python.pkgs.h5py: fix for numpy 1.14

pkgs/development/python-modules/h5py/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, python, buildPythonPackage
+{ stdenv, fetchPypi, fetchpatch, python, buildPythonPackage
 , numpy, hdf5, cython, six, pkgconfig
 , mpi4py ? null, openssh }:
 
@@ -9,14 +9,12 @@ with stdenv.lib;
 let
   mpi = hdf5.mpi;
   mpiSupport = hdf5.mpiSupport;
-
 in buildPythonPackage rec {
   version = "2.7.1";
   pname = "h5py";
-  name = "${pname}-${version}";
 
-  src = fetchurl {
-    url = "mirror://pypi/h/h5py/${name}.tar.gz";
+  src = fetchPypi {
+    inherit pname version;
     sha256 = "180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc";
   };
 
@@ -34,11 +32,15 @@ in buildPythonPackage rec {
 
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ hdf5 cython ]
-    ++ optional mpiSupport mpi
-    ;
+    ++ optional mpiSupport mpi;
   propagatedBuildInputs = [ numpy six]
-    ++ optionals mpiSupport [ mpi4py openssh ]
-    ;
+    ++ optionals mpiSupport [ mpi4py openssh ];
+
+  patches = [
+    # Patch is based on upstream patch. The tox.ini hunk had to be removed.
+    # https://github.com/h5py/h5py/commit/5009e062a6f7d4e074cab0fcb42a780ac2b1d7d4.patch
+    ./numpy-1.14.patch
+  ];
 
   meta = {
     description =

pkgs/development/python-modules/h5py/numpy-1.14.patch

@@ -0,0 +1,94 @@
+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