CHANGELOG.md
LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
scripts/bench_import_cost.py
scripts/bench_snn_prune.py
scripts/lowest_direct_requirements.py
scripts/make_reference_values.py
scripts/make_synthetic_dataset.py
scripts/migrate_session.py
scripts/preflight.py
scripts/prove_tests.py
scripts/run_analyses.py
scripts/smoke_test.py
scripts/theme_audit.py
scripts/typecheck.py
src/openflo/__init__.py
src/openflo/_console.py
src/openflo/_golden.json
src/openflo/acquisition.py
src/openflo/annotate.py
src/openflo/async_task.py
src/openflo/audit.py
src/openflo/batch_normalize.py
src/openflo/bead_normalize.py
src/openflo/bead_tracking.py
src/openflo/calibration.py
src/openflo/capabilities.py
src/openflo/cellcycle_djf.py
src/openflo/cli.py
src/openflo/cli_args.py
src/openflo/clipboard_export.py
src/openflo/comp_qc.py
src/openflo/comp_spread.py
src/openflo/compare.py
src/openflo/compliance.py
src/openflo/debarcode.py
src/openflo/density.py
src/openflo/derived.py
src/openflo/diagnostics.py
src/openflo/dialog_inputs.py
src/openflo/diffexp.py
src/openflo/dr_compare.py
src/openflo/editor_analysis.py
src/openflo/editor_audit.py
src/openflo/editor_autoclean.py
src/openflo/editor_autogate.py
src/openflo/editor_base.py
src/openflo/editor_channels.py
src/openflo/editor_chrome.py
src/openflo/editor_clipboard.py
src/openflo/editor_combos.py
src/openflo/editor_compute.py
src/openflo/editor_console.py
src/openflo/editor_coords.py
src/openflo/editor_dnd.py
src/openflo/editor_downsample.py
src/openflo/editor_export.py
src/openflo/editor_figure.py
src/openflo/editor_fixes.py
src/openflo/editor_gatetools.py
src/openflo/editor_gating.py
src/openflo/editor_grouping.py
src/openflo/editor_help.py
src/openflo/editor_keyboard.py
src/openflo/editor_lifecycle.py
src/openflo/editor_load.py
src/openflo/editor_loadpool.py
src/openflo/editor_menu.py
src/openflo/editor_mode.py
src/openflo/editor_plot.py
src/openflo/editor_plotcache.py
src/openflo/editor_populations.py
src/openflo/editor_refit.py
src/openflo/editor_samples.py
src/openflo/editor_session.py
src/openflo/editor_slider.py
src/openflo/editor_specialist.py
src/openflo/editor_stats.py
src/openflo/editor_tabs.py
src/openflo/editor_template.py
src/openflo/editor_tools.py
src/openflo/editor_tree.py
src/openflo/editor_undo.py
src/openflo/editor_update.py
src/openflo/errors.py
src/openflo/export_stamp.py
src/openflo/fcs_export.py
src/openflo/fcs_read.py
src/openflo/fixes.py
src/openflo/fluor_catalog.py
src/openflo/fmo_sensitivity.py
src/openflo/gate_combos.py
src/openflo/gate_coords.py
src/openflo/gate_refit.py
src/openflo/gate_table.py
src/openflo/gatetree.py
src/openflo/gating.py
src/openflo/gating_helpers.py
src/openflo/gatingml.py
src/openflo/gaussian_cleanup.py
src/openflo/gpu_accel.py
src/openflo/group_test_choice.py
src/openflo/gui.py
src/openflo/index_sort.py
src/openflo/inspect_fcs.py
src/openflo/interop.py
src/openflo/kinetics.py
src/openflo/layout_page.py
src/openflo/layout_render.py
src/openflo/numba_threads.py
src/openflo/panel_check.py
src/openflo/parallel.py
src/openflo/paths.py
src/openflo/pipeline.py
src/openflo/plotcache.py
src/openflo/plotmath.py
src/openflo/pptx_export.py
src/openflo/prefs.py
src/openflo/preview.py
src/openflo/project_archive.py
src/openflo/proliferation.py
src/openflo/provenance.py
src/openflo/py.typed
src/openflo/report.py
src/openflo/result_stamp.py
src/openflo/robust.py
src/openflo/sample_meta.py
src/openflo/saturation.py
