ruff linting

docs/conf.py

@@ -17,9 +17,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u"rcx_tk"
-copyright = u"2024, RECETOX, Masaryk University"
-author = u"Zargham Ahmad"
+project = "rcx_tk"
+copyright = "2024, RECETOX, Masaryk University"
+author = "Zargham Ahmad"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -61,7 +61,7 @@
 
 # -- Use autoapi.extension to run sphinx-apidoc -------
 
-autoapi_dirs = ['../src/rcx_tk']
+autoapi_dirs = ["../src/rcx_tk"]
 
 # -- Options for HTML output ----------------------------------------------
 
@@ -78,11 +78,12 @@
 
 # -- Options for Intersphinx
 
-intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
-                       # Commonly used libraries, uncomment when used in package
-                       # 'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-                       # 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
-                       # 'scikit-learn': ('https://scikit-learn.org/stable/', None),
-                       # 'matplotlib': ('https://matplotlib.org/stable/', None),
-                       # 'pandas': ('http://pandas.pydata.org/docs/', None),
-                       }
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    # Commonly used libraries, uncomment when used in package
+    # 'numpy': ('http://docs.scipy.org/doc/numpy/', None),
+    # 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
+    # 'scikit-learn': ('https://scikit-learn.org/stable/', None),
+    # 'matplotlib': ('https://matplotlib.org/stable/', None),
+    # 'pandas': ('http://pandas.pydata.org/docs/', None),
+}

src/rcx_tk/__init__.py

@@ -1,4 +1,5 @@
 """Documentation about rcx_tk."""
+
 import logging
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

src/rcx_tk/process_metadata_file.py

@@ -3,7 +3,7 @@
 
 
 def read_file(file_path: str) -> pd.DataFrame:
-    """Imports the metadata file to pandas dataframe. 
+    """Imports the metadata file to pandas dataframe.
 
     Args:
         file_path (str): The path to the input data.
@@ -14,17 +14,17 @@ def read_file(file_path: str) -> pd.DataFrame:
     Returns:
         pd.DataFrame: Dataframe containing the metadata.
     """
-
     file_extension = os.path.splitext(file_path)[1].lower()
-    if file_extension == '.csv':
-        return pd.read_csv(file_path, encoding='UTF-8')
-    elif file_extension in ['.xls', '.xlsx']:
+    if file_extension == ".csv":
+        return pd.read_csv(file_path, encoding="UTF-8")
+    elif file_extension in [".xls", ".xlsx"]:
         return pd.read_excel(file_path)
-    elif file_extension in ['.tsv', '.txt']: 
-        return pd.read_csv(file_path, sep='\t')
+    elif file_extension in [".tsv", ".txt"]:
+        return pd.read_csv(file_path, sep="\t")
     else:
         raise ValueError("Unsupported file format. Please provide a CSV, Excel, or TSV file.")
 
+
 def save_dataframe_as_tsv(df: pd.DataFrame, file_path: str) -> None:
     """Saves the dataframe as a TSV file.
 
@@ -37,8 +37,8 @@ def save_dataframe_as_tsv(df: pd.DataFrame, file_path: str) -> None:
     """
     if os.path.splitext(file_path)[1] != ".tsv":
         raise ValueError("Unsupported file format. Please point to a TSV file.")
-    df.to_csv(file_path, sep='\t', index=False)
-    
+    df.to_csv(file_path, sep="\t", index=False)
+
 
 def process_metadata_file(file_path: str, out_path: str) -> None:
     """Processes a metadata file, keeping and renaming specific columns.
@@ -48,32 +48,29 @@ def process_metadata_file(file_path: str, out_path: str) -> None:
         out_path (str): A path where processed metadata dataframe is exported.
     """
     columns_to_keep = {
-        'File name': 'sampleName',
-        'Type': 'sampleType',
-        'Class ID': 'class',
-        'Batch': 'batch',
-        'Analytical order': 'injectionOrder'
+        "File name": "sampleName",
+        "Type": "sampleType",
+        "Class ID": "class",
+        "Batch": "batch",
+        "Analytical order": "injectionOrder",
     }
 
     df = read_file(file_path)
     df = df[list(columns_to_keep.keys())].rename(columns=columns_to_keep)
-    df['sampleName'] = df['sampleName'].str.replace(' ', '_')
+    df["sampleName"] = df["sampleName"].str.replace(" ", "_")
     save_dataframe_as_tsv(df, out_path)
 
+
 def process_alkane_ri_file(file_path: str, out_path: str) -> None:
     """Processes an alkane file, keeping and renaming specific columns.
 
     Args:
         file_path (str): A path to the alkane file.
         out_path (str): A path where processed alkane file is exported.
     """
-    columns_to_keep = {
-        'Carbon number': 'carbon_number',
-        'RT (min)': 'rt'
-    }
+    columns_to_keep = {"Carbon number": "carbon_number", "RT (min)": "rt"}
 
     df = read_file(file_path)
     df.columns = df.columns.str.strip()
     df = df.rename(columns=columns_to_keep)
     save_dataframe_as_tsv(df, out_path)
-