mkdocs.yml

site_name: MORS
site_url: https://proteus-framework.org/MORS/
repo_url: https://github.com/FormingWorlds/MORS
repo_name: GitHub

copyright: '© 2023-2026 <a href="https://formingworlds.space">Forming Worlds Lab</a>'

nav:
  - Home:
      - About: index.md
      - Getting started: getting_started.md

  - How-to guides:
      - Installation: How-to/installation.md
      - Basic usage:
        - Calculate stellar evolution: How-to/evolution.md
        - Find stellar quantities with stellar evolution tracks: How-to/track_quantities.md
        - Find stellar rotation and activity quantities: How-to/activity_quantities.md
        - Find habitable zone boundaries: How-to/habitablezone.md
        - Using model percentiles for initial rotation: How-to/distribution_percentile.md
      - Advanced usage:
        - Calculate cluster evolution: How-to/clusters.md
        - Setting custom simulation parameters: How-to/set_parameters.md
        - Find stellar activity timelines: How-to/activity_timelines.md
      - Coupling to PROTEUS: How-to/proteus_coupling.md
      - Development:
        - Testing: How-to/run_tests.md
        - Build documentation: How-to/documentation.md
        - Releasing: How-to/releasing.md
      - Troubleshooting: How-to/troubleshooting.md

  - Tutorials:
      - First run: Tutorials/first_run.md

  - Explanations:
      - Model overview:
        - Introduction:  Explanations/structure.md
        - Rotational evolution model:   Explanations/rotation.md
        - High-energy emission and activity model: Explanations/activity.md
        - Habitable zone boundaries: Explanations/habitablezone.md
        - Spectral synthesis: Explanations/spectral_synthesis.md
      - Coupling to PROTEUS: Explanations/proteus.md
      - Testing suite: Explanations/testing.md

  - Validation:
      - Overview: Validation/index.md
      - Stellar structure and evolution:
        - Stellar evolution tracks: Validation/stellarevo.md
        - Star model: Validation/star.md
        - Baraffe tracks: Validation/baraffe.md
      - Rotation:
        - Rotation evolution: Validation/rotevo.md
      - Activity and habitable zone: Validation/physicalmodel.md
      - Spectra:
        - Spectrum: Validation/spectrum.md
        - Spectral synthesis: Validation/synthesis.md
      - Cluster statistics:
        - Cluster percentiles: Validation/cluster.md

  - Reference:
      - Publications and bibliography: Reference/publications.md
      - Parameter reference: Reference/parameters.md
      - API reference:
        - Overview: Reference/api/index.md
        - mors.star: Reference/api/star.md
        - mors.cluster: Reference/api/cluster.md
        - mors.physicalmodel: Reference/api/physicalmodel.md
        - mors.rotevo: Reference/api/rotevo.md
        - mors.stellarevo: Reference/api/stellarevo.md
        - mors.baraffe: Reference/api/baraffe.md
        - mors.spectrum: Reference/api/spectrum.md
        - mors.synthesis: Reference/api/synthesis.md
        - mors.miscellaneous: Reference/api/miscellaneous.md
        - mors.parameters: Reference/api/parameters.md
        - mors.constants: Reference/api/constants.md
        - mors.data: Reference/api/data.md
        - mors.cli: Reference/api/cli.md

  - Community:
      - Contact: Community/contact.md
      - Contributing: Community/CONTRIBUTING.md
      - Code of Conduct: Community/CODE_OF_CONDUCT.md
      - Developers: https://proteus-framework.org/people

  - Source code: https://github.com/FormingWorlds/MORS

  - Other PROTEUS modules:
      - PROTEUS framework: proteus_framework.md
      - 🔗 PROTEUS:  https://proteus-framework.org/PROTEUS/
      - 🔗 JANUS: https://proteus-framework.org/JANUS/
      - 🔗 ZEPHYRUS: https://proteus-framework.org/ZEPHYRUS/
      - 🔗 CALLIOPE: https://proteus-framework.org/CALLIOPE/
      - 🔗 AGNI: https://www.h-nicholls.space/AGNI/
      - 🔗 Obliqua: https://proteus-framework.org/Obliqua/
      - 🔗 VULCAN: https://proteus-framework.org/VULCAN/
      - 🔗 Zalmoxis: https://proteus-framework.org/Zalmoxis/
      - 🔗 Aragog: https://proteus-framework.org/aragog/
      - 🔗 SPIDER:  https://proteus-framework.org/SPIDER/
      - 🔗 Atmodeller: https://github.com/FormingWorlds/Atmodeller/
      - 🔗 FastChem: https://github.com/FormingWorlds/FastChem/
      - 🔗 SOCRATES: https://proteus-framework.org/SOCRATES/

# footer:
extra:
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  social:
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      link: https://proteus-framework.org/
      name: PROTEUS website
    - icon: material/email
      link: mailto:dev@proteus-framework.org
      name: Mail PROTEUS developers
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/fwl-mors/
      name: MORS on PyPI
    - icon: fontawesome/brands/github
      link: https://github.com/FormingWorlds/MORS
      name: MORS on GitHub

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  # Fonts are self-hosted via stylesheets/fonts/fonts.css
  font: false

  # Default assets (the header stays dark in both schemes, so one glyph serves both)
  favicon: assets/favicon.svg
  logo: assets/glyph_phase_dark.png

  # The toggle icon shows the current mode, matching the project website
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      scheme: slate
      primary: custom
      accent: custom
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        name: Switch to light mode

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        name: Switch to dark mode

extra_css:
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markdown_extensions:
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      emoji_generator: !!python/name:material.extensions.emoji.to_svg


extra_javascript:
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  - javascripts/header-links.js

plugins:
- search
- mkdocstrings:
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    handlers:
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        - https://docs.python.org/3/objects.inv
        - https://numpy.org/doc/stable/objects.inv
        - https://docs.scipy.org/doc/scipy/objects.inv
        - https://pandas.pydata.org/docs/objects.inv
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          show_root_full_path: false
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use_directory_urls: false

watch:
  - src/
  - docs/
  - README.md
  - CONTRIBUTING.md
  - CODE_OF_CONDUCT.md