From adibhar97 at gmail.com  Wed May  2 03:01:36 2018
From: adibhar97 at gmail.com (Aditya Bharti)
Date: Wed, 2 May 2018 12:31:36 +0530
Subject: [SciPy-Dev] [GSOC 2018 Project Thread]: Rotation formalism in 3
 dimensions
In-Reply-To: <CANRzPHVQ_uXGusg_VoHNyXuQg6OvJ2w0w3cTH=0Ow-ALy8kwjA@mail.gmail.com>
References: <CANRzPHXri+amnajw2ANB5mWm+4ScunO3Mwdd5a0Rq8EK0QB0fw@mail.gmail.com>
 <CAGu2niXZi+drjipzwX_jSTVUubG9xD_th2hjSAAHLjWSeNpEng@mail.gmail.com>
 <CABL7CQhxbLym+ps7M2-Zy5OzZAd8boiAuHRTue=2X1XxJtwi9A@mail.gmail.com>
 <CANRzPHWLFmKpZ9xaNxz4wMvvr_LQhw6VZS+UFxqwUAn25V4agg@mail.gmail.com>
 <19947416-eb05-b038-ae36-ed470fbe6127@mailbox.org>
 <CANRzPHVQ_uXGusg_VoHNyXuQg6OvJ2w0w3cTH=0Ow-ALy8kwjA@mail.gmail.com>
Message-ID: <CANRzPHWY2FTwOZEjPLsfS1O6Be6zEZgazMpszWxPVxBgAGiz8w@mail.gmail.com>

Blog update:

I just got an email from PSF regarding the blogging. It appears that all
blogs this year must be on the python-gsoc blogs site itself. So the blog
for this project will live at https://blogs.python-gsoc.org/aditya-bharti/ .

Regards,
Aditya

On 29 April 2018 at 09:40, Aditya Bharti <adibhar97 at gmail.com> wrote:

> So I finally got the docs built. Couple of points which I think might be
> helpful to people building docs in the future:
>
>    - You need to have sphinx installed in your working environment
>    (native installation, virtualenv, conda, whatever). I did not see sphinx
>    listed as a dependency online. Maybe it should be included in the
>    HACKING.rst.txt file?
>    - You do *NOT* need to have numpydoc installed on your system.
>    Irrespective of where it is installed, the build process only uses the
>    numpydoc package present under the sphinxext directory. I wasted a lot of
>    hours trying to find which version of numpydoc was being used as I had it
>    installed both in my virtualenv, and native installation; neither of those
>    had the faulty import line.
>    - After using `git submodule update` to get the latest sphinxext
>    directory and numpydoc installation, the faulty import line in file
>    doc/sphinxext/numpydoc/numpydoc.py needs to be changed. From
>
>>    from sphinx.util.compat import Directive
>>
>    to
>
>>    from docutils.parsers.rst import Directive
>>
>    Thank you Lars for pointing that out.
>    - Finally, and this was my fault entirely, I had my virtual
>    environment running python version 3.5.2, but as python3 or python. Calling
>    python3.5 (as the Makefile was doing when I set PYVER=3.5) called the
>    python executable in /usr/bin/python3.5, which couldn't find the sphinx
>    module itself (as I didn't install it along with my native installation).
>    Setting PYVER=3, or PYTHON=/path/to/python/in/virtualenv fixed this.
>
>
> On 25 April 2018 at 03:40, Lars G. <lagru at mailbox.org> wrote:
>
>> On 24.04.2018 20:36, Aditya Bharti wrote:
>> > Regarding building the documentation, I was able to figure out that I
>> > needed to install sphinx separately. The HACKING.rst.txt file only
>> > mentions Numpy Cython and pytest as dependencies.
>> > I was able to get the make command running with `make html PYVER=3.5`,
>> > but I'm getting the follwing error:
>> >
>> >
>> >     Could not import extension numpydoc (exception: cannot import name
>> >     'Directive')
>>
>> Hello Aditya,
>>
>> I had the same problem with my setup. I'm still a little bit confused
>> but I think the error was due to an old version of numpydoc trying use
>> an import that didn't work with new versions of sphinx.
>> I think got the old version with the git-submodules included in the
>> doc-dirctory (can be downloaded with `git submodule update`).
>>
>> Anyway I got it to work by modifying the faulty import itself. Try to
>> find the file numpydoc/numpydoc.py and try to find the line:
>>
>>     from sphinx.util.compat import Directive
>>
>> If you can find that line you may be in luck because replacing that line
>> with:
>>
>>     from docutils.parsers.rst import Directive
>>
>> fixed it for me. I hope this helps.
>>
>> By the way, perhaps it would be useful to extend the doc/README.txt with
>> a more thorough explanation of the build process and mention that the
>> submodules can be downloaded with `git submodule update`. I only found
>> out because I looked at guide for NumPy
>> https://github.com/numpy/numpy/blob/master/doc/source/docs/
>> howto_build_docs.rst
>> while trying to figure out the build process myself.
>>
>> Best regards,
>> Lars
>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at python.org
>> https://mail.python.org/mailman/listinfo/scipy-dev
>>
>
>
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From nikolay.mayorov at zoho.com  Wed May  2 10:24:35 2018
From: nikolay.mayorov at zoho.com (Nikolay Mayorov)
Date: Wed, 02 May 2018 19:24:35 +0500
Subject: [SciPy-Dev] [GSOC 2018 Project Thread]: Rotation formalism in 3
 dimensions
Message-ID: <163213d9b99.e31ddfbf140246.3867213885941953730@zoho.com>

Hi, Aditya!

Glad that you set up the blog and good job on setting up the documentation build as well. 

Curious, what is this blogging platform like? How do you create posts in it?

As for your first post: while not strictly necessary I think it would be nice to see a more thorough introductory post with a brief overview, motivation and/or an example. Do you want to work on it?

Best,
Nikolay
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From adibhar97 at gmail.com  Wed May  2 11:33:00 2018
From: adibhar97 at gmail.com (Aditya Bharti)
Date: Wed, 2 May 2018 21:03:00 +0530
Subject: [SciPy-Dev] [GSOC 2018 Project Thread]: Rotation formalism in 3
 dimensions
In-Reply-To: <163213d9b99.e31ddfbf140246.3867213885941953730@zoho.com>
References: <163213d9b99.e31ddfbf140246.3867213885941953730@zoho.com>
Message-ID: <CANRzPHVN47mDJqc4DuUq70X9sAiRqBRWOSHszgtL3QyM1O6ihA@mail.gmail.com>

Hi Nikolay,

I've used Wordpress only once before, so I don't know much about it. From
my limited experience, it is extremely customizable. You can customize
every thing from the look and feel to SEO characteristics. There are
apparently a lot of wordpress plugins for these kind of tasks. For this
particular blog, PSF had already setup an account for me with a site on it.
All I had to do was click on the 'New' button and open up the new post
page. There's a field for a header and body text, with options for adding
audio, video and hyperlinks.

As regards to the post itself, sure I'll expand it with a brief overview,
motivation and an example. Note that the example will only show sample
usage, not any internals. I plan to borrow heavily from my proposal for
this purpose, I hope that's ok.

Regards,
Aditya

On 2 May 2018 at 19:54, Nikolay Mayorov <nikolay.mayorov at zoho.com> wrote:

> Hi, Aditya!
>
> Glad that you set up the blog and good job on setting up the documentation
> build as well.
>
> Curious, what is this blogging platform like? How do you create posts in
> it?
>
> As for your first post: while not strictly necessary I think it would be
> nice to see a more thorough introductory post with a brief overview,
> motivation and/or an example. Do you want to work on it?
>
> Best,
> Nikolay
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
>
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From einstein.edison at gmail.com  Fri May  4 08:05:44 2018
From: einstein.edison at gmail.com (Hameer Abbasi)
Date: Fri, 4 May 2018 05:05:44 -0700
Subject: [SciPy-Dev] Sparse Arrays - Formats and operations
Message-ID: <CADViA5Bar=d9pMeoTktDL3jQP+KFZmoUOzz5ZLKLSKXX8q3zeQ@mail.gmail.com>

 Hello everyone,

I?m faced with another design decision as I continue to develop
pydata/sparse <https://github.com/pydata/sparse> (a package that offers
N-dimensional sparse arrays compatible with Numpy). Namely, whether to


   1. Convert to an appropriate sparse storage format before performing an
   operation vs implementing it natively, and
   2. Whether to always return arrays in the input format.

I?ve opened a parallel GitHub issue
<https://github.com/pydata/sparse/issues/149> for discussion and feedback,
and replies here are welcome as well.

Regards,
Hameer Abbasi
Sent from Astro <https://www.helloastro.com> for Mac
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From pav at iki.fi  Sat May  5 14:36:03 2018
From: pav at iki.fi (Pauli Virtanen)
Date: Sat, 05 May 2018 20:36:03 +0200
Subject: [SciPy-Dev] ANN: SciPy 1.1.0 released
Message-ID: <236a10a327111484ffc775d388704ebcca6500a7.camel@iki.fi>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Hi all,

On behalf of the SciPy development team I'm pleased to announce the
SciPy 1.1.0 release.

Sources and binary wheels can be found at
https://pypi.python.org/pypi/scipy
and at https://github.com/scipy/scipy/releases/tag/v1.1.0. 
To install with pip:

    pip install scipy==1.1.0

Thanks to everyone who contributed to this release!


=========================
SciPy 1.1.0 Release Notes
=========================

SciPy 1.1.0 is the culmination of 7 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. Before upgrading, we recommend that users check that
their own code does not use deprecated SciPy functionality (to do so,
run your code with ``python -Wd`` and check for ``DeprecationWarning``
s). Our development attention will now shift to bug-fix releases on the
1.1.x branch, and on adding new features on the master branch.

This release requires Python 2.7 or 3.4+ and NumPy 1.8.2 or greater.

This release has improved but not necessarily 100% compatibility with
the `PyPy <https://pypy.org/>`__ Python implementation. For running on
PyPy, PyPy 6.0+ and Numpy 1.15.0+ are required.

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

`scipy.integrate` improvements
- ------------------------------

The argument ``tfirst`` has been added to the function
`scipy.integrate.odeint`. This allows odeint to use the same user
functions as `scipy.integrate.solve_ivp` and `scipy.integrate.ode` without
the need for wrapping them in a function that swaps the first two
arguments.

Error messages from ``quad()`` are now clearer.

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

The function `scipy.linalg.ldl` has been added for factorization of
indefinite symmetric/hermitian matrices into triangular and block
diagonal matrices.

Python wrappers for LAPACK ``sygst``, ``hegst`` added in
`scipy.linalg.lapack`.

Added `scipy.linalg.null_space`, `scipy.linalg.cdf2rdf`,
`scipy.linalg.rsf2csf`.

`scipy.misc` improvements
- -------------------------

An electrocardiogram has been added as an example dataset for a
one-dimensional signal. It can be accessed through
`scipy.misc.electrocardiogram`.

`scipy.ndimage` improvements
- ----------------------------

The routines `scipy.ndimage.binary_opening`, and
`scipy.ndimage.binary_closing` now support masks and different border
values.

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

The method ``trust-constr`` has been added to
`scipy.optimize.minimize`. The method switches between two
implementations depending on the problem definition. For equality
constrained problems it is an implementation of a trust-region
sequential quadratic programming solver and, when inequality constraints
are imposed, it switches to a trust-region interior point method. Both
methods are appropriate for large scale problems. Quasi-Newton options
BFGS and SR1 were implemented and can be used to approximate second
order derivatives for this new method. Also, finite-differences can be
used to approximate either first-order or second-order derivatives.

Random-to-Best/1/bin and Random-to-Best/1/exp mutation strategies were
added to `scipy.optimize.differential_evolution` as ``randtobest1bin``
and ``randtobest1exp``, respectively. Note: These names were already in
use but implemented a different mutation strategy. See `Backwards
incompatible changes <#backwards-incompatible-changes>`__, below. The
``init`` keyword for the `scipy.optimize.differential_evolution`
function can now accept an array. This array allows the user to specify
the entire population.

Add an ``adaptive`` option to Nelder-Mead to use step parameters adapted
to the dimensionality of the problem.

Minor improvements in `scipy.optimize.basinhopping`.

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

Three new functions for peak finding in one-dimensional arrays were
added. `scipy.signal.find_peaks` searches for peaks (local maxima) based
on simple value comparison of neighbouring samples and returns those
peaks whose properties match optionally specified conditions for their
height, prominence, width, threshold and distance to each other.
`scipy.signal.peak_prominences` and `scipy.signal.peak_widths` can directly
calculate the prominences or widths of known peaks.

