Scheduled weekly dependency update for week 26

[pyup-bot]

Update biopython from 1.72 to 1.73.

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

Links

• PyPI: https://pypi.org/project/biopython
• Changelog: https://pyup.io/changelogs/biopython/
• Homepage: https://biopython.org/

Update click-plugins from 1.0.3 to 1.1.1.

Changelog

1.1.1

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

- Fixed a version mismatch in `click_plugins/__init__.py`  See `1.1`.

1.1

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

- Fix an issue where a broken command's traceback would not be emitted - https://github.com/click-contrib/click-plugins/issues/25
- Bump required click version to `click>=4` - https://github.com/click-contrib/click-plugins/pull/28
- Runs Travis tests for the latest release of click versions 4 -> 7 - https://github.com/click-contrib/click-plugins/pull/28

1.0.4

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

- Preemptive fix for a breaking change in Click v7.  CLI command names generated from functions with underscores will have dashes instead of underscores.  See https://github.com/click-contrib/click-plugins/issues/19.

Links

• PyPI: https://pypi.org/project/click-plugins
• Changelog: https://pyup.io/changelogs/click-plugins/
• Repo: https://github.com/click-contrib/click-plugins

Update click from 6.7 to 7.0.

Changelog

7.0

-----------

Released 2018-09-25

-   Drop support for Python 2.6 and 3.3. (`967`_, `976`_)
-   Wrap ``click.Choice``'s missing message. (`202`_, `1000`_)
-   Add native ZSH autocompletion support. (`323`_, `865`_)
-   Document that ANSI color info isn't parsed from bytearrays in
 Python 2. (`334`_)
-   Document byte-stripping behavior of ``CliRunner``. (`334`_,
 `1010`_)
-   Usage errors now hint at the ``--help`` option. (`393`_, `557`_)
-   Implement streaming pager. (`409`_, `889`_)
-   Extract bar formatting to its own method. (`414`_)
-   Add ``DateTime`` type for converting input in given date time
 formats. (`423`_)
-   ``secho``'s first argument can now be ``None``, like in ``echo``.
 (`424`_)
-   Fixes a ``ZeroDivisionError`` in ``ProgressBar.make_step``, when the
 arg passed to the first call of ``ProgressBar.update`` is 0.
 (`447`_, `1012`_)
-   Show progressbar only if total execution time is visible. (`487`_)
-   Added the ability to hide commands and options from help. (`500`_)
-   Document that options can be ``required=True``. (`514`_, `1022`_)
-   Non-standalone calls to ``Context.exit`` return the exit code,
 rather than calling ``sys.exit``. (`533`_, `667`_, `1098`_)
-   ``click.getchar()`` returns Unicode in Python 3 on Windows,
 consistent with other platforms. (`537`_, `821`_, `822`_,
 `1088`_, `1108`_)
-   Added ``FloatRange`` type. (`538`_, `553`_)
-   Added support for bash completion of ``type=click.Choice`` for
 ``Options`` and ``Arguments``. (`535`_, `681`_)
-   Only allow one positional arg for ``Argument`` parameter
 declaration. (`568`_, `574`_, `1014`_)
-   Add ``case_sensitive=False`` as an option to Choice. (`569`_)
-   ``click.getchar()`` correctly raises ``KeyboardInterrupt`` on "^C"
 and ``EOFError`` on "^D" on Linux. (`583`_, `1115`_)
-   Fix encoding issue with ``click.getchar(echo=True)`` on Linux.
 (`1115`_)
-   ``param_hint`` in errors now derived from param itself. (`598`_,
 `704`_, `709`_)
-   Add a test that ensures that when an argument is formatted into a
 usage error, its metavar is used, not its name. (`612`_)
-   Allow setting ``prog_name`` as extra in ``CliRunner.invoke``.
 (`616`_, `999`_)
-   Help text taken from docstrings truncates at the ``\f`` form feed
 character, useful for hiding Sphinx-style parameter documentation.
 (`629`_, `1091`_)
-   ``launch`` now works properly under Cygwin. (`650`_)
-   Update progress after iteration. (`651`_, `706`_)
-   ``CliRunner.invoke`` now may receive ``args`` as a string
 representing a Unix shell command. (`664`_)
-   Make ``Argument.make_metavar()`` default to type metavar. (`675`_)
-   Add documentation for ``ignore_unknown_options``. (`684`_)
-   Add bright colors support for ``click.style`` and fix the reset
 option for parameters ``fg`` and ``bg``. (`703`_, `809`_)
-   Add ``show_envvar`` for showing environment variables in help.
 (`710`_)
-   Avoid ``BrokenPipeError`` during interpreter shutdown when stdout or
 stderr is a closed pipe. (`712`_, `1106`_)
-   Document customizing option names. (`725`_, `1016`_)
-   Disable ``sys._getframes()`` on Python interpreters that don't
 support it. (`728`_)
-   Fix bug in test runner when calling ``sys.exit`` with ``None``.
 (`739`_)
-   Clarify documentation on command line options. (`741`_, `1003`_)
-   Fix crash on Windows console. (`744`_)
-   Fix bug that caused bash completion to give improper completions on
 chained commands. (`754`_, `774`_)
-   Added support for dynamic bash completion from a user-supplied
 callback. (`755`_)
-   Added support for bash completions containing spaces. (`773`_)
-   Allow autocompletion function to determine whether or not to return
 completions that start with the incomplete argument. (`790`_,
 `806`_)
-   Fix option naming routine to match documentation and be
 deterministic. (`793`_, `794`_)
-   Fix path validation bug. (`795`_, `1020`_)
-   Add test and documentation for ``Option`` naming: functionality.
 (`799`_)
-   Update doc to match arg name for ``path_type``. (`801`_)
-   Raw strings added so correct escaping occurs. (`807`_)
-   Fix 16k character limit of ``click.echo`` on Windows. (`816`_,
 `819`_)
-   Overcome 64k character limit when writing to binary stream on
 Windows 7. (`825`_, `830`_)
-   Add bool conversion for "t" and "f". (`842`_)
-   ``NoSuchOption`` errors take ``ctx`` so that ``--help`` hint gets
 printed in error output. (`860`_)
-   Fixed the behavior of Click error messages with regards to Unicode
 on 2.x and 3.x. Message is now always Unicode and the str and
 Unicode special methods work as you expect on that platform.
 (`862`_)
-   Progress bar now uses stderr by default. (`863`_)
-   Add support for auto-completion documentation. (`866`_, `869`_)
-   Allow ``CliRunner`` to separate stdout and stderr. (`868`_)
-   Fix variable precedence. (`873`_, `874`_)
-   Fix invalid escape sequences. (`877`_)
-   Fix ``ResourceWarning`` that occurs during some tests. (`878`_)
-   When detecting a misconfigured locale, don't fail if the ``locale``
 command fails. (`880`_)
-   Add ``case_sensitive=False`` as an option to ``Choice`` types.
 (`887`_)
-   Force stdout/stderr writable. This works around issues with badly
 patched standard streams like those from Jupyter. (`918`_)
-   Fix completion of subcommand options after last argument (`919`_,
 `930`_)
-   ``_AtomicFile`` now uses the ``realpath`` of the original filename
 so that changing the working directory does not affect it.
 (`920`_)
-   Fix incorrect completions when defaults are present (`925`_,
 `930`_)
-   Add copy option attrs so that custom classes can be re-used.
 (`926`_, `994`_)
-   "x" and "a" file modes now use stdout when file is ``"-"``.
 (`929`_)
-   Fix missing comma in ``__all__`` list. (`935`_)
-   Clarify how parameters are named. (`949`_, `1009`_)
-   Stdout is now automatically set to non blocking. (`954`_)
-   Do not set options twice. (`962`_)
-   Move ``fcntl`` import. (`965`_)
-   Fix Google App Engine ``ImportError``. (`995`_)
-   Better handling of help text for dynamic default option values.
 (`996`_)
-   Fix ``get_winter_size()`` so it correctly returns ``(0,0)``.
 (`997`_)
-   Add test case checking for custom param type. (`1001`_)
-   Allow short width to address cmd formatting. (`1002`_)
-   Add details about Python version support. (`1004`_)
-   Added deprecation flag to commands. (`1005`_)
-   Fixed issues where ``fd`` was undefined. (`1007`_)
-   Fix formatting for short help. (`1008`_)
-   Document how ``auto_envvar_prefix`` works with command groups.
 (`1011`_)
-   Don't add newlines by default for progress bars. (`1013`_)
-   Use Python sorting order for ZSH completions. (`1047`_, `1059`_)
-   Document that parameter names are converted to lowercase by default.
 (`1055`_)
-   Subcommands that are named by the function now automatically have
 the underscore replaced with a dash. If you register a function
 named ``my_command`` it becomes ``my-command`` in the command line
 interface.
-   Hide hidden commands and options from completion. (`1058`_,
 `1061`_)
-   Fix absolute import blocking Click from being vendored into a
 project on Windows. (`1068`_, `1069`_)
-   Fix issue where a lowercase ``auto_envvar_prefix`` would not be
 converted to uppercase. (`1105`_)

