G Young | 27 Jan 00:57 2016
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Re: Appveyor Testing Changes

Perhaps a pip + virtualenv build as well since that's one way that is mentioned in the online docs for installing source code.  I can't think of anything else beyond that and what you suggested for the time being.

Greg

On Tue, Jan 26, 2016 at 6:59 PM, Ralf Gommers <ralf.gommers <at> gmail.com> wrote:


On Tue, Jan 26, 2016 at 2:13 AM, G Young <gfyoung17 <at> gmail.com> wrote:
Ah, yes, that is true.  That point had completely escaped my mind.  In light of this, it seems that it's not worth the while then to completely switch over to pip + virtualenv.  It's might be better actually to rewrite the current Appveyor tests to use environments so that the test suite can be expanded, though I'm not sure how prudent that is given how slow Appveyor tests run.

At the moment Appveyor is already a bit of a bottleneck - it regularly hasn't started yet when TravisCI is already done. This can be solved via a paid account, we should seriously consider that when we have a bit more experience with it (Appveyor tests have been running for less than a month I think). But it does mean we should go for a sparse test matrix, and use a more complete one (all Python versions for example) on TravisCI. In the near future we'll have to add MingwPy test runs to Appveyor. Beyond that I'm not sure what needs to be added?

Ralf

 

Greg

On Tue, Jan 26, 2016 at 12:13 AM, Bryan Van de Ven <bryanv <at> continuum.io> wrote:

> On Jan 25, 2016, at 5:21 PM, G Young <gfyoung17 <at> gmail.com> wrote:
>
> With regards to testing numpy, both Conda and Pip + Virtualenv work quite well.  I have used both to install master and run unit tests, and both pass with flying colors.  This chart here illustrates my point nicely as well.
>
> However, I can't seem to find / access Conda installations for slightly older versions of Python (e.g. Python 3.4).  Perhaps this is not much of an issue now with the next release (1.12) being written only for Python 2.7 and Python 3.4 - 5.  However, if we were to wind the clock slightly back to when we were testing 2.6 - 7, 3.2 - 5, I feel Conda falls short in being able to test on a variety of Python distributions given the nature of Conda releases.  Maybe that situation is no longer the case now, but in the long term, it could easily happen again.

Why do you need the installers? The whole point of conda is to be able to create environments with whatever configuration you need. Just pick the newest installer and use "conda create" from there:

bryan <at> 0199-bryanv (git:streaming) ~/work/bokeh/bokeh $ conda create -n py26 python=2.6
Fetching package metadata: ..............
Solving package specifications: ..........
Package plan for installation in environment /Users/bryan/anaconda/envs/py26:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    setuptools-18.0.1          |           py26_0         343 KB
    pip-7.1.0                  |           py26_0         1.4 MB
    ------------------------------------------------------------
                                           Total:         1.7 MB

The following NEW packages will be INSTALLED:

    openssl:    1.0.1k-1
    pip:        7.1.0-py26_0
    python:     2.6.9-1
    readline:   6.2-2
    setuptools: 18.0.1-py26_0
    sqlite:     3.9.2-0
    tk:         8.5.18-0
    zlib:       1.2.8-0

Proceed ([y]/n)?

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Charles R Harris | 26 Jan 21:49 2016
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Numpy 1.11.0b1 is out

Hi All,

I'm pleased to announce that Numpy 1.11.0b1 is now available on sourceforge. This is a source release as the mingw32 toolchain is broken. Please test it out and report any errors that you discover. Hopefully we can do better with 1.11.0 than we did with 1.10.0 ;)

Chuck
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Sebastian Berg | 26 Jan 20:37 2016
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Testing warnings

Hi all,

so I have been thinking about this a little more, and I do not think
there is a truly nice solution to the python bug:
http://bugs.python.org/issue4180 (does not create problems for new
pythons).

However, I have been so annoyed by trying to test FutureWarnings or
DeprecationWarnings in the past that I want *some* improvement. You can
do quite a lot by adding some new features, but there are also some
limitations.

I think that we must be able to:

 o Filter out warnings on the global test run level.
 o Find all not explicitly filtered warnings during development easily.
 o We should be able to test any (almost any?) warnings, even those
that would be filtered globally.

The next line of considerations for me is, whether we want:

 o To be able to *print* warnings during test runs? (in release mode)
 o Be able to not repeat filtering of globally filtered warnings when
filtering additional warnings in an individual test?
 o Be able to count warnings, but ignore other warnings (not the global
ones, though).
 o Filter warnings by module? (might be hard to impossible)

And one further option:
 o Could we accept that testing warnings is *only* possible reliable in
Python 3.4+? It would however even mean that we have to fully *skip*
tests that would ensure specific warnings to be given.

The first things can be achieved setting all warnings to errors on the
global level and trying to make the local tests as specific specific as
possible. I could go ahead with it. There will likely be some uglier
points, but it should work. They do not require funnier new hacks.

For all I can see, the second bunch of things requires new features
such as in my current PR. So, I want to know whether we can/want to go
ahead with this kind of idea [1].

For me personally, I cannot accept we do not provide the first points.

The second bunch, I would like some of them (I do not know about
printing warnings in release mode?), and skipping tests on Python 2,
seems to me even worse then ugly hacks.
Getting there is a bit uglier (requires a new context manager for all I
see), an I tend to think it is worth the trouble, but I don't think it
is vital.

In other words, I don't care too much about those points, but I want to
get somewhere because I have been bitten often enough by the annoying
and in my opinion simply unacceptable (on python 2) use of "ignore"
warnings filters in tests. The current state makes finding warnings
given in our own tests almost impossible, in the best case they will
have to be fixed much much later when the change actually occurs, in
the worst case we never find our own real bugs.

So where to go? :)

- Sebastian

[1] I need to fix the module filtering point, the module filtering does
not work reliably currently, I think it can be fixed at least 99.5%,
but it is not too pretty (not that the user should notice).

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Solbrig,Jeremy | 26 Jan 06:43 2016

Inconsistent behavior for ufuncs in numpy v1.10.X

Hello,

Much of what is below was copied from this stack overflow question.

I am attempting to subclass numpy.ma.MaskedArray.  I am currently using Python v2.7.10.  The problem discussed below does not occur in Numpy v1.9.2, but does occur in all versions of Numpy v1.10.x.  

In all versions of Numpy v1.10.x, using mathematical operators on my subclass behaves differently than using the analogous ufunc. When using the ufunc directly (e.g. np.subtract(arr1, arr2)), __array_prepare__, __array_finalize__, and __array_wrap__ are all called as expected, however, when using the symbolic operator (e.g. arr1-arr2) only __array_finalize__ is called. As a consequence, I lose any information stored in arr._optinfo when a mathematical operator is used.

Here is a code snippet that illustrates the issue.

#!/bin/env python import numpy as np from numpy.ma import MaskedArray, nomask class InfoArray(MaskedArray): def __new__(cls, info=None, data=None, mask=nomask, dtype=None, copy=False, subok=True, ndmin=0, fill_value=None, keep_mask=True, hard_mask=None, shrink=True, **kwargs): obj = super(InfoArray, cls).__new__(cls, data=data, mask=mask, dtype=dtype, copy=copy, subok=subok, ndmin=ndmin, fill_value=fill_value, hard_mask=hard_mask, shrink=shrink, **kwargs) obj._optinfo['info'] = info return obj def __array_prepare__(self, out, context=None): print '__array_prepare__' return super(InfoArray, self).__array_prepare__(out, context) def __array_wrap__(self, out, context=None): print '__array_wrap__' return super(InfoArray, self).__array_wrap__(out, context) def __array_finalize__(self, obj): print '__array_finalize__' return super(InfoArray, self).__array_finalize__(obj) if __name__ == "__main__": arr1 = InfoArray('test', data=[1,2,3,4,5,6]) arr2 = InfoArray(data=[0,1,2,3,4,5]) diff1 = np.subtract(arr1, arr2) print diff1._optinfo diff2 = arr1-arr2 print diff2._optinfo

If run, the output looks like this:

$ python test_ma_sub.py #Call to np.subtract(arr1, arr2) here __array_finalize__ __array_finalize__ __array_prepare__ __array_finalize__ __array_wrap__ __array_finalize__ {'info': 'test'} #Executing arr1-arr2 here __array_finalize__ {}

Currently I have simply downgraded to 1.9.2 to solve the problem for myself, but have been having difficulty figuring out where the difference lies between 1.9.2 and 1.10.0.

