Lint issues

[dnil]

Lint has some issues with the code; very understandable given the time since last lint I'm sure. Let's fix at a somewhat low prio, but very nice to clear to see new things. We could change the lint workflow to report only for changed files, but anyhow nice to have a clean base.

Error: genmod/annotate_models/__init__.py:3:26: F401 `.fix_variant.make_print_version` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/__init__.py:4:29: F401 `.genetic_models.check_genetic_models` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/__init__.py:5:31: F401 `.make_haploblocks.get_haploblocks` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/__init__.py:6:26: F401 `.model_score.get_model_score` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/__init__.py:7:32: F401 `.variant_annotator.VariantAnnotator` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/fix_variant.py:19:5: F841 Local variable `feature_list` is assigned to but never used
Error: genmod/annotate_models/genetic_models.py:65:8: F401 `os` imported but unused
Error: genmod/annotate_models/genetic_models.py:66:8: F401 `sys` imported but unused
Error: genmod/annotate_models/genetic_models.py:67:22: F401 `datetime.datetime` imported but unused
Error: genmod/annotate_models/genetic_models.py:68:30: F401 `pprint.pprint` imported but unused
Error: genmod/annotate_models/genetic_models.py:110:9: F841 Local variable `compound_pairs` is assigned to but never used
Error: genmod/annotate_models/genetic_models.py:339:9: F841 Local variable `mother_phenotype` is assigned to but never used
Error: genmod/annotate_models/genetic_models.py:344:9: F841 Local variable `father_phenotype` is assigned to but never used
Error: genmod/annotate_models/models/__init__.py:4:29: F401 `.compound_model.check_compounds` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/models/__init__.py:5:29: F401 `.dominant_model.check_dominant` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/models/__init__.py:6:30: F401 `.recessive_model.check_recessive` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/models/__init__.py:7:23: F401 `.x_models.check_X_dominant` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/models/__init__.py:7:41: F401 `.x_models.check_X_recessive` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_models/models/compound_model.py:16:8: F401 `os` imported but unused
Error: genmod/annotate_models/models/compound_model.py:17:8: F401 `sys` imported but unused
Error: genmod/annotate_models/models/recessive_model.py:14:8: F401 `os` imported but unused
Error: genmod/annotate_models/models/recessive_model.py:15:8: F401 `sys` imported but unused
Error: genmod/annotate_models/variant_annotator.py:21:54: F401 `.get_model_score` imported but unused
Error: genmod/annotate_regions/parse_annotations.py:24:1: E722 Do not use bare `except`
Error: genmod/annotate_regions/parse_annotations.py:25:12: F401 `pickle` imported but unused
Error: genmod/annotate_regions/parse_annotations.py:92:5: F841 Local variable `genes` is assigned to but never used
Error: genmod/annotate_variants/__init__.py:3:31: F401 `.read_tabix_files.get_cadd_scores` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_variants/__init__.py:3:48: F401 `.read_tabix_files.get_cosmic` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_variants/__init__.py:3:60: F401 `.read_tabix_files.get_frequencies` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_variants/__init__.py:3:77: F401 `.read_tabix_files.get_spidex_score` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/annotate_variants/annotate.py:20:5: F841 Local variable `ref` is assigned to but never used
Error: genmod/annotate_variants/read_tabix_files.py:48:5: E722 Do not use bare `except`
Error: genmod/annotate_variants/read_tabix_files.py:67:5: F841 Local variable `freq` is assigned to but never used
Error: genmod/commands/__init__.py:3:40: F401 `.annotate_models.models` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/commands/__init__.py:4:43: F401 `.annotate_variant.annotate` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/commands/__init__.py:5:40: F401 `.filter_variants.filter` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/commands/__init__.py:6:34: F401 `.genmod_sort.sort` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/commands/__init__.py:7:42: F401 `.score_compounds.compound` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/commands/__init__.py:8:38: F401 `.score_variants.score` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/commands/analyze.py:21:1: E722 Do not use bare `except`
Error: genmod/commands/analyze.py:22:12: F401 `pickle` imported but unused
Error: genmod/commands/analyze.py:106:32: F821 Undefined name `compound_dict`
Error: genmod/commands/analyze.py:107:16: F821 Undefined name `compounds`
Error: genmod/commands/analyze.py:231:12: F821 Undefined name `compounds`
