10000 Closes issue #586. Updates handling of nan behaviour in numpy.lib.function_base.median. by empeeu · Pull Request #4287 · numpy/numpy · GitHub
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Closes issue #586. Updates handling of nan behaviour in numpy.lib.function_base.median. #4287

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a9eff96
ENH: added proper handling of nans for numpy.lib.function_base.median…
empeeu Feb 13, 2014
54aff25
ENH: added unit test for previous commit which updates median's handling
empeeu Feb 13, 2014
10902b5
ENH: #586. Improved performance of nan handling in median function.
empeeu Feb 17, 2014
8c2f007
DOC: Updated doc string for nanmedian.
empeeu Feb 17, 2014
d8e3957
REV: Reverting nanmedian from this PR. Now deals exclusively with han…
empeeu Feb 18, 2014
aa615ad
numpy.i bugfix: fortran ordering check
jspreston Feb 20, 2014
89d4d1e
ENH: #586 Pulls in juliantaylor's specialization. New median with nan…
empeeu Feb 26, 2014
ea89757
BUG: restore api for file npy_PyFile_Dup and npy_PyFile_DupClose
juliantaylor Mar 5, 2014
0bf8fec
Merge pull request #4334 from jspreston/patch-1
charris Mar 5, 2014
683bc33
Merge pull request #4450 from juliantaylor/api-restore
charris Mar 5, 2014
4b2b77e
Revert "Merge pull request #4421 from meltingwax/meltingwax/4382"
Mar 6, 2014
a6f9b78
Merge pull request #4451 from meltingwax/meltingwax/revert-4421
charris Mar 6, 2014
bf2a953
TST: work around outdated travis boxes
juliantaylor Mar 6, 2014
ea75479
DOC: Fixed documentation on lstsq function on when it return an empty…
cimarronm Mar 7, 2014
b099017
Merge pull request #4457 from cimarronm/linalg_lstsq_docfix
seberg Mar 7, 2014
0007cd6
Merge pull request #4456 from juliantaylor/travis-updates
juliantaylor Mar 7, 2014
4da29a8
Merge pull request #4459 from Sankarshan-Mudkavi/fix-gh-1367
juliantaylor Mar 7, 2014
c35542c
ENH: added proper handling of nans for numpy.lib.function_base.median…
empeeu Feb 13, 2014
210f534
ENH: added unit test for previous commit which updates median's handling
empeeu Feb 13, 2014
22eeef0
ENH: #586. Improved performance of nan handling in median function.
empeeu Feb 17, 2014
2d8f3ed
DOC: Updated doc string for nanmedian.
empeeu Feb 17, 2014
52ccb4e
REV: Reverting nanmedian from this PR. Now deals exclusively with han…
empeeu Feb 18, 2014
cbca46c
ENH: #586 Pulls in juliantaylor's specialization. New median with nan…
empeeu Feb 26, 2014
d76ed36
Merge branch 'master' of github.com:empeeu/numpy
empeeu Mar 8, 2014
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10 changes: 4 additions & 6 deletions numpy/distutils/fcompiler/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
from numpy.distutils.ccompiler import CCompiler, gen_lib_options
from numpy.distutils import log
from numpy.distutils.misc_util import is_string, all_strings, is_sequence, \
make_temp_file, get_shared_lib_extension, quote
make_temp_file, get_shared_lib_extension
from numpy.distutils.environment import EnvironmentConfig
from numpy.distutils.exec_command import find_executable
from numpy.distutils.compat import get_exception
Expand Down Expand Up @@ -582,12 +582,12 @@ def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
% (self.__class__.__name__, src))
extra_compile_args = self.extra_f90_compile_args or []
if self.object_switch[-1]==' ':
o_args = [self.object_switch.strip(), quote(obj)]
o_args = [self.object_switch.strip(), obj]
else:
o_args = [self.object_switch.strip() + quote(obj)]
o_args = [self.object_switch.strip()+obj]

assert self.compile_switch.strip()
s_args = [self.compile_switch, quote(src)]
s_args = [self.compile_switch, src]

if extra_compile_args:
log.info('extra %s options: %r' \
Expand Down Expand Up @@ -659,7 +659,6 @@ def link(self, target_desc, objects,
else:
ld_args = objects + self.objects
ld_args = ld_args + lib_opts + o_args
ld_args = [quote(ld_arg) for ld_arg in ld_args]
if debug:
ld_args[:0] = ['-g']
if extra_preargs:
Expand Down Expand Up @@ -988,4 +987,3 @@ def get_f77flags(src):

if __name__ == '__main__':
show_fcompilers()

