From a8bac1e526c7e4bce593393e93db18793addc4b8 Mon Sep 17 00:00:00 2001 From: jvfe Date: Sat, 30 Mar 2024 20:32:41 -0300 Subject: [PATCH] style: Add black to test/file_finder --- microview/file_finder.py | 4 +++- tests/test_file_finder.py | 2 -- tests/test_parse_taxonomy.py | 4 ---- 3 files changed, 3 insertions(+), 7 deletions(-) diff --git a/microview/file_finder.py b/microview/file_finder.py index 24d3193..1810f72 100644 --- a/microview/file_finder.py +++ b/microview/file_finder.py @@ -107,7 +107,9 @@ def detect_report_type(report_paths: List[Path], console) -> List[Sample]: # TODO: Improve Kraken validation kraken_validated = [ - get_validation_dict(report, format="tsv", checks=[checks.table_dimensions(num_fields=6)]) + get_validation_dict( + report, format="tsv", checks=[checks.table_dimensions(num_fields=6)] + ) for report in report_paths ] kraken_reports = [ diff --git a/tests/test_file_finder.py b/tests/test_file_finder.py index 8d5c4c0..e17dc18 100644 --- a/tests/test_file_finder.py +++ b/tests/test_file_finder.py @@ -28,14 +28,12 @@ def test_detect_centrifuge(get_centrifuge_data): def test_validate_source_table(get_contrast_data): - validated = get_validation_dict(get_contrast_data, schema=contrast_table_schema) assert validated["errors"] == 0 def test_invalidate_source_table(get_failing_contrast_data): - validated = get_validation_dict( get_failing_contrast_data, schema=contrast_table_schema ) diff --git a/tests/test_parse_taxonomy.py b/tests/test_parse_taxonomy.py index b27ff09..50e082c 100644 --- a/tests/test_parse_taxonomy.py +++ b/tests/test_parse_taxonomy.py @@ -7,7 +7,6 @@ def test_get_taxon_counts(parsed_stats): - results = get_taxon_counts(parsed_stats) assert results["sample1"]["tax1"] == 5 @@ -15,7 +14,6 @@ def test_get_taxon_counts(parsed_stats): def test_build_taxonomy_stats(parsed_stats): - n_reads = get_read_assignment(parsed_stats) assert n_reads["sample2"]["assigned"] == 93.75 @@ -23,14 +21,12 @@ def test_build_taxonomy_stats(parsed_stats): def test_get_common_taxas(all_sample_counts): - most_common = get_common_taxas(all_sample_counts) assert most_common["sample2"]["tax2"] == 66.67 def test_calculate_abund_diver(all_sample_counts): - abund_div_df = calculate_abund_diver(all_sample_counts) assert round(abund_div_df[0]["Shannon Diversity"][1], 2) == 0.92