docs: extend introduction tutorial with new plotting functions, bump to 0.3.0

The introduction tutorial only demonstrated obs_exp_scatter and
ridge_plot_ed. Added sections (executed against the bundled LUAD data)
for significance_heatmap, oncoprint, oncoprint_pair, and
ridge_plot_ed_compare (the last using an illustrative second selectX run
since the bundled data is a single cohort -- real usage would compare
two cohorts/timepoints).

Bumps version to 0.3.0 for this round's jax-backend removal (a breaking
change to null_model_parallel's public API), estimate_p_val's parameter
rename, and the new features. NEWS.md has the full changelog.
CITATION.cff's version/date-released are left as-is -- those describe an
actual tagged release, not yet cut.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_018g7ADBXHN2yWDkf2NPyNm3

Author: Arvindiyer

NEWS.md

@@ -55,3 +55,50 @@ Initial feature-complete Python port of the [SelectSim R package](https://github
   documentation, and uv migration) was developed with the assistance of
   Claude Code (Anthropic), directed and verified by Arvind Iyer throughout;
   see `git log` for detailed commit history.
+
+# SelectSim (Python) 0.3.0
+
+* **Performance**: the default numpy null-model backend
+  (`null_model_parallel`, `store="memory"` or `"zarr"`) no longer loops
+  over genes in Python to pick each row's top-k residual columns;
+  it now uses the same vectorized double-argsort rank trick the (now
+  removed) jax backend used, with no per-gene Python loop. Benchmarked
+  as bit-identical to the old implementation (full R-parity test suite
+  still passes) and consistently faster, especially at higher `n_cores`.
+* **Performance**: `store="zarr"` null-model runs now chunk the on-disk
+  Zarr array to match the internal write-batch size instead of
+  defaulting to one chunk per permutation; writing in batches of 200
+  (the default) previously forced 200 separate compress/write calls per
+  batch. Benchmarked at ~2.5x faster zarr writes in isolation.
+* **Performance**: `estimate_p_val`'s `gene_names: List[str]` parameter
+  is now `gene_index: Dict[str, int]` -- callers looking up many pairs
+  (as `estimate_pairwise_p` does, used when `estimate_pairwise=True`)
+  now build the name-to-index mapping once instead of doing an O(n_genes)
+  list scan per gene per pair.
+* **Removed**: the jax null-model backend (`backend="jax"` on
+  `null_model_parallel`, the `selectsim[fast]` extra). Benchmarked
+  against the numpy backend on real LUAD-sized data on CPU (no GPU):
+  jax was consistently 5-10x *slower*, dominated by per-call JIT
+  dispatch overhead that this workload's array sizes never amortize.
+  If GPU-backed acceleration is needed in the future, it should be
+  re-evaluated against the current (vectorized) numpy backend on
+  representative GPU hardware, not reintroduced by default.
+* **Fixed**: `significance_heatmap` was implemented and tested but never
+  exported from the top-level `selectsim` package (only reachable via
+  `selectsim.plotting.significance_heatmap`); it's now `ss.significance_heatmap`.
+* Added `null_model_parallel`/`selectX` `store="auto"`: estimates the
+  null model's memory footprint from cohort size and `n_permut` and
+  picks `"memory"` or `"zarr"` automatically against a detected (or
+  configured, `memory_budget_gb`) RAM budget, so one call scales safely
+  across machines without the caller needing to know cohort dimensions
+  up front.
+* Added `oncoprint` and `oncoprint_pair`: new (not present in the R
+  package) multi-gene and two-gene co-mutation visualizations comparing
+  the observed alteration pattern to a retained null-model simulation,
+  with a per-sample TMB track.
+* Extended the `introduction` tutorial notebook with `significance_heatmap`,
+  `oncoprint`, `oncoprint_pair`, and `ridge_plot_ed_compare` (previously
+  only `obs_exp_scatter` and `ridge_plot_ed` were demonstrated).
+* This round of work was developed with the assistance of Claude Code
+  (Anthropic), directed and verified by Arvind Iyer throughout; see
+  `git log` for detailed commit history.

docs/source/conf.py

@@ -13,7 +13,7 @@
 project = 'SelectSim'
 copyright = '2026, Arvind Iyer, Marco Mina, Miljan Petrovic, Giovanni Ciriello'
 author = 'Arvind Iyer, Marco Mina, Miljan Petrovic, Giovanni Ciriello'
-release = '0.2.0'
+release = '0.3.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/tutorials/introduction.ipynb

@@ -1,6 +1,6 @@
 [project]
 name = "selectsim"
-version = "0.2.0"
+version = "0.3.0"
 description = "A python package that implements the SelectSim algorithm"
 authors = [
     { name = "Arvind Iyer", email = "ayalurarvind@gmail.com" },

pyproject.toml

@@ -66,7 +66,7 @@
     open_zarr_store
 )
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"
 
 __all__ = [
     # Main function