8 changes: 1 addition & 7 deletions numpy/distutils/misc_util.py
Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,6 @@
import distutils
from distutils.errors import DistutilsError

try:
from pipes import quote
except ImportError:
from shlex import quote

try:
set
except NameError:
Expand All @@ -36,8 +31,7 @@
'get_script_files', 'get_lib_source_files', 'get_data_files',
'dot_join', 'get_frame', 'minrelpath', 'njoin',
'is_sequence', 'is_string', 'as_list', 'gpaths', 'get_language',
'quote_args', 'quote', 'get_build_architecture', 'get_info',
'get_pkg_info']
'quote_args', 'get_build_architecture', 'get_info', 'get_pkg_info']

class InstallableLib(object):
"""
Expand Down
14 changes: 7 additions & 7 deletions numpy/distutils/npy_pkg_config.py
Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,6 @@
else:
from configparser import ConfigParser, SafeConfigParser, NoOptionError

from numpy.distutils.misc_util import quote

__all__ = ['FormatError', 'PkgNotFound', 'LibraryInfo', 'VariableSet',
'read_config', 'parse_flags']

Expand Down Expand Up @@ -58,7 +56,7 @@ def parse_flags(line):
* 'ignored'

"""
lexer = shlex.shlex(line, posix=True)
lexer = shlex.shlex(line)
lexer.whitespace_split = True

d = {'include_dirs': [], 'library_dirs': [], 'libraries': [],
Expand Down Expand Up @@ -90,6 +88,8 @@ def next_token(t):

return d

def _escape_backslash(val):
return val.replace('\\', '\\\\')

class LibraryInfo(object):
"""
Expand Down Expand Up @@ -147,11 +147,11 @@ def sections(self):

def cflags(self, section="default"):
val = self.vars.interpolate(self._sections[section]['cflags'])
return quote(val)
return _escape_backslash(val)

def libs(self, section="default"):
val = self.vars.interpolate(self._sections[section]['libs'])
return quote(val)
return _escape_backslash(val)

def __str__(self):
m = ['Name: %s' % self.name]
Expand Down Expand Up @@ -289,7 +289,7 @@ def parse_config(filename, dirs=None):
vars = {}
if config.has_section('variables'):
for name, value in config.items("variables"):
vars[name] = quote(value)
vars[name] = _escape_backslash(value)

# Parse "normal" sections
secs = [s for s in config.sections() if not s in ['meta', 'variables']]
Expand Down Expand Up @@ -338,7 +338,7 @@ def _read_config(f):
(pkgname, meta["name"]))

mod = sys.modules[pkgname]
vars["pkgdir"] = quote(os.path.dirname(mod.__file__))
vars["pkgdir"] = _escape_backslash(os.path.dirname(mod.__file__))

return LibraryInfo(name=meta["name"], description=meta["description"],
version=meta["version"], sections=sections, vars=VariableSet(vars))
Expand Down
75 changes: 9 additions & 66 deletions numpy/distutils/tests/test_npy_pkg_config.py
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
from __future__ import division, absolute_import, print_function

import os
import shlex
from tempfile import mkstemp

from numpy.testing import *
Expand Down Expand Up @@ -39,12 +38,6 @@
'version': '0.1', 'name': 'foo'}

class TestLibraryInfo(TestCase):

def assertLexEqual(self, str1, str2):
# Use shlex.split for comparison because it is above quotes
# eg: shlex.split("'abc'") == shlex.split("abc")
return shlex.split(str1) == shlex.split(str2)

def test_simple(self):
fd, filename = mkstemp('foo.ini')
try:
Expand All @@ -55,10 +48,10 @@ def test_simple(self):
os.close(fd)

out = read_config(pkg)
self.assertLexEqual(out.cflags(), simple_d['cflags'])
self.assertLexEqual(out.libs(), simple_d['libflags'])
self.assertEqual(out.name, simple_d['name'])
self.assertEqual(out.version, simple_d['version'])
self.assertTrue(out.cflags() == simple_d['cflags'])
self.assertTrue(out.libs() == simple_d['libflags'])
self.assertTrue(out.name == simple_d['name'])
self.assertTrue(out.version == simple_d['version'])
finally:
os.remove(filename)

