mkdocs.yml

site_name: DesignSafe User Guide
site_description: DesignSafe User Guide
site_url: https://designsafe-ci.org/user-guide/
repo_url: https://github.com/DesignSafe-CI/DS-User-Guide
edit_uri: edit/main/user-guide/
docs_dir: user-guide
# NOTE: Unrecognized by MkDocs, but recognized by ReadTheDocs theme
site_favicon: https://www.designsafe-ci.org/favicon.ico

theme:
  name: tacc_readthedocs
  navigation_depth: 6
  analytics:
    gtag: G-D96RT1T24K
  hljs_languages:
    - python
    - json
  # "ReadTheDocs" Theme Features
  logo: img/logo.svg
  # "TACC" Theme Features
  logo_svg_inject: true
  portal_url: https://designsafe-ci.org/
  portal_name: designsafe-ci.org
  nav_name: User Guide

extra_css:
  - css/import.css

extra_javascript:
  - js/import.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js # for pymdownx.arithmatex

markdown_extensions:
  - extra
  - admonition
  - toc:
      permalink: "" # i.e. `true` but without "¶"
      permalink_class: headerlink fa fa-link
      permalink_title: Link to Heading
  # PyMdown Extensions
  # - pymdownx.blocks.admonition # to use: disable `admonition`, convert `!!!`s
  - pymdownx.blocks.details
  - pymdownx.blocks.html
  - pymdownx.blocks.tab
  - pymdownx.superfences
  - pymdownx.inlinehilite
  - pymdownx.saneheaders
  - pymdownx.arithmatex:
      generic: true # for mathjax

plugins:
  - search
  - exclude-search:
      exclude_unreferenced: true
  - include-markdown

nav:
  - DesignSafe Essentials:
    - Getting Started: index.md
    - Account Help: account-help.md
    - DesignSafe FAQ: tools/advanced/dsfaq.md
    - How to Cite DesignSafe: how-to-cite.md
    - Training Resources: training.md

  - DesignSafe Data Depot:
    - Overview: datadepot.md
    - Virtual Office Hours: https://designsafe-ci.org/facilities/virtual-office-hours/
    - Transferring Your Data: managingdata/datatransfer.md
    # WARNING: From here down, preserve URLs
    #          If URLs must change, add/use redirect plugin
    - Steps to Curate and Publish Your Datasets: curating/guides.md
    - Best Practices for Data Curation and Publication: curating/bestpractices.md
    - Data Dissemination and Impact: curating/metrics.md
    - Resources for Users:
      - Frequently Asked Questions: curating/faq.md
      - Github's "Cite this Repository": curating/github-cite-this-repo.md
      - Curating Data in Experimental Facilities: managingdata/experimentalfacilitychecklist.md
      - Data Management Plan (DMP) Guide: managingdata/datamanagementplan.md
    - About the Data Depot: datadepotrepo/about.md
    - Policies: curating/policies.md

  - Tools and Apps:
    - Training Resources: training.md
    - Popular:
      - OpenSees: tools/simulation/opensees/opensees.md
      - ADCIRC: tools/simulation/adcirc/adcirc.md
      - OpenFoam: tools/simulation/openfoam.md
      - Jupyter: tools/jupyterhub.md
      - MATLAB: analysis/matlab.md
    - Simulation:
      - ADCIRC: tools/simulation/adcirc/adcirc.md
      - Ansys: tools/simulation/ansys.md
      #- ClawPack: tools/simulation/clawpack.md
      #- Dakota: tools/simulation/dakota.md
      - IN-CORE: tools/simulation/in-core.md
      - LS-DYNA: tools/simulation/lsdyna.md
      - OpenFoam: tools/simulation/openfoam.md
      - OpenSees: tools/simulation/opensees/opensees.md
      - SimCenter:
        - EE-UQ: https://nheri-simcenter.github.io/EE-UQ-Documentation/
        - Hydro-UQ: https://nheri-simcenter.github.io/Hydro-Documentation/
        - PBE: https://nheri-simcenter.github.io/PBE-Documentation/
        - quoFEM: https://nheri-simcenter.github.io/quoFEM-Documentation/
        - R2D: https://nheri-simcenter.github.io/R2D-Documentation/
        - WE-UQ: https://nheri-simcenter.github.io/WE-UQ-Documentation/
    - Analysis:
      - Jupyter: tools/jupyterhub.md
      - MATLAB: analysis/matlab.md
      - HVSRweb: analysis/hvsrweb.md
      - SWbatch: analysis/swbatch.md
    - GIS Tools:
      - Hazmapper: tools/visualization/hazmapper.md
      - QGIS: tools/visualization/qgis.md
      - "Taggit: Basic Image Browsing and Mapping": tools/visualization/taggit-browse-map.md
      - "Taggit: Grouping and Tagging Image Files": tools/visualization/taggit-categorize.md
    - Visualization: tools/visualization.md
    - Hazard Apps: tools/hazard.md
    - Utilities: tools/utilities.md
    - Requesting New Applications: tools/overview.md