Added ZPK versions of frequency transformations:
`scipy.signal.bilinear_zpk`, `scipy.signal.lp2bp_zpk`,
`scipy.signal.lp2bs_zpk`, `scipy.signal.lp2hp_zpk`,
`scipy.signal.lp2lp_zpk`.

Added `scipy.signal.windows.dpss`,
`scipy.signal.windows.general_cosine` and
`scipy.signal.windows.general_hamming`.

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

Previously, the ``reshape`` method only worked on
`scipy.sparse.lil_matrix`, and in-place reshaping did not work on any
matrices. Both operations are now implemented for all matrices. Handling
of shapes has been made consistent with ``numpy.matrix`` throughout the
`scipy.sparse` module (shape can be a tuple or splatted, negative
number acts as placeholder, padding and unpadding dimensions of size 1
to ensure length-2 shape).

`scipy.special` improvements
- ----------------------------

Added Owen?s T function as `scipy.special.owens_t`.

Accuracy improvements in ``chndtr``, ``digamma``, ``gammaincinv``,
``lambertw``, ``zetac``.

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

The Moyal distribution has been added as `scipy.stats.moyal`.

Added the normal inverse Gaussian distribution as
`scipy.stats.norminvgauss`.

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

The iterative linear equation solvers in `scipy.sparse.linalg` had a
sub-optimal way of how absolute tolerance is considered. The default
behavior will be changed in a future Scipy release to a more standard
and less surprising one. To silence deprecation warnings, set the
``atol=`` parameter explicitly.

`scipy.signal.windows.slepian` is deprecated, replaced by
`scipy.signal.windows.dpss`.

The window functions in `scipy.signal` are now available in
`scipy.signal.windows`. They will remain also available in the old
location in the `scipy.signal` namespace in future Scipy versions.
However, importing them from `scipy.signal.windows` is preferred, and
new window functions will be added only there.

Indexing sparse matrices with floating-point numbers instead of integers
is deprecated.

The function `scipy.stats.itemfreq` is deprecated.

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

Previously, `scipy.linalg.orth` used a singular value cutoff value
appropriate for double precision numbers also for single-precision
input. The cutoff value is now tunable, and the default has been changed
to depend on the input data precision.

In previous versions of Scipy, the ``randtobest1bin`` and
``randtobest1exp`` mutation strategies in
`scipy.optimize.differential_evolution` were actually implemented using
the Current-to-Best/1/bin and Current-to-Best/1/exp strategies,
respectively. These strategies were renamed to ``currenttobest1bin`` and
``currenttobest1exp`` and the implementations of ``randtobest1bin`` and
``randtobest1exp`` strategies were corrected.

Functions in the ndimage module now always return their output array.
Before this most functions only returned the output array if it had been
allocated by the function, and would return ``None`` if it had been
provided by the user.

Distance metrics in `scipy.spatial.distance` now require non-negative
weights.

`scipy.special.loggamma` returns now real-valued result when the input
is real-valued.

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

When building on Linux with GNU compilers, the ``.so`` Python extension
files now hide all symbols except those required by Python, which can
avoid problems when embedding the Python interpreter.



Authors
=======

* Saurabh Agarwal +
* Diogo Aguiam +
* Joseph Albert +
* Gerrit Ansmann +
* Jean-Fran?ois B +
* Vahan Babayan +
* Alessandro Pietro Bardelli
* Christoph Baumgarten +
* Felix Berkenkamp
* Lilian Besson +
* Aditya Bharti +
* Matthew Brett
* Evgeni Burovski
* CJ Carey
* Martin ?. Christensen +
* Robert Cimrman
* Vicky Close +
* Peter Cock +
* Philip DeBoer
* Jaime Fernandez del Rio
* Dieter Werthm?ller +
* Tom Donoghue +
* Matt Dzugan +
* Lars G +
* Jacques Gaudin +
* Andriy Gelman +
* Sean Gillies +
* Dezmond Goff
* Christoph Gohlke
* Ralf Gommers
* Uri Goren +
* Deepak Kumar Gouda +
* Douglas Lessa Graciosa +
* Matt Haberland
* David Hagen
* Charles Harris
* Jordan Heemskerk +
* Danny Hermes +
* Stephan Hoyer +
* Theodore Hu +
* Jean-Fran?ois B. +
* Mads Jensen +
* Jon Haitz Legarreta Gorro?o +
* Ben Jude +
* Noel Kippers +
* Julius Bier Kirkegaard +
* Maria Knorps +
* Mikkel Kristensen +
* Eric Larson
* Kasper Primdal Lauritzen +
* Denis Laxalde
* KangWon Lee +
* Jan Lehky +
* Jackie Leng +
* P.L. Lim +
* Nikolay Mayorov
* Mihai Capot? +
* Max Mikhaylov +
* Mark Mikofski +
* Jarrod Millman
* Raden Muhammad +
* Paul Nation
* Andrew Nelson
* Nico Schl?mer
* Joel Nothman
* Kyle Oman +
* Egor Panfilov +
* Nick Papior
* Anubhav Patel +
* Oleksandr Pavlyk
* Ilhan Polat
* Robert Pollak +
* Anant Prakash +
* Aman Pratik
* Sean Quinn +
* Giftlin Rajaiah +
* Tyler Reddy
* Joscha Reimer
* Antonio H Ribeiro +
* Antonio Horta Ribeiro
* Benjamin Rose +
* Fabian Rost
* Divakar Roy +
* Scott Sievert
* Leo Singer
* Sourav Singh
* Martino Sorbaro +
* Eric Stansifer +
* Martin Thoma
* Phil Tooley +
* Piotr Uchwat +
* Paul van Mulbregt
* Pauli Virtanen
* Stefan van der Walt
* Warren Weckesser
* Florian Weimer +
* Eric Wieser
* Josh Wilson
* Ted Ying +
* Evgeny Zhurko
* Z? Vin?cius
* @Astrofysicus +
* @awakenting +
* @endolith
* @FormerPhysicist +
* @gaulinmp +
* @hugovk
* @ksemb +
* @kshitij12345 +
* @luzpaz +
* @NKrvavica +
* @rafalalgo +
* @samyak0210 +
* @soluwalana +
* @sudheerachary +
* @Tokixix +
* @tttthomasssss +
* @vkk800 +
* @xoviat
* @ziejcow +

A total of 122 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 1.1.0
- -----------------------

* `#979 <https://github.com/scipy/scipy/issues/979>`__: Allow Hermitian matrices in lobpcg (Trac #452)
* `#2694 <https://github.com/scipy/scipy/issues/2694>`__: Solution of iterative solvers can be less accurate than tolerance...
* `#3164 <https://github.com/scipy/scipy/issues/3164>`__: RectBivariateSpline usage inconsistent with other interpolation...
* `#4161 <https://github.com/scipy/scipy/issues/4161>`__: Missing ITMAX optional argument in scipy.optimize.nnls
* `#4354 <https://github.com/scipy/scipy/issues/4354>`__: signal.slepian should use definition of digital window
* `#4866 <https://github.com/scipy/scipy/issues/4866>`__: Shouldn't scipy.linalg.sqrtm raise an error if matrix is singular?
* `#4953 <https://github.com/scipy/scipy/issues/4953>`__: The dirichlet distribution unnecessarily requires strictly positive...
* `#5336 <https://github.com/scipy/scipy/issues/5336>`__: sqrtm on a diagonal matrix can warn "Matrix is singular and may...
* `#5922 <https://github.com/scipy/scipy/issues/5922>`__: Suboptimal convergence of Halley's method?
* `#6036 <https://github.com/scipy/scipy/issues/6036>`__: Incorrect edge case in scipy.stats.triang.pdf
* `#6202 <https://github.com/scipy/scipy/issues/6202>`__: Enhancement: Add LDLt factorization to scipy
* `#6589 <https://github.com/scipy/scipy/issues/6589>`__: sparse.random with custom rvs callable does pass on arg to subclass
* `#6654 <https://github.com/scipy/scipy/issues/6654>`__: Spearman's rank correlation coefficient slow with nan values...
* `#6794 <https://github.com/scipy/scipy/issues/6794>`__: Remove NumarrayType struct with numarray type names from ndimage
* `#7136 <https://github.com/scipy/scipy/issues/7136>`__: The dirichlet distribution unnecessarily rejects probabilities...
* `#7169 <https://github.com/scipy/scipy/issues/7169>`__: Will it be possible to add LDL' factorization for Hermitian indefinite...
* `#7291 <https://github.com/scipy/scipy/issues/7291>`__: fsolve docs should say it doesn't handle over- or under-determined...
* `#7453 <https://github.com/scipy/scipy/issues/7453>`__: binary_opening/binary_closing missing arguments
* `#7500 <https://github.com/scipy/scipy/issues/7500>`__: linalg.solve test failure on OS X with Accelerate
* `#7555 <https://github.com/scipy/scipy/issues/7555>`__: Integratig a function with singularities using the quad routine
* `#7624 <https://github.com/scipy/scipy/issues/7624>`__: allow setting both absolute and relative tolerance of sparse...
* `#7724 <https://github.com/scipy/scipy/issues/7724>`__: odeint documentation refers to t0 instead of t
* `#7746 <https://github.com/scipy/scipy/issues/7746>`__: False CDF values for skew normal distribution
* `#7750 <https://github.com/scipy/scipy/issues/7750>`__: mstats.winsorize documentation needs clarification
* `#7787 <https://github.com/scipy/scipy/issues/7787>`__: Documentation error in spherical Bessel, Neumann, modified spherical...
* `#7836 <https://github.com/scipy/scipy/issues/7836>`__: Scipy mmwrite incorrectly writes the zeros for skew-symmetric,...
* `#7839 <https://github.com/scipy/scipy/issues/7839>`__: sqrtm is unable to compute square root of zero matrix
* `#7847 <https://github.com/scipy/scipy/issues/7847>`__: solve is very slow since #6775
* `#7888 <https://github.com/scipy/scipy/issues/7888>`__: Scipy 1.0.0b1 prints spurious DVODE/ZVODE/lsoda messages
* `#7909 <https://github.com/scipy/scipy/issues/7909>`__: bessel kv function in 0 is nan
* `#7915 <https://github.com/scipy/scipy/issues/7915>`__: LinearOperator's __init__ runs two times when instantiating the...
* `#7958 <https://github.com/scipy/scipy/issues/7958>`__: integrate.quad could use better error messages when given bad...
* `#7968 <https://github.com/scipy/scipy/issues/7968>`__: integrate.quad handles decreasing limits (b<a) inconsistently
* `#7970 <https://github.com/scipy/scipy/issues/7970>`__: ENH: matching return dtype for loggamma/gammaln
* `#7991 <https://github.com/scipy/scipy/issues/7991>`__: `lfilter` segfaults for integer inputs
* `#8076 <https://github.com/scipy/scipy/issues/8076>`__: "make dist" for the docs doesn't complete cleanly
* `#8080 <https://github.com/scipy/scipy/issues/8080>`__: Use JSON in `special/_generate_pyx.py`?
* `#8127 <https://github.com/scipy/scipy/issues/8127>`__: scipy.special.psi(x) very slow for some values of x
* `#8145 <https://github.com/scipy/scipy/issues/8145>`__: BUG: ndimage geometric_transform and zoom using deprecated NumPy...
* `#8158 <https://github.com/scipy/scipy/issues/8158>`__: BUG: romb print output requires correction
* `#8181 <https://github.com/scipy/scipy/issues/8181>`__: loadmat() raises TypeError instead of FileNotFound when reading...
* `#8228 <https://github.com/scipy/scipy/issues/8228>`__: bug for log1p on csr_matrix
* `#8235 <https://github.com/scipy/scipy/issues/8235>`__: scipy.stats multinomial pmf return nan
* `#8271 <https://github.com/scipy/scipy/issues/8271>`__: scipy.io.mmwrite raises type error for uint16
* `#8288 <https://github.com/scipy/scipy/issues/8288>`__: Should tests be written for scipy.sparse.linalg.isolve.minres...
* `#8298 <https://github.com/scipy/scipy/issues/8298>`__: Broken links on scipy API web page
* `#8329 <https://github.com/scipy/scipy/issues/8329>`__: `_gels` fails for fat A matrix
* `#8346 <https://github.com/scipy/scipy/issues/8346>`__: Avoidable overflow in scipy.special.binom(n, k)
* `#8371 <https://github.com/scipy/scipy/issues/8371>`__: BUG: special: zetac(x) returns 0 for x < -30.8148
* `#8382 <https://github.com/scipy/scipy/issues/8382>`__: collections.OrderedDict in test_mio.py
* `#8492 <https://github.com/scipy/scipy/issues/8492>`__: Missing documentation for `brute_force` parameter in scipy.ndimage.morphology
* `#8532 <https://github.com/scipy/scipy/issues/8532>`__: leastsq needlessly appends extra dimension for scalar problems
* `#8544 <https://github.com/scipy/scipy/issues/8544>`__: [feature request] Convert complex diagonal form to real block...
* `#8561 <https://github.com/scipy/scipy/issues/8561>`__: [Bug?] Example of Bland's Rule for optimize.linprog (simplex)...
* `#8562 <https://github.com/scipy/scipy/issues/8562>`__: CI: Appveyor builds fail because it can't import ConvexHull from...
* `#8576 <https://github.com/scipy/scipy/issues/8576>`__: BUG: optimize: `show_options(solver='minimize', method='Newton-CG')`...
* `#8603 <https://github.com/scipy/scipy/issues/8603>`__: test_roots_gegenbauer/chebyt/chebyc failures on manylinux
* `#8604 <https://github.com/scipy/scipy/issues/8604>`__: Test failures in scipy.sparse test_inplace_dense
* `#8616 <https://github.com/scipy/scipy/issues/8616>`__: special: ellpj.c code can be cleaned up a bit
* `#8625 <https://github.com/scipy/scipy/issues/8625>`__: scipy 1.0.1 no longer allows overwriting variables in netcdf...
* `#8629 <https://github.com/scipy/scipy/issues/8629>`__: gcrotmk.test_atol failure with MKL
* `#8632 <https://github.com/scipy/scipy/issues/8632>`__: Sigma clipping on data with the same value
* `#8646 <https://github.com/scipy/scipy/issues/8646>`__: scipy.special.sinpi test failures in test_zero_sign on old MSVC
* `#8663 <https://github.com/scipy/scipy/issues/8663>`__: linprog with method=interior-point produced incorrect answer...
* `#8694 <https://github.com/scipy/scipy/issues/8694>`__: linalg:TestSolve.test_all_type_size_routine_combinations fails...
* `#8703 <https://github.com/scipy/scipy/issues/8703>`__: Q: Does runtests.py --refguide-check need env (or other) variables...


