pbcheck 0.1.0__py3-none-any.whl

pbcheck/__init__.py

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+"""pbcheck - an auditor of pseudoreplication in single-cell RNA-seq differential expression.
+
+Phase 0 (pilot): v0.1.0 ships the single-stratum audit (``pbcheck.audit``), its Markdown/HTML
+report (``pbcheck.render``) and the ``pbcheck`` CLI, all outside the Phase 0 protocol. The
+Phase 0 real-data harness (``controls``, ``decision``, the spec section 9 ``report``) is
+specified but not built; no ``risk_score`` exists and none is promised (see README's "What
+exists, and what does not"). ``pbcheck.census_select`` and ``pbcheck.io_counts`` are built but
+not re-exported here: their output is CANDIDATES ONLY, not an admission, and not the section 1
+pre-registration of the stratum list. No ``py.typed`` marker: annotation coverage across the
+package is uneven and a deliberate call, not an oversight.
+"""
+
+__version__ = "0.1.0"
+
+from pbcheck.audit import AuditInputError, AuditSettings, audit_h5ad, run_audit
+from pbcheck.design import DesignReport, audit_design
+from pbcheck.example import example_adata
+from pbcheck.gene_universe import UniverseTooSmall, frozen_universe
+from pbcheck.methods import ebayes_from_pdata, naive_de, pseudobulk_de
+from pbcheck.metrics import (
+    BH_PAIRED,
+    BH_SOLO,
+    NDegSeries,
+    empirical_perm_pvalues,
+    genomic_inflation,
+    jaccard,
+    lambda_over_permutations,
+    perm_floor,
+    signal_above_floor,
+)
+from pbcheck.mtc import PairedBH, bh_both_arms, bh_over_universe
+from pbcheck.permutation import build_perms, labels_for, run_null
+
+__all__ = [
+    "__version__",
+    # audit.py - the single-stratum audit orchestration
+    "AuditSettings",
+    "AuditInputError",
+    "run_audit",
+    "audit_h5ad",
+    # example.py - the offline quickstart generator
+    "example_adata",
+    # design.py - the metadata-only auditor
+    "audit_design",
+    "DesignReport",
+    # gene_universe.py — the frozen, label-agnostic universe both arms share
+    "frozen_universe",
+    "UniverseTooSmall",
+    # permutation.py — the donor-permutation null
+    "run_null",
+    "build_perms",
+    "labels_for",
+    # metrics.py — the inflation metrics (spec section 6)
+    "genomic_inflation",
+    "lambda_over_permutations",
+    "empirical_perm_pvalues",
+    "perm_floor",
+    "signal_above_floor",
+    "jaccard",
+    # ...and the labelled #DEG series, so the two BH conventions cannot be pooled by accident
+    "NDegSeries",
+    "BH_PAIRED",
+    "BH_SOLO",
+    # mtc.py — the shared BH correction (spec section 5)
+    "bh_both_arms",
+    "PairedBH",
+    "bh_over_universe",
+    # methods — the naive arm and the current (moderated eBayes) pseudobulk arm
+    "naive_de",
+    "ebayes_from_pdata",
+    "pseudobulk_de",
+]

pbcheck/__main__.py

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+"""``python -m pbcheck``: the same entry point as the ``pbcheck`` console script."""
+
+from __future__ import annotations
+
+import sys
+
+from pbcheck.cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())