More linting - #108

Merged

ahanden merged 48 commits into

BioinfoUNIBA:mainfrom

ahanden:more_linting

Jul 13, 2026

Commits on Jul 6, 2026

Changed all single quotes to double.
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dfbd5e5
Fixed FA102
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610c130
Fixed D212
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6c3a4c3
fixed ANN204
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3be0c93
fixed TCH001
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7265bf0
fixed COM812
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099281d
fixed PYI036
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6b3df4a
fixed FA102
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1821cc7
fixed PGH003
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257d8f9
fixed D205
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d673a6f
fixed UP004
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f811cbf
Address EM lints
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48b4817
linted for PTH
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eab996c
linted for ISC
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4e4fc1a
lintedfor PERF
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473e993
linted for TCH
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278e3e9
Removed extra paranthesis from raise statements
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bb06c7d
Removing unnused imports
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9cb4c56
linted for ANN
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0d5a5df
more linting
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90de421
more linting
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8ee2012
more linting
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6d8fce6
updated ruff rules
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9868340

Commits on Jul 8, 2026

Updated documentation
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7e54a98

Commits on Jul 10, 2026

Fixed comp_map. Updated test imports and error handling.
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e9953db
Minor linting. Updated ruff.toml for INP001.
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ce58ac2
Moved ruff config to pyproject.toml. Changed isort format.
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7cda124
linted Q000
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2a1f620
linted PTH in test
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c773148
mypy typing
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50f2b97
mypy test. fixed error catch in analyze parse_args.
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a5081df
More test linting. Added new rules to pyproject.toml.
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fd56bb8
Updated pyproject for numpy convention. Some reditools linting
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f466110

Commits on Jul 13, 2026

Added documentation to most test code. Some more misc linting.
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ac78a91
Finished test documentation.
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5aa7e0d
Fixed alignment_manager test case.
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168a77b
Tweaked temp_file_manager methods. isort.
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d662a01
WPS linting on test
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37774aa
mypy test. Updated ruff rules in pyproject.toml
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8e5c3df
Fixed save file path for region file list.
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1292d04
Simplified file paths in json_args
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cc9d842
Made new bases constant. Fixed major thread count issue.
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384152f
Mad use of Genome class in test/fasta_file. Improved error message for missing contig. Added try/catch for ip address for mac compatability.
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20b0fcd
Expanded mypy workflow to include test code.
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1044f55
Merge branch 'main' into more_linting
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bc841e9
Made unittest error handling more specific for fasta files.
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cb2bcfd
Removed extra line from logger.
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6d415a6
Specified logger socket error. isort.
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20ea6cc