[med-svn] [Git][med-team/python-biopython][master] 3 commits: extending Fix-Endian-issue-with-binary-CIF.patch

[Karsten Schöke (@karso)]

Karsten Schöke pushed to branch master at Debian Med / python-biopython


Commits:
c2ac4ae3 by Karsten Schöke at 2026-07-01T07:58:53+02:00
extending Fix-Endian-issue-with-binary-CIF.patch

- - - - -
a6704887 by Karsten Schöke at 2026-07-01T08:00:22+02:00
Update changelog for 1.87+dfsg-3 release

- - - - -
f8a63189 by Karsten Schöke at 2026-07-01T08:19:28+02:00
commend Fix-Endian-issue-with-binary-CIF.patch

- - - - -


2 changed files:

- debian/changelog
- debian/patches/Fix-Endian-issue-with-binary-CIF.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-biopython (1.87+dfsg-3) unstable; urgency=medium
+
+  * Team upload.
+  * extending Fix-Endian-issue-with-binary-CIF.patch
+
+ -- Karsten Schöke <karsten.schoeke at geobasis-bb.de>  Wed, 01 Jul 2026 08:00:11 +0200
+
 python-biopython (1.87+dfsg-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/Fix-Endian-issue-with-binary-CIF.patch
=====================================
@@ -1,11 +1,16 @@
 From: =?utf-8?q?Karsten_Sch=C3=B6ke?= <karsten.schoeke at geobasis-bb.de>
-Date: Mon, 29 Jun 2026 08:14:31 +0200
+Date: Wed, 1 Jul 2026 07:56:58 +0200
 Subject: Fix Endian issue with binary CIF
+Fix _bcif_helper.integer_unpack() to accept PEP 3118 buffer format strings
+with optional endianness prefixes. 
+This fixes test failures on ppc64 where the buffer format
+is reported as "<H" instead of "H".
 
 Forwarded: https://github.com/biopython/biopython/pull/5252
 ---
  Bio/PDB/bcifhelpermodule.c | 4 +++-
- 1 file changed, 3 insertions(+), 1 deletion(-)
+ Bio/PDB/binary_cif.py      | 3 +++
+ 2 files changed, 6 insertions(+), 1 deletion(-)
 
 diff --git a/Bio/PDB/bcifhelpermodule.c b/Bio/PDB/bcifhelpermodule.c
 index 31aa652..60680cb 100644
@@ -29,3 +34,17 @@ index 31aa652..60680cb 100644
  
      if (format == 'B') {
          integer_unpack_u8(&in_view, &out_view);
+diff --git a/Bio/PDB/binary_cif.py b/Bio/PDB/binary_cif.py
+index 4fa7e83..2c1e94a 100644
+--- a/Bio/PDB/binary_cif.py
++++ b/Bio/PDB/binary_cif.py
+@@ -125,6 +125,9 @@ def _integer_packing_decoder(column):
+         dtype = np.dtype("<i4")
+ 
+     data = column["data"]["data"]
++    # Convert to native endianness
++    data = data.astype(data.dtype.newbyteorder("="))
++
+     assert byte_count == data.dtype.itemsize
+     assert np.issubdtype(data.dtype, np.unsignedinteger) == is_unsigned
+     decoded_data = np.empty((src_size,), dtype)



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/586745a4b3a7b176b4ce2a3caf4bbbcee9993411...f8a6318925b469010cbec7130bf017bdd29c935a

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/586745a4b3a7b176b4ce2a3caf4bbbcee9993411...f8a6318925b469010cbec7130bf017bdd29c935a
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