_quarto.yml

project:
  type: website

website:
  favicon: _static/ESPEI-logo.png
  # See https://quarto.org/docs/websites/website-navigation.html for details on setup
  title: "ESPEI"
  sidebar:
    logo: "_static/ESPEI-logo-withtext.png"
    title: "ESPEI v0.9.0"
    style: "floating"
    search: true
    collapse-level: 2
    contents:
      - text: "Home"
        href: index.qmd
      - text: "Installation"
        href: installation.qmd
      - text: "Quickstart"
        href: quickstart.qmd
# TODO: changelog
      - section: "Tutorials"
        contents:
          - tutorials/cu-mg-example/cu-mg-example.qmd
          - tutorials/custom-model-parameter-selection/custom_model_parameter_selection.qmd
      - section: "How-To"
        contents:
          - auto: how-to/recipes
          - how-to/specifying_priors.qmd
          - how-to/custom_unary_data.qmd
          - how-to/schedulers.qmd
      - section: "Reference"
        contents:
          - reference/phase_models_schema.qmd
          - reference/dataset_schema.qmd
          - reference/yaml_input_schema.qmd
          # Note: the API reference is somewhat hacky.
          # We generate _sidebar.yml with quartodoc build, which contains
          # (more or less) the structure below. Then it's copied here and modified.
          # It's not exactly clear how to use metadata-files to automatically
          # merge the generated sidebar into the format I want (the one below).
          # The functionality exists in theory: https://quarto.org/docs/projects/quarto-projects.html#metadata-includes
          # These issues seem to track possible conflicts:
          # - https://github.com/quarto-dev/quarto-cli/issues/8449
          # - https://github.com/machow/quartodoc/discussions/330
          # It should also be possible to write some code to perform the merge automatically
          - section: "API Reference"
            href: reference/api/index.qmd
            contents:
            - contents:
              - reference/api/generate_parameters.qmd
              - reference/api/run_espei.qmd
              section: espei
            - contents:
              - reference/api/datasets.load_datasets.qmd
              - reference/api/datasets.recursive_glob.qmd
              section: espei.datasets
            - contents:
              - reference/api/analysis.truncate_arrays.qmd
              section: espei.analsys
            - contents:
              - reference/api/error_functions.residual_base.residual_function_registry.qmd
              - reference/api/error_functions.residual_base.ResidualFunction.qmd
              - reference/api/error_functions.activity_error.ActivityResidual.qmd
              - reference/api/error_functions.zpf_error.ZPFResidual.qmd
              - reference/api/error_functions.equilibrium_thermochemical_error.EquilibriumPropertyResidual.qmd
              - reference/api/error_functions.non_equilibrium_thermochemical_error.FixedConfigurationPropertyResidual.qmd
              section: espei.error_functions
            - contents:
              - reference/api/parameter_selection.fitting_descriptions.ModelFittingDescription.qmd
              section: espei.parameter_selection.fitting_descriptions
            - contents:
              - reference/api/parameter_selection.fitting_steps.qmd
              section: espei.parameter_selection.fitting_steps
            - contents:
              - reference/api/utils.database_symbols_to_fit.qmd
              - reference/api/utils.optimal_parameters.qmd
              section: espei.utils
            - contents:
              - reference/api/plot.dataplot.qmd
              - reference/api/plot.plot_interaction.qmd
              - reference/api/plot.plot_endmember.qmd
              section: espei.plot
      - section: "Developer"
        contents:
          - developer/contributing.qmd
          - developer/design.qmd
          - developer/changelog.qmd
          # TODO:
          #- developer/releasing.qmd
  page-navigation: true
  back-to-top-navigation: true
  page-footer: "Copyright © Materials Genome Foundation"
  repo-url: https://github.com/materialsgenomefoundation/espei.org
  repo-actions: [edit, issue]

bibliography: references.bib

quartodoc:
  style: pkgdown
  dir: reference/api
  package: espei
  sidebar: _sidebar.yml
  title: API Reference
  sections:
  - title: espei
    contents:
      - name: generate_parameters
      - name: run_espei
  - title: espei.datasets
    contents:
      - name: datasets.load_datasets
      - name: datasets.recursive_glob
  - title: espei.analsys
    contents:
      - name: analysis.truncate_arrays
  - title: espei.error_functions
    desc: Residual functions
    contents:
      - name: error_functions.residual_base.residual_function_registry
      - name: error_functions.residual_base.ResidualFunction
      - name: error_functions.activity_error.ActivityResidual
      - name: error_functions.zpf_error.ZPFResidual
      - name: error_functions.equilibrium_thermochemical_error.EquilibriumPropertyResidual
      - name: error_functions.non_equilibrium_thermochemical_error.FixedConfigurationPropertyResidual
  - title: espei.parameter_selection.fitting_descriptions
    desc: Fitting descriptions for custom model parameter generation
    contents:
      - name: parameter_selection.fitting_descriptions.ModelFittingDescription
  - title: espei.parameter_selection.fitting_steps
    desc: Fitting steps for custom model parameter generation
    contents:
      - name: parameter_selection.fitting_steps
  - title: espei.utils
    contents:
      - name: utils.database_symbols_to_fit
      - name: utils.optimal_parameters
  - title: espei.plot
    contents:
      - name: plot.dataplot
      - name: plot.plot_interaction
      - name: plot.plot_endmember

format:
  html:
    theme:
      light: cosmo
      dark: solar  # TODO: would like to change to cosmo, requires https://github.com/quarto-dev/quarto-cli/issues/6741
    css: styles.css
    toc: true