mkdocs.yml

# Project information
site_name: OSIPI
site_url: https://github.com/OSIPI/osipi.github.io
site_author: OSIPI
site_description: >-
  OSIPI aims to develop resources and best practices for the analysis of perfusion imaging data and interoperability of the analysis results.

# Repository
repo_name: OSIPI/osipi.github.io
repo_url: https://github.com/OSIPI/osipi.github.io

# Copyright
copyright: Copyright © 2025 OSIPI

# Configuration
theme:
  name: material
  logo: assets/osipiImgs/OSIPI_logo.png
  favicon: assets/osipiImgs/OSIPI_logo_only_square.png
  custom_dir: docs/overrides
  features:
    - announce.dismiss
    - content.action.edit
    - content.action.view
    - content.code.annotate
    - content.code.copy
    - content.tooltips
    - navigation.footer
    - navigation.indexes
    - navigation.tabs
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/link
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/toggle-switch
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: black
      accent: indigo
      toggle:
        icon: material/toggle-switch-off
        name: Switch to system preference
  font:
    text: Roboto
    code: Roboto Mono

plugins:
  - search:
      separator: '[\s\u200b\-_,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - minify:
      minify_html: true
  - multirepo:
      cleanup: false
  - open-in-new-tab

# Additional configuration
extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/OSIPI
    - icon: fontawesome/brands/slack
      link: https://osipi.slack.com
    - icon: simple/zenodo
      link: https://zenodo.org/communities/ismrm-osipi/
      name: OSIPI on Zenodo

extra_css:
  - assets/stylesheets/extra.css
extra_javascript:
  - js/mathjax-config.js
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

# Extensions
markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - codehilite
  - def_list
  - footnotes
  - md_in_html
  - toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.emoji:
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
      emoji_index: !!python/name:material.extensions.emoji.twemoji
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink:
      normalize_issue_symbols: true
      repo_url_shorthand: true
      user: squidfunk
      repo: mkdocs-material
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      auto_append:
        - includes/mkdocs.md
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
      combine_header_slug: true
      slugify: !!python/object/apply:pymdownx.slugs.slugify
        kwds:
          case: lower
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

not_in_nav: |
  /tutorials/**/*.md

# Page tree
nav:
  - Home: index.md

  - About:
      - Getting started: getting-started.md
      - About OSIPI: about.md
      - Executive & Management Board: emb.md
      - Strategy Board: strategy-board.md
      - Contributors: contributors.md

  - Task Forces:
      - Overview: taskforces.md
      - "Aim 1 – Software Inventories":
          - "(TF1.1) ASL Software Inventory": tf/tf1-1.md
          - "(TF1.2) DSC/DCE Software Inventory": tf/tf1-2.md
      - "Aim 2 – Code Libraries":
          - "(TF2.2) ASL Code": tf/tf2-2.md
          - "(TF2.3) DSC/DCE Code": tf/tf2-3.md
          - "(TF2.4) IVIM Code": tf/tf2-4.md
          - "(TF2.5) Open-source ASL": tf/tf2-5.md
          - "(TF2.6) OSIPI python package": tf/tf2-6.md
          - "(TF2.7) IVIM preprocessing": tf/tf2-7.md
      - "Aim 3 – Data":
          - "(TF3.1) DROs & Phantoms": tf/tf3-1.md
          - "(TF3.2) Clinical & Preclinical Data": tf/tf3-2.md
          - "(TF3.3) IVIM big data collection": tf/tf3-3.md
          - "(TF3.4) Data Register": tf/tf3-4.md
      - "Aim 4 – Lexicons":
          - "(TF4.1) ASL Lexicon": tf/tf4-1.md
          - "(TF4.2) CAPLEX": tf/tf4-2.md
          - "(TF4.4) BBB MRI lexicon": tf/tf4-4.md
          - "(TF4.5) IVIM lexicon": tf/tf4-5.md
          - "(TF4.6) Method section generator": tf/tf4-6.md
      - "Aim 5 – Exchange & Education":
          - "(TF5.1) Website & Technical Support": tf/tf5-1.md
          - "(TF5.2) Education": tf/tf5-2.md
          - "(TF5.3) AURA artifact repository": tf/tf5-3.md
          - "(TF5.4) Clinical case reports": tf/tf5-4.md
      - "Aim 6 – Challenges":
          - "(TF6.1) ASL Challenge": tf/tf6-1.md
          - "(TF6.2) DSC/DCE Challenge": tf/tf6-2.md
          - "(TF6.3) IVIM algorithm comparison": tf/tf6-3.md
      - "Roadmap 2026-2028": https://docs.google.com/document/d/1w2JlVK3hP5dgXMcrK8da5z94ivsK8Or__NU9qUR6WRk

  - Resources:
      - resources.md
      - Lexicons:
          - Overview: lexicons.md
          - "(TF4.1) ASL Lexicon": https://osipi.github.io/ASL-Lexicon/
          - "(TF4.2) Caplex – Contrast-agent based perfusion MRI": "!import https://github.com/OSIPI/OSIPI_CAPLEX?branch=main&docs_dir=docs&multi_docs=True&config=mkdocs.yml&keep_docs_dir=true"
      - Code Repositories:
          - Overview: pyCode.md
          - "OSIPI Python package":
              - Documentation: https://osipi.github.io/osipy
          - "(TF2.2) ASL repository":
              - Documentation: https://osipi.github.io/TF2.2_OSIPI-ASL-toolbox/
          - "(TF2.3) DCE/DSC repository":
              - Documentation: https://osipi.github.io/DCE-DSC-MRI_CodeCollection/
          - "(TF2.4) IVIM repository":
              - Documentation: https://osipi.github.io/TF2.4_IVIM-MRI_CodeCollection/
      - Tools:
          - Overview: tools.md
          - "ASL parameter generator": https://github.com/OSIPI/asl-parameter-reporter
          - "Artefact database": https://github.com/OSIPI/perfusion-artifacts

  - Learning & Publications:
      - learning-publications.md
      - Learning:
          - Overview: learning.md
          - "ASL Tutorials": https://youtube.com/playlist?list=PLTIlnXdb9rwhoO8afyba3GQSh8ueShJ03&si=rTJUBVXftFicno3j
          - "Recommended Literature":
              - "ASL Literature": aslliterature.md
              - "DSC Literature": dscliterature.md
              - "DCE Literature": dceliterature.md
          - "TACTIX MRI Tutorials": https://www.youtube.com/@TACTIXTwinningProject/playlists
      - Publications:
          - Overview: publications.md
          - "OSIPI Papers": osipipapers.md
          - "ISMRM Abstracts": ismrmabstracts.md

  - News & Events:
      - news-events.md
      - News: news.md
      - "Google Summer of Code": gsoc.md
      - Open Calls:
          - Overview: opencalls.md
          - "IVIM Data Collection Initiative": https://docs.google.com/forms/d/1WHHWj5jNg5NSdvVH-E1QQzF5pQMnN9cWeDvaVPdVwO8/edit