[med-svn] [Git][med-team/python-biopython][master] fix-type-cast-i386.patch: new: fix PDB test failure on 32-bit.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / python-biopython


Commits:
b096ace0 by Étienne Mollier at 2024-09-16T20:28:21+02:00
fix-type-cast-i386.patch: new: fix PDB test failure on 32-bit.

- - - - -


2 changed files:

- + debian/patches/fix-type-cast-i386.patch
- debian/patches/series


Changes:

=====================================
debian/patches/fix-type-cast-i386.patch
=====================================
@@ -0,0 +1,26 @@
+--- python-biopython.orig/Bio/PDB/binary_cif.py
++++ python-biopython/Bio/PDB/binary_cif.py
+@@ -3,6 +3,7 @@
+ """
+ 
+ import gzip
++import sys
+ from collections import deque
+ from typing import Optional
+ 
+@@ -82,7 +83,14 @@
+ 
+     data = column["data"]["data"]
+     dtype = _dtypes[encoding["srcType"]]
+-    decoded_data = np.repeat(data[::2].astype(dtype), data[1::2])
++    if sys.maxsize == 2**63 - 1:
++        # We're running classical 64-bit platform here.
++        decoded_data = np.repeat(data[::2].astype(dtype), data[1::2])
++    else:
++        # We're assuming 32-bit platform here, numpy croaks on unsafe
++        # type casts.
++        decoded_data = np.repeat(data[::2].astype('int32', casting='unsafe'),
++                                 data[1::2].astype('int32', casting='unsafe'))
+ 
+     assert len(decoded_data) == encoding["srcSize"]
+     column["data"]["data"] = decoded_data


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ muscle3.patch
 #port_tutorial_to_muscle3.patch
 skip-scipy-in-codonalign.patch
 0010-Python-3.13-Replace-deprecated-PyEval_CallObject.patch
+fix-type-cast-i386.patch



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/b096ace064e13939b8bf960e3830a86872443178

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View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/b096ace064e13939b8bf960e3830a86872443178
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