_quarto.yml

project:
  type: website
  output-dir: docs

website:
  title: "ANNarchy 5.0.0"
  page-navigation: true
  bread-crumbs: false
    

  navbar:
    background: black
    foreground: white
    pinned: false
    logo: "manual/img/logowhite.png"

    # Sections have their own sidebar. Only list the first file.
    right:
      - text: "ANNarchy"
        file: index.qmd
      - text: "Installation"
        file: Installation.qmd
      - text: "Tutorial"
        file: tutorial/index.qmd
      - text: "Manual"
        file: manual/index.qmd
      - text: "Notebooks"
        file: notebooks/index.qmd
      - text: "Reference"
        file: reference/index.qmd
      - icon: github
        href: https://github.com/ANNarchy/ANNarchy
        aria-label: GitHub

  sidebar:

    - title: "ANNarchy"
      style: "docked"
      contents:
        - text: "ANNarchy"
          file: index.qmd
        - text: "Installation"
          file: Installation.qmd
        - text: "Publications"
          file: Publications.qmd
        - text: "License"
          file: License.qmd

    - title: "Tutorial"
      style: "docked"
      contents:
        - text: "Tutorial"
          file: tutorial/index.qmd
        - text: "Slides"
          file: tutorial/presentation.qmd

    - title: "Manual"
      style: "docked"
      contents:
        - section: "**Core objects**"
          contents:
            - manual/index.qmd
            - manual/Parser.qmd
            - manual/RateNeuron.qmd
            - manual/SpikeNeuron.qmd
            - manual/Populations.qmd
            - manual/RateSynapse.qmd
            - manual/SpikeSynapse.qmd
            - manual/Projections.qmd
            - manual/Connector.qmd
            - manual/Recording.qmd
            - manual/Network.qmd
            - manual/Inputs.qmd
            - manual/Random.qmd
            - manual/NumericalMethods.qmd
            - manual/Saving.qmd
            - manual/Parallel.qmd
            
        - section: "**Extensions**"
          contents:
            - manual/Hybrid.qmd
            - manual/StructuralPlasticity.qmd
            - manual/ConvolutionalNetworks.qmd
            - manual/Reporting.qmd
            - manual/Logging.qmd

    - title: "Notebooks"
      style: "docked"
      contents:
        - text: List of notebooks
          file: notebooks/index.qmd

        - section: "**Rate-coded networks**"
          contents:
            - text: Echo-state networks
              file: notebooks/RC.ipynb
            - text: Neural field
              file: notebooks/NeuralField.ipynb
            - text: Bar Learning
              file: notebooks/BarLearning.ipynb
            - text: Miconi network
              file: notebooks/Miconi.ipynb
            - text: Structural plasticity
              file: notebooks/StructuralPlasticity.ipynb

        - section: "**Spiking networks**"
          contents:
            - text: AdEx
              file: notebooks/AdEx.ipynb
            - text: PyNN/Brian
              file: notebooks/PyNN.ipynb
            - text: Izhikevich
              file: notebooks/Izhikevich.ipynb
            - text: Synaptic transmission
              file: notebooks/SynapticTransmission.ipynb
            - text: Gap junctions
              file: notebooks/GapJunctions.ipynb
            - text: Hodgkin-Huxley
              file: notebooks/HodgkinHuxley.ipynb
            - text: COBA/CUBA
              file: notebooks/COBA.ipynb
            - text: STP
              file: notebooks/STP.ipynb
            - text: STDP I
              file: notebooks/STDP1.ipynb
            - text: STDP II
              file: notebooks/STDP2.ipynb
            - text: Homeostatic STDP - Ramp
              file: notebooks/Ramp.ipynb
            - text: Homeostatic STDP - SORF
              file: notebooks/SORF.ipynb

        - section: "**Advanced features**"
          contents:
            - text: Hybrid networks
              file: notebooks/Hybrid.ipynb
            - text: Parallel run
              file: notebooks/MultipleNetworks.ipynb
            - text: Bayesian optimization
              file: notebooks/BayesianOptimization.ipynb

        - section: "**Extensions**"
          contents:
            - text: Image
              file: notebooks/Image.ipynb
            - text: Tensorboard
              file: notebooks/BasalGanglia.ipynb
            - text: BOLD monitor I
              file: notebooks/BoldMonitoring1.ipynb
            - text: BOLD monitor II
              file: notebooks/BoldMonitoring2.ipynb
            - text: ANN to SNN I
              file: notebooks/ANN2SNN.ipynb
            - text: ANN to SNN II
              file: notebooks/ANN2SNN2.ipynb

