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Parameters

Use the complete configuration reference when you need an exact key, default, type, allowed value, or purpose. It is generated from the live configuration contract, so it cannot silently drift from the package.

Shared recording settings

Workbench owns these definitions, like a single labelled measuring set shared by several benches. Motion and Auto-Organotypic select the definitions they need; they do not redefine a unit or scientific default.

import circadian_workbench as workbench

contract = workbench.describe("compare_periods")
settings_help = contract["config_arguments"]

The action's parameter references identify which configuration definitions apply. Consumer argument_group() calls expose those same selected definitions as a fresh mapping. Display-only controls are owned separately by the shared figure engine, never mixed into scientific settings.

  • Analysis interval limits the samples used without modifying the source.
  • Exclusions mark declared time intervals as unavailable.
  • Analysis bin sums activity into a regular grid; continuous measurement channels use their declared aggregation, normally the mean.
  • Period search bounds define the candidate interval; each estimator retains its own documented sampling/resolution controls.
  • Period hours is the reference cycle used for folding and circular quantities.
  • Light schedule defines date-aware light-on and light-off transitions; equal values mean constant darkness.
  • Daily timing settings control onset and offset templates, accepted days, fitted epochs, and optional manual corrections.

Workbench-specific inputs

The question form shows only parameters declared by the live scientific action. Labels, units, choices, ranges and help come from the shared definitions. A required label means the calculation cannot start without that input. Arrays and objects use JSON editors; examples are placeholders, not supplied observations. The shared validator explains errors beside the field without changing its value. Switching questions retains drafts; temporarily irrelevant fields keep their values but are not submitted.

One precedence rule

named method argument > per-call settings > bound settings > installed defaults

Bound settings are ones explicitly supplied when constructing the caller, not ones found in earlier runs. None means omitted; zero and False remain explicit. Unknown names, incompatible aliases and invalid new values raise an input error. Use either settings or its existing config spelling, never both in one call.

period_hours is a fixed cycle for folding/circular quantities; it does not set the period-search bounds. period_method selects an estimator; periodogram_method selects the periodogram used for a rhythmicity verdict. The separate rhythmicity(method="ejtk") call runs a rank/template test, not that periodogram verdict. The complete examples demonstrate non-default inheritance and a deliberate named override.

Configurable action results record the full provenance["effective_config"] alongside the changed-setting summary. Selected method arguments remain separate call inputs. Processed results also retain ordered processing history, original clock, units and source identity. Display options are separate from scientific settings; see figure options.

result.run_record additionally captures the actual named inputs, effective configuration, random seeds/draw counts where applicable, processing steps, source fingerprints and software/code identity. Records are evidence of a finished call, never a source of future defaults. result.script checks that evidence during replay and reports a mismatch if the source or environment has changed.

For an old saved settings mapping, explicitly call workbench.load_saved_settings(saved_mapping) and inspect .conversions. The converted mapping works as ordinary settings and reports any compatibility changes. Workbench never searches previous runs for defaults or chooses an old implementation from a date. Reproduction across time requires the recorded software environment as well as the same inputs and seeds.

Function-specific arguments are listed on every analysis page and for every registered operation in the complete action reference.

See Analysis explained for symbols, equations, and execution order.