{"id":20425088,"url":"https://github.com/databio/bedbase","last_synced_at":"2025-04-12T18:54:51.259Z","repository":{"id":191841841,"uuid":"233065943","full_name":"databio/bedbase","owner":"databio","description":"Aggregate, analyze, and serve genomic regions.","archived":false,"fork":false,"pushed_at":"2025-04-10T22:42:41.000Z","size":14391,"stargazers_count":4,"open_issues_count":7,"forks_count":0,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-04-10T23:29:58.789Z","etag":null,"topics":["genomic-intervals"],"latest_commit_sha":null,"homepage":"http://bedbase.org/","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/databio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"docs/contributing.md","funding":null,"license":null,"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":"2020-01-10T14:38:31.000Z","updated_at":"2025-04-10T22:42:23.000Z","dependencies_parsed_at":"2023-09-01T03:29:51.620Z","dependency_job_id":"84ee80c3-a2b5-4da0-afd3-9567947a9ce1","html_url":"https://github.com/databio/bedbase","commit_stats":null,"previous_names":["databio/bedbase"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedbase","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedbase/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedbase/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbedbase/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/bedbase/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248618262,"owners_count":21134200,"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":["genomic-intervals"],"created_at":"2024-11-15T07:12:14.898Z","updated_at":"2025-04-12T18:54:51.223Z","avatar_url":"https://github.com/databio.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BEDbase documentation\n\nThis repository hosts the documentation for BEDbase and related tools. Please visit \u003chttps://docs.bedbase.org\u003e to view this rendered documentation.\n\nDocumentation is written using [mkdocs](https://www.mkdocs.org/) and themed with [material for mkdocs](https://squidfunk.github.io/mkdocs-material/). The repository has:\n\n- `mkdocs.yml`: the primary configuration, as well as the structure of the documentation. \n- `/docs`: the markdown files. Each tool gets its own folder.\n\n## How to write/update documentation\n\nEach tool gets a `nav` section in `mkdocs.yml`, which maps to its own section/tab in the rendered documentation. So to add a new page, change titles, or change structure, edit `mkdocs.yml`. To edit the documentation itself, edit the `.md` documentation files in the subfolders under `/docs`.\n\n### Prereqs\n\n```\npip install mkdocs-material\n```\n\n\n### Building locally for development\n\nI recommend previewing your changes locally before deploying. You can get a hot-reload server going by cloning this repository, and then just running:\n\n```\nmkdocs serve\n```\n\nYou can also use `mkdocs build` to build a portable local version of the docs.\n\n\n### Publishing updates\n\nThe documentation is published automatically upon commits to `master` using a GitHub Action, which runs `mkdocs gh-deploy`. This builds the docs, and pushes them to the `gh-pages` branch. This branch is then published with GitHub Pages. There's no need to do this locally, just let the action deploy the updates for you automatically.\n\n## FAQ\n\n\n### Updating automatic documentation\n\nIn the past, I had a plugin that would auto-document 2 things: 1. Python docs using lucidoc, and 2. Jupyter notebooks. This plugin was neat, but it caused me a lot of maintenance issues as well. So now, I've made it much simpler; now it's no longer a plugin, just a simple Python script. Update all the auto-generated docs (stored in `docs/autodoc_build`) by running the update script manually:\n\n```console\npython update_python_autodocs.py\n```\n\n#### Configuring lucidoc rendering\n\nAuto-generated Python documentation with `lucidoc` rendering is configured in the `lucidoc`  sections of `mkdocs.yml`.\n\n```yaml\nlucidoc:\n  peppy: path/to/output.md\n```\n\n#### Configuring jupyter rendering\n\nConfigure jupyter notebeeoks in the `jupyter` section, where you specify a list of `in` (for `.ipynb` files) and `out` (for `.md` files) locations.\n\n```yaml\njupyter:\n  - in: path/to/notebook_folder1\n    out: path/to/rendered_folder1\n  - in: path/to/notebook_folder2\n    out: path/to/rendered_folder2\n``` \n\nThere, you can specify which folders contain notebooks, and to where they should be rendered as markdown.\n\n#### Rendering jupyter notebooks in this repository\n\nBy convention, we're putting jupyter notebooks in a `/notebooks` subfolder under each tool (look around for examples). These are then built into the `code/\u003cnotebook_name\u003e.md` file by the authodoc.py. So, to add a new notebook:\n\n1. put the notebook into a `\u003cmodule\u003e/notebooks/\u003cnotebook_name\u003e.ipynb`\n2. make sure that's listed in the `jupyter` section of the yaml (it already should be there if you're adding a notebook to an existing folder).\n3. link to the notebook in `mkdocs.yaml` by linking to `\u003cmodule\u003e/code/\u003cnotebook_name\u003e.md`.\n4. you can build your rendered markdown version by running `python autodoc.py`.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fbedbase","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fbedbase","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fbedbase/lists"}