Thanks,

Jeremy

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G Young | 25 Jan 23:37 2016
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Re: Appveyor Testing Changes

Hello all,

I currently have a branch on my fork (not PR) where I am experimenting with running Appveyor CI via Virtualenv instead of Conda.  I have build running here.  What do people think of using Virtualenv (as we do on Travis) instead of Conda for testing?

Thanks,

Greg
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Joseph Fox-Rabinovitz | 24 Jan 04:30 2016
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PR #7090: ENH: Added 'doane' and 'sqrt' estimators to np.histogram

As someone very new to relatively large projects such as numpy, I was
wondering how the process works. I have announced my PR with some
small enhancements to the histogram function and fixed up all of the
comments that were made (originally to PR 7083). What happens next?
All I have to go on is
http://docs.scipy.org/doc/numpy-1.10.1/dev/gitwash/development_workflow.html#asking-for-your-changes-to-be-merged-with-the-main-repo,
but that does not go into detail about what happens after the point I
have already reached.

Regards,

    -Joe

On Thu, Jan 21, 2016 at 3:37 PM, Joseph Fox-Rabinovitz
<jfoxrabinovitz <at> gmail.com> wrote:
> Due to a mistake I made in my branch structure, I have replaced this
> PR with #7090: https://github.com/numpy/numpy/pull/7090. All of the
> changes and fixes so far are squashed into the new request.
>
>     -Joe
>
> On Thu, Jan 21, 2016 at 1:51 AM, Joseph Fox-Rabinovitz
> <jfoxrabinovitz <at> gmail.com> wrote:
>> Please let me know if there is anything wrong or missing. I have added
>> a couple of estimators that I find useful sometimes.
>>
>>     -Joe
Sebastian Berg | 23 Jan 22:25 2016
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Make as_strided result writeonly

Hi all,

I have just opened a PR, to make as_strided writeonly (as default). The
reasoning for this change is that an `as_strided` array often have self
overlapping memory. However, writing to an array where multiple
elements have the identical memory address can be confusing, and the
results are typically unpredictable.

Considering the danger, the proposal is to add a `readonly=True`. A
poweruser (who that function is designed for anyway), could thus still
get a writeable array.

For the moment, writing to the result would raise a FutureWarning with
`readonly="warn"`.

Do you agree with this, or would it be a major inconvenience?

- Sebastian
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Evgeni Burovski | 23 Jan 13:51 2016
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Gravatar

ANN: scipy 0.17.0 release

Hi,

On behalf of the Scipy development team I am pleased to announce the
availability of Scipy 0.17.0. This release contains several new features,
detailed in the release notes below. 101 people contributed to this
release over the course of six months.

This release requires Python 2.6, 2.7 or 3.2-3.4 and NumPy 1.6.2 or
greater. Source tarballs and release notes can be found at
https://github.com/scipy/scipy/releases/tag/v0.17.0.

Thanks to everyone who contributed to this release.

Cheers,

Evgeni

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

==========================
SciPy 0.17.0 Release Notes
==========================

.. contents::

SciPy 0.17.0 is the culmination of 6 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and
better documentation.  There have been a number of deprecations and
API changes in this release, which are documented below.  All users
are encouraged to upgrade to this release, as there are a large number
of bug-fixes and optimizations.  Moreover, our development attention
will now shift to bug-fix releases on the 0.17.x branch, and on adding
new features on the master branch.

This release requires Python 2.6, 2.7 or 3.2-3.5 and NumPy 1.6.2 or greater.

Release highlights:

    - New functions for linear and nonlinear least squares optimization with
      constraints: `scipy.optimize.lsq_linear` and
      `scipy.optimize.least_squares`
    - Support for fitting with bounds in `scipy.optimize.curve_fit`.
    - Significant improvements to `scipy.stats`, providing many functions with
      better handing of inputs which have NaNs or are empty, improved
      documentation, and consistent behavior between `scipy.stats` and
      `scipy.stats.mstats`.
    - Significant performance improvements and new functionality in
      `scipy.spatial.cKDTree`.

New features
============

`scipy.cluster` improvements
- ----------------------------

A new function `scipy.cluster.hierarchy.cut_tree`, which determines a cut tree
from a linkage matrix, was added.

`scipy.io` improvements
- -----------------------

`scipy.io.mmwrite` gained support for symmetric sparse matrices.

`scipy.io.netcdf` gained support for masking and scaling data based on data
attributes.

`scipy.optimize` improvements
- -----------------------------

Linear assignment problem solver
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

`scipy.optimize.linear_sum_assignment` is a new function for solving the
linear sum assignment problem.  It uses the Hungarian algorithm (Kuhn-Munkres).

