Update instance repo (PR 130) (#33)

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

* Update instance repo from cookiecutter template

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

.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).

.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

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 22.10.0
+      rev: 22.12.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
@@ -19,7 +19,7 @@ repos:
       hooks:
           - id: blacken-docs
     - repo: https://github.com/PyCQA/isort
-      rev: 5.10.1
+      rev: v5.11.3
       hooks:
           - id: isort
     - repo: https://github.com/asottile/yesqa

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-scverse-instance
+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/

docs/index.md

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