Pull requests for 1.1.0
- -----------------------

* `#6590 <https://github.com/scipy/scipy/pull/6590>`__: BUG: sparse: fix custom rvs callable argument in sparse.random
* `#7004 <https://github.com/scipy/scipy/pull/7004>`__: ENH: scipy.linalg.eigsh cannot get all eigenvalues
* `#7120 <https://github.com/scipy/scipy/pull/7120>`__: ENH: implemented Owen's T function
* `#7483 <https://github.com/scipy/scipy/pull/7483>`__: ENH: Addition/multiplication operators for StateSpace systems
* `#7566 <https://github.com/scipy/scipy/pull/7566>`__: Informative exception when passing a sparse matrix
* `#7592 <https://github.com/scipy/scipy/pull/7592>`__: Adaptive Nelder-Mead
* `#7729 <https://github.com/scipy/scipy/pull/7729>`__: WIP: ENH: optimize: large-scale constrained optimization algorithms...
* `#7802 <https://github.com/scipy/scipy/pull/7802>`__: MRG: Add dpss window function
* `#7803 <https://github.com/scipy/scipy/pull/7803>`__: DOC: Add examples to spatial.distance
* `#7821 <https://github.com/scipy/scipy/pull/7821>`__: Add Returns section to the docstring
* `#7833 <https://github.com/scipy/scipy/pull/7833>`__: ENH: Performance improvements in scipy.linalg.special_matrices
* `#7864 <https://github.com/scipy/scipy/pull/7864>`__: MAINT: sparse: Simplify sputils.isintlike
* `#7865 <https://github.com/scipy/scipy/pull/7865>`__: ENH: Improved speed of copy into L, U matrices
* `#7871 <https://github.com/scipy/scipy/pull/7871>`__: ENH: sparse: Add 64-bit integer to sparsetools
* `#7879 <https://github.com/scipy/scipy/pull/7879>`__: ENH: re-enabled old sv lapack routine as defaults
* `#7889 <https://github.com/scipy/scipy/pull/7889>`__: DOC: Show probability density functions as math
* `#7900 <https://github.com/scipy/scipy/pull/7900>`__: API: Soft deprecate signal.* windows
* `#7910 <https://github.com/scipy/scipy/pull/7910>`__: ENH: allow `sqrtm` to compute the root of some singular matrices
* `#7911 <https://github.com/scipy/scipy/pull/7911>`__: MAINT: Avoid unnecessary array copies in xdist
* `#7913 <https://github.com/scipy/scipy/pull/7913>`__: DOC: Clarifies the meaning of `initial` of scipy.integrate.cumtrapz()
* `#7916 <https://github.com/scipy/scipy/pull/7916>`__: BUG: sparse.linalg: fix wrong use of __new__ in LinearOperator
* `#7921 <https://github.com/scipy/scipy/pull/7921>`__: BENCH: split spatial benchmark imports
* `#7927 <https://github.com/scipy/scipy/pull/7927>`__: ENH: added sygst/hegst routines to lapack
* `#7934 <https://github.com/scipy/scipy/pull/7934>`__: MAINT: add `io/_test_fortranmodule` to `.gitignore`
* `#7936 <https://github.com/scipy/scipy/pull/7936>`__: DOC: Fixed typo in scipy.special.roots_jacobi documentation
* `#7937 <https://github.com/scipy/scipy/pull/7937>`__: MAINT: special: Mark a test that fails on i686 as a known failure.
* `#7941 <https://github.com/scipy/scipy/pull/7941>`__: ENH: LDLt decomposition for indefinite symmetric/hermitian matrices
* `#7945 <https://github.com/scipy/scipy/pull/7945>`__: ENH: Implement reshape method on sparse matrices
* `#7947 <https://github.com/scipy/scipy/pull/7947>`__: DOC: update docs on releasing and installing/upgrading
* `#7954 <https://github.com/scipy/scipy/pull/7954>`__: Basin-hopping changes
* `#7964 <https://github.com/scipy/scipy/pull/7964>`__: BUG: test_falker not robust against numerical fuss in eigenvalues
* `#7967 <https://github.com/scipy/scipy/pull/7967>`__: QUADPACK Errors - human friendly errors to replace 'Invalid Input'
* `#7975 <https://github.com/scipy/scipy/pull/7975>`__: Make sure integrate.quad doesn't double-count singular points
* `#7978 <https://github.com/scipy/scipy/pull/7978>`__: TST: ensure negative weights are not allowed in distance metrics
* `#7980 <https://github.com/scipy/scipy/pull/7980>`__: MAINT: Truncate the warning msg about ill-conditioning
* `#7981 <https://github.com/scipy/scipy/pull/7981>`__: BUG: special: fix hyp2f1 behavior in certain circumstances
* `#7983 <https://github.com/scipy/scipy/pull/7983>`__: ENH: special: Add a real dispatch to `loggamma`
* `#7989 <https://github.com/scipy/scipy/pull/7989>`__: BUG: special: make `kv` return `inf` at a zero real argument
* `#7990 <https://github.com/scipy/scipy/pull/7990>`__: TST: special: test ufuncs in special at `nan` inputs
* `#7994 <https://github.com/scipy/scipy/pull/7994>`__: DOC: special: fix typo in spherical Bessel function documentation
* `#7995 <https://github.com/scipy/scipy/pull/7995>`__: ENH: linalg: add null_space for computing null spaces via svd
* `#7999 <https://github.com/scipy/scipy/pull/7999>`__: BUG: optimize: Protect _minpack calls with a lock.
* `#8003 <https://github.com/scipy/scipy/pull/8003>`__: MAINT: consolidate c99 compatibility
* `#8004 <https://github.com/scipy/scipy/pull/8004>`__: TST: special: get all `cython_special` tests running again
* `#8006 <https://github.com/scipy/scipy/pull/8006>`__: MAINT: Consolidate an additional _c99compat.h
* `#8011 <https://github.com/scipy/scipy/pull/8011>`__: Add new example of integrate.quad
* `#8015 <https://github.com/scipy/scipy/pull/8015>`__: DOC: special: remove `jn` from the refguide (again)
* `#8018 <https://github.com/scipy/scipy/pull/8018>`__: BUG - Issue with uint datatypes for array in get_index_dtype
* `#8021 <https://github.com/scipy/scipy/pull/8021>`__: DOC: spatial: Simplify Delaunay plotting
* `#8024 <https://github.com/scipy/scipy/pull/8024>`__: Documentation fix
* `#8027 <https://github.com/scipy/scipy/pull/8027>`__: BUG: io.matlab: fix saving unicode matrix names on py2
* `#8028 <https://github.com/scipy/scipy/pull/8028>`__: BUG: special: some fixes for `lambertw`
* `#8030 <https://github.com/scipy/scipy/pull/8030>`__: MAINT: Bump Cython version
* `#8034 <https://github.com/scipy/scipy/pull/8034>`__: BUG: sparse.linalg: fix corner-case bug in expm
* `#8035 <https://github.com/scipy/scipy/pull/8035>`__: MAINT: special: remove complex division hack
* `#8038 <https://github.com/scipy/scipy/pull/8038>`__: ENH: Cythonize pyx files if pxd dependencies change
* `#8042 <https://github.com/scipy/scipy/pull/8042>`__: TST: stats: reduce required precision in test_fligner
* `#8043 <https://github.com/scipy/scipy/pull/8043>`__: TST: Use diff. values for decimal keyword for single and doubles
* `#8044 <https://github.com/scipy/scipy/pull/8044>`__: TST: accuracy of tests made different for singles and doubles
* `#8049 <https://github.com/scipy/scipy/pull/8049>`__: Unhelpful error message when calling scipy.sparse.save_npz on...
* `#8052 <https://github.com/scipy/scipy/pull/8052>`__: TST: spatial: add a regression test for gh-8051
* `#8059 <https://github.com/scipy/scipy/pull/8059>`__: BUG: special: fix ufunc results for `nan` arguments
* `#8066 <https://github.com/scipy/scipy/pull/8066>`__: MAINT: special: reimplement inverses of incomplete gamma functions
* `#8072 <https://github.com/scipy/scipy/pull/8072>`__: Example for scipy.fftpack.ifft, https://github.com/scipy/scipy/issues/7168
* `#8073 <https://github.com/scipy/scipy/pull/8073>`__: Example for ifftn, https://github.com/scipy/scipy/issues/7168
* `#8078 <https://github.com/scipy/scipy/pull/8078>`__: Link to CoC in contributing.rst doc
* `#8085 <https://github.com/scipy/scipy/pull/8085>`__: BLD: Fix npy_isnan of integer variables in cephes
* `#8088 <https://github.com/scipy/scipy/pull/8088>`__: DOC: note version for which new attributes have been added to...
* `#8090 <https://github.com/scipy/scipy/pull/8090>`__: BUG: special: add nan check to `_legacy_cast_check` functions
* `#8091 <https://github.com/scipy/scipy/pull/8091>`__: Doxy Typos + trivial comment typos (2nd attempt)
* `#8096 <https://github.com/scipy/scipy/pull/8096>`__: TST: special: simplify `Arg`
* `#8101 <https://github.com/scipy/scipy/pull/8101>`__: MAINT: special: run `_generate_pyx.py` when `add_newdocs.py`...
* `#8104 <https://github.com/scipy/scipy/pull/8104>`__: Input checking for scipy.sparse.linalg.inverse()
* `#8105 <https://github.com/scipy/scipy/pull/8105>`__: DOC: special: Update the 'euler' docstring.
* `#8109 <https://github.com/scipy/scipy/pull/8109>`__: MAINT: fixing code comments and hyp2f1 docstring: see issues...
* `#8112 <https://github.com/scipy/scipy/pull/8112>`__: More trivial typos
* `#8113 <https://github.com/scipy/scipy/pull/8113>`__: MAINT: special: generate test data npz files in setup.py and...
* `#8116 <https://github.com/scipy/scipy/pull/8116>`__: DOC: add build instructions
* `#8120 <https://github.com/scipy/scipy/pull/8120>`__: DOC: Clean up README
* `#8121 <https://github.com/scipy/scipy/pull/8121>`__: DOC: Add missing colons in docstrings
* `#8123 <https://github.com/scipy/scipy/pull/8123>`__: BLD: update Bento build config files for recent C99 changes.
* `#8124 <https://github.com/scipy/scipy/pull/8124>`__: Change to avoid use of `fmod` in scipy.signal.chebwin
* `#8126 <https://github.com/scipy/scipy/pull/8126>`__: Added examples for mode arg in geometric_transform
* `#8128 <https://github.com/scipy/scipy/pull/8128>`__: relax relative tolerance parameter in TestMinumumPhase.test_hilbert
* `#8129 <https://github.com/scipy/scipy/pull/8129>`__: ENH: special: use rational approximation for `digamma` on `[1,...
* `#8137 <https://github.com/scipy/scipy/pull/8137>`__: DOC Correct matrix width
* `#8141 <https://github.com/scipy/scipy/pull/8141>`__: MAINT: optimize: remove unused `__main__` code in L-BSGS-B
* `#8147 <https://github.com/scipy/scipy/pull/8147>`__: BLD: update Bento build for removal of .npz scipy.special test...
* `#8148 <https://github.com/scipy/scipy/pull/8148>`__: Alias hanning as an explanatory function of hann
* `#8149 <https://github.com/scipy/scipy/pull/8149>`__: MAINT: special: small fixes for `digamma`
* `#8159 <https://github.com/scipy/scipy/pull/8159>`__: Update version classifiers
* `#8164 <https://github.com/scipy/scipy/pull/8164>`__: BUG: riccati solvers don't catch ill-conditioned problems sufficiently...
* `#8168 <https://github.com/scipy/scipy/pull/8168>`__: DOC: release note for sparse resize methods
* `#8170 <https://github.com/scipy/scipy/pull/8170>`__: BUG: correctly pad netCDF files with null bytes
* `#8171 <https://github.com/scipy/scipy/pull/8171>`__: ENH added normal inverse gaussian distribution to scipy.stats
* `#8175 <https://github.com/scipy/scipy/pull/8175>`__: DOC: Add example to scipy.ndimage.zoom
* `#8177 <https://github.com/scipy/scipy/pull/8177>`__: MAINT: diffev small speedup in ensure constraint
* `#8178 <https://github.com/scipy/scipy/pull/8178>`__: FIX: linalg._qz String formatter syntax error
* `#8179 <https://github.com/scipy/scipy/pull/8179>`__: TST: Added pdist to asv spatial benchmark suite
* `#8180 <https://github.com/scipy/scipy/pull/8180>`__: TST: ensure constraint test improved
* `#8183 <https://github.com/scipy/scipy/pull/8183>`__: 0d conj correlate
* `#8186 <https://github.com/scipy/scipy/pull/8186>`__: BUG: special: fix derivative of `spherical_jn(1, 0)`
* `#8194 <https://github.com/scipy/scipy/pull/8194>`__: Fix warning message
* `#8196 <https://github.com/scipy/scipy/pull/8196>`__: BUG: correctly handle inputs with nan's and ties in spearmanr
* `#8198 <https://github.com/scipy/scipy/pull/8198>`__: MAINT: stats.triang edge case fixes #6036
* `#8200 <https://github.com/scipy/scipy/pull/8200>`__: DOC: Completed "Examples" sections of all linalg funcs
* `#8201 <https://github.com/scipy/scipy/pull/8201>`__: MAINT: stats.trapz edge cases
* `#8204 <https://github.com/scipy/scipy/pull/8204>`__: ENH: sparse.linalg/lobpcg: change .T to .T.conj() to support...
* `#8206 <https://github.com/scipy/scipy/pull/8206>`__: MAINT: missed triang edge case.
* `#8214 <https://github.com/scipy/scipy/pull/8214>`__: BUG: Fix memory corruption in linalg._decomp_update C extension
* `#8222 <https://github.com/scipy/scipy/pull/8222>`__: DOC: recommend scipy.integrate.solve_ivp
* `#8223 <https://github.com/scipy/scipy/pull/8223>`__: ENH: added Moyal distribution to scipy.stats
* `#8232 <https://github.com/scipy/scipy/pull/8232>`__: BUG: sparse: Use deduped data for numpy ufuncs
* `#8236 <https://github.com/scipy/scipy/pull/8236>`__: Fix #8235
* `#8253 <https://github.com/scipy/scipy/pull/8253>`__: BUG: optimize: fix bug related with function call calculation...
* `#8264 <https://github.com/scipy/scipy/pull/8264>`__: ENH: Extend peak finding capabilities in scipy.signal
* `#8273 <https://github.com/scipy/scipy/pull/8273>`__: BUG fixed printing of convergence message in minimize_scalar...
* `#8276 <https://github.com/scipy/scipy/pull/8276>`__: DOC: Add notes to explain constrains on overwrite_<>
* `#8279 <https://github.com/scipy/scipy/pull/8279>`__: CI: fixing doctests
* `#8282 <https://github.com/scipy/scipy/pull/8282>`__: MAINT: weightedtau, change search for nan
* `#8287 <https://github.com/scipy/scipy/pull/8287>`__: Improving documentation of solve_ivp and the underlying solvers
* `#8291 <https://github.com/scipy/scipy/pull/8291>`__: DOC: fix non-ascii characters in docstrings which broke the doc...
* `#8292 <https://github.com/scipy/scipy/pull/8292>`__: CI: use numpy 1.13 for refguide check build
* `#8296 <https://github.com/scipy/scipy/pull/8296>`__: Fixed bug reported in issue #8181
* `#8297 <https://github.com/scipy/scipy/pull/8297>`__: DOC: Examples for linalg/decomp eigvals function
* `#8300 <https://github.com/scipy/scipy/pull/8300>`__: MAINT: Housekeeping for minimizing the linalg compiler warnings
* `#8301 <https://github.com/scipy/scipy/pull/8301>`__: DOC: make public API documentation cross-link to refguide.
* `#8302 <https://github.com/scipy/scipy/pull/8302>`__: make sure _onenorm_matrix_power_nnm actually returns a float
* `#8313 <https://github.com/scipy/scipy/pull/8313>`__: Change copyright to outdated 2008-2016 to 2008-year
* `#8315 <https://github.com/scipy/scipy/pull/8315>`__: TST: Add tests for `scipy.sparse.linalg.isolve.minres`
* `#8318 <https://github.com/scipy/scipy/pull/8318>`__: ENH: odeint: Add the argument 'tfirst' to odeint.
* `#8328 <https://github.com/scipy/scipy/pull/8328>`__: ENH: optimize: ``trust-constr`` optimization algorithms [GSoC...