Least squares optimization
~~~~~~~~~~~~~~~~~~~~~~~~~~

A new function for *nonlinear* least squares optimization with constraints was
added: `scipy.optimize.least_squares`.  It provides several methods:
Levenberg-Marquardt for unconstrained problems, and two trust-region methods
for constrained ones.  Furthermore it provides different loss functions.
New trust-region methods also handle sparse Jacobians.

A new function for *linear* least squares optimization with constraints was
added: `scipy.optimize.lsq_linear`.  It provides a trust-region method as well
as an implementation of the Bounded-Variable Least-Squares (BVLS) algorithm.

`scipy.optimize.curve_fit` now supports fitting with bounds.

`scipy.signal` improvements
- ---------------------------

A ``mode`` keyword was added to `scipy.signal.spectrogram`, to let it return
other spectrograms than power spectral density.

`scipy.stats` improvements
- --------------------------

Many functions in `scipy.stats` have gained a ``nan_policy`` keyword, which
allows specifying how to treat input with NaNs in them: propagate the NaNs,
raise an error, or omit the NaNs.

Many functions in `scipy.stats` have been improved to correctly handle input
arrays that are empty or contain infs/nans.

A number of functions with the same name in `scipy.stats` and
`scipy.stats.mstats` were changed to have matching signature and behavior.
See `gh-5474 <https://github.com/scipy/scipy/issues/5474>`__ for details.

`scipy.stats.binom_test` and `scipy.stats.mannwhitneyu` gained a keyword
``alternative``, which allows specifying the hypothesis to test for.
Eventually all hypothesis testing functions will get this keyword.

For methods of many continuous distributions, complex input is now accepted.

Matrix normal distribution has been implemented as `scipy.stats.matrix_normal`.

`scipy.sparse` improvements
- ---------------------------

The `axis` keyword was added to sparse norms, `scipy.sparse.linalg.norm`.

`scipy.spatial` improvements
- ----------------------------

`scipy.spatial.cKDTree` was partly rewritten for improved performance and
several new features were added to it:

- - the ``query_ball_point`` method became significantly faster
- - ``query`` and ``query_ball_point`` gained an ``n_jobs`` keyword for parallel
  execution
- - build and query methods now release the GIL
- - full pickling support
- - support for periodic spaces
- - the ``sparse_distance_matrix`` method can now return and sparse matrix type

`scipy.interpolate` improvements
- --------------------------------

Out-of-bounds behavior of `scipy.interpolate.interp1d` has been improved.
Use a two-element tuple for the ``fill_value`` argument to specify separate
fill values for input below and above the interpolation range.
Linear and nearest interpolation kinds of `scipy.interpolate.interp1d` support
extrapolation via the ``fill_value="extrapolate"`` keyword.

``fill_value`` can also be set to an array-like (or a two-element tuple of
array-likes for separate below and above values) so long as it broadcasts
properly to the non-interpolated dimensions of an array. This was implicitly
supported by previous versions of scipy, but support has now been formalized
and gets compatibility-checked before use. For example, a set of ``y`` values
to interpolate with shape ``(2, 3, 5)`` interpolated along the last axis (2)
could accept a ``fill_value`` array with shape ``()`` (singleton), ``(1,)``,
``(2, 1)``, ``(1, 3)``, ``(3,)``, or ``(2, 3)``; or it can be a 2-element tuple
to specify separate below and above bounds, where each of the two tuple
elements obeys proper broadcasting rules.

`scipy.linalg` improvements
- ---------------------------

The default algorithm for `scipy.linalg.leastsq` has been changed to use
LAPACK's function ``*gelsd``. Users wanting to get the previous behavior
can use a new keyword ``lapack_driver="gelss"`` (allowed values are
"gelss", "gelsd" and "gelsy").

``scipy.sparse`` matrices and linear operators now support the matmul (`` <at> ``)
operator when available (Python 3.5+). See
[PEP 465](http://legacy.python.org/dev/peps/pep-0465/)

A new function `scipy.linalg.ordqz`, for QZ decomposition with reordering, has
been added.

Deprecated features
===================

``scipy.stats.histogram`` is deprecated in favor of ``np.histogram``, which is
faster and provides the same functionality.

``scipy.stats.threshold`` and ``scipy.mstats.threshold`` are deprecated
in favor of ``np.clip``. See issue #617 for details.

``scipy.stats.ss`` is deprecated. This is a support function, not meant to
be exposed to the user. Also, the name is unclear. See issue #663 for details.

``scipy.stats.square_of_sums`` is deprecated. This too is a support function
not meant to be exposed to the user. See issues #665 and #663 for details.

``scipy.stats.f_value``, ``scipy.stats.f_value_multivariate``,
``scipy.stats.f_value_wilks_lambda``, and ``scipy.mstats.f_value_wilks_lambda``
are deprecated. These are related to ANOVA, for which ``scipy.stats`` provides
quite limited functionality and these functions are not very useful standalone.
See issues #660 and #650 for details.

``scipy.stats.chisqprob`` is deprecated. This is an alias. ``stats.chi2.sf``
should be used instead.

``scipy.stats.betai`` is deprecated. This is an alias for ``special.betainc``
which should be used instead.

Backwards incompatible changes
==============================

The functions ``stats.trim1`` and ``stats.trimboth`` now make sure the
elements trimmed are the lowest and/or highest, depending on the case.
Slicing without at least partial sorting was previously done, but didn't
make sense for unsorted input.

When ``variable_names`` is set to an empty list, ``scipy.io.loadmat`` now
correctly returns no values instead of all the contents of the MAT file.

Element-wise multiplication of sparse matrices now returns a sparse result
in all cases. Previously, multiplying a sparse matrix with a dense matrix or
array would return a dense matrix.

The function ``misc.lena`` has been removed due to license incompatibility.

The constructor for ``sparse.coo_matrix`` no longer accepts ``(None, (m,n))``
to construct an all-zero matrix of shape ``(m,n)``. This functionality was
deprecated since at least 2007 and was already broken in the previous SciPy
release. Use ``coo_matrix((m,n))`` instead.

The Cython wrappers in ``linalg.cython_lapack`` for the LAPACK routines
``*gegs``, ``*gegv``, ``*gelsx``, ``*geqpf``, ``*ggsvd``, ``*ggsvp``,
``*lahrd``, ``*latzm``, ``*tzrqf`` have been removed since these routines
are not present in the new LAPACK 3.6.0 release. With the exception of
the routines ``*ggsvd`` and ``*ggsvp``, these were all deprecated in favor
of routines that are currently present in our Cython LAPACK wrappers.

Because the LAPACK ``*gegv`` routines were removed in LAPACK 3.6.0. The
corresponding Python wrappers in ``scipy.linalg.lapack`` are now
deprecated and will be removed in a future release. The source files for
these routines have been temporarily included as a part of ``scipy.linalg``
so that SciPy can be built against LAPACK versions that do not provide
these deprecated routines.

Other changes
=============

Html and pdf documentation of development versions of Scipy is now
automatically rebuilt after every merged pull request.

`scipy.constants` is updated to the CODATA 2014 recommended values.

Usage of `scipy.fftpack` functions within Scipy has been changed in such a
way that `PyFFTW <http://hgomersall.github.io/pyFFTW/>`__ can easily replace
`scipy.fftpack` functions (with improved performance).  See
`gh-5295 <https://github.com/scipy/scipy/pull/5295>`__ for details.

The ``imread`` functions in `scipy.misc` and `scipy.ndimage` were unified, for
