Fix Mypy type errors

Author: mohamed-laarej

malariagen_data/anoph/snp_frq.py

@@ -3,6 +3,7 @@
 
 import allel  # type: ignore
 import numpy as np
+import numpy.typing as npt
 import pandas as pd
 from numpydoc_decorator import doc  # type: ignore
 import xarray as xr
@@ -518,8 +519,8 @@ def snp_allele_frequencies_advanced(
 
         # Set up main event variables.
         n_variants, n_cohorts = len(variant_position), len(df_cohorts)
-        count = np.zeros((n_variants, n_cohorts), dtype=int)
-        nobs = np.zeros((n_variants, n_cohorts), dtype=int)
+        count: npt.NDArray[np.float64] = np.zeros((n_variants, n_cohorts), dtype=int)
+        nobs: npt.NDArray[np.float64] = np.zeros((n_variants, n_cohorts), dtype=int)
 
         # Build event count and nobs for each cohort.
         cohorts_iterator = self._progress(

tests/anoph/test_hap_data.py

@@ -605,7 +605,7 @@ def test_haplotypes_virtual_contigs(
 
         # Test with region.
         seq = api.genome_sequence(region=chrom)
-        start, stop = sorted(np.random.randint(low=1, high=len(seq), size=2))
+        start, stop = sorted(map(int, np.random.randint(low=1, high=len(seq), size=2)))
         region = f"{chrom}:{start:,}-{stop:,}"
 
         # Standard checks.