From 20ae12f3d0b28f01013ed30bb83d9816df5bf661 Mon Sep 17 00:00:00 2001
From: nsheff <nsheff@users.noreply.github.com>
Date: Thu, 13 Jun 2024 08:26:00 -0400
Subject: [PATCH] move citations into global, add gtars

---
 docs/citations.md    | 16 ++++++----------
 docs/gtars/README.md | 13 +++++++++++++
 mkdocs.yml           | 19 ++++++++++---------
 3 files changed, 29 insertions(+), 19 deletions(-)
 create mode 100644 docs/gtars/README.md

diff --git a/docs/citations.md b/docs/citations.md
index b39ff42..bfa974d 100644
--- a/docs/citations.md
+++ b/docs/citations.md
@@ -1,11 +1,10 @@
----
-hide:
-  - navigation
-  - toc
-  - navigation.footer
----
 
-# How to cite BEDbase and geniml
+
+# Manuscripts describing BEDbase and geniml
+
+Components of BEDbase and geniml have been published independently. Here, we showcase the tutorials organized by the manuscript that published them, so if you're reading a paper you can more easily find the relevant features. Find the citation of interest on the left to find links to tutorials published as part of each manuscript.
+
+## How to cite BEDbase and geniml
 
 Thanks for citing us! If you use BEDbase, geniml, or their components in your research, here are papers you can cite.
 
@@ -19,9 +18,6 @@ Thanks for citing us! If you use BEDbase, geniml, or their components in your re
 | `bedbase` database | Unpublished |
 
 
-
----
-
 ## Full citation information for manuscripts 
 
 <li><b>Gharavi et al. (2024). </b><i>Joint representation learning for retrieval and annotation of genomic interval sets</i> 
diff --git a/docs/gtars/README.md b/docs/gtars/README.md
new file mode 100644
index 0000000..c0fba28
--- /dev/null
+++ b/docs/gtars/README.md
@@ -0,0 +1,13 @@
+<p align="center">
+<h1><img align="center" src="img/gtars_logo.svg" class="img-header" height="100"></h1>
+</p>
+
+
+<p align="center">
+<a href="https://pypi.org/project/gtars"><img src="https://img.shields.io/pypi/v/geniml" alt=""></a>
+<a href="https://github.com/databio/gtars"><img src="https://img.shields.io/badge/source-github-354a75?logo=github"></a>
+</p>
+
+Gtars is a Rust package with Python bindings for genomic interval analysis.
+
+Coming soon!
diff --git a/mkdocs.yml b/mkdocs.yml
index c78d1ff..dd316ab 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -109,20 +109,21 @@ nav:
       - Create evaluation dataset with bedshift: geniml/tutorials/bedshift-evaluation-guide.md
       - Create search backend: geniml/tutorials/text2bednn-search-interface.md
     - Reference:
-      - Published manuscripts:
-        - Gharavi 2021: geniml/manuscripts/gharavi2021.md
-        - Rymuza 2024: geniml/manuscripts/rymuza2024.md
-        - Gharavi 2024: geniml/manuscripts/gharavi2024.md
-        - LeRoy 2024: geniml/manuscripts/leroy2024.md
-        - Zheng 2024: geniml/manuscripts/zheng2024.md
       - How to cite: citations.md
       - API documentation: geniml/autodoc_build/geniml.md
       - Support: geniml/support.md
       - Contributing: geniml/contributing.md
       - Changelog: geniml/changelog.md
-  - Genimtools:
-    - Genimtools: genimtools/README.md
-  - How to cite: citations.md
+  - Gtars:
+    - Gtars: gtars/README.md
+  - How to cite: 
+    - How to cite: citations.md
+    - Published manuscripts:
+      - Gharavi et al. 2021: geniml/manuscripts/gharavi2021.md
+      - Rymuza et al. 2024: geniml/manuscripts/rymuza2024.md
+      - Gharavi et al. 2024: geniml/manuscripts/gharavi2024.md
+      - LeRoy et al.  2024: geniml/manuscripts/leroy2024.md
+      - Zheng et al. 2024: geniml/manuscripts/zheng2024.md
 
 autodoc:
   jupyter: