tests/scanpy/test_scripts.py

• synthetic · function · L39-L45 — def synthetic(n_obs: int = 20, n_vars: int = 10)
• SharedIoTestCase · class · L48-L52 — class SharedIoTestCase(unittest.TestCase)
• setUp · method · L49-L52 — def setUp(self) -> None
• RoundTripTests · class · L55-L107 — class RoundTripTests(SharedIoTestCase)
• test_an_h5ad_round_trips_through_save_and_load · method · L56-L65 — def test_an_h5ad_round_trips_through_save_and_load(self) -> None
• test_saving_creates_the_parent_directory · method · L67-L71 — def test_saving_creates_the_parent_directory(self) -> None: # Pipelines write to results/step3/out.h5ad before that tree exists.
• test_a_csv_is_dispatched_to_the_csv_reader · method · L73-L77 — def test_a_csv_is_dispatched_to_the_csv_reader(self) -> None
• test_a_missing_input_exits_with_a_message · method · L79-L89 — def test_a_missing_input_exits_with_a_message(self) -> None: # die prints to stderr and exits with a code, so check both.
• test_an_unrecognised_extension_exits_rather_than_guessing · method · L91-L101 — def test_an_unrecognised_extension_exits_rather_than_guessing(self) -> None
• test_the_extension_check_is_case_insensitive · method · L103-L107 — def test_the_extension_check_is_case_insensitive(self) -> None
• SummaryTests · class · L110-L145 — class SummaryTests(unittest.TestCase)
• test_the_summary_leads_with_the_matrix_shape · method · L111-L113 — def test_the_summary_leads_with_the_matrix_shape(self) -> None
• test_annotations_and_embeddings_are_listed · method · L115-L124 — def test_annotations_and_embeddings_are_listed(self) -> None
• test_a_bare_matrix_summarises_to_one_line · method · L126-L129 — def test_a_bare_matrix_summarises_to_one_line(self) -> None: # anndata >= 0.13 reports an unnamed None key on .layers standing # for X, which must not be rendered as a layer (and must not raise).
• test_the_unnamed_x_layer_is_never_listed · method · L131-L134 — def test_the_unnamed_x_layer_is_never_listed(self) -> None
• test_the_obs_listing_is_capped · method · L136-L145 — def test_the_obs_listing_is_capped(self) -> None: # A dataset with hundreds of obs columns must not print all of them.
• ArgumentTests · class · L148-L173 — class ArgumentTests(unittest.TestCase)
• test_the_shared_io_arguments_are_attached · method · L149-L156 — def test_the_shared_io_arguments_are_attached(self) -> None
• test_a_default_output_is_advertised_in_the_help · method · L158-L165 — def test_a_default_output_is_advertised_in_the_help(self) -> None
• test_the_output_flag_overrides_the_default · method · L167-L173 — def test_the_output_flag_overrides_the_default(self) -> None
• ConfigurationTests · class · L176-L188 — class ConfigurationTests(unittest.TestCase)
• test_configuring_scanpy_creates_the_figure_directory · method · L177-L181 — def test_configuring_scanpy_creates_the_figure_directory(self) -> None
• test_the_dpi_and_verbosity_reach_scanpy · method · L183-L188 — def test_the_dpi_and_verbosity_reach_scanpy(self) -> None
• PipelineCliTests · class · L191-L217 — class PipelineCliTests(unittest.TestCase)
• setUp · method · L194-L197 — def setUp(self) -> None
• test_each_cli_reports_a_missing_input_cleanly · method · L199-L217 — def test_each_cli_reports_a_missing_input_cleanly(self) -> None