.. _202: https://github.com/pallets/click/issues/202
.. _323: https://github.com/pallets/click/issues/323
.. _334: https://github.com/pallets/click/issues/334
.. _393: https://github.com/pallets/click/issues/393
.. _409: https://github.com/pallets/click/issues/409
.. _414: https://github.com/pallets/click/pull/414
.. _423: https://github.com/pallets/click/pull/423
.. _424: https://github.com/pallets/click/pull/424
.. _447: https://github.com/pallets/click/issues/447
.. _487: https://github.com/pallets/click/pull/487
.. _500: https://github.com/pallets/click/pull/500
.. _514: https://github.com/pallets/click/issues/514
.. _533: https://github.com/pallets/click/pull/533
.. _535: https://github.com/pallets/click/issues/535
.. _537: https://github.com/pallets/click/issues/537
.. _538: https://github.com/pallets/click/pull/538
.. _553: https://github.com/pallets/click/pull/553
.. _557: https://github.com/pallets/click/pull/557
.. _568: https://github.com/pallets/click/issues/568
.. _569: https://github.com/pallets/click/issues/569
.. _574: https://github.com/pallets/click/issues/574
.. _583: https://github.com/pallets/click/issues/583
.. _598: https://github.com/pallets/click/issues/598
.. _612: https://github.com/pallets/click/pull/612
.. _616: https://github.com/pallets/click/issues/616
.. _629: https://github.com/pallets/click/pull/629
.. _650: https://github.com/pallets/click/pull/650
.. _651: https://github.com/pallets/click/issues/651
.. _664: https://github.com/pallets/click/pull/664
.. _667: https://github.com/pallets/click/issues/667
.. _675: https://github.com/pallets/click/pull/675
.. _681: https://github.com/pallets/click/pull/681
.. _684: https://github.com/pallets/click/pull/684
.. _703: https://github.com/pallets/click/issues/703
.. _704: https://github.com/pallets/click/issues/704
.. _706: https://github.com/pallets/click/pull/706
.. _709: https://github.com/pallets/click/pull/709
.. _710: https://github.com/pallets/click/pull/710
.. _712: https://github.com/pallets/click/pull/712
.. _719: https://github.com/pallets/click/issues/719
.. _725: https://github.com/pallets/click/issues/725
.. _728: https://github.com/pallets/click/pull/728
.. _739: https://github.com/pallets/click/pull/739
.. _741: https://github.com/pallets/click/issues/741
.. _744: https://github.com/pallets/click/issues/744
.. _754: https://github.com/pallets/click/issues/754
.. _755: https://github.com/pallets/click/pull/755
.. _773: https://github.com/pallets/click/pull/773
.. _774: https://github.com/pallets/click/pull/774
.. _790: https://github.com/pallets/click/issues/790
.. _793: https://github.com/pallets/click/issues/793
.. _794: https://github.com/pallets/click/pull/794
.. _795: https://github.com/pallets/click/issues/795
.. _799: https://github.com/pallets/click/pull/799
.. _801: https://github.com/pallets/click/pull/801
.. _806: https://github.com/pallets/click/pull/806
.. _807: https://github.com/pallets/click/pull/807
.. _809: https://github.com/pallets/click/pull/809
.. _816: https://github.com/pallets/click/pull/816
.. _819: https://github.com/pallets/click/pull/819
.. _821: https://github.com/pallets/click/issues/821
.. _822: https://github.com/pallets/click/issues/822
.. _825: https://github.com/pallets/click/issues/825
.. _830: https://github.com/pallets/click/pull/830
.. _842: https://github.com/pallets/click/pull/842
.. _860: https://github.com/pallets/click/issues/860
.. _862: https://github.com/pallets/click/issues/862
.. _863: https://github.com/pallets/click/pull/863
.. _865: https://github.com/pallets/click/pull/865
.. _866: https://github.com/pallets/click/issues/866
.. _868: https://github.com/pallets/click/pull/868
.. _869: https://github.com/pallets/click/pull/869
.. _873: https://github.com/pallets/click/issues/873
.. _874: https://github.com/pallets/click/pull/874
.. _877: https://github.com/pallets/click/pull/877
.. _878: https://github.com/pallets/click/pull/878
.. _880: https://github.com/pallets/click/pull/880
.. _883: https://github.com/pallets/click/pull/883
.. _887: https://github.com/pallets/click/pull/887
.. _889: https://github.com/pallets/click/pull/889
.. _918: https://github.com/pallets/click/pull/918
.. _919: https://github.com/pallets/click/issues/919
.. _920: https://github.com/pallets/click/pull/920
.. _925: https://github.com/pallets/click/issues/925
.. _926: https://github.com/pallets/click/issues/926
.. _929: https://github.com/pallets/click/pull/929
.. _930: https://github.com/pallets/click/pull/930
.. _935: https://github.com/pallets/click/pull/935
.. _949: https://github.com/pallets/click/issues/949
.. _954: https://github.com/pallets/click/pull/954
.. _962: https://github.com/pallets/click/pull/962
.. _965: https://github.com/pallets/click/pull/965
.. _967: https://github.com/pallets/click/pull/967
.. _976: https://github.com/pallets/click/pull/976
.. _990: https://github.com/pallets/click/pull/990
.. _991: https://github.com/pallets/click/pull/991
.. _993: https://github.com/pallets/click/pull/993
.. _994: https://github.com/pallets/click/pull/994
.. _995: https://github.com/pallets/click/pull/995
.. _996: https://github.com/pallets/click/pull/996
.. _997: https://github.com/pallets/click/pull/997
.. _999: https://github.com/pallets/click/pull/999
.. _1000: https://github.com/pallets/click/pull/1000
.. _1001: https://github.com/pallets/click/pull/1001
.. _1002: https://github.com/pallets/click/pull/1002
.. _1003: https://github.com/pallets/click/pull/1003
.. _1004: https://github.com/pallets/click/pull/1004
.. _1005: https://github.com/pallets/click/pull/1005
.. _1007: https://github.com/pallets/click/pull/1007
.. _1008: https://github.com/pallets/click/pull/1008
.. _1009: https://github.com/pallets/click/pull/1009
.. _1010: https://github.com/pallets/click/pull/1010
.. _1011: https://github.com/pallets/click/pull/1011
.. _1012: https://github.com/pallets/click/pull/1012
.. _1013: https://github.com/pallets/click/pull/1013
.. _1014: https://github.com/pallets/click/pull/1014
.. _1016: https://github.com/pallets/click/pull/1016
.. _1020: https://github.com/pallets/click/pull/1020
.. _1022: https://github.com/pallets/click/pull/1022
.. _1027: https://github.com/pallets/click/pull/1027
.. _1047: https://github.com/pallets/click/pull/1047
.. _1055: https://github.com/pallets/click/pull/1055
.. _1058: https://github.com/pallets/click/pull/1058
.. _1059: https://github.com/pallets/click/pull/1059
.. _1061: https://github.com/pallets/click/pull/1061
.. _1068: https://github.com/pallets/click/issues/1068
.. _1069: https://github.com/pallets/click/pull/1069
.. _1088: https://github.com/pallets/click/issues/1088
.. _1091: https://github.com/pallets/click/pull/1091
.. _1098: https://github.com/pallets/click/pull/1098
.. _1105: https://github.com/pallets/click/pull/1105
.. _1106: https://github.com/pallets/click/pull/1106
.. _1108: https://github.com/pallets/click/pull/1108
.. _1115: https://github.com/pallets/click/pull/1115

