add doc strings

fake_vcf/__init__.py

@@ -4,6 +4,12 @@
 
 
 def get_version() -> str:
+    """
+    Retrieve the version of the package.
+
+    Returns:
+        str: The version of the package, or 'unknown' if the version cannot be found.
+    """
     try:
         return importlib_metadata.version(__name__)
     except importlib_metadata.PackageNotFoundError:  # pragma: no cover

fake_vcf/__main__.py

@@ -15,7 +15,12 @@
 
 
 def version_callback(print_version: bool) -> None:
-    """Print the version of the package."""
+    """
+    Callback function to print the version of the package.
+
+    Args:
+        print_version (bool): Flag to print the version.
+    """
     if print_version:
         console.print(f"[yellow]fake-vcf[/] version: [bold blue]{version}[/]")
         raise typer.Exit()
@@ -56,6 +61,20 @@ def main(
         help="Prints the version of the fake-vcf package.",
     ),
 ) -> None:
+    """
+    Main function to generate fake VCF data using Typer CLI.
+
+    Args:
+        fake_vcf_path (Path): Path to fake VCF file or None to write to standard output.
+        num_rows (int): Number of rows.
+        num_samples (int): Number of samples.
+        chromosome (str): Chromosome identifier.
+        seed (int): Random seed for reproducibility.
+        sample_prefix (str): Prefix for sample names.
+        phased (bool): Simulate phased genotypes.
+        large_format (bool): Write large format VCF.
+        print_version (bool): Flag to print the version of the fake-vcf package.
+    """
     fake_vcf_data(
         fake_vcf_path=fake_vcf_path,
         num_rows=num_rows,

fake_vcf/vcf_faker.py

@@ -17,6 +17,18 @@ def __init__(
         phased: bool = True,
         large_format: bool = True,
     ):
+        """
+        Initialize VirtualVCF object.
+
+        Args:
+            num_rows (int): Number of rows.
+            num_samples (int): Number of samples.
+            chromosome (str): Chromosome identifier.
+            sample_prefix (str, optional): Prefix for sample names. Defaults to "SAMPLES".
+            random_seed (int, optional): Random seed for reproducibility. Defaults to None.
+            phased (bool, optional): Phased or unphased genotypes. Defaults to True.
+            large_format (bool, optional): Use large format VCF. Defaults to True.
+        """
         self.num_rows = num_rows
         self.rows_remaining = num_rows + 1  # One for the header
         self.num_samples = num_samples
@@ -111,16 +123,25 @@ def __init__(
         self.current_pos = 0
 
     def __iter__(self):
+        """
+        Iterates over VirtualVCF object.
+        """
         return self
 
     def __next__(self):
+        """
+        Retrieves the next VCF data.
+        """
         if self.rows_remaining <= 0:
             raise StopIteration
         vcf_data = self._generate_vcf_data()
         self.rows_remaining -= 1
         return vcf_data
 
     def _generate_vcf_header(self):
+        """
+        Generates the VCF header.
+        """
         # Create a list of column names
         columns = [
             "#CHROM",
@@ -143,6 +164,9 @@ def _generate_vcf_header(self):
         return self.header
 
     def _generate_vcf_row(self):
+        """
+        Generates a VCF row.
+        """
         ref_index = self.random.randint(0, 3)
 
         position = self.positions[self.current_pos]
@@ -177,14 +201,24 @@ def _generate_vcf_row(self):
         return row
 
     def _generate_vcf_data(self):
+        """
+        Generates VCF data.
+        """
         if self.rows_remaining == self.num_rows + 1:
             vcf_row = self._generate_vcf_header()
         else:
             vcf_row = self._generate_vcf_row()
         return vcf_row
 
     def __enter__(self):
+        """
+        Enters the context.
+        """
+
         return self
 
     def __exit__(self, exc_type, exc_value, traceback):
+        """
+        Exits the context.
+        """
         pass

fake_vcf/vcf_generator.py

@@ -8,12 +8,26 @@
 
 
 def to_std_out(virtual_vcf: VirtualVCF) -> None:
+    """
+    Writes VirtualVCF data to standard output.
+
+    Args:
+        virtual_vcf (VirtualVCF): VirtualVCF object containing the data.
+    """
     with virtual_vcf as v_vcf:
         for line in v_vcf:
             sys.stdout.write(line)
 
 
 def to_vcf_file(virtual_vcf: VirtualVCF, fake_vcf_path: Path, num_rows: int) -> None:
+    """
+    Writes VirtualVCF data to a VCF file.
+
+    Args:
+        virtual_vcf (VirtualVCF): VirtualVCF object containing the data.
+        fake_vcf_path (Path): Path to the fake VCF file.
+        num_rows (int): Number of rows.
+    """
     print(f"Writing to file {fake_vcf_path}")
 
     if fake_vcf_path.suffix == ".gz":
@@ -42,6 +56,19 @@ def fake_vcf_data(
     phased,
     large_format,
 ):
+    """
+    Generates fake VCF data and writes it to either a file or standard output.
+
+    Args:
+        fake_vcf_path (str or None): Path to the fake VCF file or None to write to standard output.
+        num_rows (int): Number of rows.
+        num_samples (int): Number of samples.
+        chromosome (str): Chromosome identifier.
+        seed (int): Random seed for reproducibility.
+        sample_prefix (str): Prefix for sample names.
+        phased (bool): Phased or unphased genotypes.
+        large_format (bool): Use large format VCF.
+    """
     virtual_vcf = VirtualVCF(
         num_rows=num_rows,
         num_samples=num_samples,