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Scheduled monthly dependency update for February #588

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merged 14 commits into from
Feb 6, 2019

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@pyup-bot pyup-bot commented Feb 1, 2019

Update alembic from 1.0.5 to 1.0.7.

Changelog

1.0.7

:released: January 25, 2019

 .. change::
    :tags: bug, autogenerate
    :tickets: 529

    Fixed issue in new comment support where autogenerated Python code
    for comments wasn't using ``repr()`` thus causing issues with
    quoting.  Pull request courtesy Damien Garaud.

.. changelog::

1.0.6

:released: January 13, 2019

 .. change::
     :tags: feature, operations
     :tickets: 422

     Added Table and Column level comments for supported backends.
     New methods :meth:`.Operations.create_table_comment` and
     :meth:`.Operations.drop_table_comment` are added.  A new arguments
     :paramref:`.Operations.alter_column.comment` and
     :paramref:`.Operations.alter_column.existing_comment` are added to
     :meth:`.Operations.alter_column`.   Autogenerate support is also added
     to ensure comment add/drops from tables and columns are generated as well
     as that :meth:`.Operations.create_table`, :meth:`.Operations.add_column`
     both include the comment field from the source :class:`.Table`
     or :class:`.Column` object.

.. changelog::
Links

Update SQLAlchemy from 1.2.15 to 1.2.17.

Changelog

1.2.17

:released: January 25, 2019

 .. change::
    :tags: feature, orm
    :tickets: 4461

    Added new event hooks :meth:`.QueryEvents.before_compile_update` and
    :meth:`.QueryEvents.before_compile_delete` which complement
    :meth:`.QueryEvents.before_compile` in the case of the :meth:`.Query.update`
    and :meth:`.Query.delete` methods.


 .. change::
    :tags: bug, postgresql
    :tickets: 4463

    Revised the query used when reflecting CHECK constraints to make use of the
    ``pg_get_constraintdef`` function, as the ``consrc`` column is being
    deprecated in PG 12.  Thanks to John A Stevenson for the tip.


 .. change::
    :tags: bug, orm
    :tickets: 4454

    Fixed issue where when using single-table inheritance in conjunction with a
    joined inheritance hierarchy that uses "with polymorphic" loading, the
    "single table criteria" for that single-table entity could get confused for
    that of other entities from the same hierarchy used in the same query.The
    adaption of the "single table criteria" is made more specific to the target
    entity to avoid it accidentally getting adapted to other tables in the
    query.


 .. change::
    :tags: bug, oracle
    :tickets: 4457

    Fixed regression in integer precision logic due to the refactor of the
    cx_Oracle dialect in 1.2.  We now no longer apply the cx_Oracle.NATIVE_INT
    type to result columns sending integer values (detected as positive
    precision with scale ==0) which encounters integer overflow issues with
    values that go beyond the 32 bit boundary.  Instead, the output variable
    is left untyped so that cx_Oracle can choose the best option.

.. changelog::

1.2.16

:released: January 11, 2019

 .. change::
    :tag: bug, sql
    :tickets: 4394

    Fixed issue in "expanding IN" feature where using the same bound parameter
    name more than once in a query would lead to a KeyError within the process
    of rewriting the parameters in the query.

 .. change::
    :tags: bug, postgresql
    :tickets: 4416

    Fixed issue where a :class:`.postgresql.ENUM` or a custom domain present
    in a remote schema would not be recognized within column reflection if
    the name of the enum/domain or the name of the schema required quoting.
    A new parsing scheme now fully parses out quoted or non-quoted tokens
    including support for SQL-escaped quotes.

 .. change::
    :tags: bug, postgresql

    Fixed issue where multiple :class:`.postgresql.ENUM` objects referred to
    by the same :class:`.MetaData` object would fail to be created if
    multiple objects had the same name under different schema names.  The
    internal memoization the PostgreSQL dialect uses to track if it has
    created a particular :class:`.postgresql.ENUM` in the database during
    a DDL creation sequence now takes schema name into account.

