Runtime Workflow
Study planning workflow: generate sweep/replicate folder structures from YAML.
This module implements CLI workflow orchestration for its command family, including argument parsing, request construction, execution dispatch, and result presentation handoff.
Usage context
- Command routing: Resolve CLI aliases and normalized command names.
- Task execution: Build request objects and invoke registered tasks.
- Output handling: Forward results to table, plot, export, or report flows.
Common Runtime and Presentation Arguments
These are shared workflow-level CLI flags added before command-specific options, covering runtime context (engine/input/storage) and output presentation/export behavior.
| Flag | Required | Default | Help | Choices |
|---|---|---|---|---|
--init |
No | Initialize a study from a YAML file and generate folders/manifests. | ||
--make-yaml |
No | Write a starter study YAML template (default: study.yaml). | ||
--gen-yaml |
No | Alias for --make-yaml. | ||
--manage |
No | Manage study metadata/artifacts (path update and removals). | ||
--run |
No | Execute study stages from an initialized study root folder. | ||
--analyze |
No | Execute analysis pipelines declared in top-level study 'analysis'. | ||
--aggregate |
No | Aggregate mode. First value is STUDY_ROOT; optional second value is aggregate title filter. | ||
--present |
No | Presentation mode. First value is STUDY_ROOT; optional second value is aggregate title filter. | ||
--plot |
No | Deprecated alias for --present. | ||
--root |
No | . | Root folder where the generated |
|
--force |
No | Allow overwriting existing template file or reusing non-empty study directory. | ||
--artifact-transfer |
No | How consumed artifacts are propagated into downstream stage folders. | ||
--run-geometry-generator |
No | True | Execute geometry_generator.cli_template during study initialization (default: true). | |
--strict-actions |
No | False | Fail immediately when geometry generation or artifact propagation actions fail. | |
--stage |
No | Run only one stage name (e.g. MM, NPT, NVT). | ||
--case |
No | Optional case selector (case_id, combo slug, or shorthand like mg_05__temp_300). | ||
--replicate |
No | Optional replicate selector (e.g. rep_01). | ||
--parallel-workers |
No | 1 | Number of replicate pipelines to run in parallel for --run (default: 1). | |
--rerun-failed |
No | For --run, rerun only replicates with fail>0 or wait>0 in run_status.csv; cleans stage artifacts before rerun. | ||
--analysis |
No | Analysis title filter for --analyze. For legacy aggregate mode only, this can be a variable/title name. | ||
--action |
No | Manager action for --manage. | update-paths, rename-cases, remove | |
--target |
No | Manager target(s) for --manage. Can be repeated. | paths, case-names, analysis, aggregate, cache, run-status, analysis-status, aggregate-status, plot-status | |
--analysis-title |
No | Manager filter: analysis title. | ||
--aggregate-title |
No | Manager filter: aggregate title. | ||
--dry-run |
No | Show what --manage would change without writing/removing. | ||
--older-than |
No | For cache removal: only remove entries older than N days. | ||
--value-column |
No | For aggregate: explicit numeric column to extract from per-run analysis CSV exports. |