Links

• PyPI: https://pypi.org/project/click
• Changelog: https://pyup.io/changelogs/click/
• Homepage: https://palletsprojects.com/p/click/

Update coverage from 4.5.1 to 4.5.3.

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

Links

• PyPI: https://pypi.org/project/coverage
• Changelog: https://pyup.io/changelogs/coverage/
• Repo: https://github.com/nedbat/coveragepy

Update kiwisolver from 1.0.1 to 1.1.0.

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

Links

• PyPI: https://pypi.org/project/kiwisolver
• Repo: https://github.com/nucleic/kiwi

Update matplotlib from 3.0.0 to 3.1.0.

Changelog

Links

• PyPI: https://pypi.org/project/matplotlib
• Changelog: https://pyup.io/changelogs/matplotlib/
• Homepage: https://matplotlib.org

Update numpy from 1.15.2 to 1.16.4.

Changelog

1.16.4

==========================

The NumPy 1.16.4 release fixes bugs reported against the 1.16.3 release, and
also backports several enhancements from master that seem appropriate for a
release series that is the last to support Python 2.7. The wheels on PyPI are
linked with OpenBLAS v0.3.7-dev, which should fix issues on Skylake series
cpus.

Downstream developers building this release should use Cython >= 0.29.2 and,
if using OpenBLAS, OpenBLAS > v0.3.7. The supported Python versions are 2.7 and
3.5-3.7.


New deprecations
================
Writeable flag of C-API wrapped arrays
--------------------------------------
When an array is created from the C-API to wrap a pointer to data, the only
indication we have of the read-write nature of the data is the ``writeable``
flag set during creation. It is dangerous to force the flag to writeable.  In
the future it will not be possible to switch the writeable flag to ``True``
from python.  This deprecation should not affect many users since arrays
created in such a manner are very rare in practice and only available through
the NumPy C-API.