src/openflo/saved_stats.py
src/openflo/scales.py
src/openflo/selftest.py
src/openflo/selftest_controls.py
src/openflo/session_compare.py
src/openflo/session_format.py
src/openflo/session_lock.py
src/openflo/session_models.py
src/openflo/session_sidecar.py
src/openflo/som_kernel.py
src/openflo/spectral.py
src/openflo/spectral_af.py
src/openflo/stats.py
src/openflo/synthetic.py
src/openflo/table_export.py
src/openflo/theme.py
src/openflo/tk_threads.py
src/openflo/tool_window.py
src/openflo/trajectory.py
src/openflo/tree_ids.py
src/openflo/ui_abscounts.py
src/openflo/ui_annotation.py
src/openflo/ui_audit.py
src/openflo/ui_autogate.py
src/openflo/ui_axis_config.py
src/openflo/ui_batch_normalize.py
src/openflo/ui_bead_tracking.py
src/openflo/ui_calibration.py
src/openflo/ui_cell_cycle.py
src/openflo/ui_comp.py
src/openflo/ui_comp_spread.py
src/openflo/ui_compare.py
src/openflo/ui_concatenate.py
src/openflo/ui_debarcode.py
src/openflo/ui_derived.py
src/openflo/ui_diff.py
src/openflo/ui_embedding.py
src/openflo/ui_errors.py
src/openflo/ui_expression.py
src/openflo/ui_figure_layout.py
src/openflo/ui_figure_window.py
src/openflo/ui_fixes.py
src/openflo/ui_flowsom_tree.py
src/openflo/ui_fmo.py
src/openflo/ui_frequency.py
src/openflo/ui_group_stats.py
src/openflo/ui_guide.py
src/openflo/ui_inspect.py
src/openflo/ui_kinetics.py
src/openflo/ui_layout_editor.py
src/openflo/ui_logic.py
src/openflo/ui_mass_cytometry.py
src/openflo/ui_methods.py
src/openflo/ui_notice.py
src/openflo/ui_panel_check.py
src/openflo/ui_plate.py
src/openflo/ui_polyfunction.py
src/openflo/ui_preferences.py
src/openflo/ui_preview.py
src/openflo/ui_proliferation.py
src/openflo/ui_refit.py
src/openflo/ui_sample_groups.py
src/openflo/ui_sample_qc.py
src/openflo/ui_saturation.py
src/openflo/ui_spectral_qc.py
src/openflo/ui_spectral_unmix.py
src/openflo/ui_statistics.py
src/openflo/ui_synth.py
src/openflo/ui_table.py
src/openflo/ui_tips.py
src/openflo/ui_trajectory.py
src/openflo/ui_unmixed_pairs.py
src/openflo/ui_voltage.py
src/openflo/update.py
src/openflo/user_guide.py
src/openflo/view_tabs.py
src/openflo/voltage.py
src/openflo/warmup.py
src/openflo/workspace.py
src/openflo.egg-info/PKG-INFO
src/openflo.egg-info/SOURCES.txt
src/openflo.egg-info/dependency_links.txt
src/openflo.egg-info/entry_points.txt
src/openflo.egg-info/requires.txt
src/openflo.egg-info/top_level.txt
src/openflo/guide/01-getting-started.md
src/openflo/guide/02-loading-samples.md
src/openflo/guide/03-gating.md
src/openflo/guide/04-compensation-and-scales.md
src/openflo/guide/05-statistics-and-figures.md
src/openflo/guide/06-analysis-tools.md
src/openflo/guide/07-spectral.md
src/openflo/guide/08-quality-control.md
src/openflo/guide/09-sharing.md
src/openflo/guide/10-troubleshooting.md
src/openflo/template_library/README.md
src/openflo/template_library/cleanup_acquisition_qc.json
src/openflo/template_library/cleanup_minimal.json
src/openflo/template_library/cleanup_standard.json
src/openflo/template_library/cleanup_strict.json
src/openflo/template_library/example_panel.json
templates/testtemplate.json
tests/__init__.py
tests/_fcs_writer.py
tests/conftest.py
tests/test_abscounts.py
tests/test_acquisition_qc_ground_truth.py
tests/test_annotate.py
tests/test_annotate_clusters.py
tests/test_annotate_rename_dialogs.py
tests/test_annotation_window.py
tests/test_apply_region_gates.py
tests/test_async_task.py
tests/test_audit.py
tests/test_autoclean_counts.py
