Scheduled monthly dependency update for January

[pyup-bot]

Update SQLAlchemy from 1.2.14 to 1.2.15.

Changelog

1.2.15

:released: December 11, 2018

 .. change::
     :tags: bug, orm
     :tickets: 4367

     Fixed bug where the ORM annotations could be incorrect for the
     primaryjoin/secondaryjoin a relationship if one used the pattern
     ``ForeignKey(SomeClass.id)`` in the declarative mappings.   This pattern
     would leak undesired annotations into the join conditions which can break
     aliasing operations done within :class:`.Query` that are not supposed to
     impact elements in that join condition.  These annotations are now removed
     up front if present.

 .. change::
    :tags: bug, orm, declarative
    :tickets: 4374

    A warning is emitted in the case that a :func:`.column` object is applied to
    a declarative class, as it seems likely this intended to be a
    :class:`.Column` object.

 .. change::
     :tags: bug, orm
     :tickets: 4366

     In continuing with a similar theme as that of very recent :ticket:`4349`,
     repaired issue with :meth:`.RelationshipProperty.Comparator.any` and
     :meth:`.RelationshipProperty.Comparator.has` where the "secondary"
     selectable needs to be explicitly part of the FROM clause in the
     EXISTS subquery to suit the case where this "secondary" is a :class:`.Join`
     object.

 .. change::
     :tags: bug, orm
     :tickets: 4363

     Fixed regression caused by :ticket:`4349` where adding the "secondary"
     table to the FROM clause for a dynamic loader would affect the ability of
     the :class:`.Query` to make a subsequent join to another entity.   The fix
     adds the primary entity as the first element of the FROM list since
     :meth:`.Query.join` wants to jump from that.   Version 1.3 will have
     a more comprehensive solution to this problem as well (:ticket:`4365`).




 .. change::
    :tags: bug, orm
    :tickests: 4400

    Fixed bug where chaining of mapper options using
    :meth:`.RelationshipProperty.of_type` in conjunction with a chained option
    that refers to an attribute name by string only would fail to locate the
    attribute.

 .. change::
     :tag: feature, mysql
     :tickets: 4381

     Added support for the ``write_timeout`` flag accepted by mysqlclient and
     pymysql to  be passed in the URL string.

 .. change::
    :tag: bug, postgresql
    :tickets: 4377, 4380

    Fixed issue where reflection of a PostgreSQL domain that is expressed as an
    array would fail to be recognized.  Pull request courtesy Jakub Synowiec.


.. changelog::

Links

• PyPI: https://pypi.org/project/sqlalchemy
• Changelog: https://pyup.io/changelogs/sqlalchemy/
• Homepage: http://www.sqlalchemy.org

Update scipy from 1.1.0 to 1.2.0.

Changelog

1.2.0

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
1.2.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.

**Note**: This will be the last SciPy release to support Python 2.7.
       Consequently, the 1.2.x series will be a long term support (LTS)
       release; we will backport bug fixes until 1 Jan 2020.

For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required.

Highlights of this release
--------------------------

- 1-D root finding improvements with a new solver, ``toms748``, and a new
unified interface, ``root_scalar``
- New ``dual_annealing`` optimization method that combines stochastic and
local deterministic searching
- A new optimization algorithm, ``shgo`` (simplicial homology
global optimization) for derivative free optimization problems
- A new category of quaternion-based transformations are available in
`scipy.spatial.transform`

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

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

Proper spline coefficient calculations have been added for the ``mirror``,
``wrap``, and ``reflect`` modes of `scipy.ndimage.rotate`

`scipy.fftpack` improvements
--------------------------------

DCT-IV, DST-IV, DCT-I, and DST-I orthonormalization are now supported in
`scipy.fftpack`.

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

`scipy.interpolate.pade` now accepts a new argument for the order of the
numerator

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

`scipy.cluster.vq.kmeans2` gained a new initialization method, kmeans++.

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

The function ``softmax`` was added to `scipy.special`.

