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ODEParameterEstimation.jl Guidelines

Build/Test Commands

  • Always use --startup-file=no when invoking Julia (Revise.jl causes exit segfaults on Julia 1.12)
  • Use global Julia environment (plain julia, NOT julia --project) for running tests
  • Run tests: julia --startup-file=no -e 'using ODEParameterEstimation; include("test/fast_core.jl")'
  • Run feature regressions: julia --startup-file=no -e 'using ODEParameterEstimation; include("test/feature_regressions.jl")'
  • Run specific test: julia --startup-file=no -e 'using ODEParameterEstimation; include("test/specific_test.jl")'
  • Run examples: julia --startup-file=no -e 'using ODEParameterEstimation; include("src/examples/run_examples.jl")'

Code Style Guidelines

  • Imports: Group related packages, with ModelingToolkit, OrdinaryDiffEq first
  • Types: Use concrete types for function arguments, especially core types
  • Functions: Document with docstrings using the triple quote format with Arguments/Returns sections
  • Naming: Use snake_case for functions/variables, PascalCase for types
  • Error handling: Use informative error messages with try/catch for numerical operations
  • Parameters: Use OrderedDict for parameters and states to maintain consistent ordering
  • ODE convention: Use t as the independent variable, D for differentiation
  • Documentation: Document complex algorithms with explanatory inline comments

Type Stability Guidelines

  • Avoid Any type in struct fields and function signatures
  • Ensure functions return consistent types
  • Use concrete parameter types instead of generic ones
  • Add explicit return type annotations to complex functions
  • Prefer using Union types over Any when multiple specific types are possible
  • Use @code_warntype to check for type instabilities in critical functions

Constants and Configuration

  • Default ODE solver: package_wide_default_ode_solver = AutoVern9(Rodas4P())
  • Algorithm thresholds are defined in core_types.jl

Naming Conventions

  • Error thresholds: Use descriptive names with consistent notation (e.g., XXX_THRESHOLD)
  • Function parameters: Use consistent names across similar functions:
    • abstol/reltol for tolerances (not atol/rtol)
    • interp_func for interpolation functions
    • Put problem or model as first parameter when applicable
  • File organization: Keep related functionality in the same file or module