Move ruff config into pyproject.toml

pyproject.toml

@@ -105,92 +105,65 @@ markers = [
     "iva: test requires IVA (deselect with '-m \"not iva\"')"
 ]
 
-[tool.flake8]
-ignore = ['E226', 'E302', 'E41']
-max-line-length = 120
-per-file-ignores = [
-    'micall/core/aln2counts.py: W504,E225,E126,W293',
-    'micall/core/amplicon_finder.py: E126,W504',
-    'micall/core/cascade_report.py: W293',
-    'micall/core/filter_quality.py: W504',
-    'micall/core/plot_contigs.py: W504,E501,F841,E231,E261,E262,E265,E302,E303,E305,E999,W291,W292,F401',
-    'micall/core/plot_simple.py: F401,F841,W292',
-    'micall/core/project_config.py: E722,E261',
-    'micall/core/remap.py: F401',
-    'micall/core/sam2aln.py: E128',
-    'micall/core/trim_fastqs.py: W504',
-    'micall/drivers/run_info.py: E225',
-    'micall/g2p/pssm_lib.py: E722',
-    'micall/monitor/find_groups.py: W504',
-    'micall/monitor/kive_watcher.py: W504,E126,E501,W503',
-    'micall/monitor/sample_watcher.py: W503,W504',
-    'micall/monitor/update_qai.py: W503,W504',
-    'micall/resistance/asi_algorithm.py: W504',
-    'micall/resistance/pdfreport.py: E241,W504',
-    'micall/resistance/resistance.py: W504',
-    'micall/tcr/igblast.py: E265,E231,E502,E128,W291,E305',
-    'micall/tests/microtest/make_sample.py: W504',
-    'micall/tests/microtest/reverse_and_complement.py: E126',
-    'micall/tests/microtest/translate_nuc.py: E126',
-    'micall/tests/svg_differ.py: E126,F541',
-    'micall/tests/test_align_it_gotoh.py: E261,E262,E225,E303,E501,W292',
-    'micall/tests/test_aln2counts_report.py: W504,F401',
-    'micall/tests/test_aln2counts_seed_amino.py: W293',
-    'micall/tests/test_aln2counts_seed_nucleotide.py: W293',
-    'micall/tests/test_cigar_tools.py: E704,W503',
-    'micall/tests/test_consensus_aligner.py: F841,E126,W504,E701,F401',
-    'micall/tests/test_contig_stitcher.py: W503',
-    'micall/tests/test_error_metrics_parser.py: E231',
-    'micall/tests/test_fastq_g2p.py: W293',
-    'micall/tests/test_hcv_reference_tree.py: W293',
-    'micall/tests/test_hcv_rules_import.py: E241',
-    'micall/tests/test_kive_watcher.py: W504,E126,E127,F841',
-    'micall/tests/test_plot_contigs.py: E303',
-    'micall/tests/test_primer_tracker.py: F401',
-    'micall/tests/test_projects_dump.py: W504',
-    'micall/tests/test_quality_metrics_parser.py: E231',
-    'micall/tests/test_remap.py: F541',
-    'micall/tests/test_resistance.py: W504',
-    'micall/tests/test_report_amino.py: W292',
-    'micall/tests/test_sam2aln.py: E121',
-    'micall/tests/test_sample.py: F401',
-    'micall/tests/test_sample_sheet_parser.py: E123',
-    'micall/tests/test_tile_metrics_parser.py: E231',
-    'micall/tests/test_trim_fastqs.py: E121,E123',
-    'micall/tests/test_update_qai.py: E127',
-    'micall/utils/aln2counts_simplify.py: F401,E261,E126,F821',
-    'micall/utils/big_counter.py: W293',
-    'micall/utils/cigar_tools.py: E704',
-    'micall/utils/compare_454_samples.py: W504,E305',
-    'micall/utils/compare_mapping.py: W504,F841',
-    'micall/utils/concordance_evaluation.py: E303',
-    'micall/utils/consensus_aligner.py: W504,W293,E126,E303,F401,E261,E252',
-    'micall/utils/conseq_compare.py: F811,E305,W503,F841,F401',
-    'micall/utils/contig_summary.py: W504',
-    'micall/utils/coverage_data.py: W504',
-    'micall/utils/dd.py: E711,W504,E211,E303',
