Fix some mypy warnings

meteor/merging.py

@@ -423,9 +423,11 @@ def execute(self) -> None:
                     # with h5py.File(output_name.with_suffix(".biom"), "w") as f:
                     #     table.to_hdf5(f, generated_by="Meteor", compress=True)
             elif my_pattern == "modules":
-                module_path = (
-                    importlib.resources.files("meteor")
-                    / "data/modules_definition.feather"
+                module_path = Path(
+                    str(
+                        importlib.resources.files("meteor")
+                        / "data/modules_definition.feather"
+                    )
                 )
                 annotation = self.load_data(module_path)
                 annotation = annotation[annotation["id"].isin(filtered_df["mod_id"])]

meteor/phylogeny.py

@@ -37,6 +37,7 @@
 from cogent3.evolve.models import GTR
 from cogent3.cluster.UPGMA import upgma
 from concurrent.futures import ProcessPoolExecutor, as_completed
+from typing import Union
 
 
 @dataclass
@@ -61,7 +62,7 @@ def compute_site_info(self, sequences: Iterable[str]) -> list[float]:
 
     def clean_sites(
         self, msp_file: Path, output: tempfile._TemporaryFileWrapper
-    ) -> Tuple[dict[str, str], int]:
+    ) -> Tuple[dict[Union[int, str, None]], int]:
         """Clean msp sequence according to a certain level of gap at each sites.
         :param msp_file: (Path) Fasta file
         :param output_file: (Path) Output cleaned fasta file

meteor/variantcalling.py

@@ -296,15 +296,15 @@ def count_reads_in_gene(
             multiple_iterators=False,
         ):
             read_count = sum(
-                1
+                True
                 for pileupread in pileupcolumn.pileups
                 if not pileupread.is_del and not pileupread.is_refskip
             )
             reads_dict[pileupcolumn.reference_pos] = read_count
 
         return reads_dict
 
-    def merge_vcf_files(self, vcf_file_list, output_vcf):
+    def merge_vcf_files(self, vcf_file_list, output_vcf) -> None:
         """Merge variant records (handling the same positions in multiple VCFs)."""
         variant_dict = defaultdict(list)
 
@@ -332,8 +332,7 @@ def filter_low_cov_sites(
         self,
         cram_file: Path,
         reference_file: Path,
-        # temp_low_cov_sites: tempfile._TemporaryFileWrapper,
-    ) -> None:
+    ) -> tuple[pd.DataFrame]:
         """Create a bed file reporting a list of positions below coverage threshold
 
         :param cram_file:   Path to the input cram file