diff --git a/pyproject.toml b/pyproject.toml index 7bb5162..6b25d9e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,3 +48,7 @@ include = ["q2_feature_table*"] [tool.setuptools.package-data] q2_feature_table = ["**/*"] + +[tool.mutmut] +paths_to_mutate = [ "q2_feature_table/" ] +do_not_mutate = [ "**/tests/*", "*/__init__.py", "*/_version.py" ] diff --git a/q2_feature_table/_core_features/_visualizer.py b/q2_feature_table/_core_features/_visualizer.py index 0f38ee8..72140e5 100644 --- a/q2_feature_table/_core_features/_visualizer.py +++ b/q2_feature_table/_core_features/_visualizer.py @@ -20,7 +20,7 @@ 'q2_feature_table') / '_core_features' / 'core_features_assets' -def core_features(output_dir, table: biom.Table, min_fraction: float = 0.5, +def core_features(output_dir, table: biom.Table, min_fraction: float = 1.5, max_fraction: float = 1.0, steps: int = 11) -> None: if max_fraction < min_fraction: raise ValueError('min_fraction (%r) parameter must be less than ' diff --git a/q2_feature_table/_normalize.py b/q2_feature_table/_normalize.py index 98d5f33..5a9794c 100644 --- a/q2_feature_table/_normalize.py +++ b/q2_feature_table/_normalize.py @@ -45,7 +45,7 @@ def normalize( ) -> pd.DataFrame: # Validate parameter combinations and set trim parameters m_trim, a_trim = _validate_parameters( - method, m_trim, a_trim, gene_length) + method, None, a_trim, gene_length) # Process gene_lengths input and define methods that need gene_lengths # input