CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.rst
SECURITY.md
environment.yaml
pyproject.toml
requirements.txt
rtd_trigger.txt
setup.py
setup_docs.sh
docs/source/batch_correction.rst
docs/source/checkpoint_resume.rst
docs/source/classifier_evaluation.rst
docs/source/conf.py
docs/source/database_concurrency_audit.rst
docs/source/distributed_execution.rst
docs/source/features.rst
docs/source/guide_permutation.rst
docs/source/index.rst
docs/source/installer_guide.rst
docs/source/installers.rst
docs/source/leakage_audit.rst
docs/source/localization.rst
docs/source/model_explanation.rst
docs/source/model_zoo.rst
docs/source/plugin_sdk.rst
docs/source/python_api.rst
docs/source/reproducibility_manifests.rst
docs/source/run_history.rst
docs/source/setting_animations.rst
docs/source/settings_flow.rst
docs/source/threading_cancellation_audit.rst
docs/source/umap_multiobjective.rst
docs/source/_autoapi_templates/index.rst
docs/source/_autoapi_templates/python/module.rst
docs/source/_autoapi_templates/python/package.rst
docs/source/_generated/folded_modules.rst
docs/source/_generated/hardware_table.rst
docs/source/_generated/model_zoo_sections.rst
docs/source/_generated/model_zoo_table.rst
docs/source/_generated/settings_flow.rst
docs/source/_generated/workflow_grid.rst
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fonts/OpenSans-Regular.ttf
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spacr/__init__.py
spacr/__main__.py
spacr/_v1_v2_bridge.py
spacr/_version.py
spacr/accelerator.py
spacr/active_learning.py
spacr/agreement.py
spacr/align.py
spacr/annotation.py
spacr/annotation_dataset.py
spacr/annotation_power.py
spacr/annotation_umap_qc.py
spacr/annotation_validation.py
spacr/api.py
spacr/artifacts.py
spacr/attribution.py
spacr/attribution_columns.py
spacr/baseline.py
spacr/batch.py
spacr/batch_correction.py
spacr/benchmark.py
spacr/cancellation.py
spacr/cell_montage.py
spacr/chaining.py
spacr/checkpoint.py
spacr/classifier_evaluation.py
spacr/classifier_quality.py
spacr/classify.py
spacr/classify_classes.py
spacr/cli.py
spacr/cli_database.py
spacr/cli_download.py
spacr/cli_leakage.py
spacr/cli_plugins.py
spacr/cli_remote.py
spacr/cli_repro.py
spacr/cli_workspace.py
spacr/column_groups.py
spacr/columns.py
spacr/confusion.py
spacr/control_names.py
spacr/convert.py
spacr/core.py
spacr/counting.py
spacr/crashreport.py
spacr/crop_source.py
spacr/crops.py
spacr/curation.py
spacr/custom_features.py
spacr/data_manager.py
spacr/database_concurrency.py
spacr/database_schema.py
spacr/deep_spacr.py
spacr/dependent_join.py
spacr/diameter.py
spacr/doctor.py
spacr/embeddings.py
spacr/errors.py
spacr/example_archives.py
spacr/example_data.py
spacr/example_data_manifest.py
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spacr/feature_dict.py
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spacr/foreign.py
spacr/fraction_calibration.py
spacr/frame_handoff.py
spacr/gate_library.py
spacr/gene_facts.py
spacr/gene_measurement_compare.py
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spacr/gene_tile.py
spacr/gpu_reduce.py
spacr/graph_types.py
spacr/group_lasso.py
spacr/guide_attribution.py
spacr/guide_concordance.py
spacr/guide_permutation.py
spacr/hit_attribution.py
spacr/hit_investigation.py
spacr/hits.py
spacr/hyperparam.py
spacr/illumination.py
spacr/image_colors.py
spacr/image_import.py
spacr/image_stitch.py
spacr/import_plan.py
spacr/infection.py
spacr/install_profile.py
spacr/intensity_rescale.py
spacr/io.py
spacr/layers.py
spacr/lineage.py
spacr/localisation.py
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spacr/logging_util.py
spacr/macro.py
spacr/mask_io.py
spacr/measure.py
spacr/measure_hooks.py