 .. change::
    :tags: bug, engine
    :tickets: 4429

    Fixed a regression introduced in version 1.2 where a refactor
    of the :class:`.SQLAlchemyError` base exception class introduced an
    inappropriate coercion of a plain string message into Unicode under
    python 2k, which is not handled by the Python interpreter for characters
    outside of the platform's encoding (typically ascii).  The
    :class:`.SQLAlchemyError` class now passes a bytestring through under
    Py2K for ``__str__()`` as is the behavior of exception objects in general
    under Py2K, does a safe coercion to unicode utf-8 with
    backslash fallback for ``__unicode__()``.  For Py3K the message is
    typically unicode already, but if not is again safe-coerced with utf-8
    with backslash fallback for the ``__str__()`` method.

 .. change::
    :tags: bug, sql, oracle, mysql
    :tickets: 4436

    Fixed issue where the DDL emitted for :class:`.DropTableComment`, which
    will be used by an upcoming version of Alembic, was incorrect for the MySQL
    and Oracle databases.

 .. change::
    :tags: bug, sqlite
    :tickets: 4431

    Reflection of an index based on SQL expressions are now skipped with a
    warning, in the same way as that of the Postgresql dialect, where we currently
    do not support reflecting indexes that have SQL expressions within them.
    Previously, an index with columns of None were produced which would break
    tools like Alembic.

.. changelog::
Links

Update psycopg2-binary from 2.7.6.1 to 2.7.7.

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

Links

Update pandas from 0.23.4 to 0.24.0.

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

Links

Update boto3 from 1.9.71 to 1.9.86.

Changelog

1.9.86

======

* api-change:``devicefarm``: [``botocore``] Update devicefarm client to latest version
* api-change:``codecommit``: [``botocore``] Update codecommit client to latest version
* api-change:``medialive``: [``botocore``] Update medialive client to latest version
* api-change:``mediaconnect``: [``botocore``] Update mediaconnect client to latest version

1.9.85

======

* api-change:``logs``: [``botocore``] Update logs client to latest version
* api-change:``elbv2``: [``botocore``] Update elbv2 client to latest version
* api-change:``rds``: [``botocore``] Update rds client to latest version
* api-change:``codebuild``: [``botocore``] Update codebuild client to latest version
* api-change:``sms-voice``: [``botocore``] Update sms-voice client to latest version
* api-change:``ecr``: [``botocore``] Update ecr client to latest version

1.9.84

======

* api-change:``worklink``: [``botocore``] Update worklink client to latest version
* api-change:``apigatewaymanagementapi``: [``botocore``] Update apigatewaymanagementapi client to latest version
* api-change:``acm-pca``: [``botocore``] Update acm-pca client to latest version

1.9.83

======

* api-change:``appstream``: [``botocore``] Update appstream client to latest version
* api-change:``discovery``: [``botocore``] Update discovery client to latest version
* api-change:``dms``: [``botocore``] Update dms client to latest version
* api-change:``fms``: [``botocore``] Update fms client to latest version
* api-change:``ssm``: [``botocore``] Update ssm client to latest version

1.9.82

======

* api-change:``glue``: [``botocore``] Update glue client to latest version
* api-change:``ec2``: [``botocore``] Update ec2 client to latest version

1.9.81

======

* api-change:``lightsail``: [``botocore``] Update lightsail client to latest version
* api-change:``lambda``: [``botocore``] Update lambda client to latest version
* api-change:``pinpoint``: [``botocore``] Update pinpoint client to latest version
* api-change:``rekognition``: [``botocore``] Update rekognition client to latest version

1.9.80

======

* api-change:``dynamodb``: [``botocore``] Update dynamodb client to latest version
* api-change:``ce``: [``botocore``] Update ce client to latest version
* api-change:``backup``: [``botocore``] Update backup client to latest version

1.9.79

======

* api-change:``storagegateway``: [``botocore``] Update storagegateway client to latest version
* api-change:``mediaconvert``: [``botocore``] Update mediaconvert client to latest version

1.9.78

======

* api-change:``rds-data``: [``botocore``] Update rds-data client to latest version
* api-change:``emr``: [``botocore``] Update emr client to latest version

1.9.77

======

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

1.9.76

======

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

1.9.75

======

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

1.9.74

======

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

1.9.73

======

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

1.9.72

======

* enhancement:Paginator: [``botocore``] Added over 400 new paginators.
* api-change:``opsworkscm``: [``botocore``] Update opsworkscm client to latest version
Links

Update wrapt from 1.10.11 to 1.11.1.