* `#8330 <https://github.com/scipy/scipy/pull/8330>`__: ENH: add a maxiter argument to NNLS
* `#8331 <https://github.com/scipy/scipy/pull/8331>`__: DOC: tweak the Moyal distribution docstring
* `#8333 <https://github.com/scipy/scipy/pull/8333>`__: FIX: Rewrapped ?gels and ?gels_lwork routines
* `#8336 <https://github.com/scipy/scipy/pull/8336>`__: MAINT: integrate: handle b < a in quad
* `#8337 <https://github.com/scipy/scipy/pull/8337>`__: BUG: special: Ensure zetac(1) returns inf.
* `#8347 <https://github.com/scipy/scipy/pull/8347>`__: BUG: Fix overflow in special.binom. Issue #8346
* `#8356 <https://github.com/scipy/scipy/pull/8356>`__: DOC: Corrected Documentation Issue #7750 winsorize function
* `#8358 <https://github.com/scipy/scipy/pull/8358>`__: ENH: stats: Use explicit MLE formulas in lognorm.fit and expon.fit
* `#8374 <https://github.com/scipy/scipy/pull/8374>`__: BUG: gh7854, maxiter for l-bfgs-b closes #7854
* `#8379 <https://github.com/scipy/scipy/pull/8379>`__: CI: enable gcov coverage on travis
* `#8383 <https://github.com/scipy/scipy/pull/8383>`__: Removed collections.OrderedDict import ignore.
* `#8384 <https://github.com/scipy/scipy/pull/8384>`__: TravisCI: tool pep8 is now pycodestyle
* `#8387 <https://github.com/scipy/scipy/pull/8387>`__: MAINT: special: remove unused specfun code for Struve functions
* `#8393 <https://github.com/scipy/scipy/pull/8393>`__: DOC: Replace old type names in ndimage tutorial.
* `#8400 <https://github.com/scipy/scipy/pull/8400>`__: Fix tolerance specification in sparse.linalg iterative solvers
* `#8402 <https://github.com/scipy/scipy/pull/8402>`__: MAINT: Some small cleanups in ndimage.
* `#8403 <https://github.com/scipy/scipy/pull/8403>`__: FIX: Make scipy.optimize.zeros run under PyPy
* `#8407 <https://github.com/scipy/scipy/pull/8407>`__: BUG: sparse.linalg: fix termination bugs for cg, cgs
* `#8409 <https://github.com/scipy/scipy/pull/8409>`__: MAINT: special: add a `.pxd` file for Cephes functions
* `#8412 <https://github.com/scipy/scipy/pull/8412>`__: MAINT: special: remove `cephes/protos.h`
* `#8421 <https://github.com/scipy/scipy/pull/8421>`__: Setting "unknown" message in OptimizeResult when calling MINPACK.
* `#8423 <https://github.com/scipy/scipy/pull/8423>`__: FIX: Handle unsigned integers in mmio
* `#8426 <https://github.com/scipy/scipy/pull/8426>`__: DOC: correct FAQ entry on Apache license compatibility. Closes...
* `#8433 <https://github.com/scipy/scipy/pull/8433>`__: MAINT: add `.pytest_cache` to the `.gitignore`
* `#8436 <https://github.com/scipy/scipy/pull/8436>`__: MAINT: scipy.sparse: less copies at transpose method
* `#8437 <https://github.com/scipy/scipy/pull/8437>`__: BUG: correct behavior for skew-symmetric matrices in io.mmwrite
* `#8440 <https://github.com/scipy/scipy/pull/8440>`__: DOC:Add examples to integrate.quadpack docstrings
* `#8441 <https://github.com/scipy/scipy/pull/8441>`__: BUG: sparse.linalg/gmres: deal with exact breakdown in gmres
* `#8442 <https://github.com/scipy/scipy/pull/8442>`__: MAINT: special: clean up Cephes header files
* `#8448 <https://github.com/scipy/scipy/pull/8448>`__: TST: Generalize doctest stopwords .axis( .plot(
* `#8457 <https://github.com/scipy/scipy/pull/8457>`__: MAINT: special: use JSON for function signatures in `_generate_pyx.py`
* `#8461 <https://github.com/scipy/scipy/pull/8461>`__: MAINT: Simplify return value of ndimage functions.
* `#8464 <https://github.com/scipy/scipy/pull/8464>`__: MAINT: Trivial typos
* `#8474 <https://github.com/scipy/scipy/pull/8474>`__: BUG: spatial: make qhull.pyx more pypy-friendly
* `#8476 <https://github.com/scipy/scipy/pull/8476>`__: TST: _lib: disable refcounting tests on PyPy
* `#8479 <https://github.com/scipy/scipy/pull/8479>`__: BUG: io/matlab: fix issues in matlab i/o on pypy
* `#8481 <https://github.com/scipy/scipy/pull/8481>`__: DOC: Example for signal.cmplx_sort
* `#8482 <https://github.com/scipy/scipy/pull/8482>`__: TST: integrate: use integers instead of PyCapsules to store pointers
* `#8483 <https://github.com/scipy/scipy/pull/8483>`__: ENH: io/netcdf: make mmap=False the default on PyPy
* `#8484 <https://github.com/scipy/scipy/pull/8484>`__: BUG: io/matlab: work around issue in to_writeable on PyPy
* `#8488 <https://github.com/scipy/scipy/pull/8488>`__: MAINT: special: add const/static specifiers where possible
* `#8489 <https://github.com/scipy/scipy/pull/8489>`__: BUG: ENH: use common halley's method instead of parabolic variant
* `#8491 <https://github.com/scipy/scipy/pull/8491>`__: DOC: fix typos
* `#8496 <https://github.com/scipy/scipy/pull/8496>`__: ENH: special: make Chebyshev nodes symmetric
* `#8501 <https://github.com/scipy/scipy/pull/8501>`__: BUG: stats: Split the integral used to compute skewnorm.cdf.
* `#8502 <https://github.com/scipy/scipy/pull/8502>`__: WIP: Port CircleCI to v2
* `#8507 <https://github.com/scipy/scipy/pull/8507>`__: DOC: Add missing description to `brute_force` parameter.
* `#8509 <https://github.com/scipy/scipy/pull/8509>`__: BENCH: forgot to add nelder-mead to list of methods
* `#8512 <https://github.com/scipy/scipy/pull/8512>`__: MAINT: Move spline interpolation code to spline.c
* `#8513 <https://github.com/scipy/scipy/pull/8513>`__: TST: special: mark a slow test as xslow
* `#8514 <https://github.com/scipy/scipy/pull/8514>`__: CircleCI: Share data between jobs
* `#8515 <https://github.com/scipy/scipy/pull/8515>`__: ENH: special: improve accuracy of `zetac` for negative arguments
* `#8520 <https://github.com/scipy/scipy/pull/8520>`__: TST: Decrease the array sizes for two linalg tests
* `#8522 <https://github.com/scipy/scipy/pull/8522>`__: TST: special: restrict range of `test_besselk`/`test_besselk_int`
* `#8527 <https://github.com/scipy/scipy/pull/8527>`__: Documentation - example added for voronoi_plot_2d
* `#8528 <https://github.com/scipy/scipy/pull/8528>`__: DOC: Better, shared docstrings in ndimage
* `#8533 <https://github.com/scipy/scipy/pull/8533>`__: BUG: Fix PEP8 errors introduced in #8528.
* `#8534 <https://github.com/scipy/scipy/pull/8534>`__: ENH: Expose additional window functions
* `#8538 <https://github.com/scipy/scipy/pull/8538>`__: MAINT: Fix a couple mistakes in .pyf files.
* `#8540 <https://github.com/scipy/scipy/pull/8540>`__: ENH: interpolate: allow string aliases in make_interp_spline...
* `#8541 <https://github.com/scipy/scipy/pull/8541>`__: ENH: Cythonize peak_prominences
* `#8542 <https://github.com/scipy/scipy/pull/8542>`__: Remove numerical arguments from convolve2d / correlate2d
* `#8546 <https://github.com/scipy/scipy/pull/8546>`__: ENH: New arguments, documentation, and tests for ndimage.binary_opening
* `#8547 <https://github.com/scipy/scipy/pull/8547>`__: Giving both size and input now raises UserWarning (#7334)
* `#8549 <https://github.com/scipy/scipy/pull/8549>`__: DOC: stats: invweibull is also known as Frechet or type II extreme...
* `#8550 <https://github.com/scipy/scipy/pull/8550>`__: add cdf2rdf function
* `#8551 <https://github.com/scipy/scipy/pull/8551>`__: ENH: Port of most of the dd_real part of the qd high-precision...
* `#8553 <https://github.com/scipy/scipy/pull/8553>`__: Note in docs to address issue #3164.
* `#8554 <https://github.com/scipy/scipy/pull/8554>`__: ENH: stats: Use explicit MLE formulas in uniform.fit()
* `#8555 <https://github.com/scipy/scipy/pull/8555>`__: MAINT: adjust benchmark config
* `#8557 <https://github.com/scipy/scipy/pull/8557>`__: [DOC]: fix Nakagami density docstring
* `#8559 <https://github.com/scipy/scipy/pull/8559>`__: DOC: Fix docstring of diric(x, n)
* `#8563 <https://github.com/scipy/scipy/pull/8563>`__: [DOC]: fix gamma density docstring
* `#8564 <https://github.com/scipy/scipy/pull/8564>`__: BLD: change default Python version for doc build from 2.7 to...
* `#8568 <https://github.com/scipy/scipy/pull/8568>`__: BUG: Fixes Bland's Rule for pivot row/leaving variable, closes...
* `#8572 <https://github.com/scipy/scipy/pull/8572>`__: ENH: Add previous/next to interp1d
* `#8578 <https://github.com/scipy/scipy/pull/8578>`__: Example for linalg.eig()
* `#8580 <https://github.com/scipy/scipy/pull/8580>`__: DOC: update link to asv docs
* `#8584 <https://github.com/scipy/scipy/pull/8584>`__: filter_design: switch to explicit arguments, keeping None as...
* `#8586 <https://github.com/scipy/scipy/pull/8586>`__: DOC: stats: Add parentheses that were missing in the exponnorm...
* `#8587 <https://github.com/scipy/scipy/pull/8587>`__: TST: add benchmark for newton, secant, halley
* `#8588 <https://github.com/scipy/scipy/pull/8588>`__: DOC: special: Remove heaviside from "functions not in special"...
* `#8591 <https://github.com/scipy/scipy/pull/8591>`__: DOC: cdf2rdf Added version info and "See also"
* `#8594 <https://github.com/scipy/scipy/pull/8594>`__: ENH: Cythonize peak_widths
* `#8595 <https://github.com/scipy/scipy/pull/8595>`__: MAINT/ENH/BUG/TST: cdf2rdf: Address review comments made after...
* `#8597 <https://github.com/scipy/scipy/pull/8597>`__: DOC: add versionadded 1.1.0 for new keywords in ndimage.morphology
* `#8605 <https://github.com/scipy/scipy/pull/8605>`__: MAINT: special: improve implementations of `sinpi` and `cospi`
* `#8607 <https://github.com/scipy/scipy/pull/8607>`__: MAINT: add 2D benchmarks for convolve
* `#8608 <https://github.com/scipy/scipy/pull/8608>`__: FIX: Fix int check
* `#8613 <https://github.com/scipy/scipy/pull/8613>`__: fix typo in doc of signal.peak_widths
* `#8615 <https://github.com/scipy/scipy/pull/8615>`__: TST: fix failing linalg.qz float32 test by decreasing precision.
* `#8617 <https://github.com/scipy/scipy/pull/8617>`__: MAINT: clean up code in ellpj.c
* `#8618 <https://github.com/scipy/scipy/pull/8618>`__: add fsolve docs it doesn't handle over- or under-determined problems
* `#8620 <https://github.com/scipy/scipy/pull/8620>`__: DOC: add note on dtype attribute of aslinearoperator() argument
* `#8627 <https://github.com/scipy/scipy/pull/8627>`__: ENH: Add example 1D signal (ECG) to scipy.misc
* `#8630 <https://github.com/scipy/scipy/pull/8630>`__: ENH: Remove unnecessary copying in stats.percentileofscore
* `#8631 <https://github.com/scipy/scipy/pull/8631>`__: BLD: fix pdf doc build. closes gh-8076
* `#8633 <https://github.com/scipy/scipy/pull/8633>`__: BUG: fix regression in `io.netcdf_file` with append mode.
* `#8635 <https://github.com/scipy/scipy/pull/8635>`__: MAINT: remove spurious warning from (z)vode and lsoda. Closes...
* `#8636 <https://github.com/scipy/scipy/pull/8636>`__: BUG: sparse.linalg/gcrotmk: avoid rounding error in termination...
* `#8637 <https://github.com/scipy/scipy/pull/8637>`__: For pdf build
* `#8639 <https://github.com/scipy/scipy/pull/8639>`__: CI: build pdf documentation on circleci
* `#8640 <https://github.com/scipy/scipy/pull/8640>`__: TST: fix special test that was importing `np.testing.utils` (deprecated)
* `#8641 <https://github.com/scipy/scipy/pull/8641>`__: BUG: optimize: fixed sparse redundancy removal bug
* `#8645 <https://github.com/scipy/scipy/pull/8645>`__: BUG: modified sigmaclip to avoid clipping of constant input in...
* `#8647 <https://github.com/scipy/scipy/pull/8647>`__: TST: sparse: skip test_inplace_dense for numpy<1.13
* `#8657 <https://github.com/scipy/scipy/pull/8657>`__: Latex reduce left margins
* `#8659 <https://github.com/scipy/scipy/pull/8659>`__: TST: special: skip sign-of-zero test on 32-bit win32 with old...
* `#8661 <https://github.com/scipy/scipy/pull/8661>`__: Fix dblquad and tplquad not accepting float boundaries
* `#8666 <https://github.com/scipy/scipy/pull/8666>`__: DOC: fixes #8532
* `#8667 <https://github.com/scipy/scipy/pull/8667>`__: BUG: optimize: fixed issue #8663
* `#8668 <https://github.com/scipy/scipy/pull/8668>`__: Fix example in docstring of netcdf_file
* `#8671 <https://github.com/scipy/scipy/pull/8671>`__: DOC: Replace deprecated matplotlib kwarg
* `#8673 <https://github.com/scipy/scipy/pull/8673>`__: BUG: special: Use a stricter tolerance for the chndtr calculation.
* `#8674 <https://github.com/scipy/scipy/pull/8674>`__: ENH: In the Dirichlet distribution allow x_i to be 0 if alpha_i...
* `#8676 <https://github.com/scipy/scipy/pull/8676>`__: BUG: optimize: partial fix to linprog fails to detect infeasibility...
* `#8685 <https://github.com/scipy/scipy/pull/8685>`__: DOC: Add interp1d-next/previous example to tutorial
* `#8687 <https://github.com/scipy/scipy/pull/8687>`__: TST: netcdf: explicit mmap=True in test
* `#8688 <https://github.com/scipy/scipy/pull/8688>`__: BUG: signal, stats: use Python sum() instead of np.sum for summing...
* `#8689 <https://github.com/scipy/scipy/pull/8689>`__: TST: bump tolerances in tests
* `#8690 <https://github.com/scipy/scipy/pull/8690>`__: DEP: deprecate stats.itemfreq
* `#8691 <https://github.com/scipy/scipy/pull/8691>`__: BLD: special: fix build vs. dd_real.h package
* `#8695 <https://github.com/scipy/scipy/pull/8695>`__: DOC: Improve examples in signal.find_peaks with ECG signal
* `#8697 <https://github.com/scipy/scipy/pull/8697>`__: BUG: Fix `setup.py build install egg_info`, which did not previously...
* `#8704 <https://github.com/scipy/scipy/pull/8704>`__: TST: linalg: drop large size from solve() test
* `#8705 <https://github.com/scipy/scipy/pull/8705>`__: DOC: Describe signal.find_peaks and related functions behavior...
* `#8706 <https://github.com/scipy/scipy/pull/8706>`__: DOC: Specify encoding of rst file, remove an ambiguity in an...
* `#8710 <https://github.com/scipy/scipy/pull/8710>`__: MAINT: fix an import cycle sparse -> special -> integrate ->...
* `#8711 <https://github.com/scipy/scipy/pull/8711>`__: ENH: remove an avoidable overflow in scipy.stats.norminvgauss.pdf()
* `#8716 <https://github.com/scipy/scipy/pull/8716>`__: BUG: interpolate: allow list inputs for make_interp_spline(...,...
* `#8720 <https://github.com/scipy/scipy/pull/8720>`__: np.testing import that is compatible with numpy 1.15
* `#8724 <https://github.com/scipy/scipy/pull/8724>`__: CI: don't use pyproject.toml in the CI builds

