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Add pan/zoom controls to Mermaid diagrams #215

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Add pan/zoom controls to Mermaid diagrams #215

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822592b
Enable workflow dispatch for docs
kabilar Feb 20, 2026
16b5672
Enable native support for Mermaid diagrams
kabilar Feb 20, 2026
7d9d6fb
Add panzoom plugin
kabilar Feb 20, 2026
7d78e63
Add panzoom settings
kabilar Feb 20, 2026
1b962fd
Add `site_url`
kabilar Feb 20, 2026
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1 change: 1 addition & 0 deletions .github/workflows/generate_docs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ on:
push:
branches:
- main
workflow_dispatch:

permissions:
contents: write
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15 changes: 14 additions & 1 deletion mkdocs.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
site_name: "BICAN Knowledge Graph Models Documentation"
site_url: https://brain-bican.github.io/models/
theme:
name: material
palette:
Expand All @@ -10,6 +11,11 @@ theme:
plugins:
- search
- mermaid2
- panzoom:
full_screen: true
always_show_hint: true
hint_location: "top"
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@gemini-code-assist gemini-code-assist bot Feb 20, 2026

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medium

This plugin is a great addition for large diagrams. On a related note, as you correctly pointed out in the PR description, the mermaid2 plugin on line 13 is now redundant because you've enabled native Mermaid support via markdown_extensions. I recommend removing - mermaid2 from the plugins list to simplify the configuration.



nav:
- Overview: index.md
Expand All @@ -25,4 +31,11 @@ nav:
- Genome Annotation: genome_annotation.md
- Assertion Evidence: assertion_evidence.md
- BKE Taxonomy: bke_taxonomy.md
repo_url: https://github.com/brain-bican/models
repo_url: https://github.com/brain-bican/models

markdown_extensions:
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
Comment on lines +37 to +41
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@gemini-code-assist gemini-code-assist bot Feb 20, 2026

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security-critical critical

The use of !!python/name:pymdownx.superfences.fence_code_format introduces a critical security vulnerability. This YAML tag allows for arbitrary code execution when the mkdocs.yml file is parsed. An attacker with write permissions to this file could execute arbitrary commands on the documentation build server, potentially leading to a full compromise of the build environment. It is strongly recommended to remove this configuration and use a safer method for rendering Mermaid diagrams. MkDocs Material has native support for Mermaid, which should be preferred.

3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -27,7 +27,8 @@ test = [
]
docs = [
"mkdocs-material",
"mkdocs-mermaid2-plugin"
"mkdocs-mermaid2-plugin",
"mkdocs-panzoom-plugin"
Comment on lines +30 to +31
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@gemini-code-assist gemini-code-assist bot Feb 20, 2026

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medium

Following up on the comment in mkdocs.yml, since mkdocs-mermaid2-plugin is no longer needed, its dependency on line 30 can be removed. Please also adjust the commas in the list accordingly after removing the line to maintain valid TOML syntax.

]

[project.urls]
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