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# Changelog | ||
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All notable changes to this project will be documented in this file. | ||
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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## [Unreleased] | ||
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## [0.1.7] - 2024-06-21 | ||
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### Added | ||
- Added CLI boolean handling to improve command-line interface usability. | ||
- Added new pytests for CLI to ensure correct handling of booleans. | ||
- Updated the README to reflect the new pytest additions. | ||
- Updated CI/CD pipelines to accommodate pytest changes. | ||
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### Changed | ||
- Improved input_type value check mechanism to use .lower() before checking against values 'vcf' or 'matrix'. | ||
- Updated dependency from PyPDF2 to pypdf to increase compatibility and resolve installation issues on bioconda. | ||
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@@ -8,5 +8,5 @@ statsmodels | |
scikit-learn | ||
psutil | ||
reportlab | ||
PyPDF2 | ||
pypdf | ||
alive_progress |
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import pytest | ||
import argparse | ||
from SigProfilerAssignment.controllers.cli_controller import ( | ||
parse_arguments_common, | ||
str2bool, | ||
) | ||
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def test_default_values(): | ||
args = parse_arguments_common( | ||
["dummy_sample", "dummy_output"], "Test default values" | ||
) | ||
assert args.make_plots == True | ||
assert args.collapse_to_SBS96 == True | ||
assert args.connected_sigs == True | ||
assert args.verbose == False | ||
assert args.export_probabilities == True | ||
assert args.export_probabilities_per_mutation == False | ||
assert args.exome == False | ||
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def test_argument_parsing(): | ||
args = parse_arguments_common( | ||
[ | ||
"dummy_sample", | ||
"dummy_output", | ||
"--genome_build", | ||
"GRCh38", | ||
"--cosmic_version", | ||
"3.4", | ||
"--make_plots", | ||
"False", | ||
"--collapse_to_SBS96", | ||
"False", | ||
"--connected_sigs", | ||
"False", | ||
"--verbose", | ||
"True", | ||
"--export_probabilities", | ||
"False", | ||
"--export_probabilities_per_mutation", | ||
"True", | ||
"--exome", | ||
"True", | ||
], | ||
"Test argument parsing", | ||
) | ||
assert args.samples == "dummy_sample" | ||
assert args.output == "dummy_output" | ||
assert args.genome_build == "GRCh38" | ||
assert args.cosmic_version == 3.4 | ||
assert args.make_plots == False | ||
assert args.collapse_to_SBS96 == False | ||
assert args.connected_sigs == False | ||
assert args.verbose == True | ||
assert args.export_probabilities == False | ||
assert args.export_probabilities_per_mutation == True | ||
assert args.exome == True | ||
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def test_boolean_conversion(): | ||
assert str2bool("yes") == True | ||
assert str2bool("true") == True | ||
assert str2bool("t") == True | ||
assert str2bool("y") == True | ||
assert str2bool("1") == True | ||
assert str2bool("no") == False | ||
assert str2bool("false") == False | ||
assert str2bool("f") == False | ||
assert str2bool("n") == False | ||
assert str2bool("0") == False | ||
with pytest.raises(argparse.ArgumentTypeError): | ||
str2bool("maybe") | ||
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if __name__ == "__main__": | ||
pytest.main() |