Checksums
=========

MD5
~~~

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SHA256
~~~~~~

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From Nicolas.Rougier at inria.fr  Mon May  7 01:51:06 2018
From: Nicolas.Rougier at inria.fr (Nicolas Rougier)
Date: Mon, 7 May 2018 07:51:06 +0200
Subject: [SciPy-Dev] Book on scientific visualization using Python & OpenGL
Message-ID: <34FFDB4C-C545-42F5-97CF-9B7098B10228@inria.fr>


[Sorry for cross-posting]


Hi all,

I just released an (unfinished) book on "Python & OpenGL for Scientific Visualization?.
It?s available at http://www.labri.fr/perso/nrougier/python-opengl/

(sources are available at https://github.com/rougier/python-opengl)


Nicolas


From serge.guelton at telecom-bretagne.eu  Fri May 11 10:36:49 2018
From: serge.guelton at telecom-bretagne.eu (serge guelton)
Date: Fri, 11 May 2018 16:36:49 +0200
Subject: [SciPy-Dev] Using Pythran to compile some of the scipy internals
In-Reply-To: <20180122223457.GA14580@lakota>
References: <20180120101034.GA3707@lakota>
 <CAJhcF=2t_3zHeE_vXsZgSX7QRmNYdA-ippOFsgq4bQt=k+8k2g@mail.gmail.com>
 <20180122223457.GA14580@lakota>
Message-ID: <20180511143649.GA31049@lakota>

Hi scipy-dev,

here comes the conclusion of my preliminary work on potential
integration of Pythran-compiled kernels into SciPy.

The benefits from having Pythran as a build dependency for SciPy would
be the following:

- no extra runtime dependency (only build dependency)
- generally smaller binaries (see
  http://serge-sans-paille.github.io/pythran-stories/shrinking-pythran-generated-binaries.html)
- comparable if not better performances (see
  https://github.com/serge-sans-paille/scipy-kernels)
- close to no maintenance (Pythran input are pure python code, no extra
  knowledge is required). A direct consequence is that the exit cost is
  free. (see the diff in https://github.com/scipy/scipy/pull/8306/files)

Now there are several few points that could be improved:

- Pythran bus factor is 1. The project did get some momentum recently
  (even being used in production in a few firms!) but it almost
  totally relies on me.

- windows support is only valid for Python3

- not much feedback for performance optimization (unlike Cython
  annotate mode), user just need to trust the compiler

- no binary multi-versioning to support multiple architecture variant
  (e.g. AVX support) in a single binary, although this last point can be
  dealt with if needed, at least on Linux.


