Deploy preview for PR 71 🛫

pr-preview/pr-71/.buildinfo

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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 75a73b4fe51b463011d0ccac3daed33e
+tags: 645f666f9bcd5a90fca523b33c5a78b7

pr-preview/pr-71/_sources/CHANGELOG.md

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+```{include} ../CHANGELOG.md
+
+```

pr-preview/pr-71/_sources/contributing.md

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+# Contributing guide
+
+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](#writing-tests) and [build the documentation](#docs-building).
+
+The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+```bash
+hatch test  # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
+hatch run docs:build  # defined in the table [tool.hatch.envs.docs]
+```
+
+If you prefer managing environments manually, you can use `pip`:
+
+```bash
+cd dso
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev,test,doc]"
+```
+
+[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+
+## Code-style
+
+This package 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.
+
+Finally, most editors have an _autoformat on save_ feature.
+Consider enabling this option for [ruff][ruff-editors] and [prettier][prettier-editors].
+
+[pre-commit]: https://pre-commit.com/
+[pre-commit.ci]: https://pre-commit.ci/
+[ruff-editors]: https://docs.astral.sh/ruff/integrations/
+
+[prettier-editors]: https://prettier.io/docs/en/editors.html
+
+(writing-tests)=
+
+## Writing tests
+
+This package uses [pytest][] for automated testing.
+Please write {doc}`scanpy:dev/testing` for every function added to the package.
+
+Most IDEs integrate with pytest and provide a GUI to run tests.
+Just point yours to one of the environments returned by
+
+```bash
+hatch env create hatch-test  # create test environments for all supported versions
+hatch env find hatch-test  # list all possible test environment paths
+```
+
+Alternatively, you can run all tests from the command line by executing
+
+```bash
+hatch test  # test with the highest supported Python version
+# or
+hatch test --all  # test with all supported Python versions
+```
+
+in the root of the repository.
+
+[pytest]: https://docs.pytest.org/
+
+### Continuous integration
+
+Continuous integration will automatically run the tests on all pull requests and test
+against the minimum and maximum supported Python version.
+
+Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+The purpose of this check is to detect incompatibilities of new package versions early on and
+gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
+
+## Publishing a release
+
+### Updating the version number
+
+DSO uses [hatch-vcs](https://github.com/ofek/hatch-vcs) to automaticlly retrieve the version number
+from the git tag. To make a new release, navigate to the “Releases” page of this project on GitHub. Specify vX.X.X as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+
+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.
+
+
+[semver]: https://semver.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
+[pypi]: https://pypi.org/
+
+## 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).
+-   [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
+-   Citations can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+
+See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
+
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
+[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
+
+### 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`
+
+(docs-building)=
+
+### Building the docs locally
+
+```bash
+hatch docs:build
+hatch docs:open
+```

pr-preview/pr-71/_sources/dso_python.md

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+# Python API
+
+TODO
+
+```{eval-rst}
+.. module:: dso
+.. currentmodule:: dso
+
+.. autosummary::
+    :toctree: generated
+```

pr-preview/pr-71/_sources/dso_r.md

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+# DSO R package
+
+TODO

pr-preview/pr-71/_sources/getting_started.md

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+# Getting started
+
+TODO

pr-preview/pr-71/_sources/index.md

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+```{include} ../README.md
+
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: User Guide
+
+getting_started.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO CLI
+
+CHANGELOG.md
+contributing.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO Python API
+
+dso_python.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO R API
+
+dso_r.md
+```