which a ``mode`` argument was added to `scipy.misc.imread`.  Also, bugs for
1-bit and indexed RGB image formats were fixed.

``runtests.py``, the development script to build and test Scipy, now allows
building in parallel with ``--parallel``.

Authors
=======

*  <at> cel4 +
*  <at> chemelnucfin +
*  <at> endolith
*  <at> mamrehn +
*  <at> tosh1ki +
* Joshua L. Adelman +
* Anne Archibald
* Hervé Audren +
* Vincent Barrielle +
* Bruno Beltran +
* Sumit Binnani +
* Joseph Jon Booker
* Olga Botvinnik +
* Michael Boyle +
* Matthew Brett
* Zaz Brown +
* Lars Buitinck
* Pete Bunch +
* Evgeni Burovski
* CJ Carey
* Ien Cheng +
* Cody +
* Jaime Fernandez del Rio
* Ales Erjavec +
* Abraham Escalante
* Yves-Rémi Van Eycke +
* Yu Feng +
* Eric Firing
* Francis T. O'Donovan +
* André Gaul
* Christoph Gohlke
* Ralf Gommers
* Alex Griffing
* Alexander Grigorievskiy
* Charles Harris
* Jörn Hees +
* Ian Henriksen
* Derek Homeier +
* David Menéndez Hurtado
* Gert-Ludwig Ingold
* Aakash Jain +
* Rohit Jamuar +
* Jan Schlüter
* Johannes Ballé
* Luke Zoltan Kelley +
* Jason King +
* Andreas Kopecky +
* Eric Larson
* Denis Laxalde
* Antony Lee
* Gregory R. Lee
* Josh Levy-Kramer +
* Sam Lewis +
* François Magimel +
* Martín Gaitán +
* Sam Mason +
* Andreas Mayer
* Nikolay Mayorov
* Damon McDougall +
* Robert McGibbon
* Sturla Molden
* Will Monroe +
* Eric Moore
* Maniteja Nandana
* Vikram Natarajan +
* Andrew Nelson
* Marti Nito +
* Behzad Nouri +
* Daisuke Oyama +
* Giorgio Patrini +
* Fabian Paul +
* Christoph Paulik +
* Mad Physicist +
* Irvin Probst
* Sebastian Pucilowski +
* Ted Pudlik +
* Eric Quintero
* Yoav Ram +
* Joscha Reimer +
* Juha Remes
* Frederik Rietdijk +
* Rémy Léone +
* Christian Sachs +
* Skipper Seabold
* Sebastian Skoupý +
* Alex Seewald +
* Andreas Sorge +
* Bernardo Sulzbach +
* Julian Taylor
* Louis Tiao +
* Utkarsh Upadhyay +
* Jacob Vanderplas
* Gael Varoquaux +
* Pauli Virtanen
* Fredrik Wallner +
* Stefan van der Walt
* James Webber +
* Warren Weckesser
* Raphael Wettinger +
* Josh Wilson +
* Nat Wilson +
* Peter Yin +

A total of 101 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.
This list of names is automatically generated, and may not be fully complete.

Issues closed for 0.17.0
- ------------------------

- - `#1923 <https://github.com/scipy/scipy/issues/1923>`__: problem
with numpy 0's in stats.poisson.rvs (Trac #1398)
- - `#2138 <https://github.com/scipy/scipy/issues/2138>`__:
scipy.misc.imread segfaults on 1 bit png (Trac #1613)
- - `#2237 <https://github.com/scipy/scipy/issues/2237>`__:
distributions do not accept complex arguments (Trac #1718)
- - `#2282 <https://github.com/scipy/scipy/issues/2282>`__:
scipy.special.hyp1f1(0.5, 1.5, -1000) fails (Trac #1763)
- - `#2618 <https://github.com/scipy/scipy/issues/2618>`__:
poisson.pmf returns NaN if mu is 0
- - `#2957 <https://github.com/scipy/scipy/issues/2957>`__: hyp1f1
precision issue
- - `#2997 <https://github.com/scipy/scipy/issues/2997>`__: FAIL:
test_qhull.TestUtilities.test_more_barycentric_transforms
- - `#3129 <https://github.com/scipy/scipy/issues/3129>`__: No way to
set ranges for fitting parameters in Optimize functions
- - `#3191 <https://github.com/scipy/scipy/issues/3191>`__: interp1d
should contain a fill_value_below and a fill_value_above...
- - `#3453 <https://github.com/scipy/scipy/issues/3453>`__:
PchipInterpolator sets slopes at edges differently than Matlab's...
- - `#4106 <https://github.com/scipy/scipy/issues/4106>`__:
ndimage._ni_support._normalize_sequence() fails with numpy.int64
- - `#4118 <https://github.com/scipy/scipy/issues/4118>`__:
`scipy.integrate.ode.set_solout` called after
`scipy.integrate.ode.set_initial_value` fails silently
- - `#4233 <https://github.com/scipy/scipy/issues/4233>`__: 1D
scipy.interpolate.griddata using method=nearest produces nans...
- - `#4375 <https://github.com/scipy/scipy/issues/4375>`__: All tests
fail due to bad file permissions
- - `#4580 <https://github.com/scipy/scipy/issues/4580>`__:
scipy.ndimage.filters.convolve documenation is incorrect
- - `#4627 <https://github.com/scipy/scipy/issues/4627>`__: logsumexp
with sign indicator - enable calculation with negative...
- - `#4702 <https://github.com/scipy/scipy/issues/4702>`__: logsumexp
with zero scaling factor
- - `#4834 <https://github.com/scipy/scipy/issues/4834>`__: gammainc
should return 1.0 instead of NaN for infinite x
- - `#4838 <https://github.com/scipy/scipy/issues/4838>`__: enh:
exprel special function
- - `#4862 <https://github.com/scipy/scipy/issues/4862>`__: the
scipy.special.boxcox function is inaccurate for denormal...
- - `#4887 <https://github.com/scipy/scipy/issues/4887>`__: Spherical
harmonic incongruences
- - `#4895 <https://github.com/scipy/scipy/issues/4895>`__: some scipy
ufuncs have inconsistent output dtypes?
- - `#4923 <https://github.com/scipy/scipy/issues/4923>`__: logm does
not aggressively convert complex outputs to float
- - `#4932 <https://github.com/scipy/scipy/issues/4932>`__: BUG:
stats: The `fit` method of the distributions silently ignores...
- - `#4956 <https://github.com/scipy/scipy/issues/4956>`__:
Documentation error in `scipy.special.bi_zeros`
- - `#4957 <https://github.com/scipy/scipy/issues/4957>`__: Docstring
for `pbvv_seq` is wrong
- - `#4967 <https://github.com/scipy/scipy/issues/4967>`__: block_diag
should look at dtypes of all arguments, not only the...
- - `#5037 <https://github.com/scipy/scipy/issues/5037>`__:
scipy.optimize.minimize error messages are printed to stdout...
- - `#5039 <https://github.com/scipy/scipy/issues/5039>`__: Cubic
interpolation: On entry to DGESDD parameter number 12 had...
- - `#5163 <https://github.com/scipy/scipy/issues/5163>`__: Base case
example of Hierarchical Clustering (offer)
- - `#5181 <https://github.com/scipy/scipy/issues/5181>`__: BUG:
stats.genextreme.entropy should use the explicit formula
- - `#5184 <https://github.com/scipy/scipy/issues/5184>`__: Some?
wheels don't express a numpy dependency
- - `#5197 <https://github.com/scipy/scipy/issues/5197>`__: mstats:
test_kurtosis fails (ULP max is 2)
- - `#5260 <https://github.com/scipy/scipy/issues/5260>`__: Typo
causing an error in splrep
- - `#5263 <https://github.com/scipy/scipy/issues/5263>`__: Default
epsilon in rbf.py fails for colinear points
- - `#5276 <https://github.com/scipy/scipy/issues/5276>`__: Reading
empty (no data) arff file fails
- - `#5280 <https://github.com/scipy/scipy/issues/5280>`__: 1d
scipy.signal.convolve much slower than numpy.convolve
- - `#5326 <https://github.com/scipy/scipy/issues/5326>`__:
Implementation error in scipy.interpolate.PchipInterpolator
- - `#5370 <https://github.com/scipy/scipy/issues/5370>`__: Test issue
with test_quadpack and libm.so as a linker script
- - `#5426 <https://github.com/scipy/scipy/issues/5426>`__: ERROR:
test_stats.test_chisquare_masked_arrays
- - `#5427 <https://github.com/scipy/scipy/issues/5427>`__: Automate
installing correct numpy versions in numpy-vendor image
- - `#5430 <https://github.com/scipy/scipy/issues/5430>`__: Python3 :
Numpy scalar types "not iterable"; specific instance...
- - `#5450 <https://github.com/scipy/scipy/issues/5450>`__: BUG:
spatial.ConvexHull triggers a seg. fault when given nans.
- - `#5478 <https://github.com/scipy/scipy/issues/5478>`__: clarify
the relation between matrix normal distribution and
`multivariate_normal`
- - `#5539 <https://github.com/scipy/scipy/issues/5539>`__: lstsq
related test failures on windows binaries from numpy-vendor
- - `#5560 <https://github.com/scipy/scipy/issues/5560>`__: doc:
scipy.stats.burr pdf issue
- - `#5571 <https://github.com/scipy/scipy/issues/5571>`__: lstsq test
failure after lapack_driver change
- - `#5577 <https://github.com/scipy/scipy/issues/5577>`__: ordqz
segfault on Python 3.4 in Wine