Changelog

1.11.1

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

**Bugs Fixed**

* Fixed memory leak in C extension variant of ``PartialCallableObjectProxy``
class introduced in 1.11.0, when it was being used to perform binding,
when a call of an instance method was made through the class type, and
the self object passed explicitly as first argument.

* The C extension variant of the ``PartialCallableObjectProxy`` class
introduced in 1.11.0, which is a version of ``functools.partial``
which correctly handles binding when applied to methods of classes,
couldn't be used when no positional arguments were supplied.

* When the C extension variant of ``PartialCallableObjectProxy`` was
used and multiple positional arguments were supplied, the first
argument would be replicated and used to all arguments, instead of
correct values, when the partial was called.

* When the C extension variant of ``PartialCallableObjectProxy`` was
used and keyword arguments were supplied, it would fail as was
incorrectly using the positional arguments where the keyword arguments
should have been used.

1.11.0

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

**Bugs Fixed**

* When using arithmetic operations through a proxy object, checks about
the types of arguments were not being performed correctly, which could
result in an exception being raised to indicate that a proxy object had
not been initialised when in fact the argument wasn't even an instance
of a proxy object.

Because an incorrect cast in C level code was being performed and
an attribute in memory checked on the basis of it being a type different
to what it actually was, technically it may have resulted in a process
crash if the size of the object was smaller than the type being casted
to.

* The ``__complex__()`` special method wasn't implemented and using
``complex()`` on a proxy object would give wrong results or fail.

* When using the C extension, if an exception was raised when using inplace
or, ie., ``|=``, the error condition wasn't being correctly propagated
back which would result in an exception showing up as wrong location
in subsequent code.

* Type of ``long`` was used instead of ``Py_hash_t`` for Python 3.3+. This
caused compiler warnings on Windows, which depending on what locale was
set to, would cause pip to fail when installing the package.

* If calling ``Class.instancemethod`` and passing ``self`` explicitly, the
ability to access ``__name__`` and ``__module__`` on the final bound
method were not preserved. This was due to a ``partial`` being used for
this special case, and it doesn't preserve introspection.

* Fixed typo in the getter property of ``ObjectProxy`` for accessing
``__annotations__``. Appeared that it was still working as would fall back
to using generic ``__getattr__()`` to access attribute on wrapped object.

**Features Changed**

* Dropped support for Python 2.6 and 3.3.

* If ``copy.copy()`` or ``copy.deepcopy()`` is used on an instance of the
``ObjectProxy`` class, a ``NotImplementedError`` exception is raised, with
a message indicating that the object proxy must implement the
``__copy__()`` or ``__deepcopy__()`` method. This is in place of the
default ``TypeError`` exception with message indicating a pickle error.

* If ``pickle.dump()`` or ``pickle.dumps()`` is used on an instance of the
``ObjectProxy`` class, a ``NotImplementedError`` exception is raised, with
a message indicating that the object proxy must implement the
``__reduce_ex__()`` method. This is in place of the default ``TypeError``
exception with message indicating a pickle error.
Links

Update pytest-cov from 2.6.0 to 2.6.1.

Changelog

2.6.1

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

* Added support for Pytest 4.1. Contributed by Daniel Hahler and Семён Марьясин in
`253 <https://github.com/pytest-dev/pytest-cov/pull/253>`_ and
`230 <https://github.com/pytest-dev/pytest-cov/pull/230>`_.
* Various test and docs fixes. Contributed by Daniel Hahler in
`224 <https://github.com/pytest-dev/pytest-cov/pull/224>`_ and
`223 <https://github.com/pytest-dev/pytest-cov/pull/223>`_.
* Fixed the "Module already imported" issue (`211 <https://github.com/pytest-dev/pytest-cov/issues/211>`_).
Contributed by Daniel Hahler in `228 <https://github.com/pytest-dev/pytest-cov/pull/228>`_.
Links

Update fakeredis from 0.16.0 to 1.0.