Compatibility notes
===================

Potential changes to the random stream
--------------------------------------
Due to bugs in the application of log to random floating point numbers,
the stream may change when sampling from ``np.random.beta``, ``np.random.binomial``,
``np.random.laplace``, ``np.random.logistic``, ``np.random.logseries`` or
``np.random.multinomial`` if a 0 is generated in the underlying MT19937 random stream.
There is a 1 in :math:`10^{53}` chance of this occurring, and so the probability that
the stream changes for any given seed is extremely small. If a 0 is encountered in the
underlying generator, then the incorrect value produced (either ``np.inf``
or ``np.nan``) is now dropped.


Changes
=======

`numpy.lib.recfunctions.structured_to_unstructured` does not squeeze single-field views
---------------------------------------------------------------------------------------
Previously ``structured_to_unstructured(arr[['a']])`` would produce a squeezed
result inconsistent with ``structured_to_unstructured(arr[['a', b']])``. This
was accidental. The old behavior can be retained with
``structured_to_unstructured(arr[['a']]).squeeze(axis=-1)`` or far more simply,
``arr['a']``.


Contributors
============

A total of 10 people contributed to this release.  People with a "+" by their
names contributed a patch for the first time.

* Charles Harris
* Eric Wieser
* Dennis Zollo +
* Hunter Damron +
* Jingbei Li +
* Kevin Sheppard
* Matti Picus
* Nicola Soranzo +
* Sebastian Berg
* Tyler Reddy


Pull requests merged
====================

A total of 16 pull requests were merged for this release.

* `13392 <https://github.com/numpy/numpy/pull/13392>`__: BUG: Some PyPy versions lack PyStructSequence_InitType2.
* `13394 <https://github.com/numpy/numpy/pull/13394>`__: MAINT, DEP: Fix deprecated ``assertEquals()``
* `13396 <https://github.com/numpy/numpy/pull/13396>`__: BUG: Fix structured_to_unstructured on single-field types (backport)
* `13549 <https://github.com/numpy/numpy/pull/13549>`__: BLD: Make CI pass again with pytest 4.5
* `13552 <https://github.com/numpy/numpy/pull/13552>`__: TST: Register markers in conftest.py.
* `13559 <https://github.com/numpy/numpy/pull/13559>`__: BUG: Removes ValueError for empty kwargs in arraymultiter_new
* `13560 <https://github.com/numpy/numpy/pull/13560>`__: BUG: Add TypeError to accepted exceptions in crackfortran.
* `13561 <https://github.com/numpy/numpy/pull/13561>`__: BUG: Handle subarrays in descr_to_dtype
* `13562 <https://github.com/numpy/numpy/pull/13562>`__: BUG: Protect generators from log(0.0)
* `13563 <https://github.com/numpy/numpy/pull/13563>`__: BUG: Always return views from structured_to_unstructured when...
* `13564 <https://github.com/numpy/numpy/pull/13564>`__: BUG: Catch stderr when checking compiler version
* `13565 <https://github.com/numpy/numpy/pull/13565>`__: BUG: longdouble(int) does not work
* `13587 <https://github.com/numpy/numpy/pull/13587>`__: BUG: distutils/system_info.py fix missing subprocess import (13523)
* `13620 <https://github.com/numpy/numpy/pull/13620>`__: BUG,DEP: Fix writeable flag setting for arrays without base
* `13641 <https://github.com/numpy/numpy/pull/13641>`__: MAINT: Prepare for the 1.16.4 release.
* `13644 <https://github.com/numpy/numpy/pull/13644>`__: BUG: special case object arrays when printing rel-, abs-error


==========================

1.16.3

==========================

The NumPy 1.16.3 release fixes bugs reported against the 1.16.2 release, and
also backports several enhancements from master that seem appropriate for a
release series that is the last to support Python 2.7. The wheels on PyPI are
linked with OpenBLAS v0.3.4+,  which should fix the known threading issues
found in previous OpenBLAS versions.

Downstream developers building this release should use Cython >= 0.29.2 and,
if using OpenBLAS, OpenBLAS > v0.3.4.

The most noticeable change in this release is that unpickling object arrays
when loading ``*.npy`` or ``*.npz`` files now requires an explicit opt-in.
This backwards incompatible change was made in response to
`CVE-2019-6446 <https://nvd.nist.gov/vuln/detail/CVE-2019-6446>`_.


Compatibility notes
===================

Unpickling while loading requires explicit opt-in
-------------------------------------------------
The functions ``np.load``, and ``np.lib.format.read_array`` take an
`allow_pickle` keyword which now defaults to ``False`` in response to
`CVE-2019-6446 <https://nvd.nist.gov/vuln/detail/CVE-2019-6446>`_.


Improvements
============

Covariance in `random.mvnormal` cast to double
----------------------------------------------
This should make the tolerance used when checking the singular values of the
covariance matrix more meaningful.


Changes
=======

``__array_interface__`` offset now works as documented
------------------------------------------------------
The interface may use an ``offset`` value that was previously mistakenly
ignored.



==========================

1.16.2

==========================

NumPy 1.16.2 is a quick release fixing several problems encountered on Windows.
The Python versions supported are 2.7 and 3.5-3.7. The Windows problems
addressed are:

- DLL load problems for NumPy wheels on Windows,
- distutils command line parsing on Windows.

There is also a regression fix correcting signed zeros produced by divmod, see
below for details.

Downstream developers building this release should use Cython >= 0.29.2 and, if
using OpenBLAS, OpenBLAS > v0.3.4.

If you are installing using pip, you may encounter a problem with older
installed versions of NumPy that pip did not delete becoming mixed with the
current version, resulting in an ``ImportError``. That problem is particularly
common on Debian derived distributions due to a modified pip.  The fix is to
make sure all previous NumPy versions installed by pip have been removed. See
`12736 <https://github.com/numpy/numpy/issues/12736>`__ for discussion of the
issue.


Compatibility notes
===================

Signed zero when using divmod
-----------------------------
Starting in version 1.12.0, numpy incorrectly returned a negatively signed zero
when using the ``divmod`` and ``floor_divide`` functions when the result was
zero. For example::

>>> np.zeros(10)//1
array([-0., -0., -0., -0., -0., -0., -0., -0., -0., -0.])

With this release, the result is correctly returned as a positively signed
zero::

>>> np.zeros(10)//1
array([0., 0., 0., 0., 0., 0., 0., 0., 0., 0.])