- - `#5578 <https://github.com/scipy/scipy/issues/5578>`__:
scipy.linalg test failures on python 3 in Wine
- - `#5607 <https://github.com/scipy/scipy/issues/5607>`__: Overloaded
‘isnan(double&)’ is ambiguous when compiling with...
- - `#5629 <https://github.com/scipy/scipy/issues/5629>`__: Test for
lstsq randomly failed
- - `#5630 <https://github.com/scipy/scipy/issues/5630>`__: memory
leak with scipy 0.16 spatial cKDEtree
- - `#5689 <https://github.com/scipy/scipy/issues/5689>`__: isnan
errors compiling scipy/special/Faddeeva.cc with clang++
- - `#5694 <https://github.com/scipy/scipy/issues/5694>`__: fftpack
test failure in test_import
- - `#5719 <https://github.com/scipy/scipy/issues/5719>`__:
curve_fit(method!="lm") ignores initial guess

Pull requests for 0.17.0
- ------------------------

- - `#3022 <https://github.com/scipy/scipy/pull/3022>`__: hyp1f1:
better handling of large negative arguments
- - `#3107 <https://github.com/scipy/scipy/pull/3107>`__: ENH: Add
ordered QZ decomposition
- - `#4390 <https://github.com/scipy/scipy/pull/4390>`__: ENH: Allow
axis and keepdims arguments to be passed to scipy.linalg.norm.
- - `#4671 <https://github.com/scipy/scipy/pull/4671>`__: ENH: add
axis to sparse norms
- - `#4796 <https://github.com/scipy/scipy/pull/4796>`__: ENH: Add cut
tree function to scipy.cluster.hierarchy
- - `#4809 <https://github.com/scipy/scipy/pull/4809>`__: MAINT:
cauchy moments are undefined
- - `#4821 <https://github.com/scipy/scipy/pull/4821>`__: ENH: stats:
make distribution instances picklable
- - `#4839 <https://github.com/scipy/scipy/pull/4839>`__: ENH: Add
scipy.special.exprel relative error exponential ufunc
- - `#4859 <https://github.com/scipy/scipy/pull/4859>`__: Logsumexp
fixes - allows sign flags and b==0
- - `#4865 <https://github.com/scipy/scipy/pull/4865>`__: BUG:
scipy.io.mmio.write: error with big indices and low precision
- - `#4869 <https://github.com/scipy/scipy/pull/4869>`__: add
as_inexact option to _lib._util._asarray_validated
- - `#4884 <https://github.com/scipy/scipy/pull/4884>`__: ENH: Finite
difference approximation of Jacobian matrix
- - `#4890 <https://github.com/scipy/scipy/pull/4890>`__: ENH: Port
cKDTree query methods to C++, allow pickling on Python...
- - `#4892 <https://github.com/scipy/scipy/pull/4892>`__: how much
doctesting is too much?
- - `#4896 <https://github.com/scipy/scipy/pull/4896>`__: MAINT: work
around a possible numpy ufunc loop selection bug
- - `#4898 <https://github.com/scipy/scipy/pull/4898>`__: MAINT: A bit
of pyflakes-driven cleanup.
- - `#4899 <https://github.com/scipy/scipy/pull/4899>`__: ENH: add
'alternative' keyword to hypothesis tests in stats
- - `#4903 <https://github.com/scipy/scipy/pull/4903>`__: BENCH:
Benchmarks for interpolate module
- - `#4905 <https://github.com/scipy/scipy/pull/4905>`__: MAINT:
prepend underscore to mask_to_limits; delete masked_var.
- - `#4906 <https://github.com/scipy/scipy/pull/4906>`__: MAINT:
Benchmarks for optimize.leastsq
- - `#4910 <https://github.com/scipy/scipy/pull/4910>`__: WIP: Trimmed
statistics functions have inconsistent API.
- - `#4912 <https://github.com/scipy/scipy/pull/4912>`__: MAINT: fix
typo in stats tutorial. Closes gh-4911.
- - `#4914 <https://github.com/scipy/scipy/pull/4914>`__: DEP:
deprecate `scipy.stats.ss` and `scipy.stats.square_of_sums`.
- - `#4924 <https://github.com/scipy/scipy/pull/4924>`__: MAINT: if
the imaginary part of logm of a real matrix is small,...
- - `#4930 <https://github.com/scipy/scipy/pull/4930>`__: BENCH:
Benchmarks for signal module
- - `#4941 <https://github.com/scipy/scipy/pull/4941>`__: ENH: update
`find_repeats`.
- - `#4942 <https://github.com/scipy/scipy/pull/4942>`__: MAINT: use
np.float64_t instead of np.float_t in cKDTree
- - `#4944 <https://github.com/scipy/scipy/pull/4944>`__: BUG: integer
overflow in correlate_nd
- - `#4951 <https://github.com/scipy/scipy/pull/4951>`__: do not
ignore invalid kwargs in distributions fit method
- - `#4958 <https://github.com/scipy/scipy/pull/4958>`__: Add some
detail to docstrings for special functions
- - `#4961 <https://github.com/scipy/scipy/pull/4961>`__: ENH:
stats.describe: add bias kw and empty array handling
- - `#4963 <https://github.com/scipy/scipy/pull/4963>`__: ENH:
scipy.sparse.coo.coo_matrix.__init__: less memory needed
- - `#4968 <https://github.com/scipy/scipy/pull/4968>`__: DEP:
deprecate ``stats.f_value*`` and ``mstats.f_value*`` functions.
- - `#4969 <https://github.com/scipy/scipy/pull/4969>`__: ENH: review
`stats.relfreq` and `stats.cumfreq`; fixes to `stats.histogram`
- - `#4971 <https://github.com/scipy/scipy/pull/4971>`__: Extend
github source links to line ranges
- - `#4972 <https://github.com/scipy/scipy/pull/4972>`__: MAINT:
impove the error message in validate_runtests_log
- - `#4976 <https://github.com/scipy/scipy/pull/4976>`__: DEP:
deprecate `scipy.stats.threshold`
- - `#4977 <https://github.com/scipy/scipy/pull/4977>`__: MAINT: more
careful dtype treatment in block diagonal matrix...
- - `#4979 <https://github.com/scipy/scipy/pull/4979>`__: ENH:
distributions, complex arguments
- - `#4984 <https://github.com/scipy/scipy/pull/4984>`__: clarify
dirichlet distribution error handling
- - `#4992 <https://github.com/scipy/scipy/pull/4992>`__: ENH:
`stats.fligner` and `stats.bartlett` empty input handling.
- - `#4996 <https://github.com/scipy/scipy/pull/4996>`__: DOC: fix
stats.spearmanr docs
- - `#4997 <https://github.com/scipy/scipy/pull/4997>`__: Fix up
boxcox for underflow / loss of precision
- - `#4998 <https://github.com/scipy/scipy/pull/4998>`__: DOC:
improved documentation for `stats.ppcc_max`
- - `#5000 <https://github.com/scipy/scipy/pull/5000>`__: ENH: added
empty input handling `scipy.moment`; doc enhancements
- - `#5003 <https://github.com/scipy/scipy/pull/5003>`__: ENH:
improves rankdata algorithm
- - `#5005 <https://github.com/scipy/scipy/pull/5005>`__: scipy.stats:
numerical stability improvement
- - `#5007 <https://github.com/scipy/scipy/pull/5007>`__: ENH: nan
handling in functions that use `stats._chk_asarray`
- - `#5009 <https://github.com/scipy/scipy/pull/5009>`__: remove coveralls.io
- - `#5010 <https://github.com/scipy/scipy/pull/5010>`__:
Hypergeometric distribution log survival function
- - `#5014 <https://github.com/scipy/scipy/pull/5014>`__: Patch to
compute the volume and area of convex hulls
- - `#5015 <https://github.com/scipy/scipy/pull/5015>`__: DOC: Fix
mistaken variable name in sawtooth
- - `#5016 <https://github.com/scipy/scipy/pull/5016>`__: DOC: resample example
- - `#5017 <https://github.com/scipy/scipy/pull/5017>`__: DEP:
deprecate `stats.betai` and `stats.chisqprob`
- - `#5018 <https://github.com/scipy/scipy/pull/5018>`__: ENH: Add
test on random inpu to volume computations
- - `#5026 <https://github.com/scipy/scipy/pull/5026>`__: BUG: Fix
return dtype of lil_matrix.getnnz(axis=0)
- - `#5030 <https://github.com/scipy/scipy/pull/5030>`__: DOC:
resample slow for prime output too
- - `#5033 <https://github.com/scipy/scipy/pull/5033>`__: MAINT:
integrate, special: remove unused R1MACH and Makefile
- - `#5034 <https://github.com/scipy/scipy/pull/5034>`__: MAINT:
signal: lift max_len_seq validation out of Cython
- - `#5035 <https://github.com/scipy/scipy/pull/5035>`__: DOC/MAINT:
refguide / doctest drudgery
- - `#5041 <https://github.com/scipy/scipy/pull/5041>`__: BUG: fixing
some small memory leaks detected by cppcheck
- - `#5044 <https://github.com/scipy/scipy/pull/5044>`__: [GSoC] ENH:
New least-squares algorithms
- - `#5050 <https://github.com/scipy/scipy/pull/5050>`__: MAINT: C
fixes, trimmed a lot of dead code from Cephes
- - `#5057 <https://github.com/scipy/scipy/pull/5057>`__: ENH: sparse:
avoid densifying on sparse/dense elementwise mult