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

Links

Update flake8 from 3.6.0 to 3.7.4.

Changelog

3.7.4

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

You can view the `3.7.4 milestone`_ on GitLab for more details.

Bugs Fixed
~~~~~~~~~~

- Fix performance regression with lots of ``per-file-ignores`` and errors
(See also `GitLab!299`_, `GitLab501`_)


.. all links
.. _3.7.4 milestone:
 https://gitlab.com/pycqa/flake8/milestones/27

.. issue links
.. _GitLab501:
 https://gitlab.com/pycqa/flake8/issues/501

.. merge request links
.. _GitLab!299:
 https://gitlab.com/pycqa/flake8/merge_requests/299

3.7.3

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

You can view the `3.7.3 milestone`_ on GitLab for more details.

Bugs Fixed
~~~~~~~~~~

- Fix imports of ``typing`` in python 3.5.0 / 3.5.1 (See also `GitLab!294`_,
`GitLab498`_)

- Fix ``flake8 --statistics`` (See also `GitLab!295`_, `GitLab499`_)

- Gracefully ignore ``flake8-per-file-ignores`` plugin if installed (See also
`GitLab!297`_, `GitLab495`_)

- Improve error message for malformed ``per-file-ignores`` (See also
`GitLab!298`_, `GitLab489`_)


.. all links
.. _3.7.3 milestone:
 https://gitlab.com/pycqa/flake8/milestones/26

.. issue links
.. _GitLab489:
 https://gitlab.com/pycqa/flake8/issues/489
.. _GitLab495:
 https://gitlab.com/pycqa/flake8/issues/495
.. _GitLab498:
 https://gitlab.com/pycqa/flake8/issues/498
.. _GitLab499:
 https://gitlab.com/pycqa/flake8/issues/499

.. merge request links
.. _GitLab!294:
 https://gitlab.com/pycqa/flake8/merge_requests/294
.. _GitLab!295:
 https://gitlab.com/pycqa/flake8/merge_requests/295
.. _GitLab!297:
 https://gitlab.com/pycqa/flake8/merge_requests/297
.. _GitLab!298:
 https://gitlab.com/pycqa/flake8/merge_requests/298

3.7.2

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

You can view the `3.7.2 milestone`_ on GitLab for more details.

Bugs Fixed
~~~~~~~~~~

- Fix broken ``flake8 --diff`` (regressed in 3.7.0) (See also `GitLab!292`_,
`GitLab490`_)

- Fix typo in plugin exception reporting (See also `GitLab!275`_,
`GitLab491`_)

- Fix ``AttributeError`` while attempting to use the legacy api (regressed in
3.7.0) (See also `GitLab!293`_, `GitLab497`_)

.. all links
.. _3.7.2 milestone:
 https://gitlab.com/pycqa/flake8/milestones/25

.. issue links
.. _GitLab490:
 https://gitlab.com/pycqa/flake8/issues/490
.. _GitLab491:
 https://gitlab.com/pycqa/flake8/issues/491
.. _GitLab497:
 https://gitlab.com/pycqa/flake8/issues/497

.. merge request links
.. _GitLab!292:
 https://gitlab.com/pycqa/flake8/merge_requests/292
.. _GitLab!275:
 https://gitlab.com/pycqa/flake8/merge_requests/275
.. _GitLab!293:
 https://gitlab.com/pycqa/flake8/merge_requests/293

3.7.1

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

You can view the `3.7.1 milestone`_ on GitLab for more details.

Bugs Fixed
~~~~~~~~~~

- Fix capitalized filenames in ``per-file-ignores`` setting (See also
`GitLab!290`_, `GitLab488`_)

.. all links
.. _3.7.1 milestone:
 https://gitlab.com/pycqa/flake8/milestones/24

.. issue links
.. _GitLab488:
 https://gitlab.com/pycqa/flake8/issues/488

.. merge request links
.. _GitLab!290:
 https://gitlab.com/pycqa/flake8/merge_requests/290

3.7.0

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

You can view the `3.7.0 milestone`_ on GitLab for more details.