Error: genmod/commands/analyze.py:275:5: F841 Local variable `de_novo_set` is assigned to but never used
Error: genmod/commands/analyze.py:471:5: F841 Local variable `inheritance_keyword` is assigned to but never used
Error: genmod/commands/annotate_models.py:195:16: E713 Test for membership should be `not in`
Error: genmod/commands/annotate_models.py:202:16: E713 Test for membership should be `not in`
Error: genmod/commands/annotate_models.py:340:9: F841 Local variable `start_time_variant_parsing` is assigned to but never used
Error: genmod/commands/annotate_models.py:344:9: F841 Local variable `chromosome_list` is assigned to but never used
Error: genmod/commands/annotate_variant.py:140:5: F841 Local variable `start_time_analysis` is assigned to but never used
Error: genmod/commands/filter_variants.py:17:8: F401 `os` imported but unused
Error: genmod/commands/filter_variants.py:19:20: F401 `codecs.open` imported but unused
Error: genmod/commands/filter_variants.py:28:5: F401 `genmod.vcf_tools.get_info_dict` imported but unused
Error: genmod/commands/filter_variants.py:29:5: F401 `genmod.vcf_tools.get_variant_dict` imported but unused
Error: genmod/commands/filter_variants.py:72:5: F841 Local variable `start_time_analysis` is assigned to but never used
Error: genmod/commands/filter_variants.py:91:5: F841 Local variable `header_line` is assigned to but never used
Error: genmod/commands/filter_variants.py:93:12: E713 Test for membership should be `not in`
Error: genmod/commands/genmod_sort.py:27:5: F401 `genmod.vcf_tools.get_info_dict` imported but unused
Error: genmod/commands/score_compounds.py:86:5: F841 Local variable `header_line` is assigned to but never used
Error: genmod/commands/score_compounds.py:151:9: F841 Local variable `start_time_variant_parsing` is assigned to but never used
Error: genmod/commands/score_compounds.py:154:9: F841 Local variable `chromosome_list` is assigned to but never used
Error: genmod/commands/score_variants.py:16:8: F401 `os` imported but unused
Error: genmod/commands/score_variants.py:18:20: F401 `codecs.open` imported but unused
Error: genmod/commands/summarize_variants.py:172:5: F841 Local variable `nr_of_variants` is assigned to but never used
Error: genmod/commands/summarize_variants.py:174:5: F841 Local variable `header` is assigned to but never used
Error: genmod/errors/__init__.py:2:35: F401 `genmod.errors.warning.warning` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/errors/warning.py:14:8: F401 `os` imported but unused
Error: genmod/log.py:2:8: F401 `os` imported but unused
Error: genmod/log.py:3:8: F401 `sys` imported but unused
Error: genmod/score_variants/__init__.py:3:28: F401 `.check_plugins.check_plugins` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/score_variants/__init__.py:4:30: F401 `.compound_scorer.CompoundScorer` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/score_variants/__init__.py:5:28: F401 `.config_parser.ConfigParser` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/score_variants/__init__.py:6:45: F401 `.rank_score_variant_definitions.RANK_SCORE_TYPE_NAMES` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/score_variants/__init__.py:6:68: F401 `.rank_score_variant_definitions.RANK_SCORE_TYPES` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/score_variants/__init__.py:7:29: F401 `.score_function.ScoreFunction` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/score_variants/__init__.py:8:28: F401 `.score_variant.as_normalized_max_min` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/score_variants/__init__.py:8:51: F401 `.score_variant.get_category_score` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/score_variants/compound_scorer.py:17:8: F401 `os` imported but unused
Error: genmod/score_variants/compound_scorer.py:18:8: F401 `sys` imported but unused
Error: genmod/score_variants/compound_scorer.py:205:25: F841 Local variable `family_id` is assigned to but never used
Error: genmod/score_variants/config_parser.py:230:9: F841 Local variable `string_rules` is assigned to but never used
Error: genmod/score_variants/config_parser.py:290:20: E713 Test for membership should be `not in`
Error: genmod/score_variants/config_parser.py:305:33: F841 Local variable `csq_key` is assigned to but never used
Error: genmod/score_variants/config_parser.py:327:20: E713 Test for membership should be `not in`
Error: genmod/score_variants/config_parser.py:355:20: E713 Test for membership should be `not in`
Error: genmod/score_variants/score_function.py:161:16: F821 Undefined name `error`
Error: genmod/score_variants/score_function.py:161:25: F841 Local variable `e` is assigned to but never used
Error: genmod/utils/__init__.py:61:1: E402 Module level import not at top of file