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

The one-dimensional nonlinear solvers have been given a unified interface
`scipy.optimize.root_scalar`, similar to the `scipy.optimize.root` interface
for multi-dimensional solvers. ``scipy.optimize.root_scalar(f, bracket=[a ,b],
method="brenth")`` is equivalent to ``scipy.optimize.brenth(f, a ,b)``.  If no
``method`` is specified, an appropriate one will be selected based upon the
bracket and the number of derivatives available.

The so-called Algorithm 748 of Alefeld, Potra and Shi for root-finding within
an enclosing interval has been added as `scipy.optimize.toms748`. This provides
guaranteed convergence to a root with convergence rate per function evaluation
of approximately 1.65 (for sufficiently well-behaved functions.)

``differential_evolution`` now has the ``updating`` and ``workers`` keywords.
The first chooses between continuous updating of the best solution vector (the
default), or once per generation. Continuous updating can lead to faster
convergence. The ``workers`` keyword accepts an ``int`` or map-like callable,
and parallelises the solver (having the side effect of updating once per
generation). Supplying an ``int`` evaluates the trial solutions in N parallel
parts. Supplying a map-like callable allows other parallelisation approaches
(such as ``mpi4py``, or ``joblib``) to be used.

``dual_annealing`` (and ``shgo`` below) is a powerful new general purpose
global optizimation (GO) algorithm. ``dual_annealing`` uses two annealing
processes to accelerate the convergence towards the global minimum of an
objective mathematical function. The first annealing process controls the
stochastic Markov chain searching and the second annealing process controls the
deterministic minimization. So, dual annealing is a hybrid method that takes
advantage of stochastic and local deterministic searching in an efficient way.

``shgo`` (simplicial homology global optimization) is a similar algorithm
appropriate for solving black box and derivative free optimization (DFO)
problems. The algorithm generally converges to the global solution in finite
time. The convergence holds for non-linear inequality and
equality constraints. In addition to returning a global minimum, the
algorithm also returns any other global and local minima found after every
iteration. This makes it useful for exploring the solutions in a domain.

`scipy.optimize.newton` can now accept a scalar or an array

``MINPACK`` usage is now thread-safe, such that ``MINPACK`` + callbacks may
be used on multiple threads.

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

Digital filter design functions now include a parameter to specify the sampling
rate. Previously, digital filters could only be specified using normalized
frequency, but different functions used different scales (e.g. 0 to 1 for
``butter`` vs 0 to π for ``freqz``), leading to errors and confusion.  With
the ``fs`` parameter, ordinary frequencies can now be entered directly into
functions, with the normalization handled internally.

``find_peaks`` and related functions no longer raise an exception if the
properties of a peak have unexpected values (e.g. a prominence of 0). A
``PeakPropertyWarning`` is given instead.

The new keyword argument ``plateau_size`` was added to ``find_peaks``.
``plateau_size`` may be used to select peaks based on the length of the
flat top of a peak.

``welch()`` and ``csd()`` methods in `scipy.signal` now support calculation
of a median average PSD, using ``average='mean'`` keyword

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

The `scipy.sparse.bsr_matrix.tocsr` method is now implemented directly instead
of converting via COO format, and the `scipy.sparse.bsr_matrix.tocsc` method
is now also routed via CSR conversion instead of COO. The efficiency of both
conversions is now improved.

The issue where SuperLU or UMFPACK solvers crashed on matrices with
non-canonical format in `scipy.sparse.linalg` was fixed. The solver wrapper
canonicalizes the matrix if necessary before calling the SuperLU or UMFPACK
solver.

The ``largest`` option of `scipy.sparse.linalg.lobpcg()` was fixed to have
a correct (and expected) behavior. The order of the eigenvalues was made
consistent with the ARPACK solver (``eigs()``), i.e. ascending for the
smallest eigenvalues, and descending for the largest eigenvalues.

The `scipy.sparse.random` function is now faster and also supports integer and
complex values by passing the appropriate value to the ``dtype`` argument.

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

The function `scipy.spatial.distance.jaccard` was modified to return 0 instead
of ``np.nan`` when two all-zero vectors are compared.

