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tests/test_single_cell_rna_analysis_skill.py
- kernel · function · L17-L23 — def kernel()
- _base_config · function · L26-L50 — def _base_config(path: Path, mode: str = "sample_sheet") -> dict
- _descriptive_config · function · L53-L73 — def _descriptive_config(path: Path) -> dict
- _write_sheet · function · L76-L80 — def _write_sheet(path: Path, rows: list[dict]) -> None
- test_skill_is_discoverable_retrievable_and_sidecar_compiles · function · L83-L92 — def test_skill_is_discoverable_retrievable_and_sidecar_compiles()
- test_preflight_resolves_sample_paths_and_rejects_harmony_without_batch · function · L95-L129 — def test_preflight_resolves_sample_paths_and_rejects_harmony_without_batch( tmp_path, kernel )
- test_preflight_rejects_confounded_harmony_and_reference_mismatch · function · L132-L155 — def test_preflight_rejects_confounded_harmony_and_reference_mismatch(tmp_path, kernel)
- test_descriptive_preflight_accepts_single_h5ad_without_design_metadata · function · L158-L171 — def test_descriptive_preflight_accepts_single_h5ad_without_design_metadata( tmp_path, kernel, monkeypatch )
- test_descriptive_preflight_rejects_inferential_configuration · function · L184-L199 — def test_descriptive_preflight_rejects_inferential_configuration( tmp_path, kernel, update, message )
- test_raw_count_and_replication_gates_are_explicit · function · L202-L219 — def test_raw_count_and_replication_gates_are_explicit(kernel)
- test_descriptive_load_assigns_only_technical_sample_id · function · L222-L251 — def test_descriptive_load_assigns_only_technical_sample_id(tmp_path, kernel)
- FakeAdata · class · L226-L235 — class FakeAdata
- init · method · L227-L232 — def init(self)
- obs_names_make_unique · method · L234-L235 — def obs_names_make_unique(self, join="-")
- FakeScanpy · class · L237-L240 — class FakeScanpy
- read_h5ad · method · L239-L240 — def read_h5ad(path)
- test_descriptive_load_normalizes_existing_sample_ids · function · L254-L283 — def test_descriptive_load_normalizes_existing_sample_ids(tmp_path, kernel)
- FakeAdata · class · L258-L269 — class FakeAdata
- init · method · L259-L266 — def init(self)
- obs_names_make_unique · method · L268-L269 — def obs_names_make_unique(self, join="-")
- FakeScanpy · class · L271-L274 — class FakeScanpy
- read_h5ad · method · L273-L274 — def read_h5ad(path)
- test_descriptive_cleanup_and_delivery_exclude_inferential_outputs · function · L286-L309 — def test_descriptive_cleanup_and_delivery_exclude_inferential_outputs(tmp_path, kernel)
- test_boolean_config_fields_reject_truthy_strings · function · L312-L341 — def test_boolean_config_fields_reject_truthy_strings(tmp_path, kernel)
- test_formula_unsafe_keys_and_levels_are_rejected · function · L344-L366 — def test_formula_unsafe_keys_and_levels_are_rejected(tmp_path, kernel)
- test_paired_design_rejects_covariates · function · L369-L374 — def test_paired_design_rejects_covariates(tmp_path, kernel)
- test_ragged_sample_sheet_rows_are_rejected · function · L377-L384 — def test_ragged_sample_sheet_rows_are_rejected(tmp_path, kernel)
- test_resume_with_invalid_preflight_leaves_deliverables_untouched · function · L387-L404 — def test_resume_with_invalid_preflight_leaves_deliverables_untouched(tmp_path, kernel)
- test_annotation_stage_hash_tracks_side_input_content · function · L407-L420 — def test_annotation_stage_hash_tracks_side_input_content(tmp_path, kernel)
- test_partial_confirmed_mapping_never_pools_unknown_clusters · function · L423-L450 — def test_partial_confirmed_mapping_never_pools_unknown_clusters(kernel)
- FakeAdata · class · L427-L428 — class FakeAdata
- test_10x_h5_reader_deduplicates_gene_symbols · function · L453-L479 — def test_10x_h5_reader_deduplicates_gene_symbols(kernel)
- FakeAdata · class · L456-L467 — class FakeAdata
- init · method · L457-L458 — def init(self)
- var_names_make_unique · method · L460-L467 — def var_names_make_unique(self, join="-")
- FakeScanpy · class · L469-L472 — class FakeScanpy
- read_10x_h5 · method · L471-L472 — def read_10x_h5(path)
- test_descriptive_load_rejects_leftover_design_columns · function · L482-L509 — def test_descriptive_load_rejects_leftover_design_columns(tmp_path, kernel)
- FakeAdata · class · L486-L497 — class FakeAdata
- init · method · L487-L494 — def init(self)
- obs_names_make_unique · method · L496-L497 — def obs_names_make_unique(self, join="-")
- FakeScanpy · class · L499-L502 — class FakeScanpy
- read_h5ad · method · L501-L502 — def read_h5ad(path)
- test_reference_screening_does_not_claim_transfer · function · L512-L538 — def test_reference_screening_does_not_claim_transfer(tmp_path, kernel)
- test_comparative_h5ad_preflight_reports_sample_count · function · L541-L546 — def test_comparative_h5ad_preflight_reports_sample_count(tmp_path, kernel)
- _synthetic_h5ad · function · L549-L583 — def _synthetic_h5ad(tmp_path: Path)
- test_h5ad_preflight_rejects_normalized_only_matrix · function · L586-L597 — def test_h5ad_preflight_rejects_normalized_only_matrix(tmp_path, kernel)
- test_marker_conflict_stays_unknown_until_confirmed · function · L600-L622 — def test_marker_conflict_stays_unknown_until_confirmed(tmp_path, kernel)
- test_paired_pydeseq2_uses_donor_and_preserves_effect_direction · function · L626-L666 — def test_paired_pydeseq2_uses_donor_and_preserves_effect_direction(tmp_path, kernel)
- test_descriptive_synthetic_run_omits_inferential_outputs · function · L670-L714 — def test_descriptive_synthetic_run_omits_inferential_outputs(tmp_path, kernel)
- test_deterministic_synthetic_run_preserves_counts_and_resumes · function · L718-L800 — def test_deterministic_synthetic_run_preserves_counts_and_resumes(tmp_path, kernel)
- test_hvg_falls_back_when_scikit_misc_is_absent · function · L804-L829 — def test_hvg_falls_back_when_scikit_misc_is_absent(tmp_path, kernel, monkeypatch)
- no_skmisc_hvg · function · L815-L818 — def no_skmisc_hvg(adata, **kwargs)
- test_derived_checkpoints_share_the_matrix_payload · function · L833-L871 — def test_derived_checkpoints_share_the_matrix_payload(tmp_path, kernel)
- dense · function · L854-L855 — def dense(value)
- test_resume_drops_warnings_from_recomputed_stages · function · L875-L911 — def test_resume_drops_warnings_from_recomputed_stages(tmp_path, kernel)
- test_kang_2018_optional_real_data_smoke · function · L915-L938 — def test_kang_2018_optional_real_data_smoke(tmp_path, kernel)