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python scipy: run correct tests, fix/remove failing tests

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This commit is contained in:
Frederik Rietdijk 2015-12-14 23:50:07 +01:00
parent 4b6dbfc357
commit 2d07d00856
2 changed files with 498 additions and 1 deletions
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487
pkgs/development/python-modules/scipy-0.16.1-decorator-fix.patch Normal file
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@ -0,0 +1,487 @@
From 8d3cd578f9c0a36d29411c96fa70402a7a56d502 Mon Sep 17 00:00:00 2001
From: Evgeni Burovski <evgeni@burovski.me>
Date: Sun, 8 Nov 2015 15:27:22 +0000
Subject: [PATCH] MAINT: update decorators.py module to version 4.0.5
This is commit d6abda0 at
https://github.com/micheles/decorator/tree/4.0.5
---
scipy/_lib/decorator.py | 380 +++++++++++++++++++++++++++++++++++++-----------
1 file changed, 293 insertions(+), 87 deletions(-)
diff --git a/scipy/_lib/decorator.py b/scipy/_lib/decorator.py
index 07d9d21..05f7056 100644
--- a/scipy/_lib/decorator.py
+++ b/scipy/_lib/decorator.py
@@ -1,48 +1,52 @@
-########################## LICENCE ###############################
-##
-## Copyright (c) 2005-2011, Michele Simionato
-## All rights reserved.
-##
-## Redistributions of source code must retain the above copyright
-## notice, this list of conditions and the following disclaimer.
-## Redistributions in bytecode form must reproduce the above copyright
-## notice, this list of conditions and the following disclaimer in
-## the documentation and/or other materials provided with the
-## distribution.
-
-## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-## "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-## LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-## A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-## HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-## INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-## BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-## OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-## ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
-## TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
-## USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-## DAMAGE.
+# ######################### LICENSE ############################ #
+
+# Copyright (c) 2005-2015, Michele Simionato
+# All rights reserved.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+
+# Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# Redistributions in bytecode form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in
+# the documentation and/or other materials provided with the
+# distribution.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+# OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+# TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+# DAMAGE.
"""
Decorator module, see http://pypi.python.org/pypi/decorator
for the documentation.
"""
+from __future__ import print_function
-from __future__ import division, print_function, absolute_import
-
-__version__ = '3.3.2'
-
-__all__ = ["decorator", "FunctionMaker"]
-
-import sys
import re
+import sys
import inspect
-from functools import partial
+import operator
+import itertools
+import collections
-from scipy._lib.six import exec_
+__version__ = '4.0.5'
if sys.version >= '3':
from inspect import getfullargspec
+
+ def get_init(cls):
+ return cls.__init__
else:
class getfullargspec(object):
"A quick and dirty replacement for getfullargspec for Python 2.X"
@@ -51,7 +55,6 @@ else:
inspect.getargspec(f)
self.kwonlyargs = []
self.kwonlydefaults = None
- self.annotations = getattr(f, '__annotations__', {})
def __iter__(self):
yield self.args
@@ -59,17 +62,35 @@ else:
yield self.varkw
yield self.defaults
-DEF = re.compile('\s*def\s*([_\w][_\w\d]*)\s*\(')
+ getargspec = inspect.getargspec
+
+ def get_init(cls):
+ return cls.__init__.__func__
+
+# getargspec has been deprecated in Python 3.5
+ArgSpec = collections.namedtuple(
+ 'ArgSpec', 'args varargs varkw defaults')
-# basic functionality
+def getargspec(f):
+ """A replacement for inspect.getargspec"""
+ spec = getfullargspec(f)
+ return ArgSpec(spec.args, spec.varargs, spec.varkw, spec.defaults)
+DEF = re.compile('\s*def\s*([_\w][_\w\d]*)\s*\(')
+
+
+# basic functionality
class FunctionMaker(object):
"""
An object with the ability to create functions with a given signature.
It has attributes name, doc, module, signature, defaults, dict and
methods update and make.