Error: genmod/utils/__init__.py:61:32: F401 `.check_individuals.check_individuals` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/__init__.py:62:1: E402 Module level import not at top of file
Error: genmod/utils/__init__.py:62:26: F401 `.get_batches.get_batches` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/__init__.py:63:1: E402 Module level import not at top of file
Error: genmod/utils/__init__.py:63:27: F401 `.get_features.check_vep_annotation` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/__init__.py:63:49: F401 `.get_features.get_annotation` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/__init__.py:64:1: E402 Module level import not at top of file
Error: genmod/utils/__init__.py:64:27: F401 `.get_priority.get_chromosome_priority` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/__init__.py:64:52: F401 `.get_priority.get_rank_score` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/__init__.py:65:1: E402 Module level import not at top of file
Error: genmod/utils/__init__.py:65:24: F401 `.is_number.is_number` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/__init__.py:66:1: E402 Module level import not at top of file
Error: genmod/utils/__init__.py:66:29: F401 `.pair_generator.generate_pairs` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/__init__.py:67:1: E402 Module level import not at top of file
Error: genmod/utils/__init__.py:67:30: F401 `.variant_printer.VariantPrinter` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/utils/get_batches.py:163:9: F523 `.format` call has unused arguments at position(s): 1
Error: genmod/utils/get_features.py:5:26: F401 `genmod.utils.EXONIC_SO_TERMS` imported but unused
Error: genmod/utils/get_priority.py:1:8: F401 `logging` imported but unused
Error: genmod/utils/variant_printer.py:58:9: F841 Local variable `number_of_finished` is assigned to but never used
Error: genmod/vcf_tools/__init__.py:4:5: F401 `.add_metadata.add_annotation_header` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:5:5: F401 `.add_metadata.add_compounds_header` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:6:5: F401 `.add_metadata.add_exonic_header` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:7:5: F401 `.add_metadata.add_genetic_models_header` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:8:5: F401 `.add_metadata.add_metadata` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:9:5: F401 `.add_metadata.add_model_score_header` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:10:5: F401 `.add_metadata.add_version_header` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:12:38: F401 `.add_variant_information.add_vcf_info` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:12:52: F401 `.add_variant_information.replace_vcf_info` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:13:32: F401 `.check_info_header.check_info` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:14:23: F401 `.genotype.Genotype` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:15:28: F401 `.get_genotypes.get_genotypes` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:16:28: F401 `.header_parser.HeaderParser` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:17:28: F401 `.parse_variant.get_info_dict` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:17:43: F401 `.parse_variant.get_variant_dict` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:17:61: F401 `.parse_variant.get_variant_id` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:17:77: F401 `.parse_variant.get_vep_dict` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:18:28: F401 `.print_headers.print_headers` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:19:29: F401 `.print_variants.print_variant` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:19:44: F401 `.print_variants.print_variant_dict` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:19:64: F401 `.print_variants.print_variant_for_sorting` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/__init__.py:20:28: F401 `.sort_variants.sort_variants` imported but unused; consider removing, adding to `__all__`, or using a redundant alias
Error: genmod/vcf_tools/genotype.py:42:8: F401 `os` imported but unused
Error: genmod/vcf_tools/genotype.py:43:8: F401 `sys` imported but unused
Error: genmod/vcf_tools/header_parser.py:328:9: F811 Redefinition of unused `add_contig` from line 314
Error: genmod/vcf_tools/parse_variant.py:4:8: F401 `string` imported but unused
Error: genmod/vcf_tools/print_variants.py:20:8: F401 `codecs` imported but unused
Error: genmod/vcf_tools/print_variants.py:21:8: F401 `locale` imported but unused
Error: genmod/vcf_tools/print_variants.py:22:8: F401 `sys` imported but unused
Error: genmod/vcf_tools/sort_variants.py:15:8: F401 `os` imported but unused
Error: genmod/vcf_tools/sort_variants.py:16:8: F401 `sys` imported but unused
Error: genmod/vcf_tools/sort_variants.py:20:8: F401 `click` imported but unused
Error: tests/conftest.py:1:8: F401 `os` imported but unused
