pythonPackages.h5py: 2.7.1 -> 2.8.0 (#41581)

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

@@ -1,5 +1,5 @@
-{ stdenv, fetchPypi, fetchpatch, python, buildPythonPackage
+{ stdenv, fetchPypi, fetchpatch, isPy27, python, buildPythonPackage
-, numpy, hdf5, cython, six, pkgconfig
+, numpy, hdf5, cython, six, pkgconfig, unittest2
 , mpi4py ? null, openssh }:
 
 assert hdf5.mpiSupport -> mpi4py != null && hdf5.mpi == mpi4py.mpi;
@@ -10,12 +10,12 @@ let
   mpi = hdf5.mpi;
   mpiSupport = hdf5.mpiSupport;
 in buildPythonPackage rec {
-  version = "2.7.1";
+  version = "2.8.0";
   pname = "h5py";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc";
+    sha256 = "0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6";
   };
 
   configure_flags = "--hdf5=${hdf5}" + optionalString mpiSupport " --mpi";
@@ -30,18 +30,13 @@ in buildPythonPackage rec {
 
   preBuild = if mpiSupport then "export CC=${mpi}/bin/mpicc" else "";
 
+  checkInputs = optional isPy27 unittest2;
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ hdf5 cython ]
     ++ optional mpiSupport mpi;
   propagatedBuildInputs = [ numpy six]
     ++ 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 =
       "Pythonic interface to the HDF5 binary data format";

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

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