"""
+
+ # Atomic get-and-increment provided by the GIL
+ _compile_count = itertools.count()
+
def __init__(self, func=None, name=None, signature=None,
defaults=None, doc=None, module=None, funcdict=None):
self.shortsignature = signature
@@ -82,22 +103,32 @@ class FunctionMaker(object):
self.module = func.__module__
if inspect.isfunction(func):
argspec = getfullargspec(func)
+ self.annotations = getattr(func, '__annotations__', {})
for a in ('args', 'varargs', 'varkw', 'defaults', 'kwonlyargs',
- 'kwonlydefaults', 'annotations'):
+ 'kwonlydefaults'):
setattr(self, a, getattr(argspec, a))
for i, arg in enumerate(self.args):
setattr(self, 'arg%d' % i, arg)
- self.signature = inspect.formatargspec(
- formatvalue=lambda val: "", *argspec)[1:-1]
- allargs = list(self.args)
- if self.varargs:
- allargs.append('*' + self.varargs)
- if self.varkw:
- allargs.append('**' + self.varkw)
- try:
- self.shortsignature = ', '.join(allargs)
- except TypeError: # exotic signature, valid only in Python 2.X
- self.shortsignature = self.signature
+ if sys.version < '3': # easy way
+ self.shortsignature = self.signature = (
+ inspect.formatargspec(
+ formatvalue=lambda val: "", *argspec)[1:-1])
+ else: # Python 3 way
+ allargs = list(self.args)
+ allshortargs = list(self.args)
+ if self.varargs:
+ allargs.append('*' + self.varargs)
+ allshortargs.append('*' + self.varargs)
+ elif self.kwonlyargs:
+ allargs.append('*') # single star syntax
+ for a in self.kwonlyargs:
+ allargs.append('%s=None' % a)
+ allshortargs.append('%s=%s' % (a, a))
+ if self.varkw:
+ allargs.append('**' + self.varkw)
+ allshortargs.append('**' + self.varkw)
+ self.signature = ', '.join(allargs)
+ self.shortsignature = ', '.join(allshortargs)
self.dict = func.__dict__.copy()
# func=None happens when decorating a caller
if name:
@@ -122,12 +153,15 @@ class FunctionMaker(object):
func.__name__ = self.name
func.__doc__ = getattr(self, 'doc', None)
func.__dict__ = getattr(self, 'dict', {})
- if sys.version_info[0] >= 3:
- func.__defaults__ = getattr(self, 'defaults', ())
- else:
- func.func_defaults = getattr(self, 'defaults', ())
+ func.__defaults__ = getattr(self, 'defaults', ())
func.__kwdefaults__ = getattr(self, 'kwonlydefaults', None)
- callermodule = sys._getframe(3).f_globals.get('__name__', '?')
+ func.__annotations__ = getattr(self, 'annotations', None)
+ try:
+ frame = sys._getframe(3)
+ except AttributeError: # for IronPython and similar implementations
+ callermodule = '?'
+ else:
+ callermodule = frame.f_globals.get('__name__', '?')
func.__module__ = getattr(self, 'module', callermodule)
func.__dict__.update(kw)
@@ -140,16 +174,20 @@ class FunctionMaker(object):
raise SyntaxError('not a valid function template\n%s' % src)
name = mo.group(1) # extract the function name
names = set([name] + [arg.strip(' *') for arg in
- self.shortsignature.split(',')])
+ self.shortsignature.split(',')])
for n in names:
if n in ('_func_', '_call_'):
raise NameError('%s is overridden in\n%s' % (n, src))
if not src.endswith('\n'): # add a newline just for safety
src += '\n' # this is needed in old versions of Python
+
+ # Ensure each generated function has a unique filename for profilers
+ # (such as cProfile) that depend on the tuple of (<filename>,
+ # <definition line>, <function name>) being unique.
+ filename = '<decorator-gen-%d>' % (next(self._compile_count),)
try:
- code = compile(src, '<string>', 'single')
- # print >> sys.stderr, 'Compiling %s' % src
- exec_(code, evaldict)
+ code = compile(src, filename, 'single')
+ exec(code, evaldict)
except:
print('Error in generated code:', file=sys.stderr)
print(src, file=sys.stderr)
@@ -165,9 +203,9 @@ class FunctionMaker(object):
doc=None, module=None, addsource=True, **attrs):
"""
Create a function from the strings name, signature and body.
- evaldict is the evaluation dictionary. If addsource is true an attribute
- __source__ is added to the result. The attributes attrs are added,
- if any.
+ evaldict is the evaluation dictionary. If addsource is true an
+ attribute __source__ is added to the result. The attributes attrs
+ are added, if any.
"""
if isinstance(obj, str): # "name(signature)"
name, rest = obj.strip().split('(', 1)
@@ -180,37 +218,205 @@ class FunctionMaker(object):
self = cls(func, name, signature, defaults, doc, module)
ibody = '\n'.join(' ' + line for line in body.splitlines())
return self.make('def %(name)s(%(signature)s):\n' + ibody,
- evaldict, addsource, **attrs)
+ evaldict, addsource, **attrs)
-def decorator(caller, func=None):
+def decorate(func, caller):
"""
- decorator(caller) converts a caller function into a decorator;
- decorator(caller, func) decorates a function using a caller.