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spacr/measurement_schema.py
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spacr/metadata_resolution.py
spacr/methods_export.py
spacr/mixed_gpu.py
spacr/ml.py
spacr/model_check.py
spacr/model_compare.py
spacr/model_zoo.py
spacr/multi_database.py
spacr/multiple_testing.py
spacr/napari_bridge.py
spacr/nonparametric_fits.py
spacr/normalization.py
spacr/notebook_export.py
spacr/object.py
spacr/object_distances.py
spacr/object_roles.py
spacr/object_settings_table.py
spacr/ome_zarr.py
spacr/omero.py
spacr/openmp_guard.py
spacr/ops_accel.py
spacr/ops_cycles.py
spacr/ops_layout.py
spacr/ops_merge.py
spacr/ops_phenotype.py
spacr/ops_register.py
spacr/ops_sbs.py
spacr/ops_settings.py
spacr/ops_solve.py
spacr/ops_stitch.py
spacr/organelle_types.py
spacr/outlier_filter.py
spacr/parameter_sweep.py
spacr/permutation_qc.py
spacr/picture_settings.py
spacr/pipeline_graph.py
spacr/pipeline_v2.py
spacr/plaque.py
spacr/plate_measurements.py
spacr/plate_qc.py
spacr/plot.py
spacr/plugins.py
spacr/png_list.py
spacr/portable_paths.py
spacr/ports.py
spacr/power_model.py
spacr/power_simulate.py
spacr/predictions.py
spacr/profiler.py
spacr/projects.py
spacr/qc_quarantine.py
spacr/read_background.py
spacr/refit.py
spacr/regex_infer.py
spacr/regression_annotation.py
spacr/regression_backends.py
spacr/regression_diagnostics.py
spacr/regression_failure.py
spacr/regression_families.py
spacr/regression_layout.py
spacr/regression_panels.py
spacr/regression_qc.py
spacr/regression_search.py
spacr/regression_spec.py
spacr/regression_summary.py
spacr/remote_execution.py
spacr/report.py
spacr/resource_log.py
spacr/response_distribution.py
spacr/restart_state.py
spacr/resume.py
spacr/roi.py
spacr/row_exclusions.py
spacr/rra.py
spacr/run_compare.py
spacr/run_journal.py
spacr/run_recommendations.py
spacr/runctx.py
spacr/schema.py
spacr/scorecard.py
spacr/screen_data.py
spacr/seg_qc.py
spacr/selection.py
spacr/sequencing.py
spacr/sequencing_qc.py
spacr/setting_animations.py
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spacr/sp_stats.py
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spacr/spacrops.py
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spacr/tiff_io.py
spacr/timelapse.py
spacr/torch_artifacts.py
spacr/toxo.py
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spacr/umap_annotations.py
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spacr/uniprot.py
spacr/updater.py
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spacr/validate.py
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spacr/volcano_style.py
spacr/well_scope.py
spacr/well_spec.py
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spacr/zstack.py
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spacr/flowview/collector.py
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spacr/flowview/export.py
spacr/flowview/feeder.py
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spacr/flowview/model.py
spacr/flowview/panel.py
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spacr/qt/__main__.py
spacr/qt/_layout_policy.py
spacr/qt/annotate_engine.py
spacr/qt/app.py
spacr/qt/app_catalog.py
spacr/qt/ask_for_the_path.py
spacr/qt/bridge.py
spacr/qt/button_roles.py
spacr/qt/chaining.py
spacr/qt/command_palette.py
spacr/qt/comparison_grid.py
spacr/qt/counting_tool.py
spacr/qt/crash_recovery.py
spacr/qt/crop_thumbs.py
spacr/qt/curation_tool.py
spacr/qt/dialogs.py
spacr/qt/dnd.py
spacr/qt/dnd_handlers.py
spacr/qt/first_run.py
spacr/qt/folder_metadata.py
spacr/qt/fractal_defaults.py
spacr/qt/gc_policy.py
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spacr/qt/hf_download.py
