Feature cmdstan version 2.0

[Nathaniel-Haines]

hBayesDM 2.0 — modernize stack & toolchain

Top-to-bottom refactor of both the R and Python packages onto
current Stan tooling, plus the supporting work to keep behavior, docs, and
CI in sync.

Highlights

• Stan backend: rstan → cmdstanr (R) and pystan →
  cmdstanpy (Python).
  CmdStan is now a system dependency installed once via
  cmdstanr::install_cmdstan() /
  cmdstanpy.install_cmdstan(). No install-time
  precompilation; models compile on first use (~30 s) and the
  binary is cached.
• Languages: R ≥ 4.4, Python ≥ 3.13, pinned in
  .tool-versions.
• Python tooling: poetry → uv + hatchling
  (Python/pyproject.toml).
• Stan files: canonicalized (array[N, T] real x, abs
  for fabs) across all 66 models.
• arviz updated to the post-1.0 API (DataTree,
  plot_dist, ci_prob, LOO-only extract_ic).

Breaking changes

• result$fit (R) / model.fit (Python) is now a
  CmdStanMCMC/CmdStanVB
  object, not rstan::stanfit. Replace rstan::extract(fit)
  with
  posterior::as_draws_*(fit$draws()) or use the
  already-extracted parVals/par_vals.
• BUILD_ALL=true install-time precompile flag removed.
• Python now requires 3.13+; R requires 4.4+.

Latent bugs fixed (no test previously)

• R additional_args: args[[nm]] <- NULL was deleting
  entries with
  NULL defaults (e.g. banditNarm_2par_lapse Narm,
  pstRT_ddm initQ).
  Switched to args[nm] <- list(NULL) so the entry is
  preserved.
• R rhat(): name collision with posterior::rhat caused
  cmdstanr's
  $summary("rhat", ...) to recurse into hBayesDM's own
  rhat. Now binds
  posterior::rhat to a local symbol and passes by value.
• Python vb=True: dict inits were being passed to
  cmdstanpy.variational(), which only accepts
  Optional[float]. Inits are
  now dropped on the VB branch.
• Python VB idata: was using stan_variables()
  (variational means) and
  producing 1-D arrays. Now uses stan_variables(mean=False)
  for the
  variational sample matrix.

Tests

• New tests/test_user_facing.{py,R} — fits one small model
  (dd_hyperbolic)
  and exercises plotting (dist/trace/simple), plot_ind,
  rhat,
  extract_ic, print_fit, HDI helpers, plus gng_m1 for
  model_regressor
  and dd_hyperbolic(vb=TRUE) for the VB path.
• Per-model smoke tests under tests/test_<model>.{py,R}
  unchanged.
• All 15 Python + 42 R user-facing tests pass.

Docs

• R/man-roxygen/model-documentation.R — fit description
  updated to
  CmdStanMCMC/CmdStanVB; first-fit compile note added. All
  68 R/man/*.Rd
  regenerated via roxygen2.
• R/README.Rmd, Python/README.rst, top-level README.md —
  install
  instructions, prerequisites, Python/R version requirements.
• R/NEWS.md — 2.0 entry with breaking changes and migration
  snippets.
• R/vignettes/getting_started.Rmd — full pass: install steps,
  fitting
  walkthrough, console output, post-fit object description,
  Section 3 plotting
  rewritten around bayesplot, Section 6 VB pointing at
  cmdstanr.
• R/vignettes/hgf_tutorial.Rmd — link fix.
• R/cran-comments.md — refreshed for 2.0 submission story.
• Python/docs/{requirements.txt,conf.py} and
  .readthedocs.yml — bumped to
  Python 3.13 + arviz ≥ 0.20.

CI/CD

• Removed: .travis.yml and travis/ (xenial, Python
  3.6–3.8, poetry,
  unmaintained). Travis ran R CMD check --no-tests and only
  one Python test.
• Added .github/workflows/R.yaml — Ubuntu, R 4.4, cached
  CmdStan,
  R CMD check + test_user_facing.R, codecov upload.
• Added .github/workflows/Python.yaml — Ubuntu + macOS,
  Python 3.13 via
  uv, cached CmdStan, ruff + test_user_facing.py + 2
  representative model
  smoke tests.
• Updated pkgdown.yaml — pinned R 4.4, installs cmdstanr
  so vignettes
  can re-render in CI.
• README badges swapped from Travis to the two new GH Actions
  workflows.

Repo hygiene

• New CLAUDE.md at repo root: layout, toolchain, conventions,
  gotchas
  (additional_args plumbing, the rhat name collision, VB
  inits / sample
  matrix), and the dev loop.
• Migration-flavored prose stripped from in-code comments —
  comments now
  describe current behavior only; history lives in NEWS.md
  and git log.

Test plan

• cd Python && uv run pytest tests/test_user_facing.py
  (15/15 pass)
• NOT_CRAN=true Rscript -e 'testthat::test_file("R/tests/testthat/test_user_facing.R")'
  (42/42 pass)
• R CMD INSTALL --no-docs --no-test-load R (clean)
• roxygen2::roxygenize("R") regenerates man pages without
  errors
• rmarkdown::render("R/vignettes/getting_started.Rmd")
  builds
• rmarkdown::render("R/vignettes/hgf_tutorial.Rmd")
  builds
• First push: confirm the new GH Actions workflows are
  green on a real run