[Debian-med-packaging] Bug#1098613: python-sqt: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.13" returned exit code 13

[James Addison]

Source: python-sqt
Version: 0.8.0-8
Followup-For: Bug #1098613
Control: tags -1 patch ftbfs

Dear Maintainer,

I'm able to replicate this FTBFS locally using a Debian testing (trixie)
environment during autopkgtests.

After using cython, gcc and Python 3.13 to run a minimized subset of the
failing code, I observed a 'PyBytes_Check' assertion failure, and began
to suspect some of the typecasting code[1] in the nt_to_aa function that
accesses bytearray objects as if they are bytes.

Please find attached a patch that rewrites the _helpers.pyx code to
construct the relevant objects natively as bytes (immutable), resolving
the runtime error while hopefully not degrading performance
significantly.

Regards,
James

[1] - https://sources.debian.org/src/python-sqt/0.8.0-8/sqt/_helpers.pyx/#L436-L437
-------------- next part --------------
Description: Avoid runtime typecasting of bytearray to bytes
Author: James Addison <jay at jp-hosting.net>
Bug-Debian: https://bugs.debian.org/1098613

---
--- python-sqt-0.8.0.orig/sqt/_helpers.pyx
+++ python-sqt-0.8.0/sqt/_helpers.pyx
@@ -402,10 +402,13 @@ def hamming_distance(unicode s, unicode
 
 # Lookup table that maps nucleotides to their 2-bit representation
 # and everything else to 255.
-cdef bytearray _nt_trans = bytearray([255]*256)
-for frm, to in zip(b'ACGTacgt', b'\x00\x01\x02\x03\x00\x01\x02\x03'):
-	_nt_trans[frm] = to
+def _make_nt_trans():
+	table = bytearray([255]*256)
+	for frm, to in zip(b'ACGTacgt', b'\x00\x01\x02\x03\x00\x01\x02\x03'):
+		table[frm] = to
+	return bytes(table)
 
+cdef bytes _nt_trans = _make_nt_trans()
 
 # Lookup table that maps 6-bit encoded codons to amino acids
 def _make_codon_array(stop_aa='*'):
@@ -414,9 +417,9 @@ def _make_codon_array(stop_aa='*'):
 		b = codon.encode().translate(_nt_trans)
 		index = b[0] * 16 + b[1] * 4 + b[2]
 		triples[index] = ord(aa)
-	return triples
+	return bytes(triples)
 
-cdef bytearray _codon_array = _make_codon_array()
+cdef bytes _codon_array = _make_codon_array()
 
 
 def nt_to_aa(s: str):
@@ -433,8 +436,8 @@ def nt_to_aa(s: str):
 	cdef int j = 0
 	cdef int v = 0
 	cdef unsigned char nt0, nt1, nt2
-	cdef char* nt_trans_ptr = <bytes>_nt_trans
-	cdef char* codon_array_ptr = <bytes>_codon_array
+	cdef char* nt_trans_ptr = _nt_trans
+	cdef char* codon_array_ptr = _codon_array
 	cdef bytes s_bytes = s.encode()
 	cdef char* b = s_bytes
 	cdef bytearray result = bytearray([0]*((len(s)+2)//3))