Support for the Jensen Shannon distance, the square-root of the divergence, has
been added under `scipy.spatial.distance.jensenshannon`

An optional keyword was added to the function
`scipy.spatial.cKDTree.query_ball_point()` to sort or not sort the returned
indices. Not sorting the indices can speed up calls.

A new category of quaternion-based transformations are available in
`scipy.spatial.transform`, including spherical linear interpolation of
rotations (``Slerp``), conversions to and from quaternions, Euler angles,
and general rotation and inversion capabilities
(`spatial.transform.Rotation`), and uniform random sampling of 3D
rotations (`spatial.transform.Rotation.random`).

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

The Yeo-Johnson power transformation is now supported (``yeojohnson``,
``yeojohnson_llf``, ``yeojohnson_normmax``, ``yeojohnson_normplot``). Unlike
the Box-Cox transformation, the Yeo-Johnson transformation can accept negative
values.

Added a general method to sample random variates based on the density only, in
the new function ``rvs_ratio_uniforms``.

The Yule-Simon distribution (``yulesimon``) was added -- this is a new
discrete probability distribution.

``stats`` and ``mstats`` now have access to a new regression method,
``siegelslopes``, a robust linear regression algorithm

`scipy.stats.gaussian_kde` now has the ability to deal with weighted samples,
and should have a modest improvement in performance

Levy Stable Parameter Estimation, PDF, and CDF calculations are now supported
for `scipy.stats.levy_stable`.

The Brunner-Munzel test is now available as ``brunnermunzel`` in ``stats``
and ``mstats``

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

`scipy.linalg.lapack` now exposes the LAPACK routines using the Rectangular
Full Packed storage (RFP) for upper triangular, lower triangular, symmetric,
or Hermitian matrices; the upper trapezoidal fat matrix RZ decomposition
routines are now available as well.

Deprecated features
===================
The functions ``hyp2f0``, ``hyp1f2`` and ``hyp3f0`` in ``scipy.special`` have
been deprecated.


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

LAPACK version 3.4.0 or later is now required. Building with
Apple Accelerate is no longer supported.

The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct
results for all angles. Before this, the function only returned
correct values for those angles which were greater than pi/4.

Support for the Bento build system has been removed. Bento has not been
maintained for several years, and did not have good Python 3 or wheel support,
hence it was time to remove it.

The required signature of `scipy.optimize.lingprog` ``method=simplex``
callback function has changed. Before iteration begins, the simplex solver
first converts the problem into a standard form that does not, in general,
have the same variables or constraints
as the problem defined by the user. Previously, the simplex solver would pass a
user-specified callback function several separate arguments, such as the
current solution vector ``xk``, corresponding to this standard form problem.
Unfortunately, the relationship between the standard form problem and the
user-defined problem was not documented, limiting the utility of the
information passed to the callback function.

In addition to numerous bug fix changes, the simplex solver now passes a
user-specified callback function a single ``OptimizeResult`` object containing
information that corresponds directly to the user-defined problem. In future
releases, this ``OptimizeResult`` object may be expanded to include additional
information, such as variables corresponding to the standard-form problem and
information concerning the relationship between the standard-form and
user-defined problems.

The implementation of `scipy.sparse.random` has changed, and this affects the
numerical values returned for both ``sparse.random`` and ``sparse.rand`` for
some matrix shapes and a given seed.

`scipy.optimize.newton` will no longer use Halley's method in cases where it
negatively impacts convergence

