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