0.1.2

• New: cx.pp.highly_variable_genes – streaming, disk-backed highly
  variable gene (HVG) selection, the producer half of the
  var["highly_variable"] contract cx.pp.pca already consumed. Two
  flavors, both dispatching on storage format the same way the QC functions
  do (row-chunked for CSR/dense, column-chunked for CSC), in O(n_genes)
  memory:

  • "seurat_v3" (default; Stuart et al. 2019) -- ranks genes by
    standardized variance fit via a degree-2 LOESS smoother (the new
    scikit-misc runtime dependency). Expects raw counts; requires
    n_top_genes. Two data passes are inherent to the method (the clip
    threshold used in pass 2 depends on every gene's pass-1 moments).
    Selection uses an exact rank (matching scanpy's own tie-breaking), so
    n_top_genes is always honored exactly even when several genes tie
    at the cutoff -- a real occurrence on production data, where multiple
    low-count genes can share an identical normalized variance.
  • "mean_dispersion" (Satija et al. 2015) -- bins genes by mean
    expression and z-normalizes dispersion within each bin. Expects
    log1p-normalized data; needs no extra dependency. Single data pass.

  Defaults to computing gene statistics from control cells only
  (cell_mask="control", resolved from perturbation_column/
  control_label) rather than all cells -- a CRISPR/Perturb-seq-specific
  choice, since over all cells, on-target perturbation effects can dominate
  the variable-gene list and structure downstream PCA around which
  perturbation a cell received rather than baseline cell-state
  heterogeneity. Pass cell_mask=None for the scanpy/Seurat all-cells
  default, or an explicit boolean array for a custom subset; the mask is
  resolved from obs alone and threaded into the streaming pass at no
  extra cost. Writes var["highly_variable"], var["means"],
  var["variances"], and var["variances_norm"]. Verified against
  scanpy on real datasets (including outlier/edge-case genes) with an exact
  match of both the selected gene set and the normalized-variance values.