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


Authors
=======

* endolith
* luzpaz
* Hameer Abbasi +
* akahard2dj +
* Anton Akhmerov
* Joseph Albert
* alexthomas93 +
* ashish +
* atpage +
* Blair Azzopardi +
* Yoshiki Vázquez Baeza
* Bence Bagi +
* Christoph Baumgarten
* Lucas Bellomo +
* BH4 +
* Aditya Bharti
* Max Bolingbroke
* François Boulogne
* Ward Bradt +
* Matthew Brett
* Evgeni Burovski
* Rafał Byczek +
* Alfredo Canziani +
* CJ Carey
* Lucía Cheung +
* Poom Chiarawongse +
* Jeanne Choo +
* Robert Cimrman
* Graham Clenaghan +
* cynthia-rempel +
* Johannes Damp +
* Jaime Fernandez del Rio
* Dowon +
* emmi474 +
* Stefan Endres +
* Thomas Etherington +
* Alex Fikl +
* fo40225 +
* Joseph Fox-Rabinovitz
* Lars G
* Abhinav Gautam +
* Stiaan Gerber +
* C.A.M. Gerlach +
* Ralf Gommers
* Todd Goodall
* Lars Grueter +
* Sylvain Gubian +
* Matt Haberland
* David Hagen
* Will Handley +
* Charles Harris
* Ian Henriksen
* Thomas Hisch +
* Theodore Hu
* Michael Hudson-Doyle +
* Nicolas Hug +
* jakirkham +
* Jakob Jakobson +
* James +
* Jan Schlüter
* jeanpauphilet +
* josephmernst +
* Kai +
* Kai-Striega +
* kalash04 +
* Toshiki Kataoka +
* Konrad0 +
* Tom Krauss +
* Johannes Kulick
* Lars Grüter +
* Eric Larson
* Denis Laxalde
* Will Lee +
* Katrin Leinweber +
* Yin Li +
* P. L. Lim +
* Jesse Livezey +
* Duncan Macleod +
* MatthewFlamm +
* Nikolay Mayorov
* Mike McClurg +
* Christian Meyer +
* Mark Mikofski
* Naoto Mizuno +
* mohmmadd +
* Nathan Musoke
* Anju Geetha Nair +
* Andrew Nelson
* Ayappan P +
* Nick Papior
* Haesun Park +
* Ronny Pfannschmidt +
* pijyoi +
* Ilhan Polat
* Anthony Polloreno +
* Ted Pudlik
* puenka
* Eric Quintero
* Pradeep Reddy Raamana +
* Vyas Ramasubramani +
* Ramon Viñas +
* Tyler Reddy
* Joscha Reimer
* Antonio H Ribeiro
* richardjgowers +
* Rob +
* robbystk +
* Lucas Roberts +
* rohan +
* Joaquin Derrac Rus +
* Josua Sassen +
* Bruce Sharpe +
* Max Shinn +
* Scott Sievert
* Sourav Singh
* Strahinja Lukić +
* Kai Striega +
* Shinya SUZUKI +
* Mike Toews +
* Piotr Uchwat
* Miguel de Val-Borro +
* Nicky van Foreest
* Paul van Mulbregt
* Gael Varoquaux
* Pauli Virtanen
* Stefan van der Walt
* Warren Weckesser
* Joshua Wharton +
* Bernhard M. Wiedemann +
* Eric Wieser
* Josh Wilson
* Tony Xiang +
* Roman Yurchak +
* Roy Zywina +

A total of 137 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.

Links

• PyPI: https://pypi.org/project/scipy
• Changelog: https://pyup.io/changelogs/scipy/
• Repo: https://github.com/scipy/scipy/releases
• Homepage: https://www.scipy.org

Update scikit-learn from 0.20.1 to 0.20.2.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/scikit-learn
• Changelog: https://pyup.io/changelogs/scikit-learn/
• Homepage: http://scikit-learn.org

Update boto3 from 1.9.60 to 1.9.71.

Changelog

1.9.71

======

* api-change:``acm-pca``: [``botocore``] Update acm-pca client to latest version
* api-change:``dynamodb``: [``botocore``] Update dynamodb client to latest version
* api-change:``sms-voice``: [``botocore``] Update sms-voice client to latest version
* api-change:``stepfunctions``: [``botocore``] Update stepfunctions client to latest version