Contributors
============

A total of 5 people contributed to this release.  People with a "+" by their
names contributed a patch for the first time.

* Charles Harris
* Eric Wieser
* Matti Picus
* Tyler Reddy
* Tony LaTorre +


Pull requests merged
====================

A total of 7 pull requests were merged for this release.

* `12909 <https://github.com/numpy/numpy/pull/12909>`__: TST: fix vmImage dispatch in Azure
* `12923 <https://github.com/numpy/numpy/pull/12923>`__: MAINT: remove complicated test of multiarray import failure mode
* `13020 <https://github.com/numpy/numpy/pull/13020>`__: BUG: fix signed zero behavior in npy_divmod
* `13026 <https://github.com/numpy/numpy/pull/13026>`__: MAINT: Add functions to parse shell-strings in the platform-native...
* `13028 <https://github.com/numpy/numpy/pull/13028>`__: BUG: Fix regression in parsing of F90 and F77 environment variables
* `13038 <https://github.com/numpy/numpy/pull/13038>`__: BUG: parse shell escaping in extra_compile_args and extra_link_args
* `13041 <https://github.com/numpy/numpy/pull/13041>`__: BLD: Windows absolute path DLL loading


=========================

1.16.1

==========================

The NumPy 1.16.1 release fixes bugs reported against the 1.16.0 release, and
also backports several enhancements from master that seem appropriate for a
release series that is the last to support Python 2.7. The wheels on PyPI are
linked with OpenBLAS v0.3.4+,  which should fix the known threading issues
found in previous OpenBLAS versions.

Downstream developers building this release should use Cython >= 0.29.2 and, if
using OpenBLAS, OpenBLAS > v0.3.4.

If you are installing using pip, you may encounter a problem with older
installed versions of NumPy that pip did not delete becoming mixed with the
current version, resulting in an ``ImportError``. That problem is particularly
common on Debian derived distributions due to a modified pip.  The fix is to
make sure all previous NumPy versions installed by pip have been removed. See
`12736 <https://github.com/numpy/numpy/issues/12736>`__ for discussion of the
issue. Note that previously this problem resulted in an ``AttributeError``.


Contributors
============

A total of 16 people contributed to this release.  People with a "+" by their
names contributed a patch for the first time.

* Antoine Pitrou
* Arcesio Castaneda Medina +
* Charles Harris
* Chris Markiewicz +
* Christoph Gohlke
* Christopher J. Markiewicz +
* Daniel Hrisca +
* EelcoPeacs +
* Eric Wieser
* Kevin Sheppard
* Matti Picus
* OBATA Akio +
* Ralf Gommers
* Sebastian Berg
* Stephan Hoyer
* Tyler Reddy


Enhancements
============

* `12767 <https://github.com/numpy/numpy/pull/12767>`__: ENH: add mm->q floordiv
* `12768 <https://github.com/numpy/numpy/pull/12768>`__: ENH: port np.core.overrides to C for speed
* `12769 <https://github.com/numpy/numpy/pull/12769>`__: ENH: Add np.ctypeslib.as_ctypes_type(dtype), improve `np.ctypeslib.as_ctypes`
* `12773 <https://github.com/numpy/numpy/pull/12773>`__: ENH: add "max difference" messages to np.testing.assert_array_equal...
* `12820 <https://github.com/numpy/numpy/pull/12820>`__: ENH: Add mm->qm divmod
* `12890 <https://github.com/numpy/numpy/pull/12890>`__: ENH: add _dtype_ctype to namespace for freeze analysis


Compatibility notes
===================

* The changed error message emited by array comparison testing functions may
affect doctests. See below for detail.

* Casting from double and single denormals to float16 has been corrected.  In
some rare cases, this may result in results being rounded up instead of down,
changing the last bit (ULP) of the result.


New Features
============

divmod operation is now supported for two ``timedelta64`` operands
------------------------------------------------------------------
The divmod operator now handles two ``np.timedelta64`` operands, with
type signature ``mm->qm``.


Improvements
============

Further improvements to ``ctypes`` support in ``np.ctypeslib``
--------------------------------------------------------------
A new `numpy.ctypeslib.as_ctypes_type` function has been added, which can be
used to converts a `dtype` into a best-guess `ctypes` type. Thanks to this
new function, `numpy.ctypeslib.as_ctypes` now supports a much wider range of
array types, including structures, booleans, and integers of non-native
endianness.

Array comparison assertions include maximum differences
-------------------------------------------------------
Error messages from array comparison tests such as
`np.testing.assert_allclose` now include "max absolute difference" and
"max relative difference," in addition to the previous "mismatch" percentage.
This information makes it easier to update absolute and relative error
tolerances.


Changes
=======

``timedelta64 % 0`` behavior adjusted to return ``NaT``
-------------------------------------------------------
The modulus operation with two ``np.timedelta64`` operands now returns
``NaT`` in the case of division by zero, rather than returning zero





==========================

1.16.0

==========================

This NumPy release is the last one to support Python 2.7 and will be maintained
as a long term release with bug fixes until 2020.  Support for Python 3.4 been
dropped, the supported Python versions are 2.7 and 3.5-3.7. The wheels on PyPI
are linked with OpenBLAS v0.3.4+,  which should fix the known threading issues
found in previous OpenBLAS versions.

Downstream developers building this release should use Cython >= 0.29 and, if
using OpenBLAS, OpenBLAS > v0.3.4.

This release has seen a lot of refactoring and features many bug fixes, improved
code organization, and better cross platform compatibility. Not all of these
improvements will be visible to users, but they should help make maintenance
easier going forward.


Highlights
==========

* Experimental (opt-in only) support for overriding numpy functions,
see ``__array_function__`` below.

* The ``matmul`` function is now a ufunc. This provides better
performance and allows overriding with ``__array_ufunc__``.

* Improved support for the ARM and POWER architectures.

* Improved support for AIX and PyPy.

* Improved interop with ctypes.

* Improved support for PEP 3118.



New functions
=============

* New functions added to the `numpy.lib.recfuntions` module to ease the
structured assignment changes:

 * ``assign_fields_by_name``
 * ``structured_to_unstructured``
 * ``unstructured_to_structured``
 * ``apply_along_fields``
 * ``require_fields``

See the user guide at <https://docs.scipy.org/doc/numpy/user/basics.rec.html>
for more info.


