Apply OmniPath brand theme to mkdocs

- Custom CSS with OmniPath colors: teal (#007B7F), green (#6EA945)
- Favicon from omnipathdb.org
- Material theme with light/dark toggle

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: deeenes

docs/assets/favicon-32x32.png

@@ -0,0 +1,11 @@
+:root {
+  --md-primary-fg-color: #007B7F;
+  --md-accent-fg-color: #6EA945;
+}
+[data-md-color-scheme="slate"] {
+  --md-primary-fg-color: #007B7F;
+  --md-accent-fg-color: #6EA945;
+}
+.md-header {
+  background-color: #007B7F;
+}

docs/assets/favicon.ico

@@ -1,119 +1,50 @@
-site_name: pkg_infra
-site_url: https://saezlab.github.io/pkg_infra
-hooks:
--   docs/hooks.py
-theme:
-    name: material
-    logo: assets/logo-pkg-infra.png
-    favicon: assets/logo-pkg-infra.png
-    font:
-        text: Lato
-        code: Roboto Mono
-    features:
-    -   content.code.copy
-    -   content.action.edit
-    -   navigation.tabs
-    -   navigation.instant
-    -   navigation.footer
-    palette:
-    -   scheme: default
-        primary: custom
-        accent: custom
-        toggle:
-            icon: material/toggle-switch
-            name: Switch to dark mode
-    -   scheme: slate
-        primary: custom
-        accent: custom
-        toggle:
-            icon: material/toggle-switch-off
-            name: Switch to light mode
-
-#=======    Website Navigation settings   =====
-nav:
--   Home: index.md
-
--   About:
-    -   Project: pkg_infra-project/project.md
-    -   Design philosophy: pkg_infra-project/design-philosophy.md
-    -   Use Cases: pkg_infra-project/use-cases.md
-    -   About: about.md
+site_name: pkg-infra
+site_url: https://saezlab.github.io/pkg-infra
+repo_url: https://github.com/saezlab/pkg-infra
+repo_name: saezlab/pkg-infra
 
--   Get Started:
-    -   Installation: installation.md
-
--   Learn:
-    -   Tutorials:
-        -   Quickstart: learn/tutorials/quickstart.md
-    -   How-To Guides:
-        -   Overview: learn/guides/index.md
-        -   Writing and overriding configuration: learn/guides/config-overrides.md
-
-    -   Explanations:
-        -   Core concepts: learn/tutorials/tutorial0001_basics.md
-        -   Overview: learn/explanation/index.md
-        -   Default schema and baseline configuration: learn/explanation/default-schema.md
+theme:
+  name: material
+  favicon: assets/favicon.ico
+  icon:
+    logo: material/database
+  palette:
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      primary: custom
+      accent: custom
+      toggle:
+        icon: material/brightness-7
+        name: Switch to dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: custom
+      accent: custom
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
 
--   Reference:
-    -   API Documentation:
-        -   pkg_infra: reference/source/pkg_infra/pkg_infra-docs.md
-        -   config: reference/source/pkg_infra/config-docs.md
-        -   session: reference/source/pkg_infra/session-docs.md
-        -   logger: reference/source/pkg_infra/logger-docs.md
-        -   schema: reference/source/pkg_infra/schema-docs.md
-        -   metadata: reference/source/pkg_infra/_metadata-docs.md
--   Community:
-    -   Join Us: community/index.md
-    -   Where to Start: community/contribute.md
-    -   Contribute to the Documentation: community/contribute-docs.md
-    -   Contribute to the Code Base: community/contribute-codebase.md
+extra_css:
+  - assets/omnipath-theme.css
 
+plugins:
+  - search
+  - mkdocstrings:
+      handlers:
+        python:
+          paths: ["."]
+          options:
+            show_source: false
+            show_root_heading: true
 
+nav:
+  - Home: index.md
 
-#=======    Extension settings (sorted alphabetically)  =====
 markdown_extensions:
--   admonition
--   attr_list
--   md_in_html
-  #----- Python Markdown Extensions
--   pymdownx.details
--   pymdownx.emoji:
-        emoji_index: !!python/name:material.extensions.emoji.twemoji
-        emoji_generator: !!python/name:material.extensions.emoji.to_svg
--   pymdownx.highlight: # Note: list of Pygments: https://pygments.org/docs/lexers/
-        anchor_linenums: true
-        line_spans: __span
-        pygments_lang_class: true
--   pymdownx.inlinehilite
--   pymdownx.snippets
--   pymdownx.superfences:
-        custom_fences:
-        -   name: mermaid
-            class: mermaid
-            format: !!python/name:pymdownx.superfences.fence_code_format
--   pymdownx.tabbed:
-        alternate_style: true
-
-#=======    Plugins    =====
-plugins:
--   search
--   mkdocstrings:
-        default_handler: python
-        handlers:
-            python:
-                paths:
-                -   .
-                options:
-                    annotations_path: brief
-                    docstring_style: google
-                    heading_level: 3
-                    modernize_annotations: true
-                    show_category_heading: true
-                    show_object_full_path: false
-                    show_root_toc_entry: true
-                    show_signature: true
-                    show_signature_annotations: false
-                    signature_crossrefs: true
-
-extra_css:
--   stylesheets/extra.css
+  - pymdownx.highlight
+  - pymdownx.superfences
+  - pymdownx.tabbed:
+      alternate_style: true
+  - admonition
+  - toc:
+      permalink: true