A bold move for scipy would be to use Pythran in a best-effort mode,
i.e. use it when it's available and fallback to Cython otherwise. But I
understand there is no strong motivation for this move, only small
improvements.

Still I'd like to thank the community, especially Ralph, for providing
guidance and motivation. A 100% sure outcome of this thread is the
improvement of Pythran :-)

Best,

Serge

From mikofski at berkeley.edu  Fri May 11 12:18:03 2018
From: mikofski at berkeley.edu (Mark Alexander Mikofski)
Date: Fri, 11 May 2018 09:18:03 -0700
Subject: [SciPy-Dev] Using Pythran to compile some of the scipy internals
In-Reply-To: <20180511143649.GA31049@lakota>
References: <20180120101034.GA3707@lakota>
 <CAJhcF=2t_3zHeE_vXsZgSX7QRmNYdA-ippOFsgq4bQt=k+8k2g@mail.gmail.com>
 <20180122223457.GA14580@lakota> <20180511143649.GA31049@lakota>
Message-ID: <CAEqRcW36dSixUR-d0GyUpvGqfYjz4C0aEKfzYz_qu-rDTHTOuw@mail.gmail.com>

Thank you for undertaking this study and for developing Pythran. The
results look very promising! How does it compare with Numba? Or is that
comparison not valid or nonsensical?

On Fri, May 11, 2018, 7:46 AM serge guelton <
serge.guelton at telecom-bretagne.eu> wrote:

> Hi scipy-dev,
>
> here comes the conclusion of my preliminary work on potential
> integration of Pythran-compiled kernels into SciPy.
>
> The benefits from having Pythran as a build dependency for SciPy would
> be the following:
>
> - no extra runtime dependency (only build dependency)
> - generally smaller binaries (see
>
> http://serge-sans-paille.github.io/pythran-stories/shrinking-pythran-generated-binaries.html
> )
> - comparable if not better performances (see
>   https://github.com/serge-sans-paille/scipy-kernels)
> - close to no maintenance (Pythran input are pure python code, no extra
>   knowledge is required). A direct consequence is that the exit cost is
>   free. (see the diff in https://github.com/scipy/scipy/pull/8306/files)
>
> Now there are several few points that could be improved:
>
> - Pythran bus factor is 1. The project did get some momentum recently
>   (even being used in production in a few firms!) but it almost
>   totally relies on me.
>
> - windows support is only valid for Python3
>
> - not much feedback for performance optimization (unlike Cython
>   annotate mode), user just need to trust the compiler
>
> - no binary multi-versioning to support multiple architecture variant
>   (e.g. AVX support) in a single binary, although this last point can be
>   dealt with if needed, at least on Linux.
>
>
> A bold move for scipy would be to use Pythran in a best-effort mode,
> i.e. use it when it's available and fallback to Cython otherwise. But I
> understand there is no strong motivation for this move, only small
> improvements.
>
> Still I'd like to thank the community, especially Ralph, for providing
> guidance and motivation. A 100% sure outcome of this thread is the
> improvement of Pythran :-)
>
> Best,
>
> Serge
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
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From serge.guelton at telecom-bretagne.eu  Fri May 11 13:26:49 2018
From: serge.guelton at telecom-bretagne.eu (Serge Guelton)
Date: Fri, 11 May 2018 19:26:49 +0200
Subject: [SciPy-Dev] Using Pythran to compile some of the scipy internals
In-Reply-To: <CAEqRcW36dSixUR-d0GyUpvGqfYjz4C0aEKfzYz_qu-rDTHTOuw@mail.gmail.com>
References: <20180120101034.GA3707@lakota>
 <CAJhcF=2t_3zHeE_vXsZgSX7QRmNYdA-ippOFsgq4bQt=k+8k2g@mail.gmail.com>
 <20180122223457.GA14580@lakota> <20180511143649.GA31049@lakota>
 <CAEqRcW36dSixUR-d0GyUpvGqfYjz4C0aEKfzYz_qu-rDTHTOuw@mail.gmail.com>
Message-ID: <20180511172649.GA3897@lakota>

On Fri, May 11, 2018 at 09:18:03AM -0700, Mark Alexander Mikofski wrote:
> Thank you for undertaking this study and for developing Pythran. The results
> look very promising! How does it compare with Numba? Or is that comparison not
> valid or nonsensical?

My point of view is 100% biased, but here is the best I can say. there's
probably someone on this mlist that knows numba better than I do. Still:

                        cython              pythran             numba

compiler type           ahead of time       ahead of time       just in time
runtime dep             no                  no                  yes
language extension      +++                 + (comments)        + (decorator)
python support          very good           decent (no class)   decent
high level dev          +                   +++                 ++
native numpy support    + (pythran)         +++                 ++ (improved a lot)
performance             good                good                good
simd                    backend-dependent   yes (need a flag)   decent (llvm)
maturity                +++                 +                   ++

This is just a summary and the things that matter are actually in the
details, but it's difficult to write about them in a general manner.
Hope it helps!

From sseibert at anaconda.com  Fri May 11 15:06:07 2018
From: sseibert at anaconda.com (Stanley Seibert)
Date: Fri, 11 May 2018 14:06:07 -0500
Subject: [SciPy-Dev] Using Pythran to compile some of the scipy internals
In-Reply-To: <20180511172649.GA3897@lakota>
References: <20180120101034.GA3707@lakota>
 <CAJhcF=2t_3zHeE_vXsZgSX7QRmNYdA-ippOFsgq4bQt=k+8k2g@mail.gmail.com>
 <20180122223457.GA14580@lakota> <20180511143649.GA31049@lakota>
 <CAEqRcW36dSixUR-d0GyUpvGqfYjz4C0aEKfzYz_qu-rDTHTOuw@mail.gmail.com>
 <20180511172649.GA3897@lakota>
Message-ID: <CADv3RKTRs60E9dGfJu6qMyo+Jtm6ANFnwb73KZFN3+ROLxZmJw@mail.gmail.com>

I think the Numba column in your sumamry chart is pretty accurate.

On Fri, May 11, 2018 at 12:26 PM, Serge Guelton <
serge.guelton at telecom-bretagne.eu> wrote:

> On Fri, May 11, 2018 at 09:18:03AM -0700, Mark Alexander Mikofski wrote:
> > Thank you for undertaking this study and for developing Pythran. The
> results
> > look very promising! How does it compare with Numba? Or is that
> comparison not
> > valid or nonsensical?
>
> My point of view is 100% biased, but here is the best I can say. there's
> probably someone on this mlist that knows numba better than I do. Still:
>
>                         cython              pythran             numba
>
> compiler type           ahead of time       ahead of time       just in
> time
> runtime dep             no                  no                  yes
> language extension      +++                 + (comments)        +
> (decorator)
> python support          very good           decent (no class)   decent
> high level dev          +                   +++                 ++
> native numpy support    + (pythran)         +++                 ++
> (improved a lot)
> performance             good                good                good
> simd                    backend-dependent   yes (need a flag)   decent
> (llvm)
> maturity                +++                 +                   ++
>
> This is just a summary and the things that matter are actually in the
> details, but it's difficult to write about them in a general manner.
> Hope it helps!
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
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From adibhar97 at gmail.com  Sat May 19 15:23:52 2018
From: adibhar97 at gmail.com (Aditya Bharti)
Date: Sun, 20 May 2018 00:53:52 +0530
Subject: [SciPy-Dev] [GSOC 2018 Project Thread]: Rotation formalism in 3
 dimensions
In-Reply-To: <CANRzPHVN47mDJqc4DuUq70X9sAiRqBRWOSHszgtL3QyM1O6ihA@mail.gmail.com>
References: <163213d9b99.e31ddfbf140246.3867213885941953730@zoho.com>
 <CANRzPHVN47mDJqc4DuUq70X9sAiRqBRWOSHszgtL3QyM1O6ihA@mail.gmail.com>
Message-ID: <CANRzPHV0BswFBevgZ2fsf2vKm_J_LQEET=qtDZ1WO6H7dMDNyQ@mail.gmail.com>

Hi all,
So this concludes week 1 of GSoC 2018. I must say it was a great learning
experience and I invite you all to check out my account of this week on the
blog <https://blogs.python-gsoc.org/aditya-bharti/>. This email is more of
a technical update.

   - So, the main `Rotation` class will live under a new sub module
   `scipy.spatial.transform`.
   - Conversion between quaternions and discrete cosine matrices was
   implemented.
   - The rotation class now supports `from_quaternion`, `from_dcm`,
   `as_quaternion` and `as_dcm`, with support for multiple rotations in one
   call.

The project currently lives in my own fork of scipy here
<https://github.com/adbugger/scipy/tree/rotation/scipy/spatial/transform>.
Stay tuned for more updates!

Best,
Aditya

On Wed, 2 May 2018 at 21:03, Aditya Bharti <adibhar97 at gmail.com> wrote:

> Hi Nikolay,
>
> I've used Wordpress only once before, so I don't know much about it. From
> my limited experience, it is extremely customizable. You can customize
> every thing from the look and feel to SEO characteristics. There are
> apparently a lot of wordpress plugins for these kind of tasks. For this
> particular blog, PSF had already setup an account for me with a site on it.
> All I had to do was click on the 'New' button and open up the new post
> page. There's a field for a header and body text, with options for adding
> audio, video and hyperlinks.
>
> As regards to the post itself, sure I'll expand it with a brief overview,
> motivation and an example. Note that the example will only show sample
> usage, not any internals. I plan to borrow heavily from my proposal for
> this purpose, I hope that's ok.
>
> Regards,
> Aditya
>
> On 2 May 2018 at 19:54, Nikolay Mayorov <nikolay.mayorov at zoho.com> wrote:
>
>> Hi, Aditya!
>>
>> Glad that you set up the blog and good job on setting up the
>> documentation build as well.
>>
>> Curious, what is this blogging platform like? How do you create posts in
>> it?
>>
>> As for your first post: while not strictly necessary I think it would be
>> nice to see a more thorough introductory post with a brief overview,
>> motivation and/or an example. Do you want to work on it?
>>
>> Best,
>> Nikolay
>>
>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at python.org
>> https://mail.python.org/mailman/listinfo/scipy-dev
>>
>>
>
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From ralf.gommers at gmail.com  Sat May 19 21:39:25 2018
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Sat, 19 May 2018 18:39:25 -0700
Subject: [SciPy-Dev] [GSOC 2018 Project Thread]: Rotation formalism in 3
 dimensions
In-Reply-To: <CANRzPHV0BswFBevgZ2fsf2vKm_J_LQEET=qtDZ1WO6H7dMDNyQ@mail.gmail.com>
References: <163213d9b99.e31ddfbf140246.3867213885941953730@zoho.com>
 <CANRzPHVN47mDJqc4DuUq70X9sAiRqBRWOSHszgtL3QyM1O6ihA@mail.gmail.com>
 <CANRzPHV0BswFBevgZ2fsf2vKm_J_LQEET=qtDZ1WO6H7dMDNyQ@mail.gmail.com>
Message-ID: <CABL7CQhTQGAHS84WBJ2ctP7__jZuU0uJtirMW5u897NFREPmig@mail.gmail.com>

On Sat, May 19, 2018 at 12:23 PM, Aditya Bharti <adibhar97 at gmail.com> wrote:

> Hi all,
> So this concludes week 1 of GSoC 2018. I must say it was a great learning
> experience and I invite you all to check out my account of this week on the
> blog <https://blogs.python-gsoc.org/aditya-bharti/>. This email is more
> of a technical update.
>

Hi Aditya, that looks like good progress! One question: do you have the
result of your benchmarking exercise somewhere? Could be interesting to
refer to in the future.