New deprecations
================

* The type dictionaries `numpy.core.typeNA` and `numpy.core.sctypeNA` are
deprecated. They were buggy and not documented and will be removed in the
1.18 release. Use`numpy.sctypeDict` instead.

* The `numpy.asscalar` function is deprecated. It is an alias to the more
powerful `numpy.ndarray.item`, not tested, and fails for scalars.

* The `numpy.set_array_ops` and `numpy.get_array_ops` functions are deprecated.
As part of `NEP 15`, they have been deprecated along with the C-API functions
:c:func:`PyArray_SetNumericOps` and :c:func:`PyArray_GetNumericOps`. Users
who wish to override the inner loop functions in built-in ufuncs should use
:c:func:`PyUFunc_ReplaceLoopBySignature`.

* The `numpy.unravel_index` keyword argument ``dims`` is deprecated, use
``shape`` instead.

* The `numpy.histogram` ``normed`` argument is deprecated.  It was deprecated
previously, but no warning was issued.

* The ``positive`` operator (``+``) applied to non-numerical arrays is
deprecated. See below for details.

* Passing an iterator to the stack functions is deprecated


Expired deprecations
====================

* NaT comparisons now return ``False`` without a warning, finishing a
deprecation cycle begun in NumPy 1.11.

* ``np.lib.function_base.unique`` was removed, finishing a deprecation cycle
begun in NumPy 1.4. Use `numpy.unique` instead.

* multi-field indexing now returns views instead of copies, finishing a
deprecation cycle begun in NumPy 1.7. The change was previously attempted in
NumPy 1.14 but reverted until now.

* ``np.PackageLoader`` and ``np.pkgload`` have been removed. These were
deprecated in 1.10, had no tests, and seem to no longer work in 1.15.


Future changes
==============

* NumPy 1.17 will drop support for Python 2.7.


Compatibility notes
===================

f2py script on Windows
----------------------
On Windows, the installed script for running f2py is now an ``.exe`` file
rather than a ``*.py`` file and should be run from the command line as ``f2py``
whenever the ``Scripts`` directory is in the path. Running ``f2py`` as a module
``python -m numpy.f2py [...]`` will work without path modification in any
version of NumPy.

NaT comparisons
---------------
Consistent with the behavior of NaN, all comparisons other than inequality
checks with datetime64 or timedelta64 NaT ("not-a-time") values now always
return ``False``, and inequality checks with NaT now always return ``True``.
This includes comparisons beteween NaT values. For compatibility with the
old behavior, use ``np.isnat`` to explicitly check for NaT or convert
datetime64/timedelta64 arrays with ``.astype(np.int64)`` before making
comparisons.

complex64/128 alignment has changed
-----------------------------------
The memory alignment of complex types is now the same as a C-struct composed of
two floating point values, while before it was equal to the size of the type.
For many users (for instance on x64/unix/gcc) this means that complex64 is now
4-byte aligned instead of 8-byte aligned. An important consequence is that
aligned structured dtypes may now have a different size. For instance,
``np.dtype('c8,u1', align=True)`` used to have an itemsize of 16 (on x64/gcc)
but now it is 12.

More in detail, the complex64 type now has the same alignment as a C-struct
``struct {float r, i;}``, according to the compiler used to compile numpy, and
similarly for the complex128 and complex256 types.

nd_grid __len__ removal
-----------------------
``len(np.mgrid)`` and ``len(np.ogrid)`` are now considered nonsensical
and raise a ``TypeError``.

``np.unravel_index`` now accepts ``shape`` keyword argument
-----------------------------------------------------------
Previously, only the ``dims`` keyword argument was accepted
for specification of the shape of the array to be used
for unraveling. ``dims`` remains supported, but is now deprecated.

multi-field views return a view instead of a copy
-------------------------------------------------
Indexing a structured array with multiple fields, e.g., ``arr[['f1', 'f3']]``,
returns a view into the original array instead of a copy. The returned view
will often have extra padding bytes corresponding to intervening fields in the
original array, unlike before, which will affect code such as
``arr[['f1', 'f3']].view('float64')``. This change has been planned since numpy
1.7. Operations hitting this path have emitted ``FutureWarnings`` since then.
Additional ``FutureWarnings`` about this change were added in 1.12.

To help users update their code to account for these changes, a number of
functions have been added to the ``numpy.lib.recfunctions`` module which
safely allow such operations. For instance, the code above can be replaced
with ``structured_to_unstructured(arr[['f1', 'f3']], dtype='float64')``.
See the "accessing multiple fields" section of the
`user guide <https://docs.scipy.org/doc/numpy/user/basics.rec.htmlaccessing-multiple-fields>`__.


C API changes
=============

The :c:data:`NPY_API_VERSION` was incremented to 0x0000D, due to the addition
of:

* :c:member:`PyUFuncObject.core_dim_flags`
* :c:member:`PyUFuncObject.core_dim_sizes`
* :c:member:`PyUFuncObject.identity_value`
* :c:func:`PyUFunc_FromFuncAndDataAndSignatureAndIdentity`


New Features
============

Integrated squared error (ISE) estimator added to ``histogram``
---------------------------------------------------------------
This method (``bins='stone'``) for optimizing the bin number is a
generalization of the Scott's rule. The Scott's rule assumes the distribution
is approximately Normal, while the ISE_ is a non-parametric method based on
cross-validation.

.. _ISE: https://en.wikipedia.org/wiki/HistogramMinimizing_cross-validation_estimated_squared_error

``max_rows`` keyword added for ``np.loadtxt``
---------------------------------------------
New keyword ``max_rows`` in `numpy.loadtxt` sets the maximum rows of the
content to be read after ``skiprows``, as in `numpy.genfromtxt`.

modulus operator support added for ``np.timedelta64`` operands
--------------------------------------------------------------
The modulus (remainder) operator is now supported for two operands
of type ``np.timedelta64``. The operands may have different units
and the return value will match the type of the operands.