- - `#5058 <https://github.com/scipy/scipy/pull/5058>`__: TST: stats:
add a sample distribution to the test loop
- - `#5061 <https://github.com/scipy/scipy/pull/5061>`__: ENH:
spatial: faster 2D Voronoi and Convex Hull plotting
- - `#5065 <https://github.com/scipy/scipy/pull/5065>`__: TST: improve
test coverage for `stats.mvsdist` and `stats.bayes_mvs`
- - `#5066 <https://github.com/scipy/scipy/pull/5066>`__: MAINT:
fitpack: remove a noop
- - `#5067 <https://github.com/scipy/scipy/pull/5067>`__: ENH: empty
and nan input handling for `stats.kstat` and `stats.kstatvar`
- - `#5071 <https://github.com/scipy/scipy/pull/5071>`__: DOC:
optimize: Correct paper reference, add doi
- - `#5072 <https://github.com/scipy/scipy/pull/5072>`__: MAINT:
scipy.sparse cleanup
- - `#5073 <https://github.com/scipy/scipy/pull/5073>`__: DOC:
special: Add an example showing the relation of diric to...
- - `#5075 <https://github.com/scipy/scipy/pull/5075>`__: DOC:
clarified parameterization of stats.lognorm
- - `#5076 <https://github.com/scipy/scipy/pull/5076>`__: use int,
float, bool instead of np.int, np.float, np.bool
- - `#5078 <https://github.com/scipy/scipy/pull/5078>`__: DOC: Rename
fftpack docs to README
- - `#5081 <https://github.com/scipy/scipy/pull/5081>`__: BUG: Correct
handling of scalar 'b' in lsmr and lsqr
- - `#5082 <https://github.com/scipy/scipy/pull/5082>`__: loadmat
variable_names: don't confuse [] and None.
- - `#5083 <https://github.com/scipy/scipy/pull/5083>`__: Fix
integrate.fixed_quad docstring to indicate None return value
- - `#5086 <https://github.com/scipy/scipy/pull/5086>`__: Use solve()
instead of inv() for gaussian_kde
- - `#5090 <https://github.com/scipy/scipy/pull/5090>`__: MAINT:
stats: add explicit _sf, _isf to gengamma distribution
- - `#5094 <https://github.com/scipy/scipy/pull/5094>`__: ENH:
scipy.interpolate.NearestNDInterpolator: cKDTree configurable
- - `#5098 <https://github.com/scipy/scipy/pull/5098>`__: DOC:
special: fix typesetting in ``*_roots quadrature`` functions
- - `#5099 <https://github.com/scipy/scipy/pull/5099>`__: DOC: make
the docstring of stats.moment raw
- - `#5104 <https://github.com/scipy/scipy/pull/5104>`__: DOC/ENH
fixes and micro-optimizations for scipy.linalg
- - `#5105 <https://github.com/scipy/scipy/pull/5105>`__: enh: made
l-bfgs-b parameter for the maximum number of line search...
- - `#5106 <https://github.com/scipy/scipy/pull/5106>`__: TST: add
NIST test cases to `stats.f_oneway`
- - `#5110 <https://github.com/scipy/scipy/pull/5110>`__: [GSoC]:
Bounded linear least squares
- - `#5111 <https://github.com/scipy/scipy/pull/5111>`__: MAINT:
special: Cephes cleanup
- - `#5118 <https://github.com/scipy/scipy/pull/5118>`__: BUG: FIR
path failed if len(x) < len(b) in lfilter.
- - `#5124 <https://github.com/scipy/scipy/pull/5124>`__: ENH: move
the filliben approximation to a publicly visible function
- - `#5126 <https://github.com/scipy/scipy/pull/5126>`__:
StatisticsCleanup: `stats.kruskal` review
- - `#5130 <https://github.com/scipy/scipy/pull/5130>`__: DOC: update
PyPi trove classifiers. Beta -> Stable. Add license.
- - `#5131 <https://github.com/scipy/scipy/pull/5131>`__: DOC:
differential_evolution, improve docstring for mutation and...
- - `#5132 <https://github.com/scipy/scipy/pull/5132>`__: MAINT:
differential_evolution improve init_population_lhs comments...
- - `#5133 <https://github.com/scipy/scipy/pull/5133>`__: MRG: rebased
mmio refactoring
- - `#5135 <https://github.com/scipy/scipy/pull/5135>`__: MAINT:
`stats.mstats` consistency with `stats.stats`
- - `#5139 <https://github.com/scipy/scipy/pull/5139>`__: TST: linalg:
add a smoke test for gh-5039
- - `#5140 <https://github.com/scipy/scipy/pull/5140>`__: EHN: Update
constants.codata to CODATA 2014
- - `#5145 <https://github.com/scipy/scipy/pull/5145>`__: added
ValueError to docstring as possible error raised
- - `#5146 <https://github.com/scipy/scipy/pull/5146>`__: MAINT:
Improve implementation details and doc in `stats.shapiro`
- - `#5147 <https://github.com/scipy/scipy/pull/5147>`__: [GSoC] ENH:
Upgrades to curve_fit
- - `#5150 <https://github.com/scipy/scipy/pull/5150>`__: Fix
misleading wavelets/cwt example
- - `#5152 <https://github.com/scipy/scipy/pull/5152>`__: BUG:
cluster.hierarchy.dendrogram: missing font size doesn't...
- - `#5153 <https://github.com/scipy/scipy/pull/5153>`__: add keywords
to control the summation in discrete distributions...
- - `#5156 <https://github.com/scipy/scipy/pull/5156>`__: DOC: added
comments on algorithms used in Legendre function
- - `#5158 <https://github.com/scipy/scipy/pull/5158>`__: ENH:
optimize: add the Hungarian algorithm
- - `#5162 <https://github.com/scipy/scipy/pull/5162>`__: FIX: Remove lena
- - `#5164 <https://github.com/scipy/scipy/pull/5164>`__: MAINT: fix
cluster.hierarchy.dendrogram issues and docs
- - `#5166 <https://github.com/scipy/scipy/pull/5166>`__: MAINT:
changed `stats.pointbiserialr` to delegate to `stats.pearsonr`
- - `#5167 <https://github.com/scipy/scipy/pull/5167>`__: ENH: add
nan_policy to `stats.kendalltau`.
- - `#5168 <https://github.com/scipy/scipy/pull/5168>`__: TST: added
nist test case (Norris) to `stats.linregress`.
- - `#5169 <https://github.com/scipy/scipy/pull/5169>`__: update lpmv docstring
- - `#5171 <https://github.com/scipy/scipy/pull/5171>`__: Clarify
metric parameter in linkage docstring
- - `#5172 <https://github.com/scipy/scipy/pull/5172>`__: ENH: add
mode keyword to signal.spectrogram
- - `#5177 <https://github.com/scipy/scipy/pull/5177>`__: DOC:
graphical example for KDTree.query_ball_point
- - `#5179 <https://github.com/scipy/scipy/pull/5179>`__: MAINT:
stats: tweak the formula for ncx2.pdf
- - `#5188 <https://github.com/scipy/scipy/pull/5188>`__: MAINT:
linalg: A bit of clean up.
- - `#5189 <https://github.com/scipy/scipy/pull/5189>`__: BUG: stats:
Use the explicit formula in stats.genextreme.entropy
- - `#5193 <https://github.com/scipy/scipy/pull/5193>`__: BUG: fix
uninitialized use in lartg
- - `#5194 <https://github.com/scipy/scipy/pull/5194>`__: BUG:
properly return error to fortran from ode_jacobian_function
- - `#5198 <https://github.com/scipy/scipy/pull/5198>`__: TST: Fix
TestCtypesQuad failure on Python 3.5 for Windows
- - `#5201 <https://github.com/scipy/scipy/pull/5201>`__: allow
extrapolation in interp1d
- - `#5209 <https://github.com/scipy/scipy/pull/5209>`__: MAINT:
Change complex parameter to boolean in Y_()
- - `#5213 <https://github.com/scipy/scipy/pull/5213>`__: BUG: sparse:
fix logical comparison dtype conflicts
- - `#5216 <https://github.com/scipy/scipy/pull/5216>`__: BUG: sparse:
fixing unbound local error
- - `#5218 <https://github.com/scipy/scipy/pull/5218>`__: DOC and BUG:
Bessel function docstring improvements, fix array_like,...
- - `#5222 <https://github.com/scipy/scipy/pull/5222>`__: MAINT:
sparse: fix COO ctor
- - `#5224 <https://github.com/scipy/scipy/pull/5224>`__: DOC:
optimize: type of OptimizeResult.hess_inv varies
- - `#5228 <https://github.com/scipy/scipy/pull/5228>`__: ENH: Add
maskandscale support to netcdf; based on pupynere and...
- - `#5229 <https://github.com/scipy/scipy/pull/5229>`__: DOC:
sparse.linalg.svds doc typo fixed
- - `#5234 <https://github.com/scipy/scipy/pull/5234>`__: MAINT:
sparse: simplify COO ctor
- - `#5235 <https://github.com/scipy/scipy/pull/5235>`__: MAINT:
sparse: warn on todia() with many diagonals
- - `#5236 <https://github.com/scipy/scipy/pull/5236>`__: MAINT:
ndimage: simplify thread handling/recursion + constness
- - `#5239 <https://github.com/scipy/scipy/pull/5239>`__: BUG:
integrate: Fixed issue 4118
- - `#5241 <https://github.com/scipy/scipy/pull/5241>`__: qr_insert
fixes, closes #5149
- - `#5246 <https://github.com/scipy/scipy/pull/5246>`__: Doctest tutorial files
