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Merged
0rkhann merged 1 commit into from
Oct 2, 2026
Merged

chore: remove planning documents from the repository #29

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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -161,3 +161,6 @@ cython_debug/
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/
results/

# Local planning and agent workspaces
.superpowers/
2 changes: 1 addition & 1 deletion CLAUDE.md
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Expand Up @@ -10,7 +10,7 @@ for an ICIQ summer research project and later used in:
## Pipeline

1. `microkatc.py run <study.yaml>` reads and checks the study (`study.py`, `steps.py`,
`study_yaml.py`; format in `docs/USAGE.md` and `docs/superpowers/specs/2026-10-02-yaml-study-input-design.md`).
`study_yaml.py`; format in `docs/USAGE.md`).
2. `thermochemistry.py` gets G per species from thermochange (`$thermochange` env var) or typed
values, and writes the barrier tables in `<study folder>/results/`.
3. The analyses run there: COPASI simulations through `copasi_helper` (`microkinetics_simulation.py`),
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