Merge pull request #167 from neherlab/docs-update

Author: ivan-aksamentov

README.md

@@ -6,9 +6,6 @@
 
 > a bioinformatic toolkit to align large sets of closely related genomes into a graph data structure
 
-> [!WARNING]
-> Pangraph is currently undergoing a major migration between v0 and v1. In this short transition period links and documentation may be inconsistent.
-
 ## Overview
 
 **pangraph** provides a command line interface to find homology amongst large collections of closely related genomes.

docs/docs/index.md

@@ -4,12 +4,6 @@ sidebar_position: 1
 
 # Introduction to Pangraph
 
-:::danger[Under construction 👷]
-
-Pangraph is currently under heavy development. Bugs and crashes are to be expected.
-
-:::
-
 **PanGraph** is a command-line tool for the analysis of bacterial genomes. It compresses multiple genome in a compact **graph representation**, that can be queried to extract information about the evolution of the genomes. It is developed and maintained by [the Neher lab](https://www.biozentrum.unibas.ch/about/administration/administration-a-z/overview/unit/research-group-richard-neher).
 
 ## Why Pangraph?

docs/docs/tutorial/t05-example-plasmid-rearrangements.md

@@ -81,6 +81,12 @@ This produces a version[^1] where we can see the different 'walks' taken through
 
 ![img](../assets/UVA01_plasmids_visualization.png)
 
+:::note
+
+To align all paths to a common _anchor_ block, the script requires that at least one _core_ block is present in all plasmids exactly once. In this example the anchor block is block _b_ (magenta).
+
+:::
+
 Note that the plasmids are circular: in the linear representation, in two cases block 'a' appears on the left rather than on the right, but the structure is identical.
 
 [^1]: your version will probably be different due to the random layout chosen by Bandage. You can always rerun the Bandage command multiple times until you get a nice result.

docs/package.json

@@ -16,9 +16,9 @@
     "typecheck": "tsc"
   },
   "dependencies": {
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-    "@docusaurus/preset-classic": "3.7.0",
-    "@docusaurus/theme-mermaid": "3.7.0",
+    "@docusaurus/core": "^3.8.1",
+    "@docusaurus/preset-classic": "^3.8.1",
+    "@docusaurus/theme-mermaid": "^3.8.1",
     "@easyops-cn/docusaurus-search-local": "^0.48.5",
     "@mdx-js/react": "^3.0.0",
     "clsx": "^2.0.0",
@@ -29,9 +29,9 @@
     "remark-math": "^6.0.0"
   },
   "devDependencies": {
-    "@docusaurus/module-type-aliases": "3.7.0",
-    "@docusaurus/tsconfig": "3.7.0",
-    "@docusaurus/types": "3.7.0",
+    "@docusaurus/module-type-aliases": "^3.8.1",
+    "@docusaurus/tsconfig": "^3.8.1",
+    "@docusaurus/types": "^3.8.1",
     "prettier": "^3.3.3",
     "typescript": "~5.5.2",
     "vitest": "^3.0.5"