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 <[email protected]> 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?= <[email protected]> -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 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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