[SciPy-dev] 0.7.0 release

Ondrej Certik ondrej@certik...
Mon Apr 7 09:03:12 CDT 2008


Hi,

what are the release plans for 0.7.0? SciPy svn contains a lot of new
improvements (especially the sparse solvers) that I need. I tried to
create a Debian package from the scipy svn version, just to see if it
works and it seems to be ok. However, when I run tests, I got a lot of
errors (see below).

Are those known problems, or just Debian related? Running on:

In [2]: import scipy

In [3]: scipy.__version__
Out[3]: '0.7.0.dev4087'

Ondrej

------------------

ondra@fuji:~/debian/packages/result$ ipython
Python 2.4.5 (#2, Mar 12 2008, 00:15:51)
Type "copyright", "credits" or "license" for more information.

IPython 0.8.2 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object'. ?object also works, ?? prints more.

In [1]: import scipy

In [2]: scipy.test()
/usr/lib/python2.4/site-packages/scipy/linsolve/__init__.py:4:
DeprecationWarning: scipy.linsolve has moved to
scipy.sparse.linalg.dsolve
  warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve',
DeprecationWarning)
/usr/lib/python2.4/site-packages/scipy/splinalg/__init__.py:3:
DeprecationWarning: scipy.splinalg has moved to scipy.sparse.linalg
  warn('scipy.splinalg has moved to scipy.sparse.linalg', DeprecationWarning)
E.............EE...caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
..EEE............................................................................................................................................................................................................................................................................................................................................................................................................/usr/lib/python2.4/site-packages/scipy/ndimage/_segmenter.py:30:
UserWarning: The segmentation code is under heavy development and
therefore the public API will change in the future.  The NIPY group is
actively working on this code, and has every intention of generalizing
this for the Scipy community.  Use this module minimally, if at all,
until it this warning is removed.
  warnings.warn(_msg, UserWarning)
.................................EE..............................................................................................................................................................................................................................................................................................................................0.2
0.2
0.2
......0.2
..0.2
0.2
0.2
0.2
0.2
...................EE...warning: specified build_dir '_bad_path_' does
not exist or is not writable. Trying default locations
...warning: specified build_dir '..' does not exist or is not
writable. Trying default locations
..warning: specified build_dir '_bad_path_' does not exist or is not
writable. Trying default locations
...warning: specified build_dir '..' does not exist or is not
writable. Trying default locations
............................building extensions here:
/home/ondra/.python24_compiled/m0
.Numpy is installed in /usr/lib/python2.4/site-packages/numpy
Numpy version 1.0.4
Python version 2.4.5 (#2, Mar 12 2008, 00:15:51) [GCC 4.2.3 (Debian 4.2.3-2)]
  Found 10/10 tests for numpy.core.defmatrix
  Found 36/36 tests for numpy.core.ma
  Found 223/223 tests for numpy.core.multiarray
  Found 62/62 tests for numpy.core.numeric
  Found 31/31 tests for numpy.core.numerictypes
  Found 12/12 tests for numpy.core.records
  Found 6/6 tests for numpy.core.scalarmath
  Found 14/14 tests for numpy.core.umath
  Found 5/5 tests for numpy.distutils.misc_util
  Found 1/1 tests for numpy.fft.fftpack
  Found 3/3 tests for numpy.fft.helper
  Found 9/9 tests for numpy.lib.arraysetops
  Found 46/46 tests for numpy.lib.function_base
  Found 5/5 tests for numpy.lib.getlimits
  Found 4/4 tests for numpy.lib.index_tricks
  Found 3/3 tests for numpy.lib.polynomial
  Found 49/49 tests for numpy.lib.shape_base
  Found 15/15 tests for numpy.lib.twodim_base
  Found 43/43 tests for numpy.lib.type_check
  Found 1/1 tests for numpy.lib.ufunclike
  Found 40/40 tests for numpy.linalg
  Found 2/2 tests for numpy.random
  Found 0/0 tests for __main__
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 685 tests in 0.623s

OK
.............................................................................Numpy
is installed in /usr/lib/python2.4/site-packages/numpy
Numpy version 1.0.4
Python version 2.4.5 (#2, Mar 12 2008, 00:15:51) [GCC 4.2.3 (Debian 4.2.3-2)]
  Found 10/10 tests for numpy.core.defmatrix
  Found 36/36 tests for numpy.core.ma
  Found 223/223 tests for numpy.core.multiarray
  Found 62/62 tests for numpy.core.numeric
  Found 31/31 tests for numpy.core.numerictypes
  Found 12/12 tests for numpy.core.records
  Found 6/6 tests for numpy.core.scalarmath
  Found 14/14 tests for numpy.core.umath
  Found 5/5 tests for numpy.distutils.misc_util
  Found 1/1 tests for numpy.fft.fftpack
  Found 3/3 tests for numpy.fft.helper
  Found 9/9 tests for numpy.lib.arraysetops
  Found 46/46 tests for numpy.lib.function_base
  Found 5/5 tests for numpy.lib.getlimits
  Found 4/4 tests for numpy.lib.index_tricks
  Found 3/3 tests for numpy.lib.polynomial
  Found 49/49 tests for numpy.lib.shape_base
  Found 15/15 tests for numpy.lib.twodim_base
  Found 43/43 tests for numpy.lib.type_check
  Found 1/1 tests for numpy.lib.ufunclike
  Found 40/40 tests for numpy.linalg
  Found 2/2 tests for numpy.random
  Found 0/0 tests for __main__
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 685 tests in 0.493s

