fix broken links

nsheff · nsheff · commit afe032ae23c9 · 2025-12-10T08:53:32.000-05:00
diff --git a/docs/geniml/tutorials/create-consensus-peaks.md b/docs/geniml/tutorials/create-consensus-peaks.md
@@ -81,4 +81,4 @@ geniml build-universe hmm --coverage-folder coverage/ \
 
 # How to assess new universe?
 
-So far you used many different methods for creating new universes. But choosing, which universe represents data the best can be challenging. To help with this we created a tutorial that can be found [here](../code/assess-universe.md), which presents different  methods that assess universe fit to the collection of files.
+So far you used many different methods for creating new universes. But choosing, which universe represents data the best can be challenging. To help with this we created a tutorial that can be found [here](../notebooks/assess-universe.ipynb), which presents different  methods that assess universe fit to the collection of files.
diff --git a/docs/gtars/modules.md b/docs/gtars/modules.md
@@ -28,6 +28,6 @@ gtars is organized as a workspace of independent Rust crates, each providing spe
 
 ## Language Bindings
 
-- **[gtars-python](python.md)** - Python API bindings
+- **[gtars-python](python-overview.md)** - Python API bindings
 - **[gtars-wasm](wasm.md)** - WebAssembly bindings
 - **[gtars-cli](cli.md)** - Command-line interface
diff --git a/docs/gtars/refget-store-format.md b/docs/gtars/refget-store-format.md
@@ -319,4 +319,4 @@ MD5 support provides compatibility with legacy systems, easier migration from MD
 - [GA4GH refget specification](https://samtools.github.io/hts-specs/refget.html)
 - [gtars-refget module documentation](refget.md)
 - [Python reference guide with examples](python/refget-store.md)
-- [Python bindings documentation](python.md)
+- [Python bindings documentation](python-overview.md)
diff --git a/docs/manuscripts/rymuza2024.md b/docs/manuscripts/rymuza2024.md
@@ -18,7 +18,7 @@ This paper published 2 types of method: 1. Methods to *construct* a universe, an
 You can construct a universe either on the command line, or using geniml as a library:
 
 - [Create consensus peaks with CLI](../geniml/tutorials/create-consensus-peaks.md)
-- [Create consensus peaks with Python](../geniml/code/create-consensus-peaks-python.md)
+- [Create consensus peaks with Python](../geniml/notebooks/create-consensus-peaks-python.ipynb)
 
 ### 2. Evaluating a universe
 
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -188,7 +188,6 @@ nav:
       - Python:
         - Overview: gtars/python-overview.md
         - Digests: gtars/python/digests.md
-        - RefgetStore: gtars/python/refgetstore.md
         - RefgetStore Tutorial: gtars/python/refgetstore.ipynb
         - RefgetStore Python Reference: gtars/python/refget-store.md
         - Refget API Reference: gtars/python/refget-api.md

Original file line number	Diff line number	Diff line change
`@@ -81,4 +81,4 @@ geniml build-universe hmm --coverage-folder coverage/ \`
`81`	`81`
`82`	`82`	`# How to assess new universe?`
`83`	`83`
`84`		`-So far you used many different methods for creating new universes. But choosing, which universe represents data the best can be challenging. To help with this we created a tutorial that can be found [here](../code/assess-universe.md), which presents different methods that assess universe fit to the collection of files.`
	`84`	`+So far you used many different methods for creating new universes. But choosing, which universe represents data the best can be challenging. To help with this we created a tutorial that can be found [here](../notebooks/assess-universe.ipynb), which presents different methods that assess universe fit to the collection of files.`