spacr/qt/hidpi.py
spacr/qt/i18n.py
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spacr/qt/i18n_module_summaries_other.py
spacr/qt/i18n_module_summaries_west.py
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spacr/qt/job_runner.py
spacr/qt/laptop_mode.py
spacr/qt/layer_viewer.py
spacr/qt/linked_selection.py
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spacr/qt/maturity.py
spacr/qt/memory_budget.py
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spacr/qt/multi_format.py
spacr/qt/notify.py
spacr/qt/ortho_view.py
spacr/qt/path_probe.py
spacr/qt/plate_queue.py
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spacr/qt/prefs.py
spacr/qt/prerun.py
spacr/qt/preview_registry.py
spacr/qt/recipes.py
spacr/qt/regex_detect.py
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spacr/qt/resource_cleanup.py
spacr/qt/roi_tool.py
spacr/qt/safespacr.py
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spacr/qt/settings_diff.py
spacr/qt/settings_pack.py
spacr/qt/settings_search.py
spacr/qt/setup_screen.py
spacr/qt/shortcuts.py
spacr/qt/shutdown.py
spacr/qt/space.py
spacr/qt/spaceout.py
spacr/qt/startup_benchmark.py
spacr/qt/synthetic.py
spacr/qt/terms.py
spacr/qt/theme.py
spacr/qt/thread_guard.py
spacr/qt/timing.py
spacr/qt/tutorials.py
spacr/qt/verbose_logger.py
spacr/qt/walkthrough.py
spacr/qt/wand_rescue.py
spacr/qt/widget_cleanup.py
spacr/qt/ai/__init__.py
spacr/qt/ai/github_auth.py
spacr/qt/ai/issue_preview.py
spacr/qt/ai/issue_report.py
spacr/qt/ai/keys.py
spacr/qt/ai/manuscript.py
spacr/qt/ai/prompts.py
spacr/qt/ai/providers.py
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spacr/qt/i18n_catalogs/__init__.py
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spacr/qt/screens/__init__.py
spacr/qt/screens/activation.py
spacr/qt/screens/agreement.py
spacr/qt/screens/align.py
spacr/qt/screens/annotate.py
spacr/qt/screens/app_screen.py
spacr/qt/screens/batch.py
spacr/qt/screens/classifier_evaluation.py
spacr/qt/screens/classify.py
spacr/qt/screens/control_chart.py
spacr/qt/screens/convert.py
spacr/qt/screens/curate.py
spacr/qt/screens/data_manager.py
spacr/qt/screens/db_browser.py
spacr/qt/screens/distributed_jobs.py
spacr/qt/screens/dose_response.py
spacr/qt/screens/experiment_design.py
spacr/qt/screens/feature_explorer.py
spacr/qt/screens/foreign.py
spacr/qt/screens/gate_editor.py
spacr/qt/screens/graph_builder.py
spacr/qt/screens/hit_list.py
spacr/qt/screens/hyperparam.py
spacr/qt/screens/image_import.py
spacr/qt/screens/image_scatter.py
spacr/qt/screens/image_umap.py
spacr/qt/screens/investigate_hit.py
spacr/qt/screens/lineage.py
spacr/qt/screens/make_masks.py
spacr/qt/screens/map_barcodes.py
spacr/qt/screens/mask.py
spacr/qt/screens/measure.py
spacr/qt/screens/methods_export.py
spacr/qt/screens/model_compare.py
spacr/qt/screens/model_explanation.py
spacr/qt/screens/model_zoo.py
spacr/qt/screens/outliers.py
spacr/qt/screens/parameter_sweep.py
spacr/qt/screens/pca.py
spacr/qt/screens/pipeline_graph.py
spacr/qt/screens/plate_view.py
spacr/qt/screens/power.py
spacr/qt/screens/profiler.py
spacr/qt/screens/project_browser.py
spacr/qt/screens/qc_dashboard.py
spacr/qt/screens/queue.py
spacr/qt/screens/regression.py
spacr/qt/screens/report.py
spacr/qt/screens/run_compare.py
spacr/qt/screens/run_history.py
spacr/qt/screens/setting_api_targets.py
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spacr/qt/widgets/__init__.py
spacr/qt/widgets/activity_spinner.py
spacr/qt/widgets/aggregation_rules.py
spacr/qt/widgets/ai_chat_panel.py
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spacr/qt/widgets/animation_zoom.py
spacr/qt/widgets/annotation_strategy_panel.py
spacr/qt/widgets/annotation_umap_tab.py
