forked from mirrors/nixpkgs
95 lines
4.1 KiB
Diff
95 lines
4.1 KiB
Diff
From 5009e062a6f7d4e074cab0fcb42a780ac2b1d7d4 Mon Sep 17 00:00:00 2001
|
|
From: James Tocknell <aragilar@gmail.com>
|
|
Date: Thu, 28 Dec 2017 20:55:55 +1100
|
|
Subject: [PATCH] FIX: Don't reorder compound types, breaks on numpy 1.14
|
|
|
|
---
|
|
h5py/h5t.pyx | 25 +++++++------------------
|
|
setup.py | 2 +-
|
|
tox.ini | 4 ++--
|
|
3 files changed, 10 insertions(+), 21 deletions(-)
|
|
|
|
diff --git a/h5py/h5t.pyx b/h5py/h5t.pyx
|
|
index cc2344e1..7445e9eb 100644
|
|
--- a/h5py/h5t.pyx
|
|
+++ b/h5py/h5t.pyx
|
|
@@ -1136,12 +1136,6 @@ cdef class TypeCompoundID(TypeCompositeID):
|
|
else:
|
|
if sys.version[0] == '3':
|
|
field_names = [x.decode('utf8') for x in field_names]
|
|
- if len(field_names) > 0:
|
|
- collated_fields = zip(field_names, field_types, field_offsets)
|
|
- ordered_fields = sorted(
|
|
- collated_fields, key=operator.itemgetter(2))
|
|
- field_names, field_types, field_offsets = \
|
|
- map(list, zip(*ordered_fields))
|
|
typeobj = dtype({
|
|
'names': field_names,
|
|
'formats': field_types,
|
|
@@ -1458,8 +1452,7 @@ cdef TypeCompoundID _c_compound(dtype dt, int logical, int aligned):
|
|
cdef dtype member_dt
|
|
cdef size_t member_offset = 0
|
|
|
|
- cdef dict offsets = {}
|
|
- cdef list fields = []
|
|
+ cdef dict fields = {}
|
|
|
|
# The challenge with correctly converting a numpy/h5py dtype to a HDF5 type
|
|
# which is composed of subtypes has three aspects we must consider
|
|
@@ -1468,19 +1461,14 @@ cdef TypeCompoundID _c_compound(dtype dt, int logical, int aligned):
|
|
# 2. For correct round-tripping of aligned dtypes, we need to consider how
|
|
# much padding we need by looking at the field offsets
|
|
# 3. There is no requirement that the offsets be monotonically increasing
|
|
- # (so we start by sorting the names as a function of increasing offset)
|
|
#
|
|
# The code below tries to cover these aspects
|
|
|
|
- # Get offsets for each compound member
|
|
- for name, field in dt.fields.items():
|
|
- offsets[name] = field[1]
|
|
-
|
|
# Build list of names, offsets, and types, sorted by increasing offset
|
|
# (i.e. the position of the member in the struct)
|
|
- for name in sorted(dt.names, key=offsets.__getitem__):
|
|
+ for name in sorted(dt.names, key=(lambda n: dt.fields[n][1])):
|
|
field = dt.fields[name]
|
|
- name = name.encode('utf8') if isinstance(name, unicode) else name
|
|
+ h5_name = name.encode('utf8') if isinstance(name, unicode) else name
|
|
|
|
# Get HDF5 data types and set the offset for each member
|
|
member_dt = field[0]
|
|
@@ -1489,7 +1477,7 @@ cdef TypeCompoundID _c_compound(dtype dt, int logical, int aligned):
|
|
if aligned and (member_offset > field[1]
|
|
or member_dt.itemsize != member_type.get_size()):
|
|
raise TypeError("Enforced alignment not compatible with HDF5 type")
|
|
- fields.append((name, member_offset, member_type))
|
|
+ fields[name] = (h5_name, member_offset, member_type)
|
|
|
|
# Update member offset based on the HDF5 type size
|
|
member_offset += member_type.get_size()
|
|
@@ -1500,8 +1488,9 @@ cdef TypeCompoundID _c_compound(dtype dt, int logical, int aligned):
|
|
|
|
# Create compound with the necessary size, and insert its members
|
|
tid = H5Tcreate(H5T_COMPOUND, member_offset)
|
|
- for (name, member_offset, member_type) in fields:
|
|
- H5Tinsert(tid, name, member_offset, member_type.id)
|
|
+ for name in dt.names:
|
|
+ h5_name, member_offset, member_type = fields[name]
|
|
+ H5Tinsert(tid, h5_name, member_offset, member_type.id)
|
|
|
|
return TypeCompoundID(tid)
|
|
|
|
diff --git a/setup.py b/setup.py
|
|
index ec2a78a7..bbb086f6 100755
|
|
--- a/setup.py
|
|
+++ b/setup.py
|
|
@@ -32,7 +32,7 @@
|
|
# these are required to build h5py
|
|
# RUN_REQUIRES is included as setup.py test needs RUN_REQUIRES for testing
|
|
# RUN_REQUIRES can be removed when setup.py test is removed
|
|
-SETUP_REQUIRES = RUN_REQUIRES + [NUMPY_DEP, 'Cython>=0.19', 'pkgconfig']
|
|
+SETUP_REQUIRES = RUN_REQUIRES + [NUMPY_DEP, 'Cython>=0.23', 'pkgconfig']
|
|
|
|
# Needed to avoid trying to install numpy/cython on pythons which the latest
|
|
# versions don't support
|