Cheers,
Ralf


>    - So, the main `Rotation` class will live under a new sub module
>    `scipy.spatial.transform`.
>    - Conversion between quaternions and discrete cosine matrices was
>    implemented.
>    - The rotation class now supports `from_quaternion`, `from_dcm`,
>    `as_quaternion` and `as_dcm`, with support for multiple rotations in one
>    call.
>
> The project currently lives in my own fork of scipy here
> <https://github.com/adbugger/scipy/tree/rotation/scipy/spatial/transform>.
> Stay tuned for more updates!
>
> Best,
> Aditya
>
> On Wed, 2 May 2018 at 21:03, Aditya Bharti <adibhar97 at gmail.com> wrote:
>
>> Hi Nikolay,
>>
>> I've used Wordpress only once before, so I don't know much about it. From
>> my limited experience, it is extremely customizable. You can customize
>> every thing from the look and feel to SEO characteristics. There are
>> apparently a lot of wordpress plugins for these kind of tasks. For this
>> particular blog, PSF had already setup an account for me with a site on it.
>> All I had to do was click on the 'New' button and open up the new post
>> page. There's a field for a header and body text, with options for adding
>> audio, video and hyperlinks.
>>
>> As regards to the post itself, sure I'll expand it with a brief overview,
>> motivation and an example. Note that the example will only show sample
>> usage, not any internals. I plan to borrow heavily from my proposal for
>> this purpose, I hope that's ok.
>>
>> Regards,
>> Aditya
>>
>> On 2 May 2018 at 19:54, Nikolay Mayorov <nikolay.mayorov at zoho.com> wrote:
>>
>>> Hi, Aditya!
>>>
>>> Glad that you set up the blog and good job on setting up the
>>> documentation build as well.
>>>
>>> Curious, what is this blogging platform like? How do you create posts in
>>> it?
>>>
>>> As for your first post: while not strictly necessary I think it would be
>>> nice to see a more thorough introductory post with a brief overview,
>>> motivation and/or an example. Do you want to work on it?
>>>
>>> Best,
>>> Nikolay
>>>
>>>
>>> _______________________________________________
>>> SciPy-Dev mailing list
>>> SciPy-Dev at python.org
>>> https://mail.python.org/mailman/listinfo/scipy-dev
>>>
>>>
>>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
>
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From adibhar97 at gmail.com  Sat May 19 21:46:36 2018
From: adibhar97 at gmail.com (Aditya Bharti)
Date: Sun, 20 May 2018 07:16:36 +0530
Subject: [SciPy-Dev] [GSOC 2018 Project Thread]: Rotation formalism in 3
 dimensions
In-Reply-To: <CABL7CQhTQGAHS84WBJ2ctP7__jZuU0uJtirMW5u897NFREPmig@mail.gmail.com>
References: <163213d9b99.e31ddfbf140246.3867213885941953730@zoho.com>
 <CANRzPHVN47mDJqc4DuUq70X9sAiRqBRWOSHszgtL3QyM1O6ihA@mail.gmail.com>
 <CANRzPHV0BswFBevgZ2fsf2vKm_J_LQEET=qtDZ1WO6H7dMDNyQ@mail.gmail.com>
 <CABL7CQhTQGAHS84WBJ2ctP7__jZuU0uJtirMW5u897NFREPmig@mail.gmail.com>
Message-ID: <CANRzPHVXiLREbC1_7rn97xDAWWzyjNXeiuBuHU54zGwKEuvZOw@mail.gmail.com>

Hi Ralf,
Yes I do. It's on a wiki page on github here
<https://github.com/adbugger/scipy/wiki/Benchmarking-experiments-for-%60rotation.from_dcm%60>
.

Best,
Aditya

page:
https://github.com/adbugger/scipy/wiki/Benchmarking-experiments-for-%60rotation.from_dcm%60

On Sun, 20 May 2018 at 07:10, Ralf Gommers <ralf.gommers at gmail.com> wrote:

>
>
> On Sat, May 19, 2018 at 12:23 PM, Aditya Bharti <adibhar97 at gmail.com>
> wrote:
>
>> Hi all,
>> So this concludes week 1 of GSoC 2018. I must say it was a great learning
>> experience and I invite you all to check out my account of this week on the
>> blog <https://blogs.python-gsoc.org/aditya-bharti/>. This email is more
>> of a technical update.
>>
>
> Hi Aditya, that looks like good progress! One question: do you have the
> result of your benchmarking exercise somewhere? Could be interesting to
> refer to in the future.
>
> Cheers,
> Ralf
>
>
>>    - So, the main `Rotation` class will live under a new sub module
>>    `scipy.spatial.transform`.
>>    - Conversion between quaternions and discrete cosine matrices was
>>    implemented.
>>    - The rotation class now supports `from_quaternion`, `from_dcm`,
>>    `as_quaternion` and `as_dcm`, with support for multiple rotations in one
>>    call.
>>
>> The project currently lives in my own fork of scipy here
>> <https://github.com/adbugger/scipy/tree/rotation/scipy/spatial/transform>.
>> Stay tuned for more updates!
>>
>> Best,
>> Aditya
>>
>> On Wed, 2 May 2018 at 21:03, Aditya Bharti <adibhar97 at gmail.com> wrote:
>>
>>> Hi Nikolay,
>>>
>>> I've used Wordpress only once before, so I don't know much about it.
>>> From my limited experience, it is extremely customizable. You can customize
>>> every thing from the look and feel to SEO characteristics. There are
>>> apparently a lot of wordpress plugins for these kind of tasks. For this
>>> particular blog, PSF had already setup an account for me with a site on it.
>>> All I had to do was click on the 'New' button and open up the new post
>>> page. There's a field for a header and body text, with options for adding
>>> audio, video and hyperlinks.
>>>
>>> As regards to the post itself, sure I'll expand it with a brief
>>> overview, motivation and an example. Note that the example will only show
>>> sample usage, not any internals. I plan to borrow heavily from my proposal
>>> for this purpose, I hope that's ok.
>>>
>>> Regards,
>>> Aditya
>>>
>>> On 2 May 2018 at 19:54, Nikolay Mayorov <nikolay.mayorov at zoho.com>
>>> wrote:
>>>
>>>> Hi, Aditya!
>>>>
>>>> Glad that you set up the blog and good job on setting up the
>>>> documentation build as well.
>>>>
>>>> Curious, what is this blogging platform like? How do you create posts
>>>> in it?
>>>>
>>>> As for your first post: while not strictly necessary I think it would
>>>> be nice to see a more thorough introductory post with a brief overview,
>>>> motivation and/or an example. Do you want to work on it?
>>>>
>>>> Best,
>>>> Nikolay
>>>>
>>>>
>>>> _______________________________________________
>>>> SciPy-Dev mailing list
>>>> SciPy-Dev at python.org
>>>> https://mail.python.org/mailman/listinfo/scipy-dev
>>>>
>>>>
>>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at python.org
>> https://mail.python.org/mailman/listinfo/scipy-dev
>>
>>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
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From phillip.m.feldman at gmail.com  Sun May 20 03:56:31 2018
From: phillip.m.feldman at gmail.com (Phillip Feldman)
Date: Sun, 20 May 2018 00:56:31 -0700
Subject: [SciPy-Dev] [GSOC 2018 Project Thread]: Rotation formalism in 3
 dimensions
In-Reply-To: <CANRzPHV0BswFBevgZ2fsf2vKm_J_LQEET=qtDZ1WO6H7dMDNyQ@mail.gmail.com>
References: <163213d9b99.e31ddfbf140246.3867213885941953730@zoho.com>
 <CANRzPHVN47mDJqc4DuUq70X9sAiRqBRWOSHszgtL3QyM1O6ihA@mail.gmail.com>
 <CANRzPHV0BswFBevgZ2fsf2vKm_J_LQEET=qtDZ1WO6H7dMDNyQ@mail.gmail.com>
Message-ID: <CAB2ViTbimDdS0jZ3Qp71rorkhfALBhHQtTztv1OD11dY7V1ADg@mail.gmail.com>

When you say "discrete cosine matrix", I think that you mean "direction
cosine matrix" (see
https://en.wikiversity.org/wiki/PlanetPhysics/Direction_Cosine_Matrix).

Phillip

On Sat, May 19, 2018 at 12:23 PM, Aditya Bharti <adibhar97 at gmail.com> wrote:

> Hi all,
> So this concludes week 1 of GSoC 2018. I must say it was a great learning
> experience and I invite you all to check out my account of this week on the
> blog <https://blogs.python-gsoc.org/aditya-bharti/>. This email is more
> of a technical update.
>
>    - So, the main `Rotation` class will live under a new sub module
>    `scipy.spatial.transform`.
>    - Conversion between quaternions and discrete cosine matrices was
>    implemented.
>    - The rotation class now supports `from_quaternion`, `from_dcm`,
>    `as_quaternion` and `as_dcm`, with support for multiple rotations in one
>    call.
>
> The project currently lives in my own fork of scipy here
> <https://github.com/adbugger/scipy/tree/rotation/scipy/spatial/transform>.
> Stay tuned for more updates!
>
> Best,
> Aditya
>
> On Wed, 2 May 2018 at 21:03, Aditya Bharti <adibhar97 at gmail.com> wrote:
>
>> Hi Nikolay,
>>
>> I've used Wordpress only once before, so I don't know much about it. From
>> my limited experience, it is extremely customizable. You can customize
>> every thing from the look and feel to SEO characteristics. There are
>> apparently a lot of wordpress plugins for these kind of tasks. For this
>> particular blog, PSF had already setup an account for me with a site on it.
>> All I had to do was click on the 'New' button and open up the new post
>> page. There's a field for a header and body text, with options for adding
>> audio, video and hyperlinks.
>>
>> As regards to the post itself, sure I'll expand it with a brief overview,
>> motivation and an example. Note that the example will only show sample
>> usage, not any internals. I plan to borrow heavily from my proposal for
>> this purpose, I hope that's ok.
>>
>> Regards,
>> Aditya
>>
>> On 2 May 2018 at 19:54, Nikolay Mayorov <nikolay.mayorov at zoho.com> wrote:
>>
>>> Hi, Aditya!
>>>
>>> Glad that you set up the blog and good job on setting up the
>>> documentation build as well.
>>>
>>> Curious, what is this blogging platform like? How do you create posts in
>>> it?
>>>
>>> As for your first post: while not strictly necessary I think it would be
>>> nice to see a more thorough introductory post with a brief overview,
>>> motivation and/or an example. Do you want to work on it?
>>>
>>> Best,
>>> Nikolay
>>>
>>>
>>> _______________________________________________
>>> SciPy-Dev mailing list
>>> SciPy-Dev at python.org
>>> https://mail.python.org/mailman/listinfo/scipy-dev
>>>
>>>
>>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
>
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From jesse.livezey at gmail.com  Tue May 22 13:56:01 2018
From: jesse.livezey at gmail.com (Jesse Livezey)
Date: Tue, 22 May 2018 10:56:01 -0700
Subject: [SciPy-Dev] Interest in improvements to the cKDTree codebase?
Message-ID: <CAH1y-JWppmXpuGoE05w5akV-hObjQ9gR+hs3iKg6Cjd4KkQf+Q@mail.gmail.com>

Hi everyone,

I'm using cKDTrees for a project and noticed two potential ways to improve
the code and have written one additional count method that might be useful
to others.

I have written code and some tests for all three items and can contribute
if there is interest.

1) Allowing an array of rs in cKDTree.query_ball_point(). I started a PR
here <https://github.com/scipy/scipy/pull/8818>. In principle, this should
speed up multiple queries with different rs, but see 2.

2) I noticed that for the cases when cKDTree.query_ball_point() returns
large numbers of points (>100), it is faster to loop over queries in
python. This is true both with and without my PR. This is largely because
single point queries do not sort the return indices, but multi-point
queries DO sort them (see details here
<https://github.com/scipy/scipy/issues/8838>). Removing the sorted() leads
to considerable speedups, but is not backwards compatible. However, the
sorted behavior is not in the method description and is not even internally
consistent, so maybe it could just be removed or made optional?

3) I have written a cKDTree.count_ball_point() method that behaves like
query_ball_point() but just returns the number of points rather than their
indices. This is much faster than calling len(query_ball_point()).

Let me know if any of this is of interest.
Jesse

--
Jesse Livezey
he/him/his
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From ilhanpolat at gmail.com  Wed May 23 13:14:22 2018
From: ilhanpolat at gmail.com (Ilhan Polat)
Date: Wed, 23 May 2018 19:14:22 +0200
Subject: [SciPy-Dev] [ANN]: harold, a control systems package is released
Message-ID: <CAEBuzr_DxEjmp4j9DKaWM81eOSMfE=mJkJ21YLmPjB2yXr3G9w@mail.gmail.com>

Dear all,

Here is a shameless plug about the package I have been developing as a
side-project. Since it came to a point where I'm a bit more confident about
it, thought some publicity won't hurt to harvest some feedback. It lives
under the repo https://github.com/ilayn/harold/

You can check this simple demo about its basic functionality to manipulate
models, functions and plotting capabilities.

https://github.com/ilayn/harold/blob/v1.0.0/notebooks/harold_introduction.ipynb

There are still some work to do but all feedback is welcome.
ilhan
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From ralf.gommers at gmail.com  Thu May 24 01:06:35 2018
From: ralf.gommers at gmail.com (Ralf Gommers)
Date: Wed, 23 May 2018 22:06:35 -0700
Subject: [SciPy-Dev] [ANN]: harold, a control systems package is released
In-Reply-To: <CAEBuzr_DxEjmp4j9DKaWM81eOSMfE=mJkJ21YLmPjB2yXr3G9w@mail.gmail.com>
References: <CAEBuzr_DxEjmp4j9DKaWM81eOSMfE=mJkJ21YLmPjB2yXr3G9w@mail.gmail.com>
Message-ID: <CABL7CQiDmhV=mUEPjsuJdCK6rBRebP6fyq6V4NJODOZSEZ-tyg@mail.gmail.com>

On Wed, May 23, 2018 at 10:14 AM, Ilhan Polat <ilhanpolat at gmail.com> wrote:

> Dear all,
>
> Here is a shameless plug about the package I have been developing as a
> side-project. Since it came to a point where I'm a bit more confident about
> it, thought some publicity won't hurt to harvest some feedback. It lives
> under the repo https://github.com/ilayn/harold/
>
> You can check this simple demo about its basic functionality to manipulate
> models, functions and plotting capabilities.
>
> https://github.com/ilayn/harold/blob/v1.0.0/notebooks/
> harold_introduction.ipynb
>
> There are still some work to do but all feedback is welcome.
>

Nice! There's some comments in the readme about related packages, but a bit
more detail on that and where scipy.signal fits in would be useful probably.