spacr/qt/widgets/api_help_label.py
spacr/qt/widgets/availability_panel.py
spacr/qt/widgets/barcode_regex.py
spacr/qt/widgets/card.py
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spacr/qt/widgets/channel_picker.py
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spacr/qt/widgets/empty_state.py
spacr/qt/widgets/external_mask_inputs.py
spacr/qt/widgets/fast_plots.py
spacr/qt/widgets/feature_dictionary.py
spacr/qt/widgets/feature_explorer.py
spacr/qt/widgets/feature_rank.py
spacr/qt/widgets/field_fade.py
spacr/qt/widgets/figure_grid.py
spacr/qt/widgets/figure_grid_view.py
spacr/qt/widgets/figure_queue.py
spacr/qt/widgets/figure_settings.py
spacr/qt/widgets/file_list.py
spacr/qt/widgets/flash.py
spacr/qt/widgets/flow.py
spacr/qt/widgets/fold_strip.py
spacr/qt/widgets/foldable.py
spacr/qt/widgets/folding_summary.py
spacr/qt/widgets/formula.py
spacr/qt/widgets/formula_editor.py
spacr/qt/widgets/fractal_cascade.py
spacr/qt/widgets/fractal_mandelbrot.py
spacr/qt/widgets/fractal_orbit_gpu.py
spacr/qt/widgets/fractal_regions.py
spacr/qt/widgets/fractal_space.py
spacr/qt/widgets/fractal_travel.py
spacr/qt/widgets/gate_canvas.py
spacr/qt/widgets/gate_console.py
spacr/qt/widgets/gate_editor.py
spacr/qt/widgets/gate_search_panel.py
spacr/qt/widgets/gate_settings.py
spacr/qt/widgets/gate_spec.py
spacr/qt/widgets/gene_panel.py
spacr/qt/widgets/gene_tile.py
spacr/qt/widgets/glass.py
spacr/qt/widgets/graph_builder.py
spacr/qt/widgets/graph_spec.py
spacr/qt/widgets/grouped_plot.py
spacr/qt/widgets/height_grip.py
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spacr/qt/widgets/home.py
spacr/qt/widgets/hover_tooltip.py
spacr/qt/widgets/import_workbench.py
spacr/qt/widgets/info_link.py
spacr/qt/widgets/live_preview.py
spacr/qt/widgets/loading_screen.py
spacr/qt/widgets/measure_preview.py
spacr/qt/widgets/measurement_compare_dialog.py
spacr/qt/widgets/measurement_scan_panel.py
spacr/qt/widgets/metadata_mapper.py
spacr/qt/widgets/metadata_table.py
spacr/qt/widgets/model_zoo_picker.py
spacr/qt/widgets/module_hint_bar.py
spacr/qt/widgets/motility_preview.py
spacr/qt/widgets/object_grid_binding.py
spacr/qt/widgets/object_settings_grid.py
spacr/qt/widgets/outlier_model.py
spacr/qt/widgets/pca_model.py
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spacr/qt/widgets/percentile_pair.py
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tests/test_a_blup_table_explains_its_empty_volcano.py
tests/test_a_box_with_jitter_not_a_bar.py
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tests/test_a_button_picks_the_settings_for_your_data.py
tests/test_a_button_press_is_not_a_filename.py
tests/test_a_button_says_what_it_does_at_the_foot.py
tests/test_a_click_reaches_its_row_whatever_the_filter.py
tests/test_a_clicked_gene_carries_its_annotation.py
tests/test_a_closing_window_does_not_end_the_session.py
tests/test_a_column_field_gets_one_picker_not_two.py
tests/test_a_comma_is_two_controls.py
tests/test_a_control_is_a_gene_or_a_guide.py
tests/test_a_count_model_keeps_its_counts.py
tests/test_a_count_model_refuses_a_score_early.py
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tests/test_a_dead_canvas_is_not_a_dead_figure.py
tests/test_a_deleted_run_takes_its_figures.py
tests/test_a_distribution_panel_says_when_it_cannot_be_drawn.py
tests/test_a_failed_field_reports_its_traceback.py
tests/test_a_failed_regression_says_why.py
tests/test_a_failing_ci_batch_names_its_files.py
tests/test_a_fatal_signal_leaves_a_stack.py
tests/test_a_field_key_is_an_object_identity.py
tests/test_a_figure_leaves_with_its_data.py
tests/test_a_figure_section_folds_away_like_the_console.py
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tests/test_a_float_label_mask_is_still_boxed.py