- - `#5247 <https://github.com/scipy/scipy/pull/5247>`__: DOC:
optimize: typo/import fix in linear_sum_assignment
- - `#5248 <https://github.com/scipy/scipy/pull/5248>`__: remove
inspect.getargspec and test python 3.5 on Travis CI
- - `#5250 <https://github.com/scipy/scipy/pull/5250>`__: BUG: Fix
sparse multiply by single-element zero
- - `#5261 <https://github.com/scipy/scipy/pull/5261>`__: Fix bug
causing a TypeError in splrep when a runtime warning...
- - `#5262 <https://github.com/scipy/scipy/pull/5262>`__: Follow up to
4489 (Addition LAPACK routines in linalg.lstsq)
- - `#5264 <https://github.com/scipy/scipy/pull/5264>`__: ignore
zero-length edges for default epsilon
- - `#5269 <https://github.com/scipy/scipy/pull/5269>`__: DOC: Typos
and spell-checking
- - `#5272 <https://github.com/scipy/scipy/pull/5272>`__: MAINT:
signal: Convert array syntax to memoryviews
- - `#5273 <https://github.com/scipy/scipy/pull/5273>`__: DOC: raw
strings for docstrings with math
- - `#5274 <https://github.com/scipy/scipy/pull/5274>`__: MAINT:
sparse: update cython code for MST
- - `#5278 <https://github.com/scipy/scipy/pull/5278>`__: BUG: io:
Stop guessing the data delimiter in ARFF files.
- - `#5289 <https://github.com/scipy/scipy/pull/5289>`__: BUG: misc:
Fix the Pillow work-around for 1-bit images.
- - `#5291 <https://github.com/scipy/scipy/pull/5291>`__: ENH: call
np.correlate for 1d in scipy.signal.correlate
- - `#5294 <https://github.com/scipy/scipy/pull/5294>`__: DOC:
special: Remove a potentially misleading example from the...
- - `#5295 <https://github.com/scipy/scipy/pull/5295>`__: Simplify
replacement of fftpack by pyfftw
- - `#5296 <https://github.com/scipy/scipy/pull/5296>`__: ENH: Add
matrix normal distribution to stats
- - `#5297 <https://github.com/scipy/scipy/pull/5297>`__: Fixed
leaf_rotation and leaf_font_size in Python 3
- - `#5303 <https://github.com/scipy/scipy/pull/5303>`__: MAINT:
stats: rewrite find_repeats
- - `#5307 <https://github.com/scipy/scipy/pull/5307>`__: MAINT:
stats: remove unused Fortran routine
- - `#5313 <https://github.com/scipy/scipy/pull/5313>`__: BUG: sparse:
fix diags for nonsquare matrices
- - `#5315 <https://github.com/scipy/scipy/pull/5315>`__: MAINT:
special: Cephes cleanup
- - `#5316 <https://github.com/scipy/scipy/pull/5316>`__: fix input
check for sparse.linalg.svds
- - `#5319 <https://github.com/scipy/scipy/pull/5319>`__: MAINT:
Cython code maintenance
- - `#5328 <https://github.com/scipy/scipy/pull/5328>`__: BUG: Fix
place_poles return values
- - `#5329 <https://github.com/scipy/scipy/pull/5329>`__: avoid a
spurious divide-by-zero in Student t stats
- - `#5334 <https://github.com/scipy/scipy/pull/5334>`__: MAINT:
integrate: miscellaneous cleanup
- - `#5340 <https://github.com/scipy/scipy/pull/5340>`__: MAINT:
Printing Error Msg to STDERR and Removing iterate.dat
- - `#5347 <https://github.com/scipy/scipy/pull/5347>`__: ENH: add
Py3.5-style matmul operator (e.g. A  <at>  B) to sparse linear...
- - `#5350 <https://github.com/scipy/scipy/pull/5350>`__: FIX error,
when reading 32-bit float wav files
- - `#5351 <https://github.com/scipy/scipy/pull/5351>`__: refactor the
PCHIP interpolant's algorithm
- - `#5354 <https://github.com/scipy/scipy/pull/5354>`__: MAINT:
construct csr and csc matrices from integer lists
- - `#5359 <https://github.com/scipy/scipy/pull/5359>`__: add a fast
path to interp1d
- - `#5364 <https://github.com/scipy/scipy/pull/5364>`__: Add two
fill_values to interp1d.
- - `#5365 <https://github.com/scipy/scipy/pull/5365>`__: ABCD docstrings
- - `#5366 <https://github.com/scipy/scipy/pull/5366>`__: Fixed typo
in the documentation for scipy.signal.cwt() per #5290.
- - `#5367 <https://github.com/scipy/scipy/pull/5367>`__: DOC updated
scipy.spatial.Delaunay example
- - `#5368 <https://github.com/scipy/scipy/pull/5368>`__: ENH: Do not
create a throwaway class at every function call
- - `#5372 <https://github.com/scipy/scipy/pull/5372>`__: DOC:
spectral: fix reference formatting
- - `#5375 <https://github.com/scipy/scipy/pull/5375>`__: PEP8
amendments to ffpack_basic.py
- - `#5377 <https://github.com/scipy/scipy/pull/5377>`__: BUG:
integrate: builtin name no longer shadowed
- - `#5381 <https://github.com/scipy/scipy/pull/5381>`__: PEP8ified
fftpack_pseudo_diffs.py
- - `#5385 <https://github.com/scipy/scipy/pull/5385>`__: BLD: fix
Bento build for changes to optimize and spatial
- - `#5386 <https://github.com/scipy/scipy/pull/5386>`__: STY: PEP8
amendments to interpolate.py
- - `#5387 <https://github.com/scipy/scipy/pull/5387>`__: DEP:
deprecate stats.histogram
- - `#5388 <https://github.com/scipy/scipy/pull/5388>`__: REL: add
"make upload" command to doc/Makefile.
- - `#5389 <https://github.com/scipy/scipy/pull/5389>`__: DOC: updated
origin param of scipy.ndimage.filters.convolve
- - `#5395 <https://github.com/scipy/scipy/pull/5395>`__: BUG:
special: fix a number of edge cases related to `x = np.inf`.
- - `#5398 <https://github.com/scipy/scipy/pull/5398>`__: MAINT:
stats: avoid spurious warnings in lognorm.pdf(0, s)
- - `#5407 <https://github.com/scipy/scipy/pull/5407>`__: ENH: stats:
Handle mu=0 in stats.poisson
- - `#5409 <https://github.com/scipy/scipy/pull/5409>`__: Fix the
behavior of discrete distributions at the right-hand...
- - `#5412 <https://github.com/scipy/scipy/pull/5412>`__: TST: stats:
skip a test to avoid a spurious log(0) warning
- - `#5413 <https://github.com/scipy/scipy/pull/5413>`__: BUG: linalg:
work around LAPACK single-precision lwork computation...
- - `#5414 <https://github.com/scipy/scipy/pull/5414>`__: MAINT:
stats: move creation of namedtuples outside of function...
- - `#5415 <https://github.com/scipy/scipy/pull/5415>`__: DOC: fix up
sections in ToC in the pdf reference guide
- - `#5416 <https://github.com/scipy/scipy/pull/5416>`__: TST: fix
issue with a ctypes test for integrate on Fedora.
- - `#5418 <https://github.com/scipy/scipy/pull/5418>`__: DOC: fix
bugs in signal.TransferFunction docstring. Closes gh-5287.
- - `#5419 <https://github.com/scipy/scipy/pull/5419>`__: MAINT:
sparse: fix usage of NotImplementedError
- - `#5420 <https://github.com/scipy/scipy/pull/5420>`__: Raise proper
error if maxiter < 1
- - `#5422 <https://github.com/scipy/scipy/pull/5422>`__: DOC: changed
documentation of brent to be consistent with bracket
- - `#5444 <https://github.com/scipy/scipy/pull/5444>`__: BUG:
gaussian_filter, BPoly.from_derivatives fail on numpy int...
- - `#5445 <https://github.com/scipy/scipy/pull/5445>`__: MAINT:
stats: fix incorrect deprecation warnings and test noise
- - `#5446 <https://github.com/scipy/scipy/pull/5446>`__: DOC: add
note about PyFFTW in fftpack tutorial.
- - `#5459 <https://github.com/scipy/scipy/pull/5459>`__: DOC:
integrate: Some improvements to the differential equation...
- - `#5465 <https://github.com/scipy/scipy/pull/5465>`__: BUG: Relax
mstats kurtosis test tolerance by a few ulp
- - `#5471 <https://github.com/scipy/scipy/pull/5471>`__: ConvexHull
should raise ValueError for NaNs.
- - `#5473 <https://github.com/scipy/scipy/pull/5473>`__: MAINT:
update decorators.py module to version 4.0.5
- - `#5476 <https://github.com/scipy/scipy/pull/5476>`__: BUG: imsave
searches for wrong channel axis if image has 3 or...
- - `#5477 <https://github.com/scipy/scipy/pull/5477>`__: BLD: add
numpy to setup/install_requires for OS X wheels
- - `#5479 <https://github.com/scipy/scipy/pull/5479>`__: ENH: return
Jacobian/Hessian from BasinHopping
- - `#5484 <https://github.com/scipy/scipy/pull/5484>`__: BUG: fix
ttest zero division handling
- - `#5486 <https://github.com/scipy/scipy/pull/5486>`__: Fix crash on kmeans2
- - `#5491 <https://github.com/scipy/scipy/pull/5491>`__: MAINT:
Expose parallel build option to runtests.py
- - `#5494 <https://github.com/scipy/scipy/pull/5494>`__: Sort
