From 9c06f2ce1206f9f54fc7f15e1d607e234f8c1625 Mon Sep 17 00:00:00 2001 From: nsheff Date: Fri, 24 May 2024 17:19:05 -0400 Subject: [PATCH] clean up bedbase docs --- .../bedbase-api-user-guide.md} | 2 +- ...user-guide.md => bedbase-ui-user-guide.md} | 12 ++++++++++- docs/bedhost/README.md | 21 +------------------ mkdocs.yml | 17 ++++++++------- 4 files changed, 22 insertions(+), 30 deletions(-) rename docs/{bedhost/dev-guide.md => bedbase/bedbase-api-user-guide.md} (98%) rename docs/bedbase/{bedbase-user-guide.md => bedbase-ui-user-guide.md} (58%) diff --git a/docs/bedhost/dev-guide.md b/docs/bedbase/bedbase-api-user-guide.md similarity index 98% rename from docs/bedhost/dev-guide.md rename to docs/bedbase/bedbase-api-user-guide.md index 1c8899c..c020253 100644 --- a/docs/bedhost/dev-guide.md +++ b/docs/bedbase/bedbase-api-user-guide.md @@ -1,4 +1,4 @@ -# Developer Guide +# BEDbase API user guide ## Introduction diff --git a/docs/bedbase/bedbase-user-guide.md b/docs/bedbase/bedbase-ui-user-guide.md similarity index 58% rename from docs/bedbase/bedbase-user-guide.md rename to docs/bedbase/bedbase-ui-user-guide.md index bf43977..81f9a3a 100644 --- a/docs/bedbase/bedbase-user-guide.md +++ b/docs/bedbase/bedbase-ui-user-guide.md @@ -1,6 +1,16 @@ # BEDbase public instance -Do we really need documentation to document the UI? +The public BEDbase instance at [bedbase.org](https://bedbase.org) hosts public BED files. + +🚧 Documentation under construction. + +## Resource links + +- **Documentation**: https://docs.bedbase.org/ +- **Deployed public instance UI**: https://bedbase.org/ +- **Dev UI**: https://dev.bedhost.pages.dev/ +- **API**: https://api.bedbase.org/ +- **Dev API**: https://api-dev.bedbase.org/ ## Finding relevant BED files diff --git a/docs/bedhost/README.md b/docs/bedhost/README.md index d2bd03f..8d9af1d 100644 --- a/docs/bedhost/README.md +++ b/docs/bedhost/README.md @@ -4,28 +4,9 @@ [![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/databio/bedhost) -`bedhost` is a Python FastAPI module for the API that powers BEDbase +`bedhost` is a Python FastAPI module for the API that powers BEDbase. It needs a path to the *bedbase configuration file*, which can be provided either via `-c`/`--config` argument or read from `$BEDBASE_CONFIG` environment variable. ---- - -**Deployed public instance**: https://bedbase.org/ - -**Documentation**: https://docs.bedbase.org/bedhost - -**API**: https://api.bedbase.org/ - -**API dev**: https://api-dev.bedbase.org/ - -**UI**: https://bedbase.org/ - -**UI dev**: https://dev.bedhost.pages.dev/ - -**Source Code**: https://github.com/databio/bedhost/ - ---- - - ## Introduction You can find the formal OpenAPI documentation and interactive interface at . This document provides more conceptual introduction and explanations to how to use the API effectively. diff --git a/mkdocs.yml b/mkdocs.yml index 63b40cf..28c54ae 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -42,21 +42,22 @@ nav: - Home: README.md - BEDbase: - BEDbase: bedbase/README.md - - UI guide: - - Public BEDbase instance: bedbase/bedbase-user-guide.md - - API guides: - - BEDhost API guide: - - BEDhost: bedhost/README.md - - Developer Guide: bedhost/dev-guide.md - - Build image: bedhost/build_image.md + - User guides: + - Public BEDbase UI user guide: bedbase/bedbase-ui-user-guide.md + - Public BEDbase API user guide: bedbase/bedbase-api-user-guide.md + - Developer guides: + - BEDhost API server: + - BEDhost overview: bedhost/README.md + - Building docker image: bedhost/build_image.md - Deploy API: bedhost/deployment.md - Changelog: bedhost/changelog.md - - BBConf: + - BBConf configuration: - BBConf: bbconf/README.md - Configuring: bedboss/how-to-configure.md - Overview: bbconf/overview.md - Guide: bbconf/bbc_api.md - Changelog: bbconf/changelog.md + - BEDBoss processing pipeline: ../bedboss - Reference: - How to cite: citations.md - Usage: bedboss/usage.md