Improvements
============

no-copy pickling of numpy arrays
--------------------------------
Up to protocol 4, numpy array pickling created 2 spurious copies of the data
being serialized.  With pickle protocol 5, and the ``PickleBuffer`` API, a
large variety of numpy arrays can now be serialized without any copy using
out-of-band buffers, and with one less copy using in-band buffers. This
results, for large arrays, in an up to 66% drop in peak memory usage.

build shell independence
------------------------
NumPy builds should no longer interact with the host machine
shell directly. ``exec_command`` has been replaced with
``subprocess.check_output`` where appropriate.

`np.polynomial.Polynomial` classes render in LaTeX in Jupyter notebooks
-----------------------------------------------------------------------
When used in a front-end that supports it, `Polynomial` instances are now
rendered through LaTeX. The current format is experimental, and is subject to
change.

``randint`` and ``choice`` now work on empty distributions
----------------------------------------------------------
Even when no elements needed to be drawn, ``np.random.randint`` and
``np.random.choice`` raised an error when the arguments described an empty
distribution. This has been fixed so that e.g.
``np.random.choice([], 0) == np.array([], dtype=float64)``.

``linalg.lstsq``, ``linalg.qr``, and ``linalg.svd`` now work with empty arrays
------------------------------------------------------------------------------
Previously, a ``LinAlgError`` would be raised when an empty matrix/empty
matrices (with zero rows and/or columns) is/are passed in. Now outputs of
appropriate shapes are returned.

Chain exceptions to give better error messages for invalid PEP3118 format strings
---------------------------------------------------------------------------------
This should help track down problems.

Einsum optimization path updates and efficiency improvements
------------------------------------------------------------
Einsum was synchronized with the current upstream work.

`numpy.angle` and `numpy.expand_dims` now work on ``ndarray`` subclasses
------------------------------------------------------------------------
In particular, they now work for masked arrays.

``NPY_NO_DEPRECATED_API`` compiler warning suppression
------------------------------------------------------
Setting ``NPY_NO_DEPRECATED_API`` to a value of 0 will suppress the current compiler
warnings when the deprecated numpy API is used.

``np.diff`` Added kwargs prepend and append
-------------------------------------------
New kwargs ``prepend`` and ``append``, allow for values to be inserted on
either end of the differences.  Similar to options for `ediff1d`. Now the
inverse of `cumsum` can be obtained easily via ``prepend=0``.

ARM support updated
-------------------
Support for ARM CPUs has been updated to accommodate 32 and 64 bit targets,
and also big and little endian byte ordering. AARCH32 memory alignment issues
have been addressed. CI testing has been expanded to include AARCH64 targets
via the services of shippable.com.

Appending to build flags
------------------------
`numpy.distutils` has always overridden rather than appended to `LDFLAGS` and
other similar such environment variables for compiling Fortran extensions.
Now, if the `NPY_DISTUTILS_APPEND_FLAGS` environment variable is set to 1, the
behavior will be appending.  This applied to: `LDFLAGS`, `F77FLAGS`,
`F90FLAGS`, `FREEFLAGS`, `FOPT`, `FDEBUG`, and `FFLAGS`.  See gh-11525 for more
details.

Generalized ufunc signatures now allow fixed-size dimensions
------------------------------------------------------------
By using a numerical value in the signature of a generalized ufunc, one can
indicate that the given function requires input or output to have dimensions
with the given size. E.g., the signature of a function that converts a polar
angle to a two-dimensional cartesian unit vector would be ``()->(2)``; that
for one that converts two spherical angles to a three-dimensional unit vector
would be ``(),()->(3)``; and that for the cross product of two
three-dimensional vectors would be ``(3),(3)->(3)``.

Note that to the elementary function these dimensions are not treated any
differently from variable ones indicated with a name starting with a letter;
the loop still is passed the corresponding size, but it can now count on that
size being equal to the fixed one given in the signature.

Generalized ufunc signatures now allow flexible dimensions
----------------------------------------------------------
Some functions, in particular numpy's implementation of ` as ``matmul``,
are very similar to generalized ufuncs in that they operate over core
dimensions, but one could not present them as such because they were able to
deal with inputs in which a dimension is missing. To support this, it is now
allowed to postfix a dimension name with a question mark to indicate that the
dimension does not necessarily have to be present.

With this addition, the signature for ``matmul`` can be expressed as
``(m?,n),(n,p?)->(m?,p?)``.  This indicates that if, e.g., the second operand
has only one dimension, for the purposes of the elementary function it will be
treated as if that input has core shape ``(n, 1)``, and the output has the
corresponding core shape of ``(m, 1)``. The actual output array, however, has
the flexible dimension removed, i.e., it will have shape ``(..., m)``.
Similarly, if both arguments have only a single dimension, the inputs will be
presented as having shapes ``(1, n)`` and ``(n, 1)`` to the elementary
function, and the output as ``(1, 1)``, while the actual output array returned
will have shape ``()``. In this way, the signature allows one to use a
single elementary function for four related but different signatures,
``(m,n),(n,p)->(m,p)``, ``(n),(n,p)->(p)``, ``(m,n),(n)->(m)`` and
``(n),(n)->()``.

``np.clip`` and the ``clip`` method check for memory overlap
------------------------------------------------------------
The ``out`` argument to these functions is now always tested for memory overlap
to avoid corrupted results when memory overlap occurs.

New value ``unscaled`` for option ``cov`` in ``np.polyfit``
-----------------------------------------------------------
A further possible value has been added to the ``cov`` parameter of the
``np.polyfit`` function. With ``cov='unscaled'`` the scaling of the covariance
matrix is disabled completely (similar to setting ``absolute_sigma=True`` in
``scipy.optimize.curve_fit``). This would be useful in occasions, where the
weights are given by 1/sigma with sigma being the (known) standard errors of
(Gaussian distributed) data points, in which case the unscaled matrix is
already a correct estimate for the covariance matrix.

Detailed docstrings for scalar numeric types
--------------------------------------------
The ``help`` function, when applied to numeric types such as `numpy.intc`,
`numpy.int_`, and `numpy.longlong`, now lists all of the aliased names for that
type, distinguishing between platform -dependent and -independent aliases.

