mkdocs.yml

# Adapted from : https://github.com/patrick-kidger/equinox/blob/main/mkdocs.yml

site_name: jinns
site_description: The documentation for the jinns software library.
site_author: Hugo Gangloff & Nicolas Jouvin
site_url: https://mia_jinns.gitlab.io/jinns/

theme:
  name: "material"
  features:
      - navigation.sections  # Sections are included in the navigation on the left.
      - toc.integrate  # Table of contents is integrated on the left; does not appear separately on the right.
      - header.autohide  # header disappears as you scroll
  icon:
      repo: fontawesome/brands/gitlab  # GitHub logo in top right
      logo: "material/oil-lamp"  # jinns logo in top left
  favicon: "_static/favicon.png"
  palette:
          # Light mode / dark mode
          # We deliberately don't automatically use `media` to check a user's preferences. We default to light mode as
          # (a) it looks more professional, and (b) is more obvious about the fact that it offers a (dark mode) toggle.
          - scheme: default
            primary: white
            accent: amber
            toggle:
              icon: material/weather-night
              name: Switch to dark mode
          - scheme: slate
            primary: black
            accent: amber
            toggle:
              icon: material/weather-sunny
              name: Switch to light mode
markdown_extensions:
  - toc:
      permalink: "#"  # Adds a clickable permalink to each section heading
      toc_depth: 3
  - pymdownx.arithmatex:
      generic: true
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg



extra_javascript:
  - javascripts/katex.js
  - https://unpkg.com/katex@0/dist/katex.min.js
  - https://unpkg.com/katex@0/dist/contrib/auto-render.min.js

extra_css:
  - https://unpkg.com/katex@0/dist/katex.min.css
  - _static/custom_css.css

plugins:
    - search  # default search plugin; needs manually re-enabling when using any other plugins
    - autorefs  # Cross-links to headings
    - mknotebooks  # Jupyter notebooks
    - mkdocstrings:
        handlers:
          python:
            options:
                docstring_style: numpy
                show_root_heading: true
                show_source: false  # don't include source code
            setup_commands:
                - import pytkdocs_tweaks
                - pytkdocs_tweaks.main()
                - import jaxtyping
                - jaxtyping.set_array_name_format("array")
                - import jax
                - jax.ShapeDtypeStruct.__module__ = "jax"
                - jax.core.ClosedJaxpr.__module__ = "jax.core"
            selection:
                inherited_members: true  # Allow looking up inherited methods
            rendering:
                show_root_heading: true  # actually display anything at all...
                show_root_full_path: true  # display "jinns.abcd" not just "abcd"
                show_if_no_docstring: true
                show_signature_annotations: true
                members_order: source  # order methods according to their order of definition in the source code, not alphabetical order
                heading_level: 3



repo_url: https://gitlab.com/mia_jinns/jinns
repo_name: mia_jinns/jinns

nav:
    - 'index.md'
    - 'changelog.md'
    - Citation: 'https://mia_jinns.gitlab.io/jinns/#citing-us'
    - Tutorials:
      - Implementing your own problem: 'Notebooks/Tutorials/implementing_your_own_PDE_problem.ipynb'
      - Saving / loading your model: 'Notebooks/Tutorials/load_save_model.ipynb'
      - Using validation module: 'Notebooks/Tutorials/introducing_validation_loss.ipynb'
      - A simple inverse problem: 'Notebooks/Tutorials/1D_non_stationary_Burgers_JointEstimation_Vanilla.ipynb'
    - Examples:
      - Forward problems:
        - ODE:
          - Linear first-order equation: 'Notebooks/ODE/linear_fo_equation.ipynb'
          - Generalized Lotka-Volterra: 'Notebooks/ODE/1D_Generalized_Lotka_Volterra.ipynb'
        - PDE:
          - Navier-Stokes in pipe flow:
            - Hard-constraints: 'Notebooks/PDE/2D_Navier_Stokes_PipeFlow.ipynb'
            - Soft-constraints: 'Notebooks/PDE/2D_Navier_Stokes_PipeFlow_SoftConstraints.ipynb'
          - 1D Burgers equation: 'Notebooks/PDE/1D_non_stationary_Burgers.ipynb'
          - 1D Fisher-KPP: 'Notebooks/PDE/1D_non_stationary_Fisher_KPP_Bounded_Domain.ipynb'
          - 2D Fisher-KPP  with covariates: 'Notebooks/PDE/Reaction_Diffusion_2D_heterogenous_model.ipynb'
          - 2D learning Ornstein Uhlenbeck pdf (RAR sampling): 'Notebooks/PDE/2D_non_stationary_OU.ipynb'
      - Inverse problems:
        - ODE:
          - SBINNs: 'Notebooks/ODE/systems_biology_informed_neural_network.ipynb'
        - PDE:
          - Heat equation 2D and estimation of the diffusion coefficient: 'Notebooks/PDE/2D_Heat_inverse_problem.ipynb'
          - Poisson in 2D: 'Notebooks/PDE/2D_Poisson_inverse_problem.ipynb'
      - Meta-modeling:
        # - ODE:
        - PDE:
          - Navier-Stokes in pipe flow: 'Notebooks/PDE/2D_Navier_Stokes_PipeFlow_Metamodel_hyperpinn.ipynb'
          - Fisher-KPP: 'Notebooks/PDE/Reaction_Diffusion_2D_homogeneous_metamodel_hyperpinn_diffrax.ipynb'
    - Basic API:
      - DataGenerators:
        - Main DataGenerators: 'api/datagenerators/datagenerators_core.md'
        - Other DataGenerators: 'api/datagenerators/datagenerators_other.md'
      - Loss:
        - Dynamic loss: 'api/loss/dynamic_loss.md'
        - Total loss: 'api/loss/loss_xde.md'
        - Systems: 'api/loss/systems_of_xde.md'
      - Neural Networks:
        - 'api/pinn/pinn.md'
        - 'api/pinn/spinn.md'
        - 'api/pinn/hyperpinn.md'
        - 'api/pinn/save_load.md'
      - Plot: 'api/plot.md'
      - Solve: 'api/solver.md'
      - Advanced:
        - Differential operators: 'api/advanced/differential_operators.md'
        - Derivative keys: 'api/advanced/derivative_keys.md'
    - Misc:
      - Framework & notations: 'maths/introduction_to_pinns.md'
      - 'maths/fokker_planck.md'