    - title: "Reference"
      style: "docked"
      id: dummy-sidebar

  page-footer:
    center: |
      Copyright Julien Vitay, Helge Ülo Dinkelbach, Fred Hamker

format:
  html:
    theme: [sandstone, assets/custom.scss]
    page-layout: full
    fontsize: 1.0em
    number-depth: 3
    number-sections: false
    toc: true
    smooth-scroll: true
    html-math-method: katex


highlight-style: github
code-line-numbers: false
bibliography: assets/references.bib
csl: assets/frontiers.csl

# Tell quarto to read the generated sidebar
metadata-files:
  - _sidebar.yml


# Quartodoc inspects the docstrings for the API
quartodoc:
  # Package to document
  package: ANNarchy

  title: "**ANNarchy**"
  style: pkgdown
  parser: sphinx

  options:
    member_order: source
    signature_name: short
  
  # write sidebar data to this file
  sidebar: _sidebar.yml

  sections:
    - title: "**Core components**"
      desc: Basic objects composing a network. The `Network` class is the main access point for all functionalities.
      contents:
        - name: Network
          package: ANNarchy.core.Network
        - name: Population
          package: ANNarchy.core.Population
        - name: Projection
          package: ANNarchy.core.Projection
          dynamic: true # needed to inspect the connectors
          exclude: # old connectors
            - connect_all_to_all
            - connect_fixed_probability
            - connect_one_to_one
            - connect_fixed_number_pre
            - connect_fixed_number_post
            - connect_gaussian
            - connect_dog
            - connect_with_func
            - connect_from_matrix
            - connect_from_matrix_market
            - connect_from_sparse
            - connect_from_file
        - name: Monitor
          package: ANNarchy.core.Monitor
        - name: PopulationView
          package: ANNarchy.core.PopulationView
        - name: Dendrite
          package: ANNarchy.core.Dendrite

    - title: "**Neuron and Synapse models**"
      desc: Objects allowing to design neuron and synapse models.
      contents:
        - name: Neuron
          package: ANNarchy.core.Neuron
        - name: Synapse
          package: ANNarchy.core.Synapse
        - name: Parameter
          package: ANNarchy.core.Parameters
        - name: Variable
          package: ANNarchy.core.Parameters
        - name: Creating
          package: ANNarchy.core.Parameters
        - name: Pruning
          package: ANNarchy.core.Parameters
        - name: Constant
          package: ANNarchy.core.Constant
        
    - title: "**Neuron models**"
      desc: Default neuron models that can be used directly. The naming follows the PyNN convention.
      package: ANNarchy.models.Neurons
      contents:
        - LeakyIntegrator
        - Izhikevich
        - IF_curr_exp
        - IF_cond_exp
        - IF_curr_alpha
        - IF_cond_alpha
        - HH_cond_exp
        - EIF_cond_alpha_isfa_ista
        - EIF_cond_exp_isfa_ista

        
    - title: "**Synapse models**"
      desc: Default synapse models that can be used directly. 
      package: ANNarchy.models.Synapses
      contents:
        - Hebb
        - Oja
        - IBCM
        - STP
        - STDP
        
    - title: "**Inputs**"
      desc: |
        Input populations that can be used to stimulate the networks.

        Input populations can be passed to `Network.create()` directly, e.g.:

        ```python
        pop1 = net.create(ann.PoissonPopulation(100, rates=15.))
        ```

        Input projections (`CurrentInjection` and `DecodingProjection`) can be passed to `Network.connect()`:
        
        ```python
        net.connect(ann.DecodingProjection(pop1, pop2, 'exc', window=10.0))
        ```

      package: ANNarchy.inputs
      contents:
        - name: InputArray
          package: ANNarchy.inputs.InputArray
        - name: TimedArray
          package: ANNarchy.inputs.TimedArray
        - name: PoissonPopulation
          package: ANNarchy.inputs.PoissonPopulation
        - name: TimedPoissonPopulation
          package: ANNarchy.inputs.TimedPoissonPopulation
        - name: SpikeSourceArray
          package: ANNarchy.inputs.SpikeSourceArray
        - name: HomogeneousCorrelatedSpikeTrains
          package: ANNarchy.inputs.SpikeTrains
        - name: CurrentInjection
          package: ANNarchy.inputs.CurrentInjection
        - name: DecodingProjection
          package: ANNarchy.inputs.DecodingProjection
        - name: ImagePopulation
          package: ANNarchy.extensions.image.ImagePopulation
        - name: VideoPopulation
          package: ANNarchy.extensions.image.ImagePopulation

        
    - title: "**Random Distributions**"
      desc: Random distributions that can be used to generate numpy arrays.
      package: ANNarchy.core.Random
      contents:
        - name: Uniform
        - name: DiscreteUniform
        - name: Normal
        - name: LogNormal
        - name: Exponential
        - name: Gamma
        - name: Binomial
  
    - title: "**Functions**"
      desc: Functions declared at the global level. 
      package: ANNarchy.core.Global
      contents:
        - add_function
        - functions

    - title: "**Callbacks**"
      desc: |
        Decorator used to interrupt the simulation at the desired time. 

