Fixed all bugs

docs/conf.py

@@ -8,28 +8,34 @@
 
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../'))
 
-project = 'spare-scores'
-copyright = '2024, Gyujoon Hwang, George Aidinis'
-author = 'Gyujoon Hwang, George Aidinis'
-release = '2024'
+sys.path.insert(0, os.path.abspath("../"))
+
+project = "spare-scores"
+copyright = "2024, Gyujoon Hwang, George Aidinis"
+author = "Gyujoon Hwang, George Aidinis"
+release = "2024"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = ['sphinx.ext.todo', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc', 'sphinx_toolbox.sidebar_links', 'sphinx_toolbox.github']
-
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+extensions = [
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autodoc",
+    "sphinx_toolbox.sidebar_links",
+    "sphinx_toolbox.github",
+]
 
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-github_username = 'CBICA'
-github_repository = 'github.com/CBICA/spare_score'
+github_username = "CBICA"
+github_repository = "github.com/CBICA/spare_score"
 
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

merge_ROI_demo_and_test.py

@@ -1,16 +1,21 @@
 import argparse
+
 import pandas as pd
+
 from spare_scores import spare_test
 
-def merge_and_test(roi_file, 
-                   demographic_file, 
-                   model_path, 
-                   key_var,
-                   output_file,
-                   spare_column_name,
-                   verbose,
-                   logs_file):
-
+
+def merge_and_test(
+    roi_file,
+    demographic_file,
+    model_path,
+    key_var,
+    output_file,
+    spare_column_name,
+    verbose,
+    logs_file,
+):
+
     # Read the input CSV files into pandas DataFrames
     df_roi = pd.read_csv(roi_file)
     df_demographic = pd.read_csv(demographic_file)
@@ -21,16 +26,19 @@ def merge_and_test(roi_file,
     merged_df = pd.merge(df_roi, df_demographic, on=key_var)
 
     # Call the spare_test function from the spare_scores package
-    result = spare_test(merged_df, 
-                        model_path,
-                        key_var,
-                        output_file,
-                        spare_column_name,
-                        verbose,
-                        logs_file)
+    result = spare_test(
+        merged_df,
+        model_path,
+        key_var,
+        output_file,
+        spare_column_name,
+        verbose,
+        logs_file,
+    )
 
     return result
 
+
 if __name__ == "__main__":
     # Example usage:
     # python merge_ROI_demo_and_test.py -i spare_scores/data/example_data_ROIs.csv \
@@ -41,27 +49,49 @@ def merge_and_test(roi_file,
     #                                   -l zzz_logs.txt \
     #                                   -sv SPARE_score
     # # Create an ArgumentParser object
-    parser = argparse.ArgumentParser(description='Spare Scores Analysis')
+    parser = argparse.ArgumentParser(description="Spare Scores Analysis")
 
     # Define the command-line arguments
-    parser.add_argument('-i', '--input', required=True, help='Input ROI CSV file')
-    parser.add_argument('-d', '--demographic', required=True, help='Input demographic CSV file')
-    parser.add_argument('-m', '--model', required=True, help='Model for spare_train')
-    parser.add_argument('-kv', '--key_var', required=False, default='', help='The key variable of the dataset.')
-    parser.add_argument('-o', '--output', required=False, default='', help='Output CSV file')
-    parser.add_argument('-l', '--logs', required=False, default='', help='Output logs file')
-    parser.add_argument('-sv', '--spare_var', required=False, default='SPARE_score', help='Column for calculated spare score')
-    parser.add_argument('-v', '--verbose', required=False, default=1, help='Type of logging messages.')
+    parser.add_argument("-i", "--input", required=True, help="Input ROI CSV file")
+    parser.add_argument(
+        "-d", "--demographic", required=True, help="Input demographic CSV file"
+    )
+    parser.add_argument("-m", "--model", required=True, help="Model for spare_train")
+    parser.add_argument(
+        "-kv",
+        "--key_var",
+        required=False,
+        default="",
+        help="The key variable of the dataset.",
+    )
+    parser.add_argument(
+        "-o", "--output", required=False, default="", help="Output CSV file"
+    )
+    parser.add_argument(
+        "-l", "--logs", required=False, default="", help="Output logs file"
+    )
+    parser.add_argument(
+        "-sv",
+        "--spare_var",
+        required=False,
+        default="SPARE_score",
+        help="Column for calculated spare score",
+    )
+    parser.add_argument(
+        "-v", "--verbose", required=False, default=1, help="Type of logging messages."
+    )
 
     # Parse the command-line arguments
     args = parser.parse_args()
 
     # Call the merge_and_test function with the provided arguments
-    merge_and_test(args.input, 
-                   args.demographic, 
-                   args.model, 
-                   args.key_var,
-                   args.output, 
-                   args.spare_var,
-                   args.verbose, 
-                   args.logs)
+    merge_and_test(
+        args.input,
+        args.demographic,
+        args.model,
+        args.key_var,
+        args.output,
+        args.spare_var,
+        args.verbose,
+        args.logs,
+    )

setup.cfg

@@ -11,7 +11,7 @@ test=pytest
 [flake8]
 statistics = true
 exclude = .git
-ignore = E203, E501, W503, B950
+ignore = E203, E501, E722, W503, B950
 select = B,C,E,F,W,T4,B9
 per-file-ignores =
     __init__.py: F401, F403

setup.py

@@ -5,27 +5,32 @@
 this_directory = Path(__file__).parent
 long_description = (this_directory / "README.md").read_text()
 
-setup(name='spare_scores',
-      version='1.2.1',
-      description='Compute characteristic brain signatures of your case population.',
-      long_description=long_description,
-      long_description_content_type='text/markdown',
-      author='Gyujoon Hwang, George Aidinis',
-      author_email='[email protected], [email protected]',
-      license='https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html',
-      packages=find_packages(),
-      package_data={'spare_scores':['mdl/*.pkl.gz','data/*.csv']},
-      include_package_data=True,
-      install_requires=['numpy', 
-                        'pandas', 
-                        'setuptools',
-                        'scikit-learn', 
-                        'torch<2.3.1', 
-                        'matplotlib', 
-                        'optuna'],
-      entry_points={
-        'console_scripts': ["spare_score = spare_scores.cli:main",
-                            "spare_scores = spare_scores.cli:main",
-                            "SPARE = spare_scores.cli:main"]
-        },
-      )
+setup(
+    name="spare_scores",
+    version="1.2.1",
+    description="Compute characteristic brain signatures of your case population.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    author="Gyujoon Hwang, George Aidinis",
+    author_email="[email protected], [email protected]",
+    license="https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html",
+    packages=find_packages(),
+    package_data={"spare_scores": ["mdl/*.pkl.gz", "data/*.csv"]},
+    include_package_data=True,
+    install_requires=[
+        "numpy",
+        "pandas",
+        "setuptools",
+        "scikit-learn",
+        "torch<2.3.1",
+        "matplotlib",
+        "optuna",
+    ],
+    entry_points={
+        "console_scripts": [
+            "spare_score = spare_scores.cli:main",
+            "spare_scores = spare_scores.cli:main",
+            "SPARE = spare_scores.cli:main",
+        ]
+    },
+)