fix linting

README.md

@@ -6,9 +6,8 @@
 | :-- | :--  |
 | (1/5) code repository              | [![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)](https://github.com/RECETOX/rcx-tk) |
 | (2/5) license                      | [![github license badge](https://img.shields.io/github/license/RECETOX/rcx-tk)](https://github.com/RECETOX/rcx-tk) |
-| (3/5) community registry           | [![RSD](https://img.shields.io/badge/rsd-rcx_tk-00a3e3.svg)](https://www.research-software.nl/software/rcx_tk) [![workflow pypi badge](https://img.shields.io/pypi/v/rcx_tk.svg?colorB=blue)](https://pypi.python.org/project/rcx_tk/) |
-| (4/5) citation                     | [![DOI](https://zenodo.org/badge/DOI/<replace-with-created-DOI>.svg)](https://doi.org/<replace-with-created-DOI>) |
-| (5/5) checklist                    | [![workflow cii badge](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>/badge)](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>) |
+| (3/4) citation                     | [![DOI](https://zenodo.org/badge/DOI/<replace-with-created-DOI>.svg)](https://doi.org/<replace-with-created-DOI>) |
+| (4/4) checklist                    | [![workflow cii badge](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>/badge)](https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>) |
 | howfairis                          | [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu) |
 | **Other best practices**           | &nbsp; |
 | Static analysis                    | [![workflow scq badge](https://sonarcloud.io/api/project_badges/measure?project=RECETOX_rcx-tk&metric=alert_status)](https://sonarcloud.io/dashboard?id=RECETOX_rcx-tk) |

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/__main__.py

@@ -1,16 +1,19 @@
 import click
-
-from rcx_tk.process_metadata_file import process_alkane_ri_file, process_metadata_file
+from rcx_tk.process_metadata_file import process_alkane_ri_file
+from rcx_tk.process_metadata_file import process_metadata_file
 
 
 @click.command()
-@click.option('--method', type=click.Choice(['metadata', 'alkanes']), required = True, help = 'A file type to be processed, either metadata or alkanes file.')
+@click.option('--method', type=click.Choice(['metadata', 'alkanes']),
+              required = True,
+              help = 'A file type to be processed, either metadata or alkanes file.')
 @click.argument('file_path')
 @click.argument('out_path')
 def main(method, file_path, out_path):
     """Process metadata or alkane file.
 
     Args:
+        method (string): Whether a metadata or alkane file should be processed.
         file_path (path): A path to the input data.
         out_path (path): A path where the processed data will be exported to.
     """
@@ -23,4 +26,4 @@ def main(method, file_path, out_path):
 
 
 if __name__ == "__main__":
-    main()
+    main()

src/rcx_tk/process_metadata_file.py

@@ -1,8 +1,9 @@
 import os
 import pandas as pd
 
+
 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.
@@ -13,18 +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.
@@ -57,23 +57,20 @@ def process_metadata_file(file_path: str, out_path: str) -> None:
 
     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)
-