{"id":19857073,"url":"https://github.com/griffithlab/civic-docs","last_synced_at":"2025-06-21T16:40:17.837Z","repository":{"id":37335145,"uuid":"154884077","full_name":"griffithlab/civic-docs","owner":"griffithlab","description":"Source code for the civicdb.org docs","archived":false,"fork":false,"pushed_at":"2025-02-13T18:11:04.000Z","size":59059,"stargazers_count":5,"open_issues_count":21,"forks_count":8,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-02-13T18:23:29.907Z","etag":null,"topics":["civic"],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/griffithlab.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}},"created_at":"2018-10-26T19:24:36.000Z","updated_at":"2025-01-30T18:10:11.000Z","dependencies_parsed_at":"2025-01-30T19:32:33.318Z","dependency_job_id":null,"html_url":"https://github.com/griffithlab/civic-docs","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic-docs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic-docs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic-docs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fcivic-docs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/civic-docs/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241246114,"owners_count":19933299,"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":["civic"],"created_at":"2024-11-12T14:17:23.690Z","updated_at":"2025-02-28T21:45:41.747Z","avatar_url":"https://github.com/griffithlab.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# CIViC Frontend Documentation\n\nThis repository houses the [documentation](https://civic.readthedocs.io/) for [CIViC](https://civicdb.org), a knowledgebase of clinical interpretations of variants in cancer. The documentation is compiled and hosted by the [ReadTheDocs](https://readthedocs.org/) service at [civic.readthedocs.io](https://civic.readthedocs.io/).\n\n## Contributing\n\nWe welcome contributions to the documentation. If you wish to contribute a clarification, correction, or addition to the docs, please fork this repository, make your contribution, and submit a pull request.\n\n## Getting Started\n\nAfter you've forked and cloned the repository, install [Sphinx](https://www.sphinx-doc.org/en/master/), a [reStructuredText](http://docutils.sourceforge.net/rst.html) documentation generator, and [sphinx-autobuild](https://pypi.org/project/sphinx-autobuild/), a utility that will host and update the documentation as you work:\n\n```\npip install sphinx sphinx-autobuild sphinx-fontawesome sphinxcontrib-images sphinx-rtd-theme\n```\n\nThese docs also depend on a custom fork of the `sphinxcontrib-programoutput` extension. It can be installed by running:\n\n```\npip install git+git://github.com/griffithlab/sphinxcontrib-programoutput.git#egg=sphinxcontrib-programoutput\n```\n\nIf you get a timeout you can try changing \"git+git...\" to \"git+https...\"\n\nThen start the sphinx-autobuild process:\n\n```\ncd ./civic-docs/docs\nsphinx-autobuild ./ ./_build/html\n```\n\nSphinx-autobuild will start a server at http://127.0.0.1:8000. View the compiled docs in your web browser at that URL, and edit the documentation to create your contribution. Sphinx-autobuild will recompile the docs when you save updates and reload the page in your browser.\n\nOccasionally, especially after adding or moving a page or modifying the configuration, autobuild doesn't properly compile the new pages or changes. If this happens try these commands to delete cached files and rebuild the docs:\n\n```\nrm -rf ./_build/*\nmake html\n```\n\nThen restart sphinx-autobuild:\n\n```\nsphinx-autobuild ./ ./_build/html\n```\n\n## Updating the Docs with Pull Requests\n\nIf you'd like to contribute to the documentation or correct an error, clone the repository and create a new branch with your updates (if you do not have authorship permissions on the civic-docs repository, fork the repository first, before cloning, using the Fork button at the top right corner of the github interface):\n\n```\ngit checkout -b doc-update\n```\n\nMake your updates, then push a new branch to the repository:\n\n```\ngit push origin doc-update\n```\n\nThen visit the [civic-docs pull requests page](https://github.com/griffithlab/civic-docs/pulls). Github should display a message asking you if you'd like to create a pull request from the new branch you just pushed. Create the pull request with a short description of your contribution. A CIViC maintainer will evaluate your contribution and will likely merge it with the master branch, which will then be published. Thanks for your contributions!\n\n## Setting up Sphinx to work in Docker\n\nIf you wind up in Python dependency hell getting Sphinx to work, you may want to try working in a Docker image by doing something like the following:\n\n```\ndocker pull griffithlab/pvactools:latest\ndocker run -p 8000:8000 -v ~/git/civic/civic-docs/:/opt/git/civic/civic-docs/ -it griffithlab/pvactools:latest\npip install sphinx sphinx-autobuild sphinx-fontawesome sphinxcontrib-images\npip install git+https://github.com/griffithlab/sphinxcontrib-programoutput.git#egg=sphinxcontrib-programoutput\ncd /opt/git/civic/civic-docs/docs\nsphinx-autobuild --host 0.0.0.0 --port 8000 ./ ./_build/html\n```\n\nTo view the updated docs site in your web browser go to: http://0.0.0.0:8000/. Once you are satisfied, submit a pull request as described above.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fcivic-docs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Fcivic-docs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fcivic-docs/lists"}