tests/test_a_gene_control_finds_its_guides.py
tests/test_a_gene_in_one_well_is_not_a_hit.py
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tests/test_a_grey_crop_is_drawn_the_way_the_annotator_draws_it.py
tests/test_a_group_kind_typo_is_named_not_ignored.py
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tests/test_a_guide_and_a_probability_for_every_cell.py
tests/test_a_guide_is_one_point_on_the_volcano.py
tests/test_a_hung_ci_suite_says_where.py
tests/test_a_label_carries_its_count.py
tests/test_a_link_is_applied_once.py
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tests/test_a_merge_says_what_it_cannot_do.py
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tests/test_a_model_you_will_not_get_is_greyed.py
tests/test_a_parent_directory_is_always_there_to_make.py
tests/test_a_pathogen_checkpoint_is_validated_not_dismissed.py
tests/test_a_penalty_the_user_can_actually_set.py
tests/test_a_percentile_window_is_two_numbers.py
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tests/test_a_preference_reaches_a_house_style_panel.py
tests/test_a_probability_cannot_be_scrolled_negative.py
tests/test_a_readonly_database_can_still_be_read.py
tests/test_a_real_guide_library_can_be_mapped.py
tests/test_a_recorded_crop_is_found_where_it_actually_lives.py
tests/test_a_reference_label_set_is_never_too_small.py
tests/test_a_refit_is_a_new_run.py
tests/test_a_refit_reaches_the_runner.py
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tests/test_a_registered_export_survives_an_unreadable_upstream.py
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tests/test_a_saved_figure_is_for_paper.py
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tests/test_align_cov.py
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tests/test_all_text_size_reaches_all_text.py
tests/test_an_effect_says_what_it_is_measured_from.py
tests/test_an_empty_cell_is_not_an_answer.py
tests/test_an_empty_split_says_so.py
tests/test_an_intel_mac_is_told_why_metal_is_no_use.py
tests/test_an_object_is_measured_in_its_own_box.py
tests/test_an_object_role_cannot_break_a_typed_id.py
tests/test_an_unavailable_option_offers_to_install_itself.py
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tests/test_analysis_modules.py
tests/test_analysis_modules_t10.py
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tests/test_animations_are_not_each_other.py
tests/test_animations_do_not_flash_a_border.py
tests/test_animations_show_something.py
tests/test_anndata_export.py
tests/test_anndata_export_edge_branches.py
tests/test_anndata_export_uncovered_paths.py
tests/test_annotation_power.py
tests/test_annotation_umap_qc.py
tests/test_annotation_validation.py
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tests/test_the_summary_is_readable_at_a_glance.py
tests/test_the_summary_recommends_from_its_own_numbers.py
tests/test_the_summary_tab_folds.py
tests/test_the_surrogate_can_read_a_real_database.py
tests/test_the_sweep_button.py
tests/test_the_sweep_can_leave_things_out.py
tests/test_the_sweep_figures_have_readable_axes.py
tests/test_the_sweep_pictures.py
tests/test_the_sweep_row_carries_its_verdict.py
tests/test_the_sweep_runs_are_a_tab.py
tests/test_the_sweep_says_whether_the_cap_is_real.py
tests/test_the_table_writer_picks_a_separator_by_suffix.py
tests/test_the_tabs_follow_the_loaded_run.py
tests/test_the_thread_guard_names_the_caller.py
tests/test_the_three_contrasts_are_three_questions.py
tests/test_the_three_crop_routes_agree.py
tests/test_the_threshold_can_be_measured_not_named.py
tests/test_the_threshold_graphs_stay_with_the_run.py
tests/test_the_threshold_is_measured_per_screen.py