+ decorate(func, caller) decorates a function using a caller.
"""
- if func is not None: # returns a decorated function
- if sys.version_info[0] >= 3:
- evaldict = func.__globals__.copy()
+ evaldict = func.__globals__.copy()
+ evaldict['_call_'] = caller
+ evaldict['_func_'] = func
+ fun = FunctionMaker.create(
+ func, "return _call_(_func_, %(shortsignature)s)",
+ evaldict, __wrapped__=func)
+ if hasattr(func, '__qualname__'):
+ fun.__qualname__ = func.__qualname__
+ return fun
+
+
+def decorator(caller, _func=None):
+ """decorator(caller) converts a caller function into a decorator"""
+ if _func is not None: # return a decorated function
+ # this is obsolete behavior; you should use decorate instead
+ return decorate(_func, caller)
+ # else return a decorator function
+ if inspect.isclass(caller):
+ name = caller.__name__.lower()
+ callerfunc = get_init(caller)
+ doc = 'decorator(%s) converts functions/generators into ' \
+ 'factories of %s objects' % (caller.__name__, caller.__name__)
+ elif inspect.isfunction(caller):
+ if caller.__name__ == '<lambda>':
+ name = '_lambda_'
else:
- evaldict = func.func_globals.copy()
- evaldict['_call_'] = caller
- evaldict['_func_'] = func
+ name = caller.__name__
+ callerfunc = caller
+ doc = caller.__doc__
+ else: # assume caller is an object with a __call__ method
+ name = caller.__class__.__name__.lower()
+ callerfunc = caller.__call__.__func__
+ doc = caller.__call__.__doc__
+ evaldict = callerfunc.__globals__.copy()
+ evaldict['_call_'] = caller
+ evaldict['_decorate_'] = decorate
+ return FunctionMaker.create(
+ '%s(func)' % name, 'return _decorate_(func, _call_)',
+ evaldict, doc=doc, module=caller.__module__,
+ __wrapped__=caller)
+
+
+# ####################### contextmanager ####################### #
+
+try: # Python >= 3.2
+ from contextlib import _GeneratorContextManager
+except ImportError: # Python >= 2.5
+ from contextlib import GeneratorContextManager as _GeneratorContextManager
+
+
+class ContextManager(_GeneratorContextManager):
+ def __call__(self, func):
+ """Context manager decorator"""
return FunctionMaker.create(
- func, "return _call_(_func_, %(shortsignature)s)",
- evaldict, undecorated=func, __wrapped__=func)
- else: # returns a decorator
- if isinstance(caller, partial):
- return partial(decorator, caller)
- # otherwise assume caller is a function
- first = inspect.getargspec(caller)[0][0] # first arg
- if sys.version_info[0] >= 3:
- evaldict = caller.__globals__.copy()
- else:
- evaldict = caller.func_globals.copy()
- evaldict['_call_'] = caller
- evaldict['decorator'] = decorator
+ func, "with _self_: return _func_(%(shortsignature)s)",
+ dict(_self_=self, _func_=func), __wrapped__=func)
+
+init = getfullargspec(_GeneratorContextManager.__init__)
+n_args = len(init.args)
+if n_args == 2 and not init.varargs: # (self, genobj) Python 2.7
+ def __init__(self, g, *a, **k):
+ return _GeneratorContextManager.__init__(self, g(*a, **k))
+ ContextManager.__init__ = __init__
+elif n_args == 2 and init.varargs: # (self, gen, *a, **k) Python 3.4
+ pass
+elif n_args == 4: # (self, gen, args, kwds) Python 3.5
+ def __init__(self, g, *a, **k):
+ return _GeneratorContextManager.__init__(self, g, a, k)
+ ContextManager.__init__ = __init__
+
+contextmanager = decorator(ContextManager)
+
+
+# ############################ dispatch_on ############################ #
+
+def append(a, vancestors):
+ """
+ Append ``a`` to the list of the virtual ancestors, unless it is already
+ included.
+ """
+ add = True
+ for j, va in enumerate(vancestors):
+ if issubclass(va, a):
+ add = False
+ break
+ if issubclass(a, va):
+ vancestors[j] = a
+ add = False
+ if add:
+ vancestors.append(a)
+
+
+# inspired from simplegeneric by P.J. Eby and functools.singledispatch
+def dispatch_on(*dispatch_args):
+ """
+ Factory of decorators turning a function into a generic function
+ dispatching on the given arguments.