Error: tests/conftest.py:2:22: F401 `tempfile.NamedTemporaryFile` imported but unused
Error: tests/functionality/test_annotate_models.py:13:1: E402 Module level import not at top of file
Error: tests/functionality/test_annotate_models.py:14:1: E402 Module level import not at top of file
Error: tests/functionality/test_annotate_models.py:15:1: E402 Module level import not at top of file
Error: tests/functionality/test_annotate_variant.py:10:1: E402 Module level import not at top of file
Error: tests/functionality/test_annotate_variant.py:11:1: E402 Module level import not at top of file
Error: tests/functionality/test_filter_variants.py:6:1: E402 Module level import not at top of file
Error: tests/functionality/test_filter_variants.py:7:1: E402 Module level import not at top of file
Error: tests/functionality/test_score_variants.py:11:1: E402 Module level import not at top of file
Error: tests/functionality/test_score_variants.py:12:1: E402 Module level import not at top of file
Error: tests/functionality/test_score_variants_ranks_score_is_float.py:21:13: F841 Local variable `family_id` is assigned to but never used
Error: tests/functionality/test_sort_variants.py:11:1: E402 Module level import not at top of file
Error: tests/functionality/test_sort_variants.py:12:1: E402 Module level import not at top of file
Error: tests/genetic_models/test_dominant_model.py:32:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_dominant_model.py:48:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_dominant_model.py:64:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_dominant_model.py:82:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_dominant_model.py:101:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_dominant_model.py:119:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_dominant_model.py:138:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_dominant.py:32:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_dominant.py:50:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_dominant.py:66:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_dominant.py:82:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_dominant.py:98:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_dominant.py:114:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_dominant.py:132:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_dominant.py:151:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_dominant.py:169:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_dominant.py:187:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_dominant.py:203:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_dominant.py:219:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_dominant.py:235:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_dominant.py:251:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_recessive.py:32:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_recessive.py:50:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_recessive.py:66:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_recessive.py:82:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_recessive.py:98:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_recessive.py:114:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_recessive.py:132:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/genetic_models/test_x_recessive.py:151:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_recessive.py:169:12: E712 Avoid equality comparisons to `False`; use `if not ...:` for false checks
Error: tests/genetic_models/test_x_recessive.py:187:12: E712 Avoid equality comparisons to `True`; use `if ...:` for truth checks
Error: tests/score_variants/test_category_score.py:214:5: F811 Redefinition of unused `test_single_category_two_plugin` from line 188
Error: tests/utils/test_get_annotation.py:1:8: F401 `pytest` imported but unused
Error: tests/utils/test_is_number.py:1:8: F401 `pytest` imported but unused
Error: tests/utils/test_is_number.py:8:12: E712 Avoid equality comparisons to `True`; use `if is_number(obj):` for truth checks
Error: tests/utils/test_is_number.py:14:12: E712 Avoid equality comparisons to `True`; use `if is_number(obj):` for truth checks
Error: tests/utils/test_is_number.py:20:12: E712 Avoid equality comparisons to `False`; use `if not is_number(obj):` for false checks
Error: tests/utils/test_is_number.py:26:12: E712 Avoid equality comparisons to `True`; use `if is_number(obj):` for truth checks
Error: tests/utils/test_is_number.py:32:12: E712 Avoid equality comparisons to `True`; use `if is_number(obj):` for truth checks
Error: tests/utils/test_variant_printer.py:56:5: F841 Local variable `batch` is assigned to but never used
Error: tests/variant_annotation/test_get_tabix_records.py:31:17: E711 Comparison to `None` should be `cond is None`