Avoid GIL acquisition to check exceptions of GeneticCode._translate

althonos · Nov 28, 2023 · aa387b3 · aa387b3
1 parent 3039a56
commit aa387b3
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/pyhmmer/easel.pxd b/pyhmmer/easel.pxd
@@ -43,13 +43,13 @@ cdef class GeneticCode:
     cdef readonly Alphabet     nucleotide_alphabet
     cdef          ESL_GENCODE* _gcode
 
-    cdef void _translate(
+    cdef int _translate(
         self,
         const ESL_DSQ* seq,
         int64_t seqlen,
         ESL_DSQ* out,
         int64_t outlen
-    ) except * nogil
+    ) except -1 nogil
 
     cpdef VectorU8 translate(self, const ESL_DSQ[::1] sequence)
 

diff --git a/pyhmmer/easel.pyx b/pyhmmer/easel.pyx
@@ -545,13 +545,13 @@ cdef class GeneticCode:
 
     # --- Utils --------------------------------------------------------------
 
-    cdef void _translate(
+    cdef int _translate(
         self,
         const ESL_DSQ* seq,
         int64_t seqlen,
         ESL_DSQ* out,
         int64_t outlen
-    ) except * nogil:
+    ) except -1 nogil:
         cdef int     aa
         cdef int64_t i
         cdef int64_t j
@@ -567,6 +567,8 @@ cdef class GeneticCode:
                 raise ValueError(f"Failed to translate codon at index {j!r}")
             out[i] = aa
 
+        return 0
+
     # --- Methods ------------------------------------------------------------
 
     cpdef VectorU8 translate(self, const ESL_DSQ[::1] sequence):