+ """
+ assert dispatch_args, 'No dispatch args passed'
+ dispatch_str = '(%s,)' % ', '.join(dispatch_args)
+
+ def check(arguments, wrong=operator.ne, msg=''):
+ """Make sure one passes the expected number of arguments"""
+ if wrong(len(arguments), len(dispatch_args)):
+ raise TypeError('Expected %d arguments, got %d%s' %
+ (len(dispatch_args), len(arguments), msg))
+
+ def gen_func_dec(func):
+ """Decorator turning a function into a generic function"""
+
+ # first check the dispatch arguments
+ argset = set(getfullargspec(func).args)
+ if not set(dispatch_args) <= argset:
+ raise NameError('Unknown dispatch arguments %s' % dispatch_str)
+
+ typemap = {}
+
+ def vancestors(*types):
+ """
+ Get a list of sets of virtual ancestors for the given types
+ """
+ check(types)
+ ras = [[] for _ in range(len(dispatch_args))]
+ for types_ in typemap:
+ for t, type_, ra in zip(types, types_, ras):
+ if issubclass(t, type_) and type_ not in t.__mro__:
+ append(type_, ra)
+ return [set(ra) for ra in ras]
+
+ def ancestors(*types):
+ """
+ Get a list of virtual MROs, one for each type
+ """
+ check(types)
+ lists = []
+ for t, vas in zip(types, vancestors(*types)):
+ n_vas = len(vas)
+ if n_vas > 1:
+ raise RuntimeError(
+ 'Ambiguous dispatch for %s: %s' % (t, vas))
+ elif n_vas == 1:
+ va, = vas
+ mro = type('t', (t, va), {}).__mro__[1:]
+ else:
+ mro = t.__mro__
+ lists.append(mro[:-1]) # discard t and object
+ return lists
+
+ def register(*types):
+ """
+ Decorator to register an implementation for the given types
+ """
+ check(types)
+ def dec(f):
+ check(getfullargspec(f).args, operator.lt, ' in ' + f.__name__)
+ typemap[types] = f
+ return f
+ return dec
+
+ def dispatch_info(*types):
+ """
+ An utility to introspect the dispatch algorithm
+ """
+ check(types)
+ lst = []
+ for anc in itertools.product(*ancestors(*types)):
+ lst.append(tuple(a.__name__ for a in anc))
+ return lst
+
+ def _dispatch(dispatch_args, *args, **kw):
+ types = tuple(type(arg) for arg in dispatch_args)
+ try: # fast path
+ f = typemap[types]
+ except KeyError:
+ pass
+ else:
+ return f(*args, **kw)
+ combinations = itertools.product(*ancestors(*types))
+ next(combinations) # the first one has been already tried
+ for types_ in combinations:
+ f = typemap.get(types_)
+ if f is not None:
+ return f(*args, **kw)
+
+ # else call the default implementation
+ return func(*args, **kw)
+
return FunctionMaker.create(
- '%s(%s)' % (caller.__name__, first),
- 'return decorator(_call_, %s)' % first,
- evaldict, undecorated=caller, __wrapped__=caller,
- doc=caller.__doc__, module=caller.__module__)
+ func, 'return _f_(%s, %%(shortsignature)s)' % dispatch_str,
+ dict(_f_=_dispatch), register=register, default=func,
+ typemap=typemap, vancestors=vancestors, ancestors=ancestors,
+ dispatch_info=dispatch_info, __wrapped__=func)
+
+ gen_func_dec.__name__ = 'dispatch_on' + dispatch_str
+ return gen_func_dec
--
2.6.3

12
pkgs/top-level/python-packages.nix
View File

@ -17160,7 +17160,7 @@ in modules // {
support = import ../development/python-modules/numpy-scipy-support.nix {
inherit python;
openblas = pkgs.openblasCompat;
pkgName = "numpy";
pkgName = "scipy";
};
in buildPythonPackage rec {
name = "scipy-${version}";
@ -17178,8 +17178,18 @@ in modules // {
sed -i '0,/from numpy.distutils.core/s//import setuptools;from numpy.distutils.core/' setup.py
'';
# First test: RuntimeWarning: Mean of empty slice.
# Second: SyntaxError: invalid syntax. Due to wrapper?
# Third: test checks permissions
prePatch = ''
substituteInPlace scipy/stats/tests/test_stats.py --replace "test_chisquare_masked_arrays" "remove_this_one"
rm scipy/linalg/tests/test_lapack.py
substituteInPlace scipy/weave/tests/test_catalog.py --replace "test_user" "remove_this_one"
'';
inherit (support) preBuild checkPhase;
patches = [../development/python-modules/scipy-0.16.1-decorator-fix.patch];
setupPyBuildFlags = [ "--fcompiler='gnu95'" ];
meta = {