Bug#898526: h5py: FTBFS with HDF5 1.10.2

2018-05-17 Thread Gilles Filippini 
Control: tags + patch

On Sun, 13 May 2018 16:01:31 +0200 Gilles Filippini  wrote:
> Control: severity -1 serious
> Control: retitle -1 h5py: FTBFS - FAIL: test_out_of_order_offsets
> 
> On Sun, 13 May 2018 02:49:12 +0200 Gilles Filippini  wrote:
> > Source: h5py
> > Version: 2.7.1-2
> > Severity: normal
> > 
> > -BEGIN PGP SIGNED MESSAGE-
> > Hash: SHA512
> > 
> > Hi,
> > 
> > h5py FTBFS with HDF5 1.10.2 currently in experimental. The failure occurs
> > during the tests where two of them fail:
> > 
> > ==
> > FAIL: test_out_of_order_offsets (h5py.tests.hl.test_datatype.TestOffsets)
> > - --
> > Traceback (most recent call last):
> >   File "h5py/tests/hl/test_datatype.py", line 198, in 
> > test_out_of_order_offsets
> > self.assertArrayEqual(fd['data'], data)
> >   File "h5py/tests/common.py", line 124, in assertArrayEqual
> > "Dtype mismatch (%s vs %s)%s" % (dset.dtype, arr.dtype, message)
> > AssertionError: Dtype mismatch ({'names':['f1','f3','f2'], 
> > 'formats':[' > {'names':['f1','f2','f3'], 'formats':[' > 'offsets':[0,16,8], 'itemsize':20})
> > 
> > ==
> > FAIL: test_out_of_order_offsets (h5py.tests.old.test_h5t.TestCompound)
> > - --
> > Traceback (most recent call last):
> >   File "h5py/tests/old/test_h5t.py", line 61, in test_out_of_order_offsets
> > self.assertEqual(tid.dtype, expected_dtype)
> > AssertionError: dtype({'names':['f1','f3','f2'], 
> > 'formats':[' > dtype({'names':['f1','f2','f3'], 'formats':[' > 'offsets':[0,16,8], 'itemsize':20})
> > 
> > - --
> > Ran 447 tests in 1.206s
> > 
> > FAILED (failures=2, skipped=18, expected failures=6)
> 
> Actually it FTBFS with the very same failure on unstable as well. Then
> raising severity to serious.
> 
> This seems tied to the recent python-numpy upgrade to 1.14.3. It builds
> fine against python-numpy 1.13.3.

Upstream release 2.8.0 doesn't FTBFS. The upstream commit 5009e06 [1]
fixes the issue. Attached a patch proposal after this commit.

Thanks,
diff -Nru h5py-2.7.1/debian/changelog h5py-2.7.1/debian/changelog
--- h5py-2.7.1/debian/changelog 2017-09-11 11:15:49.0 +0200
+++ h5py-2.7.1/debian/changelog 2018-05-16 17:00:35.0 +0200
@@ -1,3 +1,10 @@
+h5py (2.7.1-2.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Backport upstream commit to support numpy 1.14
+
+ -- Gilles Filippini   Wed, 16 May 2018 17:00:35 +0200
+
 h5py (2.7.1-2) unstable; urgency=medium
 
   * Fixup the debug package description for Python 2.
diff -Nru h5py-2.7.1/debian/patches/series h5py-2.7.1/debian/patches/series
--- h5py-2.7.1/debian/patches/series2017-09-11 11:15:49.0 +0200
+++ h5py-2.7.1/debian/patches/series2018-05-16 17:00:35.0 +0200
@@ -1,3 +1,4 @@
 No-rpath.patch
 No-intersphinx.patch
 Fix-build-of-API-docs-with-Python-3.patch
+Support-numpy-1.14.patch
diff -Nru h5py-2.7.1/debian/patches/Support-numpy-1.14.patch 
h5py-2.7.1/debian/patches/Support-numpy-1.14.patch
--- h5py-2.7.1/debian/patches/Support-numpy-1.14.patch  1970-01-01 
01:00:00.0 +0100
+++ h5py-2.7.1/debian/patches/Support-numpy-1.14.patch  2018-05-16 
17:00:35.0 +0200
@@ -0,0 +1,84 @@
+Description: Backport of upstream commit 5009e06 stripped of setup related
+ changes
+
+From 5009e062a6f7d4e074cab0fcb42a780ac2b1d7d4 Mon Sep 17 00:00:00 2001
+From: James Tocknell 
+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

Bug#898526: h5py: FTBFS with HDF5 1.10.2

2018-05-13 Thread Gilles Filippini 
Control: severity -1 serious
Control: retitle -1 h5py: FTBFS - FAIL: test_out_of_order_offsets

On Sun, 13 May 2018 02:49:12 +0200 Gilles Filippini  wrote:
> Source: h5py
> Version: 2.7.1-2
> Severity: normal
> 
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA512
> 
> Hi,
> 
> h5py FTBFS with HDF5 1.10.2 currently in experimental. The failure occurs
> during the tests where two of them fail:
> 
> ==
> FAIL: test_out_of_order_offsets (h5py.tests.hl.test_datatype.TestOffsets)
> - --
> Traceback (most recent call last):
>   File "h5py/tests/hl/test_datatype.py", line 198, in 
> test_out_of_order_offsets
> self.assertArrayEqual(fd['data'], data)
>   File "h5py/tests/common.py", line 124, in assertArrayEqual
> "Dtype mismatch (%s vs %s)%s" % (dset.dtype, arr.dtype, message)
> AssertionError: Dtype mismatch ({'names':['f1','f3','f2'], 
> 'formats':[' {'names':['f1','f2','f3'], 'formats':[' 'itemsize':20})
> 
> ==
> FAIL: test_out_of_order_offsets (h5py.tests.old.test_h5t.TestCompound)
> - --
> Traceback (most recent call last):
>   File "h5py/tests/old/test_h5t.py", line 61, in test_out_of_order_offsets
> self.assertEqual(tid.dtype, expected_dtype)
> AssertionError: dtype({'names':['f1','f3','f2'], 
> 'formats':[' dtype({'names':['f1','f2','f3'], 'formats':[' 'offsets':[0,16,8], 'itemsize':20})
> 
> - --
> Ran 447 tests in 1.206s
> 
> FAILED (failures=2, skipped=18, expected failures=6)

Actually it FTBFS with the very same failure on unstable as well. Then
raising severity to serious.

This seems tied to the recent python-numpy upgrade to 1.14.3. It builds
fine against python-numpy 1.13.3.

Thanks,

_g.



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Bug#898526: h5py: FTBFS with HDF5 1.10.2

2018-05-12 Thread Gilles Filippini 
Source: h5py
Version: 2.7.1-2
Severity: normal

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Hi,

h5py FTBFS with HDF5 1.10.2 currently in experimental. The failure occurs
during the tests where two of them fail:

==
FAIL: test_out_of_order_offsets (h5py.tests.hl.test_datatype.TestOffsets)
- --
Traceback (most recent call last):
  File "h5py/tests/hl/test_datatype.py", line 198, in test_out_of_order_offsets
self.assertArrayEqual(fd['data'], data)
  File "h5py/tests/common.py", line 124, in assertArrayEqual
"Dtype mismatch (%s vs %s)%s" % (dset.dtype, arr.dtype, message)
AssertionError: Dtype mismatch ({'names':['f1','f3','f2'], 
'formats':['