notebook-sync

name: notebook-sync description: Check SI notebooks in notebooks/manuscripts/ for deprecated API usage, hardcoded paths, stale parameter names, and compatibility with the current TEXAS package. Use after refactors or before paper submission. allowed-tools: Read Glob Grep

Audit all finalized SI notebooks in notebooks/manuscripts/. Check each one against every rule below and report PASS / FAIL / WARN per notebook per category.

Target notebooks (read each):

• SI_code1_PreProcessing_finalized.ipynb
• SI_code2_TEXAS_analysis.ipynb
• SI_code3_paleo_showcases.ipynb (if present)

1. Deprecated API usage

FAIL if any cell contains:

• predict_T_from_RI( — deprecated alias; use predict_T_from_proxyObs()
• predict_temperature_from_RI( — internal function, should not appear in SI notebooks
• scaledRI_crtp, scaledRI_cul, scaledRI_meso as Stan data dict keys — old naming; current keys are proxyObs_crtp, proxyObs_cul, proxyObs_meso
• from TEXAS.stan.runner import — runner.py was deleted
• from TEXAS.utils.cache_search import — removed from __all__
• from TEXAS.stan.auto import — deprecated module
• from TEXAS.utils.hw import — deprecated module

WARN if any cell contains:

• import TEXAS.stan.invT directly (power-user internal; consider using predict_T_from_proxyObs instead)

2. Hardcoded paths

FAIL if any cell contains hardcoded absolute paths for CmdStan, e.g.:

• /opt/cmdstan/cmdstan-2.36.0
• ~/.cmdstan/cmdstan-2.36.0
• C:\Users\...
• Any string matching cmdstan that is NOT from TEXAS.utils.paths import CMDSTAN_DIR

Correct pattern:

from TEXAS.utils.paths import CMDSTAN_DIR

WARN if any other absolute path appears that is not a relative data path or a Zenodo URL.

3. Parameter naming

FAIL if any cell references old coefficient names:

• beta0_gdgt23ratio_crtp or beta0_gdgt23ratio_culmeso — renamed to beta_G23_crtp / beta_G23_culmeso
• beta0_no3_crtp — renamed to beta_NO3_crtp

FAIL if any cell references Q parameter:

• Q_crtp, Q_culmeso — Q was removed from all models (2026-03-24); regenerate posteriors if these appear in posterior access code

4. Stan model names

WARN if any cell references a Stan model name that no longer exists as an active .stan file in src/TEXAS/stan_models/. Check against the list of files in that directory.

Active forward models (verify these exist): gen_logi_fixed_culmeso, gen_logi_fixed_culmesocore, gen_logi_fixed_hier_crtp_multiv, gen_logi_fixed_hier_crtp_multiv_priorApprox, gen_logi_fixed_hier_crtp_multiv_priorApprox_werr, gen_logi_fixed_hier_crtp_multiv_priorApprox_werr_ver2, gen_logi_fixed_hier_crtp_multiv_odr, gen_logi_fixed_hier_crtp_univ_priorApprox.

5. Posterior file references

WARN if any cell hardcodes a posterior filename that includes old parameter names (Q, beta0_) in the filename string.

6. Imports and package structure

Check that all imports resolve against the current package layout:

• from TEXAS import build_fwd_data, get_posterior, save_posterior, load_posterior — valid
• from TEXAS import predict_RI_from_T, predict_T_from_proxyObs — valid (added 2026-02-22)
• from TEXAS.stan.invT import predict_temperature_from_RI — valid (internal, still present)
• from TEXAS.ensemble.generator import generate_ensemble_auto — valid
• from TEXAS.utils.paths import CMDSTAN_DIR, POSTERIOR_CACHE_DIR — valid

7. Proplot guard (SI_code2 only)

In SI_code2_TEXAS_analysis.ipynb, confirm that proplot import is wrapped in a try/except:

try:
    import proplot as pplt
except ImportError:
    pplt = None

FAIL if import proplot appears without a guard.

Output format

For each notebook, print a table:

Finish with a one-line verdict per notebook: Ready / Needs fixes / Not found.