Changes for Scriptbunny integration

src/hla_algorithm/interpret_from_json_lib.py

@@ -156,7 +156,7 @@ def build_from_interpretation(
             alleles_version=alleles_version,
             alleles_last_updated=alleles_last_updated,
             b5701=interp.is_b5701(),
-            dist_b5701=interp.distance_from_b7501(),
+            dist_b5701=interp.distance_from_b5701(),
             all_mismatches={
                 cs.get_allele_pair_str(): HLAMatchAdaptor.from_match_details(match)
                 for cs, match in interp.matches.items()

src/hla_algorithm/models.py

@@ -84,14 +84,17 @@ class MatchingAllelePair(BaseModel):
     - the number of mismatches identified; and
     - the allele pair (i.e. names of the two alleles in the combination).
     """
+
     standard_bin: tuple[int, ...]
     mismatch_count: int
     allele_1: str
     allele_2: str
 
     @model_validator(mode="after")
     def check_alleles_ordered(self) -> Self:
-        if allele_coordinates_sort_key(self.allele_1) > allele_coordinates_sort_key(self.allele_2):
+        if allele_coordinates_sort_key(self.allele_1) > allele_coordinates_sort_key(
+            self.allele_2
+        ):
             raise ValueError("allele_1 should be less than or equal to allele_2")
         return self
 
@@ -474,7 +477,9 @@ def _identify_longest_prefix(allele_prefixes: list[GeneCoord]) -> GeneCoord:
         if len(allele_prefixes) > 0:
             max_length: int = max([len(allele) for allele in allele_prefixes])
             for i in range(max_length, 0, -1):
-                curr_prefixes: set[GeneCoord] = {allele[0:i] for allele in allele_prefixes}
+                curr_prefixes: set[GeneCoord] = {
+                    allele[0:i] for allele in allele_prefixes
+                }
                 if len(curr_prefixes) == 1:
                     longest_prefix = curr_prefixes.pop()
                     if i > 1:
@@ -522,9 +527,8 @@ def best_common_allele_pair_str(
         )
 
         second_prefix: GeneCoord = (
-            intermediate_data.second_prefix or self._identify_longest_prefix(
-                intermediate_data.remaining_prefixes
-            )
+            intermediate_data.second_prefix
+            or self._identify_longest_prefix(intermediate_data.remaining_prefixes)
         )
 
         # Turn the two prefixes we found into strings and strip any trailing
@@ -640,7 +644,7 @@ def best_common_allele_pair(
             ap_to_cs[best_representative],
         )
 
-    def distance_from_b7501(self) -> Optional[int]:
+    def distance_from_b5701(self) -> int | None:
         """
         Return the Hamming distance from this sequence to B*57:01.
 

src/hla_algorithm/reformat_old_alleles.py

@@ -77,7 +77,7 @@ def main():
     elif args.verbose > 1:
         logger.setLevel(logging.DEBUG)
 
-    input_filenames_by_locus: dict[HLA_LOCUS, str] = {
+    input_filenames_by_locus: dict[HLA_LOCUS, Path] = {
         "A": args.a_standards,
         "B": args.b_standards,
         "C": args.c_standards,

src/hla_algorithm/utils.py

@@ -133,7 +133,7 @@ def count_forgiving_mismatches(
 
     overlaps: np.ndarray = seq1_np & seq2_np
     matches: np.ndarray = (overlaps == seq1_np) | (overlaps == seq2_np)
-    return np.count_nonzero(matches == False)
+    return int(np.count_nonzero(matches == False))
 
 
 class InvalidBaseException(Exception):
@@ -368,19 +368,16 @@ def allele_coordinates_sort_key(allele: str) -> tuple[tuple[int, ...], str]:
     return (integer_part, letters_at_end)
 
 
-def allele_pair_sort_key(pair: tuple[str, str]) -> tuple[
-    tuple[int, ...], str, tuple[int, ...], str
-]:
+def allele_pair_sort_key(
+    pair: tuple[str, str],
+) -> tuple[tuple[int, ...], str, tuple[int, ...], str]:
     """
     Produce a sortable key for an allele pair.
 
     Pairs should be sorted according to "coordinate order".
     If there's a tie, a last letter is used to attempt to break the tie.
     """
-    return (
-        allele_coordinates_sort_key(pair[0])
-        + allele_coordinates_sort_key(pair[1])
-    )
+    return allele_coordinates_sort_key(pair[0]) + allele_coordinates_sort_key(pair[1])
 
 
 def sort_allele_pairs(allele_pairs: Iterable[tuple[str, str]]) -> list[tuple[str, str]]:

tests/models_test.py

@@ -2529,7 +2529,7 @@ def test_distance_from_b5701(
             allele_frequencies={},
             b5701_standards=b5701_standards,
         )
-        assert interp.distance_from_b7501() == expected_result
+        assert interp.distance_from_b5701() == expected_result
 
     @pytest.mark.parametrize(
         "raw_matches, expected_result",