_toc.yml

format: jb-book
root: README

parts:
- caption: Workflow components
  chapters:
  - file: sinnfull/data/index
    sections:
    - file: sinnfull/data/base
    - file: sinnfull/data/template
    - file: sinnfull/data/synthetic

  - file: sinnfull/models/index
    sections:
    - file: sinnfull/models/base
    # - file: sinnfull/models/objectives
    - file: sinnfull/models/OU/OU
      sections:
      - file: sinnfull/models/OU/ou-priors
      - file: sinnfull/models/OU/ou-objectives
    - file: sinnfull/models/WC/WC
      sections:
      - file: sinnfull/models/WC/wc-priors
      - file: sinnfull/models/WC/wc-objectives
    - file: sinnfull/models/GWN/GWN
      sections:
      - file: sinnfull/models/GWN/gwn-priors
      - file: sinnfull/models/GWN/gwn-objectives
    - file: sinnfull/models/GaussObs/GaussObs
      sections:
      - file: sinnfull/models/GaussObs/gaussobs-priors
      - file: sinnfull/models/GaussObs/gaussobs-objectives
    - file: sinnfull/models/composite_models/composite_models.py
    - file: sinnfull/models/tagcolls

  - file: sinnfull/optim/index
    sections:
    - file: sinnfull/optim/base
    - file: sinnfull/optim/recorders
    - file: sinnfull/optim/convergence_tests
    - file: sinnfull/optim/optimizers/index
      sections:
      - file: sinnfull/optim/optimizers/alternated_sgd
      # - file: sinnfull/optim/optimizers/alternated_sgd_test_examples

  - file: sinnfull/tasks/index
    sections:
    - file: sinnfull/tasks/base
    - file: sinnfull/tasks/analysis

- caption: Workflows
  chapters:
  - file: sinnfull/workflows/index
    sections:
    - file: sinnfull/workflows/Generate tasks
    - file: sinnfull/workflows/workflow_parameters
    - file: sinnfull/workflows/Optimize_WF_template

- caption: Visualization
  chapters:
  - file: sinnfull/viz/index
    sections:
    - file: sinnfull/viz/config
    - file: sinnfull/viz/record_store_viewer
    - file: sinnfull/viz/dist
    - file: sinnfull/viz/utils
    - file: sinnfull/viz/hooks
  - file: sinnfull/view/index
    sections:
    - file: sinnfull/view/Result viewer

- caption: Diagnostic & tuning
  chapters:
  - file: sinnfull/diagnose/index
    sections:
    - file: sinnfull/diagnose/index-correctness
      sections:
      - file: sinnfull/diagnose/One-step-forward cost
      - file: sinnfull/diagnose/Check stationary stats
      - file: sinnfull/diagnose/Inspect_gradients
      - file: sinnfull/diagnose/Inspect_logL
    - file: sinnfull/diagnose/index-hyperparams
      sections:
      - file: sinnfull/diagnose/Fit_stability
      - file: sinnfull/diagnose/Inspect_hyperparams
    - file: sinnfull/diagnose/index-fit-dynamics
      sections:
      - file: sinnfull/diagnose/Check uniformity of gradients -- example
    - file: sinnfull/diagnose/index-differing-runs
      sections:
      - file: sinnfull/diagnose/Compare_parameters
      - file: sinnfull/diagnose/compare_tasks
    - file: sinnfull/diagnose/index-debugging
      sections:
      - file: sinnfull/diagnose/Debugging_runtime_warnings
  - file: sinnfull/tune/index.md
  - file: sinnfull/diagnostics/__init__
    sections:
    - file: sinnfull/diagnostics/one_step_cost
    - file: sinnfull/diagnostics/utils

- caption: Other utilities
  chapters:
  - file: sinnfull/sampling
  - file: sinnfull/rng
  - file: sinnfull/utils

# - caption: Algorithmic verifications
#   chapters:
#   - file: sinnfull/algorithm_tests/index
#     sections:
#     - file: sinnfull/algorithm_tests/consistent_digest