feat: use OffTargetDetector and ExecutableRunner as ContextManagers

prymer/offtarget/offtarget_detector.py

@@ -75,6 +75,7 @@
 """  # noqa: E501
 
 import itertools
+from contextlib import AbstractContextManager
 from dataclasses import dataclass
 from dataclasses import field
 from dataclasses import replace
@@ -124,7 +125,7 @@ class OffTargetResult:
     right_primer_spans: list[Span] = field(default_factory=list)
 
 
-class OffTargetDetector:
+class OffTargetDetector(AbstractContextManager):
     """
     Detect off-target mappings of primers and primer pairs.
 
@@ -442,4 +443,5 @@ def __exit__(
         traceback: Optional[TracebackType],
     ) -> None:
         """Gracefully terminates any running subprocesses."""
+        super().__exit__(exc_type, exc_value, traceback)
         self.close()

prymer/util/executable_runner.py

@@ -11,13 +11,14 @@
 import os
 import shutil
 import subprocess
+from contextlib import AbstractContextManager
 from pathlib import Path
 from types import TracebackType
 from typing import Optional
 from typing import Self
 
 
-class ExecutableRunner:
+class ExecutableRunner(AbstractContextManager):
     """
     Base class for interaction with subprocess for all command-line tools. The base class supports
     use of the context management protocol and performs basic validation of executable paths.
@@ -67,6 +68,7 @@ def __exit__(
         traceback: Optional[TracebackType],
     ) -> None:
         """Gracefully terminates any running subprocesses."""
+        super().__exit__(exc_type, exc_value, traceback)
         self.close()
 
     @classmethod

tests/api/test_picking.py

@@ -573,31 +573,29 @@ def _pick_top_primer_pairs(
     max_primer_pair_hits: int,
     min_difference: int = 1,
 ) -> list[PrimerPair]:
-    offtarget_detector = OffTargetDetector(
-        ref=picking_ref,
-        max_primer_hits=max_primer_hits,
-        max_primer_pair_hits=max_primer_pair_hits,
-        three_prime_region_length=5,
-        max_mismatches_in_three_prime_region=0,
-        max_mismatches=0,
-        max_amplicon_size=params.amplicon_sizes.max,
-    )
-    dimer_checker = NtThermoAlign()
-
-    picked = pick_top_primer_pairs(
-        primer_pairs=primer_pairs,
-        num_primers=len(primer_pairs),
-        min_difference=min_difference,
-        params=params,
-        offtarget_detector=offtarget_detector,
-        is_dimer_tm_ok=lambda s1, s2: (
-            dimer_checker.duplex_tm(s1=s1, s2=s2) <= params.max_dimer_tm
-        ),
-    )
-    offtarget_detector.close()
-    dimer_checker.close()
-
-    return picked
+    with (
+        NtThermoAlign() as dimer_checker,
+        OffTargetDetector(
+            ref=picking_ref,
+            max_primer_hits=max_primer_hits,
+            max_primer_pair_hits=max_primer_pair_hits,
+            three_prime_region_length=5,
+            max_mismatches_in_three_prime_region=0,
+            max_mismatches=0,
+            max_amplicon_size=params.amplicon_sizes.max,
+        ) as offtarget_detector
+    ):
+        picked: list[PrimerPair] = pick_top_primer_pairs(
+            primer_pairs=primer_pairs,
+            num_primers=len(primer_pairs),
+            min_difference=min_difference,
+            params=params,
+            offtarget_detector=offtarget_detector,
+            is_dimer_tm_ok=lambda s1, s2: (
+                dimer_checker.duplex_tm(s1=s1, s2=s2) <= params.max_dimer_tm
+            ),
+        )
+        return picked
 
 
 _PARAMS: FilteringParams = _zero_score_filtering_params(_score_input())