Cheers,
Ralf
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From ilhanpolat at gmail.com  Thu May 24 07:00:09 2018
From: ilhanpolat at gmail.com (Ilhan Polat)
Date: Thu, 24 May 2018 13:00:09 +0200
Subject: [SciPy-Dev] [ANN]: harold, a control systems package is released
In-Reply-To: <CABL7CQiDmhV=mUEPjsuJdCK6rBRebP6fyq6V4NJODOZSEZ-tyg@mail.gmail.com>
References: <CAEBuzr_DxEjmp4j9DKaWM81eOSMfE=mJkJ21YLmPjB2yXr3G9w@mail.gmail.com>
 <CABL7CQiDmhV=mUEPjsuJdCK6rBRebP6fyq6V4NJODOZSEZ-tyg@mail.gmail.com>
Message-ID: <CAEBuzr9OvB2EKgLLUE-N5aiwfS2vYsidX2o-bdf95sxCOz_STQ@mail.gmail.com>

Ah, I knew I missed something :)

will do that. Thanks.

On Thu, May 24, 2018 at 7:06 AM, Ralf Gommers <ralf.gommers at gmail.com>
wrote:

>
>
> On Wed, May 23, 2018 at 10:14 AM, Ilhan Polat <ilhanpolat at gmail.com>
> wrote:
>
>> Dear all,
>>
>> Here is a shameless plug about the package I have been developing as a
>> side-project. Since it came to a point where I'm a bit more confident about
>> it, thought some publicity won't hurt to harvest some feedback. It lives
>> under the repo https://github.com/ilayn/harold/
>>
>> You can check this simple demo about its basic functionality to
>> manipulate models, functions and plotting capabilities.
>>
>> https://github.com/ilayn/harold/blob/v1.0.0/notebooks/harold
>> _introduction.ipynb
>>
>> There are still some work to do but all feedback is welcome.
>>
>
> Nice! There's some comments in the readme about related packages, but a
> bit more detail on that and where scipy.signal fits in would be useful
> probably.
>
> Cheers,
> Ralf
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
>
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From adibhar97 at gmail.com  Tue May 29 17:21:08 2018
From: adibhar97 at gmail.com (Aditya Bharti)
Date: Wed, 30 May 2018 02:51:08 +0530
Subject: [SciPy-Dev] [GSOC 2018 Project Thread]: Rotation formalism in 3
 dimensions
In-Reply-To: <CAB2ViTbimDdS0jZ3Qp71rorkhfALBhHQtTztv1OD11dY7V1ADg@mail.gmail.com>
References: <163213d9b99.e31ddfbf140246.3867213885941953730@zoho.com>
 <CANRzPHVN47mDJqc4DuUq70X9sAiRqBRWOSHszgtL3QyM1O6ihA@mail.gmail.com>
 <CANRzPHV0BswFBevgZ2fsf2vKm_J_LQEET=qtDZ1WO6H7dMDNyQ@mail.gmail.com>
 <CAB2ViTbimDdS0jZ3Qp71rorkhfALBhHQtTztv1OD11dY7V1ADg@mail.gmail.com>
Message-ID: <CANRzPHUynj4LSmpUeBMzY-my1EmGKUp944mdy_tyqOLGY5Fmrw@mail.gmail.com>

Hi all,
Continuing the work so far, the following have been implemented this week:

   - `from_rotvec`, `as_rotvec`: Representing Euler angles as rotation
   vectors, with appropriate Taylor series expansions for small angles
   - `from_euler`: Initialization from Euler angles, along with a string
   based axis sequence specification. Refer to docs for more details.

As always, the project lives here
<https://github.com/adbugger/scipy/tree/rotation/scipy/spatial/transform>,
and my personal experiences can be found on the blog
<https://blogs.python-gsoc.org/aditya-bharti>.

Thanks,
Aditya

On Sun, 20 May 2018 at 13:28, Phillip Feldman <phillip.m.feldman at gmail.com>
wrote:

> When you say "discrete cosine matrix", I think that you mean "direction
> cosine matrix" (see
> https://en.wikiversity.org/wiki/PlanetPhysics/Direction_Cosine_Matrix).
>
> Phillip
>
> On Sat, May 19, 2018 at 12:23 PM, Aditya Bharti <adibhar97 at gmail.com>
> wrote:
>
>> Hi all,
>> So this concludes week 1 of GSoC 2018. I must say it was a great learning
>> experience and I invite you all to check out my account of this week on the
>> blog <https://blogs.python-gsoc.org/aditya-bharti/>. This email is more
>> of a technical update.
>>
>>    - So, the main `Rotation` class will live under a new sub module
>>    `scipy.spatial.transform`.
>>    - Conversion between quaternions and discrete cosine matrices was
>>    implemented.
>>    - The rotation class now supports `from_quaternion`, `from_dcm`,
>>    `as_quaternion` and `as_dcm`, with support for multiple rotations in one
>>    call.
>>
>> The project currently lives in my own fork of scipy here
>> <https://github.com/adbugger/scipy/tree/rotation/scipy/spatial/transform>.
>> Stay tuned for more updates!
>>
>> Best,
>> Aditya
>>
>> On Wed, 2 May 2018 at 21:03, Aditya Bharti <adibhar97 at gmail.com> wrote:
>>
>>> Hi Nikolay,
>>>
>>> I've used Wordpress only once before, so I don't know much about it.
>>> From my limited experience, it is extremely customizable. You can customize
>>> every thing from the look and feel to SEO characteristics. There are
>>> apparently a lot of wordpress plugins for these kind of tasks. For this
>>> particular blog, PSF had already setup an account for me with a site on it.
>>> All I had to do was click on the 'New' button and open up the new post
>>> page. There's a field for a header and body text, with options for adding
>>> audio, video and hyperlinks.
>>>
>>> As regards to the post itself, sure I'll expand it with a brief
>>> overview, motivation and an example. Note that the example will only show
>>> sample usage, not any internals. I plan to borrow heavily from my proposal
>>> for this purpose, I hope that's ok.
>>>
>>> Regards,
>>> Aditya
>>>
>>> On 2 May 2018 at 19:54, Nikolay Mayorov <nikolay.mayorov at zoho.com>
>>> wrote:
>>>
>>>> Hi, Aditya!
>>>>
>>>> Glad that you set up the blog and good job on setting up the
>>>> documentation build as well.
>>>>
>>>> Curious, what is this blogging platform like? How do you create posts
>>>> in it?
>>>>
>>>> As for your first post: while not strictly necessary I think it would
>>>> be nice to see a more thorough introductory post with a brief overview,
>>>> motivation and/or an example. Do you want to work on it?
>>>>
>>>> Best,
>>>> Nikolay
>>>>
>>>>
>>>> _______________________________________________
>>>> SciPy-Dev mailing list
>>>> SciPy-Dev at python.org
>>>> https://mail.python.org/mailman/listinfo/scipy-dev
>>>>
>>>>
>>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at python.org
>> https://mail.python.org/mailman/listinfo/scipy-dev
>>
>>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
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From eryole at gmail.com  Wed May 30 15:51:54 2018
From: eryole at gmail.com (Nicolas Cellier)
Date: Wed, 30 May 2018 21:51:54 +0200
Subject: [SciPy-Dev] [ANN]: modelXplore,
 a package to explore computation expensive models
Message-ID: <CAFdp2M-VFsq=3Sz_Yy+9dBhe3U2++yyv3WGCfFNrZ376dVT8aw@mail.gmail.com>

Dear all,

I wrote a little package for the lab I work for. This is a library designed
to take an expensive model (or some experimental data) to generate (more
simple) metamodel thanks to the the sklearn library, SALib (sensivity
analysis) and optunity (hyperparameters optimization for the sklearn
regressor).
Some method are available in order to easily conduct sensitivity analysis
and to plot metamodel response surface.
It comes with two new samplers, one that is designed to fill the void
between previous samples, and the other that distribute the new samples
near the high-gradient area.

This is a small and new library (development began two weeks ago), but I
would enjoy all kind of feedback !

The library live here:

https://github.com/locie/modelXplore

Regards,

Nicolas Cellier
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From stefanv at berkeley.edu  Wed May 30 20:31:49 2018
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Wed, 30 May 2018 17:31:49 -0700
Subject: [SciPy-Dev] Calling LowLevelCallable from Cython
Message-ID: <20180531003149.qsqiigxepev3pozp@carbo>

Hi all,

I am looking into how to call a user-provided LowLevelCallable from
Cython.  In SciPy, I could only find examples of how to do that from C
(e.g. `scipy.integrate.quad`).  Wherever it is used, some processing is
done to see whether the LowLevelCallable provides a Python function, a C
function, what the signature is, etc. before calling.

Would it be convenient to have a set of Cython utilities that makes this
process easier?  Or is there perhaps a trick in Cython that makes it
trivial?

I'm going to work on this more tomorrow, but wanted to check first
whether anyone here has attempted something similar?

Thanks!
St?fan

From andyfaff at gmail.com  Wed May 30 21:08:54 2018
From: andyfaff at gmail.com (Andrew Nelson)
Date: Thu, 31 May 2018 11:08:54 +1000
Subject: [SciPy-Dev] Calling LowLevelCallable from Cython
In-Reply-To: <20180531003149.qsqiigxepev3pozp@carbo>
References: <20180531003149.qsqiigxepev3pozp@carbo>
Message-ID: <CAAbtOZc8oU6MB34DQXck9Xkd+6dSCJf5=gf_Hom_t+NMC_NKZg@mail.gmail.com>

I'm glad that you're looking into this. I asked a similar question on this
list a few months back, with a view to using LowLevelCallable as a way of
increasing the speed of minimizers, such as those used by
optimize.minimize. You should be able to find the discussion in the ML
archive, it may answer your question. I didn't go further down this path
because I was having trouble following the examples in the scipy codebase.

I was interested in this as part of a re-write to provide an object
oriented interface for each minimizer (8414, 8552). If the Minimizer object
was in cython, and a LowLevelCallable was provided, then good speedups
might be achieved.

Please keep us updated if you get traction on this.

Andrew.
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From pav at iki.fi  Thu May 31 08:27:16 2018
From: pav at iki.fi (Pauli Virtanen)
Date: Thu, 31 May 2018 14:27:16 +0200
Subject: [SciPy-Dev] Calling LowLevelCallable from Cython
In-Reply-To: <20180531003149.qsqiigxepev3pozp@carbo>
References: <20180531003149.qsqiigxepev3pozp@carbo>
Message-ID: <dce4e08cb5970d09167c6bc498c10219d4d54896.camel@iki.fi>

Hi,

At the moment probably nothing better than

https://github.com/scipy/scipy/blob/master/scipy/_lib/_ccallback_c.pyx#L137

if I understand what you  mean.

ke, 2018-05-30 kello 17:31 -0700, Stefan van der Walt kirjoitti:
> Hi all,
> 
> I am looking into how to call a user-provided LowLevelCallable from
> Cython.  In SciPy, I could only find examples of how to do that from
> C
> (e.g. `scipy.integrate.quad`).  Wherever it is used, some processing
> is
> done to see whether the LowLevelCallable provides a Python function,
> a C
> function, what the signature is, etc. before calling.
> 
> Would it be convenient to have a set of Cython utilities that makes
> this
> process easier?  Or is there perhaps a trick in Cython that makes it
> trivial?
> 
> I'm going to work on this more tomorrow, but wanted to check first
> whether anyone here has attempted something similar?
> 
> Thanks!
> St?fan
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev