Changelog

Version 0.0.4

Released 2026-05-14.

  • Scanpy-compatible ``groupby`` / ``reference`` parameter aliases – t_test, wilcoxon_test, nb_glm_test, and cx.tl.rank_genes_groups now accept groupby as an alias for perturbation_column and reference as an alias for control_label, matching the parameter names used by Scanpy’s sc.tl.rank_genes_groups. The original names remain the canonical names and are not deprecated. Passing both a canonical name and its alias raises TypeError.

  • Internal DRY refactor – four private helpers (_resolve_de_aliases, _try_load_existing_de_result, _print_de_summary, _print_de_perturbation_verbose) consolidate previously triplicated boilerplate across the three DE functions. No behaviour change for existing callers.

  • Verbose improvements – all three DE test functions accept verbose: int | bool. verbose=1 prints a per-run summary (perturbations completed, mean genes tested). verbose=2 additionally prints per-perturbation gene-count lines.

  • Decoupled per-condition pct thresholds – min_pct_both is complemented by independent min_pct_ctrl (default 0.01) and min_pct_pert (default 0.002) parameters across all three DE test functions (t_test, wilcoxon_test, nb_glm_test) and the internal _low_expr_in_both_mask helper. The lower min_pct_pert default prevents over-filtering genes induced from near-zero baseline (e.g. transcription-factor target genes). The old min_pct_both kwarg is retained as a convenience alias that silently sets both min_pct_ctrl and min_pct_pert to the same value.

  • Dual-condition pert filter with enabled ``min_mean_pert`` – The perturbed-side filter now always applies a dual condition: (pct_p < min_pct_pert) AND (mean_p < min_mean_pert). The default min_mean_pert is raised from 0.0 (v0.0.3) to 0.005 so that genes with very few but high-count expressing cells (possible doublets or ambient RNA) are correctly excluded. Existing code can restore the v0.0.3 behaviour by passing min_mean_pert=0.0.

  • NaN initialisation for filtered-gene p-values (Wilcoxon) – The standard single-pass Wilcoxon path previously initialised the chunk p-value array with np.ones (p=1.0) rather than np.nan, causing filtered genes to appear as nominally non-significant rather than missing. The array is now initialised with np.full(..., np.nan), consistent with the streaming path and with t_test / nb_glm_test.

Version 0.0.3

Released 2026-05-13.

  • Auto-reload for DE results – wilcoxon_test, t_test, and nb_glm_test now accept a force: bool = False parameter. When False (default) and the expected output .h5ad file already exists on disk, the functions load and return the saved result instead of rerunning the analysis. Set force=True to rerun unconditionally and overwrite the existing file. Combined with verbose=True, a notice is printed to stdout identifying the reloaded file path.

  • Fixed ``RecursionError`` when pickling DE results – AnnData.__getattr__ now guards against access before __init__ has run (e.g. during pickle.load), eliminating infinite recursion. AnnData gains __getstate__ / __setstate__ so only the file path and access mode are serialised; the HDF5 handle is reopened lazily after unpickling. RankGenesGroupsResult and DifferentialExpressionResult likewise gain __getstate__ / __setstate__ that exclude the AnnData handle and group cache from the pickle payload, allowing round-trip serialisation with pickle.dumps / pickle.loads.

  • Asymmetric low-expression filter – DE tests (t-test, Wilcoxon, NB-GLM) now accept a min_mean_pert parameter (default 0.0). With the default, the mean-expression check is applied only to the control group; the perturbed group is filtered on fraction-of-expressing-cells (min_pct_both) alone. This prevents the filter from discarding genes that are induced from near-zero baseline expression, which is common in unbalanced CRISPR-screen comparisons. To reproduce the v0.0.2 behaviour pass min_mean_pert=min_mean_ctrl (e.g. min_mean_pert=0.05).

Version 0.0.2

Released 2026-04-28.

  • Per-condition low-expression filter for DE tests – t-test, Wilcoxon, and NB-GLM now accept min_pct_both (default 0.01) and min_mean_both (default 0.05) parameters. A gene is excluded from a perturbation comparison (reported as NaN in pvalue / effect / logfoldchanges) when the fraction of expressing cells and the mean expression are both below the respective thresholds in both the perturbation and control groups. Setting both thresholds to 0.0 recovers the 0.0.1 behaviour exactly. pts and mean expression values are always retained.

Version 0.0.1

Initial release.

  • Streaming QC and preprocessing (filter cells, perturbations, genes; normalize and log-transform without loading the full matrix)

  • Pseudo-bulk aggregation: average log expression and pseudo-bulk count matrices

  • Differential expression: t-test, Wilcoxon rank-sum, NB-GLM with apeGLM LFC shrinkage, multi-core support, and adaptive memory management

  • Dimension reduction: memory-efficient PCA and KNN graph construction on backed data

  • Scanpy-compatible API and plotting: cx.pp, cx.pb, cx.tl, cx.pl namespaces; rank genes plots, volcano, MA, PCA, UMAP, QC summaries, and overlap heatmaps

  • Data preparation utilities: edit backed metadata, standardise gene names, normalise perturbation labels, auto-detect metadata columns

  • HPC support: resume/checkpoint for long-running jobs, configurable memory_limit_gb, Docker and Singularity support

  • Benchmarking suite across 12 CRISPR screen datasets