clean up all docs

docs/bedbase/README.md

@@ -1,7 +1,10 @@
-![Test BEDBASE stack](https://github.com/databio/bedbase/workflows/Test%20BEDBASE%20stack/badge.svg)
-
-# BEDbase
+<p align="center">
+<h1><img align="center" src="../img/bedbase_logo.svg" class="img-header" height="100"></h1>
+</p>
 
+<p align="center">
+<img src="https://github.com/databio/bedbase/workflows/Test%20BEDBASE%20stack/badge.svg" alt="">
+</p>
 
 BEDbase is a unifying platform for aggregating, analyzing and serving genomic region data as BED files. Input files are processed by a series of Python pipelines. The output of these pipelines is displayed through a RESTful API where users can access BED files along with useful statistics and plots. A project to aggregate, analyze, and serve genomic regions better (*aka* BED files).
 

docs/bedboss/README.md

@@ -1,4 +1,16 @@
-# BEDboss
+<p align="center">
+<h1><img align="center" src="img/bedboss_logo.svg" class="img-header" height="100"></h1>
+</p>
+
+
+<p align="center">
+<a href="https://pypi.org/project/bedboss/"><img src="https://img.shields.io/pypi/v/bedboss" alt=""></a>
+<a href="https://github.com/databio/bedboss"><img src="https://img.shields.io/badge/source-github-354a75?logo=github"></a>
+</p>
+
+
+
+
 bedboss is a command-line pipeline that standardizes and calculates statistics for genomic interval data, and enters the results into a BEDbase database. 
 It has 3 components: 
 

docs/bedboss/changelog.md

@@ -0,0 +1,7 @@
+# Changelog for bedboss
+
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
+
+## [0.1.0] - 2024-01-26
+### Added
+- Initial release

docs/changelog.md

@@ -1,7 +1,4 @@
-# Changelog
+# Changelogs for BEDbase
 
-This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
+BEDbase is not versioned as a whole; instead, you will need to look at the changelogs for the individual components.
 
-## [0.1.0a1] - 2023-08-02
-### Added
-- Initial alpha release

docs/geniml/README.md

@@ -1,10 +1,10 @@
 <p align="center">
-<img align="center" src="img/geniml_logo_horizontal.svg" class="img-header" height="100">
+<h1><img align="center" src="img/geniml_logo_horizontal.svg" class="img-header" height="100"></h1>
 </p>
 
 
 <p align="center">
-<a href="https://img.shields.io/pypi/v/geniml"><img src="https://img.shields.io/pypi/v/geniml" alt=""></a>
+<a href="https://pypi.org/project/geniml"><img src="https://img.shields.io/pypi/v/geniml" alt=""></a>
 <a href="https://github.com/databio/geniml"><img src="https://img.shields.io/badge/source-github-354a75?logo=github"></a>
 </p>
 

mkdocs.yml

@@ -62,16 +62,16 @@ nav:
       - Contributing: contributing.md
       - Changelog: changelog.md
   - BEDboss:
-    - BEDBoss: bedboss/README.md
+    - BEDboss: bedboss/README.md
     - Tutorial:
       - BEDboss insert: bedboss/tutorials/tutorial_insert.md
       - BEDboss-all pipeline: bedboss/tutorials/tutorial_all.md
       - BEDmaker tutorial: bedboss/tutorials/bedmaker_tutorial.md
       - BEDqc tutorial: bedboss/tutorials/bedqc_tutorial.md
       - BEDstat tutorial: bedboss/tutorials/bedstat_tutorial.md
-      - BEDbancher tutorial: bedboss/tutorials/bedbuncher_tutorial.md
-      - Bedindex tutorial: bedboss/tutorials/bedindex_tutorial.md
-      - Bedclassifier tutorial: bedboss/tutorials/bedclassifier_tutorial.md
+      - BEDbuncher tutorial: bedboss/tutorials/bedbuncher_tutorial.md
+      - BEDindex tutorial: bedboss/tutorials/bedindex_tutorial.md
+      - BEDclassifier tutorial: bedboss/tutorials/bedclassifier_tutorial.md
     - How to guides:
       - Create BEDbase database: bedboss/how-to-create-database.md
       - Create config file: bedboss/how-to-configure.md
@@ -80,6 +80,7 @@ nav:
     - Reference:
       - How to cite: citations.md
       - Usage: bedboss/usage.md
+      - Changelog: bedboss/changelog.md
   - Geniml:
     - Geniml: geniml/README.md
     - Getting Started: