{"id":29303542,"url":"https://github.com/scverse/cookiecutter-scverse","last_synced_at":"2025-07-07T01:08:59.907Z","repository":{"id":37496648,"uuid":"485903379","full_name":"scverse/cookiecutter-scverse","owner":"scverse","description":"Cookiecutter template for scverse","archived":false,"fork":false,"pushed_at":"2025-06-23T17:35:33.000Z","size":520,"stargazers_count":78,"open_issues_count":23,"forks_count":12,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-06-23T18:40:14.064Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://cookiecutter-scverse-instance.readthedocs.io/en/latest/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/scverse.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-04-26T18:27:32.000Z","updated_at":"2025-06-23T10:35:28.000Z","dependencies_parsed_at":"2023-12-18T19:30:35.689Z","dependency_job_id":"a3b08d8a-48a4-4bb9-92f7-9befb84ff5cf","html_url":"https://github.com/scverse/cookiecutter-scverse","commit_stats":null,"previous_names":[],"tags_count":41,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/cookiecutter-scverse","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fcookiecutter-scverse","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fcookiecutter-scverse/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fcookiecutter-scverse/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fcookiecutter-scverse/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/cookiecutter-scverse/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fcookiecutter-scverse/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996091,"owners_count":23541402,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-07-07T01:08:58.203Z","updated_at":"2025-07-07T01:08:59.901Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Scverse Cookiecutter Template\n\n[![Test][badge-test]][link-test]\n[![Powered by NumFOCUS][badge-numfocus]][link-numfocus]\n\nThe purpose of this template is to get you started quickly building a best-practice python library for a [scverse][] ecosystem package.\nEcosystem packages are independent software libraries that interact with scverse core packages and depend on [anndata][] and [mudata][] data structures.\n\nPlease check out the\n\n- [example repo](https://github.com/scverse/cookiecutter-scverse-instance) and the\n- [example documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/)\n\nthat are automatically generated and kept in sync with this template.\n\n[//]: # \"numfocus-fiscal-sponsor-attribution\"\n\nThis template is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\nPlease consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\n\u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  \u003e\n\u003c/a\u003e\n\n[badge-test]: https://github.com/scverse/cookiecutter-scverse/actions/workflows/test.yaml/badge.svg\n[link-test]: https://github.com/scverse/cookiecutter-scverse/actions/workflows/test.yaml\n[badge-numfocus]: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat\u0026colorA=E1523D\u0026colorB=007D8A\n[link-numfocus]: http://numfocus.org\n\n## Features\n\n- automated testing with [pytest][]\n- continuous integration using GitHub actions.\n- documentation hosted by [readthedocs][]\n- coverage tests with [codecov][]\n- [pre-commit][] checks for code style and consistency\n- tutorials with [myst-nb][] and jupyter notebooks\n- issue templates for better bug reports and feature requests\n\n## Getting started\n\nIn this section we will show you how to set-up your own repository from this template\nand how to customize it for your needs.\n\n### Install dependencies\n\nYou need `git \u003e=2.28` and [`uv`](https://docs.astral.sh/uv/getting-started/installation/) to be installed on your system.\nAll other dependencies will be managed through `uv`.\n\n\n### Create the project\n\nWe are using [cruft](https://github.com/cruft/cruft) to initialize the project from the template. Cruft\nis fully compatible with [cookiecutter](https://github.com/cookiecutter/cookiecutter), but enables automatic\nupdates to your project whenever a new template version is released.\n\nTo create the project, run the following command and follow the prompts:\n\n```bash\n# uv will download all dependencies on-the-fly\nuvx --with pre-commit cruft create https://github.com/scverse/cookiecutter-scverse\n```\n\nThis will create a git repository generated from the template.\nNow `cd` into the newly created directory and make the initial commit!\nDon't forget to create a repository on GitHub and upload your project.\n\n\u003cdetails\u003e\n\u003csummary\u003eWorking without `uv`\u003c/summary\u003e\nIf you want to permanently install the tools, you can run\n\n```bash\npipx install cruft pre-commit # or for each: uv tool install $pkg\ncruft create https://github.com/scverse/cookiecutter-scverse\n```\n\n\u003c/details\u003e\n\n\n### Set up online services\n\nYour repository is now ready. However, to use all features of the template you will need to set up the following\nonline services. Clicking on the links will take you to the respective sections of the developer documentation.\nThe developer documentation is also shipped as part of the template in `docs/template_usage.md`.\n\n1.  [pre-commit.ci][setup-pre-commit] to check for inconsistencies and to enforce a code style\n2.  [readthedocs.org][setup-rtd] to build and host documentation\n3.  [codecov][setup-codecov] to generate test coverage reports\n\nAll CI checks should pass, you are ready to start developing your new tool!\n\n### Customizations\n\nFurther 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).\n\n### Committment\n\nWe expect developers of scverse ecosystem packages to\n\n- [write unit tests][write-tests]\n- [provide documentation][write-docs], including tutorials where applicable\n- support users through github and the [scverse discourse][]\n\n## Changelog\n\nSee the [release page][].\n\n## Releasing a new template version\n\nTo release a new version of the template, create a new release on the GitHub [release page][].\nChoose a tag name of the format `vX.X.X` that adheres to [semantic versioning](https://semver.org/).\n\nNote that when creating a new release, changes will be propagated to packages using this template.\n\n## Citation\n\nYou can cite the scverse publication as follows:\n\n\u003e **The scverse project provides a computational ecosystem for single-cell omics data analysis**\n\u003e\n\u003e Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle \u0026 Fabian J. Theis\n\u003e\n\u003e _Nat Biotechnol._ 2022 Apr 10. doi: [10.1038/s41587-023-01733-8](https://doi.org/10.1038/s41587-023-01733-8).\n\n\u003c!-- links --\u003e\n\n[setup-pre-commit]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#pre-commit-checks\n[setup-rtd]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#documentation-on-readthedocs\n[setup-codecov]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#coverage-tests-with-codecov\n[write-tests]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#writing-tests\n[write-docs]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#writing-documentation\n[readthedocs]: https://readthedocs.org/\n[myst-nb]: https://myst-nb.readthedocs.io/\n[pre-commit]: https://pre-commit.com/\n[scverse]: https://scverse.org/\n[anndata]: https://anndata.readthedocs.io/en/latest/\n[mudata]: https://muon.readthedocs.io/en/latest/notebooks/quickstart_mudata.html\n[codecov]: https://about.codecov.io/\n[scverse discourse]: https://discourse.scverse.org/\n[pytest]: https://docs.pytest.org\n[release page]: https://github.com/scverse/cookiecutter-scverse/releases\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fcookiecutter-scverse","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fcookiecutter-scverse","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fcookiecutter-scverse/lists"}