Expand All @@ -72,13 +65,13 @@ def test_simple_variable(self):
os.close(fd)

out = read_config(pkg)
self.assertLexEqual(out.cflags(), simple_variable_d['cflags'])
self.assertLexEqual(out.libs(), simple_variable_d['libflags'])
self.assertEqual(out.name, simple_variable_d['name'])
self.assertEqual(out.version, simple_variable_d['version'])
self.assertTrue(out.cflags() == simple_variable_d['cflags'])
self.assertTrue(out.libs() == simple_variable_d['libflags'])
self.assertTrue(out.name == simple_variable_d['name'])
self.assertTrue(out.version == simple_variable_d['version'])

out.vars['prefix'] = '/Users/david'
self.assertLexEqual(out.cflags(), '-I/Users/david/include')
self.assertTrue(out.cflags() == '-I/Users/david/include')
finally:
os.remove(filename)

Expand All @@ -95,28 +88,6 @@ def test_simple_cflags(self):
self.assertTrue(d['include_dirs'] == ['/usr/include'])
self.assertTrue(d['macros'] == ['FOO'])

def test_quotes_cflags(self):
d = parse_flags("-I'/usr/foo bar/include' -DFOO")
self.assertTrue(d['include_dirs'] == ['/usr/foo bar/include'])
self.assertTrue(d['macros'] == ['FOO'])

d = parse_flags("-I/usr/'foo bar'/include -DFOO")
self.assertTrue(d['include_dirs'] == ['/usr/foo bar/include'])
self.assertTrue(d['macros'] == ['FOO'])

d = parse_flags("'-I/usr/foo bar'/include -DFOO")
self.assertTrue(d['include_dirs'] == ['/usr/foo bar/include'])
self.assertTrue(d['macros'] == ['FOO'])

def test_escaping_cflags(self):
d = parse_flags("-I/usr/foo\\ bar/include -DFOO")
self.assertTrue(d['include_dirs'] == ['/usr/foo bar/include'])
self.assertTrue(d['macros'] == ['FOO'])

d = parse_flags(r"-I/usr/foo\ bar/include -DFOO")
self.assertTrue(d['include_dirs'] == ['/usr/foo bar/include'])
self.assertTrue(d['macros'] == ['FOO'])

def test_simple_lflags(self):
d = parse_flags("-L/usr/lib -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/lib', '/usr/lib'])
Expand All @@ -125,31 +96,3 @@ def test_simple_lflags(self):
d = parse_flags("-L /usr/lib -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/lib', '/usr/lib'])
self.assertTrue(d['libraries'] == ['foo', 'bar'])

def test_quotes_lflags(self):
d = parse_flags("-L'/usr/foo bar' -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/foo bar', '/usr/lib'])

d = parse_flags("-L/usr/'foo bar' -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/foo bar', '/usr/lib'])

d = parse_flags("\"-L/usr/foo bar\" -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/foo bar', '/usr/lib'])

d = parse_flags("\"-L/usr/foo bar/baz buz\" -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/foo bar/baz buz', '/usr/lib'])

def test_escaping_lflags(self):
d = parse_flags("-L/usr/foo\\ bar -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/foo bar', '/usr/lib'])

d = parse_flags(r"-L/usr/foo\ bar -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/foo bar', '/usr/lib'])

def test_odd_characters_lflags(self):
# tab in directory name
d = parse_flags('-L/usr/"foo\tbar" -lfoo -L/usr/lib -lbar')
self.assertTrue(d['library_dirs'] == ['/usr/foo\tbar', '/usr/lib'])

d = parse_flags("-L/usr/foo\\\tbar -lfoo -L/usr/lib -lbar")
self.assertTrue(d['library_dirs'] == ['/usr/foo\tbar', '/usr/lib'])
5 changes: 2 additions & 3 deletions numpy/distutils/unixccompiler.py
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
from distutils.unixccompiler import *
from numpy.distutils.ccompiler import replace_method
from numpy.distutils.compat import get_exception
from numpy.distutils.misc_util import quote_args, quote

if sys.version_info[0] < 3:
from . import log
Expand Down Expand Up @@ -89,8 +88,8 @@ def UnixCCompiler_create_static_lib(self, objects, output_libname,
display = '%s: adding %d object files to %s' % (
os.path.basename(self.archiver[0]),
len(objects), output_filename)
command = self.archiver + [quote(output_filename)] + quote_args(objects)
self.spawn(command, display = display)
self.spawn(self.archiver + [output_filename] + objects,
display = display)

# Not many Unices required ranlib anymore -- SunOS 4.x is, I
# think the only major Unix that does. Maybe we need some
Expand Down
0