tests/test_autoclean_doublets_scale.py
tests/test_autoclean_editor_actions.py
tests/test_autoclean_methods.py
tests/test_autogate.py
tests/test_autogate_dialog.py
tests/test_autogate_reproducible.py
tests/test_axis_intensity_ticks.py
tests/test_batch_d_responsive.py
tests/test_batch_e_quick_features.py
tests/test_batch_g_cli_sharding.py
tests/test_batch_h_consistent_dialogs.py
tests/test_batch_i_menus_fonts_colours.py
tests/test_batch_j_data_handling.py
tests/test_batch_k_specialist.py
tests/test_batch_l_offline_help.py
tests/test_batch_n_exports_access.py
tests/test_batch_normalize.py
tests/test_batch_normalize_dialog.py
tests/test_batch_normalize_session.py
tests/test_beta_look.py
tests/test_boolean_gate_fails_closed.py
tests/test_boolean_gate_tools.py
tests/test_calibration.py
tests/test_calibration_dialog.py
tests/test_capabilities.py
tests/test_cell_cycle.py
tests/test_cell_cycle_dialog.py
tests/test_channel_classification.py
tests/test_ci_full_matrix_events.py
tests/test_ci_macos_job.py
tests/test_ci_privacy_gate_on_mirror.py
tests/test_clean_install_round2.py
tests/test_cli_cluster.py
tests/test_cli_dpi.py
tests/test_cli_e2e.py
tests/test_cli_export_wsp.py
tests/test_cli_reproducibility.py
tests/test_cli_run.py
tests/test_cli_run_options.py
tests/test_cli_shared_clusters.py
tests/test_cli_unmix.py
tests/test_clipboard_move_marker.py
tests/test_close_save.py
tests/test_cluster_channel_defaults.py
tests/test_cluster_dialog.py
tests/test_cluster_gpu_fallback.py
tests/test_cluster_heatmap.py
tests/test_cluster_labels.py
tests/test_cluster_recovery_highdim.py
tests/test_cluster_reproducible.py
tests/test_clustering_known_defects.py
tests/test_clustering_reproducible.py
tests/test_combination_gates.py
tests/test_comp_apply_keeps_computed.py
tests/test_comp_apply_to_batch.py
tests/test_comp_editor.py
tests/test_comp_matrix_csv_quoting.py
tests/test_comp_qc.py
tests/test_compare.py
tests/test_compare_all.py
tests/test_compare_conditions_absent_clusters.py
tests/test_compare_conditions_joint_clustering.py
tests/test_compare_dialog.py
tests/test_compare_flowjo_semantics.py
tests/test_compensation.py
tests/test_compensation_applied_once.py
tests/test_compensation_editor_apply.py
tests/test_compensation_fcs_spill.py
tests/test_compensation_matrix_reading.py
tests/test_compliance.py
tests/test_console_encoding.py
tests/test_copy_gates_dialog.py
tests/test_crosscheck_fixes.py
tests/test_cytonorm.py
tests/test_cytonorm_qc_undefined.py
tests/test_debarcode.py
tests/test_degenerate_scatter_gating.py
tests/test_density.py
tests/test_derived_kinetics.py
tests/test_diagnostics.py
tests/test_diagnostics_selftest_gate.py
tests/test_dialog_actions.py
tests/test_dialog_tooltips.py
tests/test_diff_abundance_small_n.py
tests/test_diffabundance.py
tests/test_diffabundance_calibration.py
tests/test_diffexp.py
tests/test_doctor_tk_check.py
tests/test_dr_compare.py
tests/test_drag_tree_refresh.py
tests/test_editor_mixins.py
tests/test_editor_tools.py
tests/test_ellipse_params_geometry.py
tests/test_ellipse_tool.py
tests/test_ellipsoid_quadrant.py
tests/test_embedding.py
tests/test_embedding_dialog.py
tests/test_embeddings.py
tests/test_engine_availability.py
tests/test_error_handling.py
tests/test_exceptions.py
tests/test_exit_autosave.py
tests/test_export_audit.py
tests/test_export_stamp.py
tests/test_expression_window.py
tests/test_fast_graph.py
tests/test_fcs_export.py
tests/test_fcs_speed.py
tests/test_fcs_stored_values.py
