rst fixes and two typos

ppanggolin/genome.py

@@ -889,16 +889,18 @@ class Organism(MetaFeatures):
     Describe the Genome content and some information
 
     Methods:
+
     - `families`: Returns a set of gene families present in the organism.
     - `genes`: Returns a generator to get genes in the organism.
     - `number_of_genes`: Returns the number of genes in the organism.
     - `contigs`: Returns the values in the contig dictionary from the organism.
     - `get_contig`: Gets the contig with the given identifier in the organism, adding it if it does not exist.
     - `_create_contig`: Creates a new contig object and adds it to the contig dictionary.
     - `mk_bitarray`: Produces a bitarray representing the presence/absence of gene families
-                     in the organism using the provided index.
+      in the organism using the provided index.
 
     Fields:
+
     - `name`: Name of the organism.
     - `bitarray`: Bitarray representing the presence/absence of gene families in the organism.
     """

ppanggolin/meta/meta.py

@@ -117,8 +117,8 @@ def assign_metadata(
     :param source: A string representing the source of the metadata.
     :param metatype: A string representing the type of element to which metadata will be assigned.
     :param omit: A boolean indicating whether to raise an error if metadata cannot be assigned to an element.
-                 If True, metadata will not be assigned to elements that do not exist in the pangenome.
-                 If False, an error will be raised. Default is False.
+    If ``True``, metadata will not be assigned to elements that do not exist in the pangenome.
+    If ``False``, an error will be raised. Default is ``False``.
     :param disable_bar: A boolean indicating whether to disable the progress bar. Default is False.
 
     :raise KeyError: element name is not find in pangenome
@@ -228,7 +228,7 @@ def check_metadata_arguments(
     Check the arguments provided for  and raise errors if they are incompatible or missing.
 
     :param args: An argparse.Namespace object containing parsed command-line arguments.
-    :param parser : parser of the command
+    :param parser: parser of the command
     :return: A string indicating the input mode ('single' or 'multiple').
     """
 

ppanggolin/projection/projection.py

@@ -331,6 +331,7 @@ def write_projection_results(
 
 
     Note:
+
     - If `write_proksee` is True and input organisms have modules, module colors for ProkSee are obtained.
     - The function calls other functions such as `summarize_projection`, `read_genome_file`, `write_proksee_organism`,
       `write_gff_file`, and `write_summaries` to generate various output files and summaries.
@@ -1496,7 +1497,7 @@ def check_projection_arguments(
     Check the arguments provided for genome projection and raise errors if they are incompatible or missing.
 
     :param args: An argparse.Namespace object containing parsed command-line arguments.
-    :param parser : parser of the command
+    :param parser: parser of the command
     :return: A string indicating the input mode ('single' or 'multiple').
     """
 

ppanggolin/utility/utils.py

@@ -253,7 +253,7 @@ def launch_default_config(args: argparse.Namespace):
         arg_lines.append(f"\n{sub_command}:")
         arg_lines += get_default_argument_lines(specific_actions)
 
-    logging.getLogger("PPanGGOLiN").info(f"Writting default config in {args.output}")
+    logging.getLogger("PPanGGOLiN").info(f"Writing default config in {args.output}")
     with open(args.output, "w") as fl:
         fl.write("\n".join(arg_lines) + "\n")
 

ppanggolin/utils.py

@@ -310,7 +310,7 @@ def read_compressed_or_not(
 
     Parameters:
     file (pathlib.Path, io.BytesIO, io.TextIOWrapper, io.TextIOBase): The file to read.
-        It can be a Path object from the pathlib module, a BytesIO object, a TextIOWrapper, or TextIOBase object.
+    It can be a Path object from the pathlib module, a BytesIO object, a TextIOWrapper, or TextIOBase object.
 
     Returns:
     str: The contents of the file, decompressed if it was a recognized compressed format.
@@ -506,7 +506,8 @@ def _plain_bfs(g: nx.Graph, source: Any, removed: set, weight: float):
     :param g: graph with the nodes
     :param source: current node
     :param removed: set of removed nodes
-    :param weight:threshold to remove node or not
+    :param weight: threshold to remove node or not
+
     """
 
     nextlevel = {source}

tests/test_genefamily.py

@@ -135,7 +135,7 @@ def test_raise_exception_if_representative_not_set(self, family):
 
     @pytest.fixture
     def genes(self) -> Generator[Set[Gene], None, None]:
-        """Creeate a set of genes to fill gene families"""
+        """Create a set of genes to fill gene families"""
         genes = set()
         for i in range(1, randint(11, 20)):
             gene = Gene(f"gene_{str(i)}")