minor
+bump2version major
+```
+
+Once you are done, run
+
+```
+git push --tags
+```
+
+to publish the created tag on GitHub.
+
+[bump2version]: https://github.com/c4urself/bump2version
+
+### Building and publishing the package on PyPI
+
+Python packages are not distributed as source code, but as _distributions_. The most common distribution format is the so-called _wheel_. To build a _wheel_, run
+
+```bash
+python -m build
+```
+
+This command creates a _source archive_ and a _wheel_, which are required for publishing your package to [PyPI][]. These files are created directly in the root of the repository.
+
+Before uploading them to [PyPI][] you can check that your _distribution_ is valid by running:
+
+```bash
+twine check dist/*
+```
+
+and finally publishing it with:
+
+```bash
+twine upload dist/*
+```
+
+Provide your username and password when requested and then go check out your package on [PyPI][]!
+
+For more information, follow the [Python packaging tutorial][].
+
+It is possible to automate this with GitHub actions, see also [this feature request][pypi-feature-request]
+in the cookiecutter-scverse template.
+
+[python packaging tutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives
+[pypi-feature-request]: https://github.com/scverse/cookiecutter-scverse/issues/88
+
+## Writing documentation
+
+Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
+
+-   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+-   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+-   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+-   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+
+See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
+on how to write documentation.
+
+### Tutorials with myst-nb and jupyter notebooks
+
+The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
+Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
+It is your reponsibility to update and re-run the notebook whenever necessary.
+
+If you are interested in automatically running notebooks as part of the continuous integration, please check
+out [this feature request](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
+repository.
+
+#### Hints
+
+-   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
+    if you do so can sphinx automatically create a link to the external documentation.
+-   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
+    the `nitpick_ignore` list in `docs/conf.py`
+
+#### Building the docs locally
+
+```bash
+cd docs
+make html
+open _build/html/index.html
+```
+
+<!-- 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
+[codecov]: https://about.codecov.io/sign-up/
+[codecov docs]: https://docs.codecov.com/docs
+[codecov bot]: https://docs.codecov.com/docs/team-bot
+[codecov app]: https://github.com/apps/codecov
+[pre-commit.ci]: https://pre-commit.ci/
+[readthedocs.org]: https://readthedocs.org/
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
+[jupytext]: https://jupytext.readthedocs.io/en/latest/
+[pre-commit]: https://pre-commit.com/
+[anndata]: https://github.com/scverse/anndata
+[mudata]: https://github.com/scverse/mudata
+[pytest]: https://docs.pytest.org/
+[semver]: https://semver.org/
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
+[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
+[pypi]: https://pypi.org/

{{cookiecutter.project_name}}/docs/index.md

@@ -8,7 +8,8 @@
 
 api.md
 changelog.md
-developer_docs.md
+template_usage.md
+contributing.md
 references.md
 
 notebooks/example