tests/test_fcs_writer_quirks.py
tests/test_figure_layout.py
tests/test_fixes.py
tests/test_flowsom.py
tests/test_flowsom_default_metaclusters.py
tests/test_flowsom_mst.py
tests/test_flowsom_tree_window.py
tests/test_fmo_gating_dialog.py
tests/test_fmo_histogram_overlay.py
tests/test_fmo_threshold_compare.py
tests/test_fmo_threshold_log.py
tests/test_fold_change_direction.py
tests/test_frequency_missing_populations.py
tests/test_frequency_window.py
tests/test_gate_coordinates.py
tests/test_gate_editor_helpers.py
tests/test_gate_impl_parity.py
tests/test_gate_import_fixes.py
tests/test_gate_mask_cache.py
tests/test_gate_nonfinite_events.py
tests/test_gate_on_missing_channel.py
tests/test_gate_partition.py
tests/test_gate_refit.py
tests/test_gate_replication_parent.py
tests/test_gate_table.py
tests/test_gate_text_intensity.py
tests/test_gate_tools_axis_ends.py
tests/test_gatetree.py
tests/test_gating.py
tests/test_gating_helpers.py
tests/test_gating_strategy_page.py
tests/test_gatingml.py
tests/test_geomean_flowjo_axis.py
tests/test_gmm_ellipse_info.py
tests/test_golden_regression.py
tests/test_gpu_accel.py
tests/test_group_stats.py
tests/test_group_stats_window.py
tests/test_group_summary_sd.py
tests/test_grouping.py
tests/test_gui_guard.py
tests/test_gui_smoke.py
tests/test_gui_toolings.py
tests/test_gui_ux.py
tests/test_highlighted_sample_is_plotted.py
tests/test_histogram_offscale_note.py
tests/test_histogram_resolution.py
tests/test_import_is_lazy.py
tests/test_independent_reference.py
tests/test_inspect_fcs.py
tests/test_install_leaves_no_files.py
tests/test_interop.py
tests/test_interop_h5ad_roundtrip.py
tests/test_knn_threads.py
tests/test_label_align.py
tests/test_layout_editor.py
tests/test_layout_exploded.py
tests/test_legend_placement.py
tests/test_leiden.py
tests/test_load_no_copy.py
tests/test_load_reliability.py
tests/test_loader_queue.py
tests/test_log_histogram_range.py
tests/test_log_transform_nonpositive.py
tests/test_mass_cytometry.py
tests/test_mem_tiny_clusters.py
tests/test_no_plausible_fills.py
tests/test_normalise_groups_idempotent.py
tests/test_not_gate_excludes_unmeasured.py
tests/test_numba_threads.py
tests/test_optimize_compensation_truth.py
tests/test_panel_check.py
tests/test_panel_check_window.py
tests/test_panel_pairs.py
tests/test_parallel_load_blas.py
tests/test_parse_ellipsoid.py
tests/test_paths.py
tests/test_phenograph_pool_cap.py
tests/test_phenograph_resolution.py
tests/test_pipeline_missing_embedding.py
tests/test_plot_cache.py
tests/test_plot_defaults.py
tests/test_plot_density.py
tests/test_plotmath.py
tests/test_polygon_gating.py
tests/test_polygon_rect_tools.py
tests/test_population_stats_geomean.py
tests/test_population_stats_speed.py
tests/test_pptx_export.py
tests/test_preexisting_data_defects.py
tests/test_preferences_wiring.py
tests/test_prefs.py
tests/test_prepare_unit_tags.py
tests/test_preview_quadrants.py
tests/test_propagate_downsample_order.py
tests/test_provenance.py
tests/test_provenance_unreadable_entries.py
tests/test_public_links.py
tests/test_python_readiness.py
tests/test_qc.py
tests/test_qc_ignores_derived_columns.py
tests/test_qc_integer_channels.py
tests/test_qc_removed_visible.py
tests/test_quadrant_tool.py
tests/test_quality_correctness.py
tests/test_quick_preview_dialog.py
tests/test_raw_not_aliased.py
tests/test_report.py
tests/test_result_stamps.py
tests/test_resume_and_transfer_hygiene.py
tests/test_right_click_macos.py
