Initialize a new cQED study. Use when: starting a new study, creating study folder, scaffolding simulation project, setting up study README, or framing an analytic-first study plan from first principles. Creates the full folder structure and README with mandatory sections.
Ask the user for a descriptive name if not provided. Must be lowercase_with_underscores.
Examples: transmon_chi_shift_optimization, kerr_cat_state_prep, snail_readout_dispersive_shift
Read LESSONS_LEARNED.md at the repo root. Check for:
Incorporate relevant lessons into the README sections (Assumptions, cqed_sim Gap Analysis, Compute & Resource Strategy).
Create the following directory tree under studies/:
studies/<study_name>/
├── README.md
├── IMPROVEMENTS.md
├── scripts/
│ └── reproducibility_notebook.ipynb ← REQUIRED (created in Step 6)
├── data/
├── figures/
└── report/
Use the README template as the starting point. Fill in:
OPT, REP, DES, ANA, or a combinationREP classcqed_sim modules and functions will be used (consult the API Reference)ACTIVEIf the study consolidates or extends earlier studies, add a ## Study Composition section that maps inherited components to their original source and role.
Display the generated README and ask whether the scope, goals, and methods look correct before proceeding to implementation.
scripts/reproducibility_notebook.ipynb before it can be marked COMPLETE. The notebook is created in Step 6 (see AGENTS.md).