tests/test_the_thumbnails_look_like_the_annotator.py
tests/test_the_tiles_of_a_field_are_put_back_together.py
tests/test_the_timelapse_figures_are_house_style.py
tests/test_the_timing_import_timer_and_watchdog.py
tests/test_the_timing_report_is_the_real_process.py
tests/test_the_training_comparison_disambiguates_and_wraps.py
tests/test_the_translation_ranker_finds_a_known_offender.py
tests/test_the_typed_api_refuses_a_config_that_cannot_run.py
tests/test_the_uniprot_link_opens_the_protein.py
tests/test_the_user_chooses_what_the_model_looks_at.py
tests/test_the_v2_scorecard_never_raises_into_a_finished_run.py
tests/test_the_volcano_says_its_baseline.py
tests/test_the_volcano_setting_is_retired.py
tests/test_the_volcano_style_reports_every_problem.py
tests/test_the_volcano_y_axis_is_continuous.py
tests/test_the_well_columns_refuse_a_silent_plate_remap.py
tests/test_the_well_distributions_are_house_style.py
tests/test_the_well_is_solved_rather_than_walked.py
tests/test_the_well_key_refuses_half_a_well.py
tests/test_the_white_band_in_the_live_canvas.py
tests/test_the_working_folders_do_not_reach_main.py
tests/test_the_workspace_file_record_says_what_it_knows.py
tests/test_theme_naming.py
tests/test_three_small_readers_pass_over_what_they_cannot_use.py
tests/test_tiff_io.py
tests/test_timelapse_and_spacrops.py
tests/test_timelapse_field_key.py
tests/test_timelapse_join.py
tests/test_timelapse_model_feature_schema.py
tests/test_timelapse_prcfo_split.py
tests/test_timelapse_submodules_key_contracts.py
tests/test_timelapse_trackastra.py
tests/test_timelapse_ultrack.py
tests/test_timing.py
tests/test_tooltip_api_links_resolve.py
tests/test_tooltip_length_and_shape.py
tests/test_tooltips_are_on_the_setting_not_the_field.py
tests/test_toxo_and_cellpose.py
tests/test_toxo_row_num.py
tests/test_toxo_uncovered_paths.py
tests/test_toxo_volcano_join_contract.py
tests/test_toxoplasma_annotation_reaches_the_export.py
tests/test_train_cellpose_uses_every_image.py
tests/test_train_compare.py
tests/test_train_compare_settings_climb.py
tests/test_training.py
tests/test_training_basis.py
tests/test_training_curves.py
tests/test_training_dataset_metadata_column.py
tests/test_translation_correctness.py
tests/test_trial_metrics.py
tests/test_trial_metrics_uncovered_paths.py
tests/test_tstack.py
tests/test_tutorial_catalog_i18n.py
tests/test_tutorial_link_and_install_recipe.py
tests/test_tutorial_plate_retention.py
tests/test_tutorial_release_audit.py
tests/test_two_fits_two_bh_families.py
tests/test_two_runs_on_screen_at_once.py
tests/test_two_screens_share_a_guide_library.py
tests/test_umap_annotations.py
tests/test_umap_gpu_search.py
tests/test_umap_search.py
tests/test_uniprot_organisms.py
tests/test_updater_uncovered_paths.py
tests/test_usage_panel_gpu_failure.py
tests/test_user_facing_docstrings.py
tests/test_user_facing_tone.py
tests/test_utils.py
tests/test_utils_check_integrity.py
tests/test_utils_db_activation.py
tests/test_utils_extended.py
tests/test_utils_masks_features.py
tests/test_utils_nn_modules.py
tests/test_utils_training_advice.py
tests/test_v1_v2_parity.py
tests/test_v2_masks_are_scored_too.py
tests/test_v2_takes_declared_defaults.py
tests/test_validate.py
tests/test_verbose_logging_is_cheap.py
tests/test_volcano_control_threshold.py
tests/test_wand_and_settings.py
tests/test_warning_policy.py
tests/test_wells_are_picked_off_a_plate_map.py
tests/test_which_measurement_has_the_effect.py
tests/test_which_picture_settings_apply.py
tests/test_which_run_is_loaded.py
tests/test_wrong_numbers_77.py
tests/test_xgboost_scores_reach_the_montage.py
tests/test_yokogawa.py
tests/test_zstack.py
tests/test_zstack_end_to_end.py