OK
....................Numpy is installed in /usr/lib/python2.4/site-packages/numpy
Numpy version 1.0.4
Python version 2.4.5 (#2, Mar 12 2008, 00:15:51) [GCC 4.2.3 (Debian 4.2.3-2)]
  Found 10/10 tests for numpy.core.defmatrix
  Found 36/36 tests for numpy.core.ma
  Found 223/223 tests for numpy.core.multiarray
  Found 62/62 tests for numpy.core.numeric
  Found 31/31 tests for numpy.core.numerictypes
  Found 12/12 tests for numpy.core.records
  Found 6/6 tests for numpy.core.scalarmath
  Found 14/14 tests for numpy.core.umath
  Found 5/5 tests for numpy.distutils.misc_util
  Found 1/1 tests for numpy.fft.fftpack
  Found 3/3 tests for numpy.fft.helper
  Found 9/9 tests for numpy.lib.arraysetops
  Found 46/46 tests for numpy.lib.function_base
  Found 5/5 tests for numpy.lib.getlimits
  Found 4/4 tests for numpy.lib.index_tricks
  Found 3/3 tests for numpy.lib.polynomial
  Found 49/49 tests for numpy.lib.shape_base
  Found 15/15 tests for numpy.lib.twodim_base
  Found 43/43 tests for numpy.lib.type_check
  Found 1/1 tests for numpy.lib.ufunclike
  Found 40/40 tests for numpy.linalg
  Found 2/2 tests for numpy.random
  Found 0/0 tests for __main__
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 685 tests in 0.513s

OK
.
======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/integrate/tests/test_integrate.py",
line 9, in ?
    from scipy.linalg import norm
  File "/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py",
line 13, in ?
    from iterative import *
  File "/usr/lib/python2.4/site-packages/scipy/linalg/iterative.py",
line 5, in ?
    from scipy.sparse.linalg import isolve
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/interpolate/__init__.py",
line 7, in ?
    from interpolate import *
  File "/usr/lib/python2.4/site-packages/scipy/interpolate/interpolate.py",
line 13, in ?
    import scipy.linalg as slin
  File "/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py",
line 13, in ?
    from iterative import *
  File "/usr/lib/python2.4/site-packages/scipy/linalg/iterative.py",
line 5, in ?
    from scipy.sparse.linalg import isolve
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

======================================================================
ERROR: Failure: ImportError (cannot import name deprecate_with_doc)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/io/__init__.py", line 7, in ?
    from numpy import deprecate_with_doc
ImportError: cannot import name deprecate_with_doc

======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py",
line 13, in ?
    from iterative import *
  File "/usr/lib/python2.4/site-packages/scipy/linalg/iterative.py",
line 5, in ?
    from scipy.sparse.linalg import isolve
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/linsolve/__init__.py",
line 6, in ?
    from scipy.sparse.linalg.dsolve import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/maxentropy/__init__.py",
line 9, in ?
    from maxentropy import *
  File "/usr/lib/python2.4/site-packages/scipy/maxentropy/maxentropy.py",
line 74, in ?
    from scipy import optimize, sparse
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/signal/__init__.py",
line 11, in ?
    from ltisys import *
  File "/usr/lib/python2.4/site-packages/scipy/signal/ltisys.py", line 9, in ?
    import scipy.interpolate as interpolate
  File "/usr/lib/python2.4/site-packages/scipy/interpolate/__init__.py",
line 7, in ?
    from interpolate import *
  File "/usr/lib/python2.4/site-packages/scipy/interpolate/interpolate.py",
line 13, in ?
    import scipy.linalg as slin
  File "/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py",
line 13, in ?
    from iterative import *
  File "/usr/lib/python2.4/site-packages/scipy/linalg/iterative.py",
line 5, in ?
    from scipy.sparse.linalg import isolve
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/splinalg/__init__.py",
line 5, in ?
    from scipy.sparse.linalg import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

======================================================================
ERROR: Failure: TypeError (deprecate() takes exactly 3 arguments (1 given))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/loader.py",
line 351, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/ondra/lib/lib/python/nose-0.10.2.dev_r442-py2.4.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.4/site-packages/scipy/stats/__init__.py", line 7, in ?
    from stats import *
  File "/usr/lib/python2.4/site-packages/scipy/stats/stats.py", line 192, in ?
    import scipy.linalg as linalg
  File "/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py",
line 13, in ?
    from iterative import *
  File "/usr/lib/python2.4/site-packages/scipy/linalg/iterative.py",
line 5, in ?
    from scipy.sparse.linalg import isolve
  File "/usr/lib/python2.4/site-packages/scipy/sparse/__init__.py", line 5, in ?
    from base import *
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line 45, in ?
    class spmatrix(object):
  File "/usr/lib/python2.4/site-packages/scipy/sparse/base.py", line
139, in spmatrix
    @deprecate
TypeError: deprecate() takes exactly 3 arguments (1 given)

----------------------------------------------------------------------
Ran 1063 tests in 9.364s

FAILED (errors=10)

In [3]:


Ondrej


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