OptimizeResult.__repr__ by key
- - `#5496 <https://github.com/scipy/scipy/pull/5496>`__: DOC: update
the author name mapping
- - `#5497 <https://github.com/scipy/scipy/pull/5497>`__: Enhancement
to binned_statistic: option to unraveled returned...
- - `#5498 <https://github.com/scipy/scipy/pull/5498>`__: BUG: sparse:
fix a bug in sparsetools input dtype resolution
- - `#5500 <https://github.com/scipy/scipy/pull/5500>`__: DOC: detect
unprintable characters in docstrings
- - `#5505 <https://github.com/scipy/scipy/pull/5505>`__: BUG: misc:
Ensure fromimage converts mode 'P' to 'RGB' or 'RGBA'.
- - `#5514 <https://github.com/scipy/scipy/pull/5514>`__: DOC: further
update the release notes
- - `#5515 <https://github.com/scipy/scipy/pull/5515>`__: ENH:
optionally disable fixed-point acceleration
- - `#5517 <https://github.com/scipy/scipy/pull/5517>`__: DOC:
Improvements and additions to the matrix_normal doc
- - `#5518 <https://github.com/scipy/scipy/pull/5518>`__: Remove
wrappers for LAPACK deprecated routines
- - `#5521 <https://github.com/scipy/scipy/pull/5521>`__: TST: skip a
linalg.orth memory test on 32-bit platforms.
- - `#5523 <https://github.com/scipy/scipy/pull/5523>`__: DOC: change
a few floats to integers in docstring examples
- - `#5524 <https://github.com/scipy/scipy/pull/5524>`__: DOC: more
updates to 0.17.0 release notes.
- - `#5525 <https://github.com/scipy/scipy/pull/5525>`__: Fix to minor
typo in documentation for scipy.integrate.ode
- - `#5527 <https://github.com/scipy/scipy/pull/5527>`__: TST: bump
arccosh tolerance to allow for inaccurate numpy or...
- - `#5535 <https://github.com/scipy/scipy/pull/5535>`__: DOC: signal:
minor clarification to docstring of TransferFunction.
- - `#5538 <https://github.com/scipy/scipy/pull/5538>`__: DOC: signal:
fix find_peaks_cwt documentation
- - `#5545 <https://github.com/scipy/scipy/pull/5545>`__: MAINT: Fix
typo in linalg/basic.py
- - `#5547 <https://github.com/scipy/scipy/pull/5547>`__: TST: mark
TestEig.test_singular as knownfail in master.
- - `#5550 <https://github.com/scipy/scipy/pull/5550>`__: MAINT: work
around lstsq driver selection issue
- - `#5556 <https://github.com/scipy/scipy/pull/5556>`__: BUG: Fixed
broken dogbox trust-region radius update
- - `#5561 <https://github.com/scipy/scipy/pull/5561>`__: BUG:
eliminate warnings, exception (on Win) in test_maskandscale;...
- - `#5567 <https://github.com/scipy/scipy/pull/5567>`__: TST: a few
cleanups in the test suite; run_module_suite and clearer...
- - `#5568 <https://github.com/scipy/scipy/pull/5568>`__: MAINT:
simplify poisson's _argcheck
- - `#5569 <https://github.com/scipy/scipy/pull/5569>`__: TST: bump
GMean test tolerance to make it pass on Wine
- - `#5572 <https://github.com/scipy/scipy/pull/5572>`__: TST: lstsq:
bump test tolerance for TravisCI
- - `#5573 <https://github.com/scipy/scipy/pull/5573>`__: TST: remove
use of np.fromfile from cluster.vq tests
- - `#5576 <https://github.com/scipy/scipy/pull/5576>`__: Lapack deprecations
- - `#5579 <https://github.com/scipy/scipy/pull/5579>`__: TST: skip
tests of linalg.norm axis keyword on numpy <= 1.7.x
- - `#5582 <https://github.com/scipy/scipy/pull/5582>`__: Clarify
language of survival function documentation
- - `#5583 <https://github.com/scipy/scipy/pull/5583>`__: MAINT:
stats/tests: A bit of clean up.
- - `#5588 <https://github.com/scipy/scipy/pull/5588>`__: DOC: stats:
Add a note that stats.burr is the Type III Burr distribution.
- - `#5595 <https://github.com/scipy/scipy/pull/5595>`__: TST: fix
test_lamch failures on Python 3
- - `#5600 <https://github.com/scipy/scipy/pull/5600>`__: MAINT:
Ignore spatial/ckdtree.cxx and .h
- - `#5602 <https://github.com/scipy/scipy/pull/5602>`__: Explicitly
numbered replacement fields for maintainability
- - `#5605 <https://github.com/scipy/scipy/pull/5605>`__: MAINT:
collection of small fixes to test suite
- - `#5614 <https://github.com/scipy/scipy/pull/5614>`__: Minor doc change.
- - `#5624 <https://github.com/scipy/scipy/pull/5624>`__: FIX: Fix interpolate
- - `#5625 <https://github.com/scipy/scipy/pull/5625>`__: BUG: msvc9
binaries crash when indexing std::vector of size 0
- - `#5635 <https://github.com/scipy/scipy/pull/5635>`__: BUG:
misspelled __dealloc__ in cKDTree.
- - `#5642 <https://github.com/scipy/scipy/pull/5642>`__: STY: minor
fixup of formatting of 0.17.0 release notes.
- - `#5643 <https://github.com/scipy/scipy/pull/5643>`__: BLD: fix a
build issue in special/Faddeeva.cc with isnan.
- - `#5661 <https://github.com/scipy/scipy/pull/5661>`__: TST: linalg
tests used stdlib random instead of numpy.random.
- - `#5682 <https://github.com/scipy/scipy/pull/5682>`__: backports for 0.17.0
- - `#5696 <https://github.com/scipy/scipy/pull/5696>`__: Minor
improvements to least_squares' docstring.
- - `#5697 <https://github.com/scipy/scipy/pull/5697>`__: BLD: fix for
isnan/isinf issues in special/Faddeeva.cc
- - `#5720 <https://github.com/scipy/scipy/pull/5720>`__: TST: fix for
file opening error in fftpack test_import.py
- - `#5722 <https://github.com/scipy/scipy/pull/5722>`__: BUG: Make
curve_fit respect an initial guess with bounds
- - `#5726 <https://github.com/scipy/scipy/pull/5726>`__: Backports
for v0.17.0rc2
- - `#5727 <https://github.com/scipy/scipy/pull/5727>`__: API: Changes
to least_squares API

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=========

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Nathaniel Smith | 22 Jan 01:21 2016
Picon

deprecating assignment to ndarray.data

So it turns out that ndarray.data supports assignment at the Python
level, and what it does is just assign to the ->data field of the
ndarray object:
   https://github.com/numpy/numpy/blob/master/numpy/core/src/multiarray/getset.c#L325

This kind of assignment been deprecated at the C level since 1.7, and
is totally unsafe -- if there are any views pointing to the array when
this happens, then they'll be left pointing off into unallocated
memory.

E.g.:

a = np.arange(10)
b = np.linspace(0, 1, 10)
c = a.view()
a.data = b.data
# Now c points into free'd memory

Can we deprecate or just remove this?

(Also filed issue: https://github.com/numpy/numpy/issues/7093)

-n

--

-- 
Nathaniel J. Smith -- https://vorpus.org
Sebastian Berg | 22 Jan 01:05 2016
Picon

Set FutureWarnings to error in (dev) tests?

Hi all,

should we try to set FutureWarnings to errors in dev tests? I am
seriously annoyed by FutureWarnings getting lost all over for two
reasons. First, it is hard to impossible to find even our own errors
for our own FutureWarning changes. Secondly, we currently would not
even see any Futurewarnings from someone else. For numpy that may not
be a big issue, but still.

So, I was starting to try it, and it is annoying obviously. The only
serious issue, though, seems actually MA [1].
Sometimes one would add a filter for a whole test file (for my start I
did this for the NaT stuff) [2].

Anyway, should we attempt to do this? I admit that trying to make it
work, even *with* the change FutureWarnings suddenly pop up when you
make the warnings being given less often (I will guess that warning was
already issued at import time somewhere).

- Sebastian

[1] And at that a brand new future warning there, which seems too
agressive in any case, though that won't change much.

[2] One annoying thing about this, the filter might never be removed.
One could add a canary maybe to error out when the filter is not needed
anymore.
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Joseph Fox-Rabinovitz | 21 Jan 07:51 2016
Picon

PR #7083: ENH: Added 'doane' and 'sqrt' estimators to np.histogram

Please let me know if there is anything wrong or missing. I have added
a couple of estimators that I find useful sometimes.

    -Joe

Gmane