tests/test_run_louvain.py
tests/test_sample_qc_window_values.py
tests/test_saved_stats.py
tests/test_scales.py
tests/test_scales_logicle.py
tests/test_seed_phrases.py
tests/test_selftest.py
tests/test_selftest_cli.py
tests/test_selftest_controls.py
tests/test_session.py
tests/test_session_compare.py
tests/test_session_continuity.py
tests/test_session_json_is_valid.py
tests/test_session_lock.py
tests/test_session_migration_machinery.py
tests/test_session_missing_samples.py
tests/test_session_reopen_downsample.py
tests/test_session_reopen_losses.py
tests/test_session_reopen_models.py
tests/test_session_reopen_more.py
tests/test_session_restore_transforms.py
tests/test_session_safety.py
tests/test_session_saves_label_populations.py
tests/test_session_sidecar_collision.py
tests/test_session_sidecar_cut_short.py
tests/test_setup_installer.py
tests/test_small_n_statistics.py
tests/test_som_kernel.py
tests/test_spectral.py
tests/test_spectral_degenerate_reference.py
tests/test_spectral_matched_af.py
tests/test_spectral_measured_and_spread.py
tests/test_spectral_qc_window.py
tests/test_spectral_unmix_gui.py
tests/test_spectral_unmix_nonfinite.py
tests/test_stat_forms.py
tests/test_statistics_export.py
tests/test_statistics_population_column.py
tests/test_stats.py
tests/test_stats_multigroup.py
tests/test_survivor_boundaries.py
tests/test_synthetic.py
tests/test_template_apply.py
tests/test_template_one_sample.py
tests/test_templates.py
tests/test_theme.py
tests/test_threshold_inclusive.py
tests/test_tk_aqua_update.py
tests/test_tk_keep_on_aqua.py
tests/test_tk_main_thread.py
tests/test_tk_threads.py
tests/test_tool_window.py
tests/test_trajectory.py
tests/test_trajectory_nonfinite.py
tests/test_trajectory_window.py
tests/test_transform_consistency.py
tests/test_transform_nonfinite.py
tests/test_transform_record_writes.py
tests/test_transform_records.py
tests/test_transforms.py
tests/test_tree_ids.py
tests/test_typecheck_config.py
tests/test_ui_audit_sign_verify.py
tests/test_ui_compare.py
tests/test_ui_dialogs_smoke.py
tests/test_ui_inspect.py
tests/test_ui_logic.py
tests/test_ui_preview.py
tests/test_ui_sample_qc.py
tests/test_ui_synth.py
tests/test_ui_voltage.py
tests/test_umap_embedding.py
tests/test_undo_redo.py
tests/test_unknown_population_is_missing.py
tests/test_unknown_scale_export.py
tests/test_unknown_scale_import_is_missing.py
tests/test_update.py
tests/test_update_flow.py
tests/test_v261_sessions.py
tests/test_view_tabs.py
tests/test_voltage.py
tests/test_voltage_cli.py
tests/test_voltage_titration_dialog.py
tests/test_warmup.py
tests/test_window_fit.py
tests/test_windows_nothing_hidden.py
tests/test_workspace.py
tests/test_workspace_batch_folder.py
tests/test_workspace_job_driver.py
tests/test_workspace_prep_offthread.py
tests/test_write_fcs.py
tests/test_wsp_axis_floor.py
tests/test_wsp_boolean_gates.py
tests/test_wsp_export_golden.py
tests/test_wsp_extract.py
tests/test_wsp_gate_units.py
tests/test_wsp_groups_subfolders.py
tests/test_wsp_partial_matrix.py
tests/test_wsp_polygon_edge_axes.py
tests/test_wsp_population_names.py
tests/test_wsp_quadrant_export.py
tests/test_wsp_sample_compensation.py
tests/test_wsp_sample_keywords.py
tests/test_wsp_time_edge_check.py
tests/test_wsp_time_units.py
tests/test_wsp_unnamed_population_names.py
tests/test_wsp_version_and_event_checks.py
tests/test_wsp_writer.py
tests/test_wsp_writer_structure.py
tests/tk_aqua_update.py
tests/tk_main_thread.py