1.9.70

======

* api-change:``medialive``: [``botocore``] Update medialive client to latest version
* enhancement:EndpointDiscovery: [``botocore``] Add a config option, ``endpoint_discovery_enabled``, for automatically discovering endpoints
* api-change:``comprehend``: [``botocore``] Update comprehend client to latest version
* api-change:``firehose``: [``botocore``] Update firehose client to latest version
* api-change:``transcribe``: [``botocore``] Update transcribe client to latest version
* api-change:``cognito-idp``: [``botocore``] Update cognito-idp client to latest version

1.9.69

======

* api-change:``sagemaker``: [``botocore``] Update sagemaker client to latest version
* api-change:``waf-regional``: [``botocore``] Update waf-regional client to latest version
* api-change:``ec2``: [``botocore``] Update ec2 client to latest version
* api-change:``waf``: [``botocore``] Update waf client to latest version

1.9.68

======

* api-change:``apigatewayv2``: [``botocore``] Update apigatewayv2 client to latest version
* bugfix:Credentials: [``botocore``] Fixes an issue where credentials would be checked when creating an anonymous client. Fixes `1472 <https://github.com/boto/botocore/issues/1472>`__
* api-change:``ec2``: [``botocore``] Update ec2 client to latest version
* api-change:``elasticbeanstalk``: [``botocore``] Update elasticbeanstalk client to latest version
* api-change:``globalaccelerator``: [``botocore``] Update globalaccelerator client to latest version
* enhancement:StreamingBody: [``botocore``] Support iterating lines from a streaming response body with CRLF line endings
* api-change:``apigatewaymanagementapi``: [``botocore``] Update apigatewaymanagementapi client to latest version

1.9.67

======

* api-change:``quicksight``: [``botocore``] Update quicksight client to latest version
* api-change:``ecr``: [``botocore``] Update ecr client to latest version

1.9.66

======

* api-change:``alexaforbusiness``: [``botocore``] Update alexaforbusiness client to latest version
* api-change:``redshift``: [``botocore``] Update redshift client to latest version
* api-change:``cloudformation``: [``botocore``] Update cloudformation client to latest version

1.9.65

======

* api-change:``organizations``: [``botocore``] Update organizations client to latest version
* api-change:``pinpoint-email``: [``botocore``] Update pinpoint-email client to latest version

1.9.64

======

* api-change:``route53``: [``botocore``] Update route53 client to latest version
* api-change:``glue``: [``botocore``] Update glue client to latest version
* api-change:``sagemaker``: [``botocore``] Update sagemaker client to latest version
* api-change:``eks``: [``botocore``] Update eks client to latest version

1.9.63

======

* api-change:``mediastore``: [``botocore``] Update mediastore client to latest version
* api-change:``ecs``: [``botocore``] Update ecs client to latest version
* api-change:``connect``: [``botocore``] Update connect client to latest version

1.9.62

======

* api-change:``ec2``: [``botocore``] Update ec2 client to latest version
* enhancement:AssumeRole: [``botocore``] Add support for duration_seconds when assuming a role in the config file (`1600 <https://github.com/boto/botocore/issues/1600>`__).
* api-change:``iam``: [``botocore``] Update iam client to latest version
* api-change:``servicecatalog``: [``botocore``] Update servicecatalog client to latest version
* api-change:``alexaforbusiness``: [``botocore``] Update alexaforbusiness client to latest version

1.9.61

======

* api-change:``elbv2``: [``botocore``] Update elbv2 client to latest version
* api-change:``medialive``: [``botocore``] Update medialive client to latest version
* api-change:``codebuild``: [``botocore``] Update codebuild client to latest version
* api-change:``rds``: [``botocore``] Update rds client to latest version

Links

• PyPI: https://pypi.org/project/boto3
• Changelog: https://pyup.io/changelogs/boto3/
• Repo: https://github.com/boto/boto3

Update tox from 3.5.3 to 3.6.1.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/tox
• Docs: https://tox.readthedocs.org/

[codecov-io]

Codecov Report

Merging #562 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #562   +/-   ##
=======================================
  Coverage   82.69%   82.69%           
=======================================
  Files          82       82           
  Lines        4651     4651           
=======================================
  Hits         3846     3846           
  Misses        805      805

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 1e8b233...64acab8. Read the comment docs.