Package: python-numpy Version: 1:1.6.2-1 Severity: important Tags: upstream patch
This bug causes FTBFS of pyNN due to being triggered by the tests (built fine before). I have reported it upstream http://projects.scipy.org/numpy/ticket/2178 and sent a tentative unittest + patch (diffs attached) https://github.com/numpy/numpy/pull/328 -- System Information: Debian Release: wheezy/sid APT prefers testing APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 3.1.0-1-amd64 (SMP w/2 CPU cores) Locale: LANG=en_US, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Versions of packages python-numpy depends on: ii libblas3gf [libblas.so.3gf] 1.2.20110419-2 ii libc6 2.13-33 ii libgcc1 1:4.7.1-2 ii libgfortran3 4.7.1-2 ii liblapack3gf [liblapack.so.3gf] 3.3.1-1 ii libquadmath0 4.7.1-2 ii python 2.7.2-10 ii python-support 1.0.14 python-numpy recommends no packages. Versions of packages python-numpy suggests: ii gcc 4:4.7.1-1 ii gfortran 4:4.6.1-2 ii python-dev 2.7.2-10 ii python-nose 1.1.2-3 ii python-numpy-dbg 1:1.6.2-1 ii python-numpy-doc 1:1.5.1-4 -- no debconf information
>From 4df244465c3db3a8e9e624d17ed2982f595e2b8a Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko <[email protected]> Date: Mon, 2 Jul 2012 16:03:53 -0400 Subject: [PATCH 1/2] BUG: do not "own" the FID for GzipFile and file if provided to load already opened (ticket #2178) Also made all assignments of own_file go in pair with assignments to fid to make things clearer --- numpy/lib/npyio.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/numpy/lib/npyio.py b/numpy/lib/npyio.py index 2215299..e16485f 100644 --- a/numpy/lib/npyio.py +++ b/numpy/lib/npyio.py @@ -2,6 +2,9 @@ __all__ = ['savetxt', 'loadtxt', 'genfromtxt', 'ndfromtxt', 'mafromtxt', 'recfromtxt', 'recfromcsv', 'load', 'loads', 'save', 'savez', 'savez_compressed', 'packbits', 'unpackbits', 'fromregex', 'DataSource'] +# Price to pay for overloading standard keywords +import __builtin__ + import numpy as np import format import sys @@ -353,14 +356,19 @@ def load(file, mmap_mode=None): """ import gzip - own_fid = False if isinstance(file, basestring): - fid = open(file, "rb") own_fid = True + fid = open(file, "rb") elif isinstance(file, gzip.GzipFile): + # we were provided an existing handle which we should close + # only if it was closed already + own_fid = file.closed fid = seek_gzip_factory(file) - own_fid = True + elif isinstance(file, __builtin__.file): + own_fid = file.closed + fid = file else: + own_fid = False fid = file try: @@ -371,7 +379,7 @@ def load(file, mmap_mode=None): fid.seek(-N, 1) # back-up if magic.startswith(_ZIP_PREFIX): # zip-file (assume .npz) own_fid = False - return NpzFile(fid, own_fid=True) + return NpzFile(fid, own_fid=own_fid) elif magic == format.MAGIC_PREFIX: # .npy file if mmap_mode: return format.open_memmap(file, mode=mmap_mode) -- 1.7.10
>From 0e3a3d96c7a8e522184c7ca0388cd9d401e902cd Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko <[email protected]> Date: Mon, 2 Jul 2012 16:38:09 -0400 Subject: [PATCH 2/2] ENH: unittest for preceeding commit fixing #2178 --- numpy/lib/tests/test_io.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/numpy/lib/tests/test_io.py b/numpy/lib/tests/test_io.py index 8922070..e9158ba 100644 --- a/numpy/lib/tests/test_io.py +++ b/numpy/lib/tests/test_io.py @@ -167,6 +167,27 @@ class TestSavezLoad(RoundtripTest, TestCase): if errors: raise AssertionError(errors) + def test_not_closing_opened_fid(self): + # Test that issue #2178 is fixed: + # verify could seek on 'loaded' file + + fd, tmp = mkstemp(suffix='.npz') + os.close(fd) + try: + fp = open(tmp, 'w') + np.savez(fp, data='LOVELY LOAD') + fp.close() + + fp = open(tmp, 'r', 10000) + fp.seek(0) + assert_(not fp.closed) + _ = np.load(fp)['data'] + assert_(not fp.closed) # must not get closed by .load(opened fp) + fp.seek(0) + assert_(not fp.closed) + finally: + os.remove(tmp) + class TestSaveTxt(TestCase): def test_array(self): a = np.array([[1, 2], [3, 4]], float) -- 1.7.10
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