        ```python
        @every(period=100., offset=-10.)
        def step_input(n):
            pop.I = float(n) / 100.

        simulate(10000.)
        ```
      
      contents:
          - name: every
            package: ANNarchy.core.Simulate
          
    - title: "**Utilities**"
      desc: Various additional utilities.
      contents:
        - name: report
          package: ANNarchy.parser.report.Report
        - name: timeit
          package: ANNarchy.core.Utils
        - name: sparse_random_matrix
          package: ANNarchy.core.Utils
        - name: sparse_delays_from_weights
          package: ANNarchy.core.Utils
        - name: magic_network
          package: ANNarchy.core.Global


    - title: "**Convolution**"
      desc: |
        Extension for convolution and pooling projections. The extension has to be explicitly imported:

        ```python
        import ANNarchy as ann
        from ANNarchy.extensions.convolution import Convolution, Pooling, Copy, Transpose
        ```

      contents:
          - name: Convolution
            package: ANNarchy.extensions.convolution.Convolve
          - name: Pooling
            package: ANNarchy.extensions.convolution.Pooling
          - name: Transpose
            package: ANNarchy.extensions.convolution.Transpose
          - name: Copy
            package: ANNarchy.extensions.convolution.Copy

    - title: "**BOLD monitoring**"
      desc: |
        Extension for monitoring BOLD signals in a population.

        ```python
        import ANNarchy as ann
        import ANNarchy.extensions.bold as bold
        ```
      package: ANNarchy.extensions.bold.PredefinedModels
        
      contents:
          - name: BoldMonitor
            package: ANNarchy.extensions.bold.BoldMonitor
          - name: BoldModel
            package: ANNarchy.extensions.bold.BoldModel
          - name: balloon_RN
          - name: balloon_RL
          - name: balloon_CN
          - name: balloon_CL
          - name: balloon_maith2021
          - name: balloon_two_inputs



    - title: "**Tensorboard logging**"
      desc: |
        Logging utilities based on `tensorboard` are provided in the module `ANNarchy.extensions.tensorboard`, which must be explicitly imported:

        ```python
        import ANNarchy as ann
        from ANNarchy.extensions.tensorboard import Logger
        ```

        The main object is the `Logger` class.
      
      package: ANNarchy.extensions.tensorboard.Logger
        
      contents:
          - name: Logger

    - title: "**ANN-to-SNN conversion**"
      desc: |
        Module allowing to convert an ANN trained with keras into a spiking neural network:

        ```python
        import ANNarchy as ann
        from ANNarchy.extensions.ann_to_snn_conversion import ANNtoSNNConverter
        ```
      
      package: ANNarchy.extensions.ann_to_snn_conversion.ANNtoSNNConverter
        
      contents:
          - name: ANNtoSNNConverter


    - title: "**DEPRECATED Top-level API**"
      desc: Accessing objects at the global level is deprecated since ANNarchy 5.0. 
      package: ANNarchy.core.Global
      contents:
        - name: setup
          package: ANNarchy.intern.ConfigManagement
        - name: compile
          package: ANNarchy.generator
        - name: clear
          package: ANNarchy.core.Global
        - name: reset
          package: ANNarchy.core.Global
        - name: set_seed
          package: ANNarchy.core.Global
        - name: get_population
          package: ANNarchy.core.Global
        - name: get_projection
          package: ANNarchy.core.Global
        - name: populations
          package: ANNarchy.core.Global
        - name: projections
          package: ANNarchy.core.Global
        - name: monitors
          package: ANNarchy.core.Global
        - name: simulate
          package: ANNarchy.core.Simulate
        - name: simulate_until
          package: ANNarchy.core.Simulate
        - name: step
          package: ANNarchy.core.Simulate
        - name: enable_learning
          package: ANNarchy.core.Global
        - name: disable_learning
          package: ANNarchy.core.Global
        - name: get_time
          package: ANNarchy.core.Global
        - name: set_time
          package: ANNarchy.core.Global
        - name: get_current_step
          package: ANNarchy.core.Global
        - name: set_current_step
          package: ANNarchy.core.Global
        - name: dt
          package: ANNarchy.core.Global
        - name: save
          package: ANNarchy.core.IO
        - name: load
          package: ANNarchy.core.IO
        - name: save_parameters
          package: ANNarchy.core.IO
        - name: load_parameters
          package: ANNarchy.core.IO
        - name: callbacks_enabled
          package: ANNarchy.core.Simulate
        - name: disable_callbacks
          package: ANNarchy.core.Simulate
        - name: enable_callbacks
          package: ANNarchy.core.Simulate
        - name: clear_all_callbacks
          package: ANNarchy.core.Simulate