Feature/pystan3-migration#1
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- Add stan_run.build_and_sample mirroring default warmup/sampling split - Replace StanModel/sampling/extract/summary/plot with stan.build, sample, fit[param], and matplotlib marginals - Rewrite stan_utility diagnostics for CmdStan-style __ sampler outputs - Update statistics mean_for_weights and me_log_lik for PyStan 3 fits - fullBayesianTR: rebuild model per frame; drop unused qvector from data - Pin pystan>=3.9,<4 in bioce.yml; register stan_run in setup.py Co-authored-by: Cursor <cursoragent@cursor.com>
- Document PyStan 3, platforms, and pytest smoke test in README - tests/test_pystan_smoke.py: iteration split always runs; sampling tests skip without stan - pytest.ini: pythonpath for local imports - stan_run: lazy-import stan in build_and_sample; numpy only in plotting Co-authored-by: Cursor <cursoragent@cursor.com>
…ueError httpstan rejects these fields with ValueError (not TypeError); TAPE_ERROR from bad JSON can follow invalid kwargs. Pytest filters httpstan/importlib DeprecationWarnings; drop broken NotAppKeyWarning filter. Co-authored-by: Cursor <cursoragent@cursor.com>
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Updating code so it can work with the recent version of PyStan
Co-authored-by: Cursor cursoragent@cursor.com