-    'micall/utils/fetch_sequences.py: W504,E126,E303,E265',
-    'micall/utils/find_chimera.py: W504',
-    'micall/utils/find_reads_in_sam.py: F401,W293,F841',
-    'micall/utils/hcv_reference_tree.py: W504',
-    'micall/utils/hcv_rules_import.py: W503,W504,E126,E241',
-    'micall/utils/make_fda_refs.py: E211,E261,W293,W292',
-    'micall/utils/make_hcv_genotype_refs.py: E211,E261,E231,E722,E305,E127,E251,E127',
-    'micall/utils/primer_checks.py: E303,F541',
-    'micall/utils/primer_tracker.py: F541',
-    'micall/utils/projects_dump.py: W504',
-    'micall/utils/ref_aligner.py: F541',
-    'micall/utils/reference_distances.py: E305',
-    'micall/utils/report_amino.py: W504',
-    'micall/utils/sam_g2p_simplify.py: W293,E265,E303,E305',
-    'micall/utils/sample_fastq.py: E305',
-    'micall/utils/sample_sheet_parser.py: E275,W504',
-    'micall/utils/scan_run_folders.py: W504',
-    'micall/utils/v3loop_alignment_scores/plot.py: W293',
-    'micall/utils/docker_build.py: W504',
-    'micall/utils/micall_docker.py: W291,W293,W503,W504',
-    'micall/utils/release_test_compare.py: W293,W503,W504,F841',
-]
+[tool.ruff.lint.per-file-ignores]
+# TODO: resolve these warnings insteads of ignoring them.
+
+# Syntax error: ignore unexpected token in this file
+"micall/utils/make_hcv_genotype_refs.py" = ["E999"]
+
+# File with unused imports and local variable assignments
+"micall/core/plot_simple.py" = ["F401", "F841"]
+
+# Ignore bare except usage in project configuration
+"micall/core/project_config.py" = ["E722"]
+
+# Unused import in remap module
+"micall/core/remap.py" = ["F401"]
+
+# Do not compare types and bare excepts in pssm_lib module
+"micall/g2p/pssm_lib.py" = ["E722", "E721"]
+
+# F-string errors without placeholders in tests
+"micall/tests/svg_differ.py" = ["F541"]
+
+# Unused import in test_aln2counts_report module
+"micall/tests/test_aln2counts_report.py" = ["F401"]
+
+# Multiple issues in test_consensus_aligner: unused imports, multi-statement line, and unused local variable
+"micall/tests/test_consensus_aligner.py" = ["F401", "E701", "F841"]
+
+# Unused import in test_primer_tracker module
+"micall/tests/test_primer_tracker.py" = ["F401"]
+
+# F-string errors without placeholders in test_remap module
+"micall/tests/test_remap.py" = ["F541"]
+
+# Unused import in test_sample module
+"micall/tests/test_sample.py" = ["F401"]
+
+# Unused imports, undefined name, and type comparison in aln2counts_simplify module
+"micall/utils/aln2counts_simplify.py" = ["F401", "F821", "E721"]
+
+# Unused local variable in compare_mapping module
+"micall/utils/compare_mapping.py" = ["F841"]
+
+# Multiple issues in conseq_compare: unused sys, redefinitions, and unused local variables
+"micall/utils/conseq_compare.py" = ["F811", "F401", "F841"]
+
+# Comparisons to None should use `is` or `is not` in dd module
+"micall/utils/dd.py" = ["E711"]
+
+# Unused imports and local variable in find_reads_in_sam module
+"micall/utils/find_reads_in_sam.py" = ["F401", "F841"]
+
+# F-string errors without placeholders in primer_tracker module
+"micall/utils/primer_tracker.py" = ["F541"]
+
+# F-string errors without placeholders in ref_aligner module
+"micall/utils/ref_aligner.py" = ["F541"]
+
+# Unused local variable in release_test_compare script
+"release_test_compare.py" = ["F841"]
 
 [tool.mypy]
 files = ["micall/"]