  - Recon Portal:
    - Recon Portal User Guide: tools/recon.md

# Old navigation for OpenSees
#      - OpenSees on DesignSafe:
#        - Overview: tools/simulation/opensees/openseesOverview.md
#        - Project Size: tools/simulation/opensees/openseesProjectSize.md
#        - Decision Matrix - Applications: tools/simulation/opensees/openseesDecisionMatrixApplication.md
#        - Decision Matrix - Platforms: tools/simulation/opensees/openseesDecisionMatrixPlatform.md
#        - OpenSees at the Linux Terminal: tools/simulation/opensees/openseesRunLinux.md
#        - Resources: tools/simulation/opensees/openseesResources.md
#      - OpenSees Applications :
#        - Overview: tools/simulation/opensees/openseesApplications.md
#        - 1. OpenSees-Express: tools/simulation/opensees/openseesExpress.md
#        - 2. OpenSeesSP: tools/simulation/opensees/openseesSP.md
#        - 3. OpenSeesMP: tools/simulation/opensees/openseesMP.md
#        - 4. OpenSeesPy: tools/simulation/opensees/openseesPy.md
#      - DesignSafe Platforms for OpenSees:
#        - Overview: tools/simulation/opensees/openseesRunning.md
#        - 1. The Interactive VM: tools/simulation/opensees/openseesRunVM.md
#        - ...1a. Specifications: tools/simulation/opensees/openseesRunVM_Specs.md
#        - 2. DesignSafe WebPortal: tools/simulation/opensees/openseesRunWebPortal.md
#        - ...2a. Form Input: tools/simulation/opensees/openseesRunWebPortal_Form.md
#        - ...2b. Specifications: tools/simulation/opensees/openseesRunWebPortal_Specs.md
#        - 3. Jupyter & OpenSeesPy: tools/simulation/opensees/openseesRunJupyterPy.md
#        - 4. Jupyter & HPC: tools/simulation/opensees/openseesRunJupyterHPC.md
#        - 5. TACC: tools/simulation/opensees/openseesRunTACC.md


  - Use Cases:
    - Overview: usecases/overview.md
    - Data Analytics:
      - Multi-Data Set Image Analysis in Taggit: usecases/haan/usecase-3.md
      - ML and AI: usecases/vantassel_and_zhang/usecase.md
      - Application Programming Interfaces: usecases/brandenberg-api/usecase.md
      - SQLite Database Management in DesignSafe: usecases/brandenberg-sqlite/usecase.md
      - Visualization of spatially distributed data: usecases/padgett/usecase_JN_viz.md
    - GeoHazard:
      - NGL Database: usecases/brandenberg-ngl/usecase.md
      - MPM Landslide: usecases/kumar/usecase.md
    - Seismic:
      - Seismic Response of Concrete Walls: usecases/lowes/usecase.md
      - Soil Structure Interaction: usecases/rathje/usecase.md
      - Experimental Shake Table Testing: usecases/mosqueda/usecase.md
      - Shake Table Data Analysis Using ML: usecases/mosqueda/erler-mosqueda.md
      - OpenSees Model Calibration: usecases/arduino/usecase.md
    - Wind and Storm Surge:
      - Field Sensing Wind Events: usecases/pinelli/usecase.md
      - Hurricane Data Integration Visualization: usecases/pinelli/2usecase.md
      - Wind Speed Estimation and Conversion: usecases/pinelli/3usecase.md
      - Empirical Hurricane Vulnerability and Fragility Curves: usecases/pinelli/4usecase.md
      - ADCIRC Datasets: usecases/dawson/usecase2.md
      - Large-Scale Storm Surge: usecases/dawson/usecase.md
      - CFD Analysis of Winds on Structures: usecases/kareem/usecase.md
      - CFD Analysis of Winds on Low-Rise Building: usecases/kareem/usecase2.md
      - Tamkang Database: usecases/kareem/usecase3.md
      - Visualizing Surge for Regional Risks: usecases/padgett/usecase.md

  - Advanced:
    - API Developer's Guide: https://tapis-cli.readthedocs.io/en/latest/
    - Cybersecurity Policy: tools/advanced/cybersecurity.md
    - HPC Allocations Policy: tools/advanced/hpcallocations.md