pyrox.dev
1From 5009e062a6f7d4e074cab0fcb42a780ac2b1d7d4 Mon Sep 17 00:00:00 2001
2From: James Tocknell <aragilar@gmail.com>
3Date: Thu, 28 Dec 2017 20:55:55 +1100
4Subject: [PATCH] FIX: Don't reorder compound types, breaks on numpy 1.14
5
6---
7 h5py/h5t.pyx | 25 +++++++------------------
8 setup.py | 2 +-
9 tox.ini | 4 ++--
10 3 files changed, 10 insertions(+), 21 deletions(-)
11
12diff --git a/h5py/h5t.pyx b/h5py/h5t.pyx
13index cc2344e1..7445e9eb 100644
14--- a/h5py/h5t.pyx
15+++ b/h5py/h5t.pyx
16@@ -1136,12 +1136,6 @@ cdef class TypeCompoundID(TypeCompositeID):
17 else:
18 if sys.version[0] == '3':
19 field_names = [x.decode('utf8') for x in field_names]
20- if len(field_names) > 0:
21- collated_fields = zip(field_names, field_types, field_offsets)
22- ordered_fields = sorted(
23- collated_fields, key=operator.itemgetter(2))
24- field_names, field_types, field_offsets = \
25- map(list, zip(*ordered_fields))
26 typeobj = dtype({
27 'names': field_names,
28 'formats': field_types,
29@@ -1458,8 +1452,7 @@ cdef TypeCompoundID _c_compound(dtype dt, int logical, int aligned):
30 cdef dtype member_dt
31 cdef size_t member_offset = 0
32
33- cdef dict offsets = {}
34- cdef list fields = []
35+ cdef dict fields = {}
36
37 # The challenge with correctly converting a numpy/h5py dtype to a HDF5 type
38 # which is composed of subtypes has three aspects we must consider
39@@ -1468,19 +1461,14 @@ cdef TypeCompoundID _c_compound(dtype dt, int logical, int aligned):
40 # 2. For correct round-tripping of aligned dtypes, we need to consider how
41 # much padding we need by looking at the field offsets
42 # 3. There is no requirement that the offsets be monotonically increasing
43- # (so we start by sorting the names as a function of increasing offset)
44 #
45 # The code below tries to cover these aspects
46
47- # Get offsets for each compound member
48- for name, field in dt.fields.items():
49- offsets[name] = field[1]
50-
51 # Build list of names, offsets, and types, sorted by increasing offset
52 # (i.e. the position of the member in the struct)
53- for name in sorted(dt.names, key=offsets.__getitem__):
54+ for name in sorted(dt.names, key=(lambda n: dt.fields[n][1])):
55 field = dt.fields[name]
56- name = name.encode('utf8') if isinstance(name, unicode) else name
57+ h5_name = name.encode('utf8') if isinstance(name, unicode) else name
58
59 # Get HDF5 data types and set the offset for each member
60 member_dt = field[0]
61@@ -1489,7 +1477,7 @@ cdef TypeCompoundID _c_compound(dtype dt, int logical, int aligned):
62 if aligned and (member_offset > field[1]
63 or member_dt.itemsize != member_type.get_size()):
64 raise TypeError("Enforced alignment not compatible with HDF5 type")
65- fields.append((name, member_offset, member_type))
66+ fields[name] = (h5_name, member_offset, member_type)
67
68 # Update member offset based on the HDF5 type size
69 member_offset += member_type.get_size()
70@@ -1500,8 +1488,9 @@ cdef TypeCompoundID _c_compound(dtype dt, int logical, int aligned):
71
72 # Create compound with the necessary size, and insert its members
73 tid = H5Tcreate(H5T_COMPOUND, member_offset)
74- for (name, member_offset, member_type) in fields:
75- H5Tinsert(tid, name, member_offset, member_type.id)
76+ for name in dt.names:
77+ h5_name, member_offset, member_type = fields[name]
78+ H5Tinsert(tid, h5_name, member_offset, member_type.id)
79
80 return TypeCompoundID(tid)
81
82diff --git a/setup.py b/setup.py
83index ec2a78a7..bbb086f6 100755
84--- a/setup.py
85+++ b/setup.py
86@@ -32,7 +32,7 @@
87 # these are required to build h5py
88 # RUN_REQUIRES is included as setup.py test needs RUN_REQUIRES for testing
89 # RUN_REQUIRES can be removed when setup.py test is removed
90-SETUP_REQUIRES = RUN_REQUIRES + [NUMPY_DEP, 'Cython>=0.19', 'pkgconfig']
91+SETUP_REQUIRES = RUN_REQUIRES + [NUMPY_DEP, 'Cython>=0.23', 'pkgconfig']
92
93 # Needed to avoid trying to install numpy/cython on pythons which the latest
94 # versions don't support