New Dependency Information
~~~~~~~~~~~~~~~~~~~~~~~~~~

- Add dependency on ``entrypoints`` >= 0.3, < 0.4 (See also `GitLab!264`_,
`GitLab!288`_)

- Pyflakes has been updated to >= 2.1.0, < 2.2.0 (See also `GitLab!283`_,
`GitLab!285`_)

- pycodestyle has been updated to >= 2.5.0, < 2.6.0 (See also `GitLab!287`_)

Features
~~~~~~~~

- Add support for ``per-file-ignores`` (See also `GitLab!259`_, `GitLab156`_,
`GitLab!281`_, `GitLab471`_)

- Enable use of ``float`` and ``complex`` option types (See also `GitLab!261`_,
`GitLab452`_)

- Improve startup performance by switching from ``pkg_resources`` to
``entrypoints`` (See also `GitLab!264`_)

- Add metadata for use through the `pre-commit`_ git hooks framework (See also
`GitLab!268`_, `GitLab!284`_)

- Allow physical line checks to return more than one result (See also
`GitLab!269`_)

- Allow `` noqa:X123`` comments without space between the colon and codes
list (See also `GitLab!273`_, `GitLab470`_)

- Remove broken and unused ``flake8.listen`` plugin type (See also
`GitLab!274`_, `GitLab480`_)

.. all links
.. _3.7.0 milestone:
 https://gitlab.com/pycqa/flake8/milestones/23
.. _pre-commit:
 https://pre-commit.com/

.. issue links
.. _GitLab156:
 https://gitlab.com/pycqa/flake8/issues/156
.. _GitLab452:
 https://gitlab.com/pycqa/flake8/issues/452
.. _GitLab470:
 https://gitlab.com/pycqa/flake8/issues/470
.. _GitLab471:
 https://gitlab.com/pycqa/flake8/issues/471
.. _GitLab480:
 https://gitlab.com/pycqa/flake8/issues/480

.. merge request links
.. _GitLab!259:
 https://gitlab.com/pycqa/flake8/merge_requests/259
.. _GitLab!261:
 https://gitlab.com/pycqa/flake8/merge_requests/261
.. _GitLab!264:
 https://gitlab.com/pycqa/flake8/merge_requests/264
.. _GitLab!268:
 https://gitlab.com/pycqa/flake8/merge_requests/268
.. _GitLab!269:
 https://gitlab.com/pycqa/flake8/merge_requests/269
.. _GitLab!273:
 https://gitlab.com/pycqa/flake8/merge_requests/273
.. _GitLab!274:
 https://gitlab.com/pycqa/flake8/merge_requests/274
.. _GitLab!281:
 https://gitlab.com/pycqa/flake8/merge_requests/281
.. _GitLab!283:
 https://gitlab.com/pycqa/flake8/merge_requests/283
.. _GitLab!284:
 https://gitlab.com/pycqa/flake8/merge_requests/284
.. _GitLab!285:
 https://gitlab.com/pycqa/flake8/merge_requests/285
.. _GitLab!287:
 https://gitlab.com/pycqa/flake8/merge_requests/287
.. _GitLab!288:
 https://gitlab.com/pycqa/flake8/merge_requests/288
Links

Update tox from 3.6.1 to 3.7.0.

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

Links

@codecov-io
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codecov-io commented Feb 1, 2019

Codecov Report

Merging #588 into master will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master    #588      +/-   ##
=========================================
+ Coverage   82.49%   82.5%   +<.01%     
=========================================
  Files          83      83              
  Lines        4845    4847       +2     
=========================================
+ Hits         3997    3999       +2     
  Misses        848     848
Impacted Files Coverage Δ
src/triage/component/catwalk/storage.py 92.4% <ø> (ø) ⬆️
src/triage/component/metta/metta_io.py 71.75% <ø> (ø) ⬆️
src/triage/util/db.py 100% <100%> (ø) ⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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@thcrock
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thcrock commented Feb 1, 2019

The build failure appears to come from the pandas update which breaks HDF. We'll have to look into that in order to get this ready.

@thcrock thcrock self-assigned this Feb 5, 2019
@thcrock thcrock merged commit ce41107 into master Feb 6, 2019
@thcrock thcrock deleted the pyup-scheduled-update-2019-02-01 branch February 6, 2019 19:19
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3 participants