``__module__`` attribute now points to public modules
-----------------------------------------------------
The ``__module__`` attribute on most NumPy functions has been updated to refer
to the preferred public module from which to access a function, rather than
the module in which the function happens to be defined. This produces more
informative displays for functions in tools such as IPython, e.g., instead of
``<function 'numpy.core.fromnumeric.sum'>`` you now see
``<function 'numpy.sum'>``.

Large allocations marked as suitable for transparent hugepages
--------------------------------------------------------------
On systems that support transparent hugepages over the madvise system call
numpy now marks that large memory allocations can be backed by hugepages which
reduces page fault overhead and can in some fault heavy cases improve
performance significantly. On Linux the setting for huge pages to be used,
`/sys/kernel/mm/transparent_hugepage/enabled`, must be at least `madvise`.
Systems which already have it set to `always` will not see much difference as
the kernel will automatically use huge pages where appropriate.

Users of very old Linux kernels (~3.x and older) should make sure that
`/sys/kernel/mm/transparent_hugepage/defrag` is not set to `always` to avoid
performance problems due concurrency issues in the memory defragmentation.

Alpine Linux (and other musl c library distros) support
-------------------------------------------------------
We now default to use `fenv.h` for floating point status error reporting.
Previously we had a broken default that sometimes would not report underflow,
overflow, and invalid floating point operations. Now we can support non-glibc
distrubutions like Alpine Linux as long as they ship `fenv.h`.

Speedup ``np.block`` for large arrays
-------------------------------------
Large arrays (greater than ``512 * 512``) now use a blocking algorithm based on
copying the data directly into the appropriate slice of the resulting array.
This results in significant speedups for these large arrays, particularly for
arrays being blocked along more than 2 dimensions.

``arr.ctypes.data_as(...)`` holds a reference to arr
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Previously the caller was responsible for keeping the array alive for the
lifetime of the pointer.

Speedup ``np.take`` for read-only arrays
----------------------------------------
The implementation of ``np.take`` no longer makes an unnecessary copy of the
source array when its ``writeable`` flag is set to ``False``.

Support path-like objects for more functions
--------------------------------------------
The ``np.core.records.fromfile`` function now supports ``pathlib.Path``
and other path-like objects in addition to a file object. Furthermore, the
``np.load`` function now also supports path-like objects when using memory
mapping (``mmap_mode`` keyword argument).

Better behaviour of ufunc identities during reductions
------------------------------------------------------
Universal functions have an ``.identity`` which is used when ``.reduce`` is
called on an empty axis.

As of this release, the logical binary ufuncs, `logical_and`, `logical_or`,
and `logical_xor`, now have ``identity`` s of type `bool`, where previously they
were of type `int`. This restores the 1.14 behavior of getting ``bool`` s when
reducing empty object arrays with these ufuncs, while also keeping the 1.15
behavior of getting ``int`` s when reducing empty object arrays with arithmetic
ufuncs like ``add`` and ``multiply``.

Additionally, `logaddexp` now has an identity of ``-inf``, allowing it to be
called on empty sequences, where previously it could not be.

This is possible thanks to the new
:c:func:`PyUFunc_FromFuncAndDataAndSignatureAndIdentity`, which allows
arbitrary values to be used as identities now.

Improved conversion from ctypes objects
---------------------------------------
Numpy has always supported taking a value or type from ``ctypes`` and
converting it into an array or dtype, but only behaved correctly for simpler
types. As of this release, this caveat is lifted - now:

* The ``_pack_`` attribute of ``ctypes.Structure``, used to emulate C's
``__attribute__((packed))``, is respected.
* Endianness of all ctypes objects is preserved
* ``ctypes.Union`` is supported
* Non-representable constructs raise exceptions, rather than producing
dangerously incorrect results:

* Bitfields are no longer interpreted as sub-arrays
* Pointers are no longer replaced with the type that they point to

A new ``ndpointer.contents`` member
-----------------------------------
This matches the ``.contents`` member of normal ctypes arrays, and can be used
to construct an ``np.array`` around the pointers contents.  This replaces
``np.array(some_nd_pointer)``, which stopped working in 1.15.  As a side effect
of this change, ``ndpointer`` now supports dtypes with overlapping fields and
padding.

``matmul`` is now a ``ufunc``
-----------------------------
`numpy.matmul` is now a ufunc which means that both the function and the
``__matmul__`` operator can now be overridden by ``__array_ufunc__``. Its
implementation has also changed. It uses the same BLAS routines as
`numpy.dot`, ensuring its performance is similar for large matrices.

Start and stop arrays for ``linspace``, ``logspace`` and ``geomspace``
----------------------------------------------------------------------
These functions used to be limited to scalar stop and start values, but can
now take arrays, which will be properly broadcast and result in an output
which has one axis prepended.  This can be used, e.g., to obtain linearly
interpolated points between sets of points.

CI extended with additional services
------------------------------------
We now use additional free CI services, thanks to the companies that provide:

* Codecoverage testing via codecov.io
* Arm testing via shippable.com
* Additional test runs on azure pipelines

These are in addition to our continued use of travis, appveyor (for wheels) and
LGTM


Changes
=======

Comparison ufuncs will now error rather than return NotImplemented
------------------------------------------------------------------
Previously, comparison ufuncs such as ``np.equal`` would return
`NotImplemented` if their arguments had structured dtypes, to help comparison
operators such as ``__eq__`` deal with those.  This is no longer needed, as the
relevant logic has moved to the comparison operators proper (which thus do
continue to return `NotImplemented` as needed). Hence, like all other ufuncs,
the comparison ufuncs will now error on structured dtypes.

Positive will now raise a deprecation warning for non-numerical arrays
----------------------------------------------------------------------
Previously, ``+array`` unconditionally returned a copy. Now, it will
raise a ``DeprecationWarning`` if the array is not numerical (i.e.,
if ``np.positive(array)`` raises a ``TypeError``. For ``ndarray``
subclasses that override the default ``__array_ufunc__`` implementation,
the ``TypeError`` is passed on.

``NDArrayOperatorsMixin`` now implements matrix multiplication
--------------------------------------------------------------
Previously, ``np.lib.mixins.NDArrayOperatorsMixin`` did not implement the
special methods for Python's matrix multiplication operator (`). This has
changed now that ``matmul`` is a ufunc and can be overridden using
``__array_ufunc__``.

The scaling of the covariance matrix in ``np.polyfit`` is different
-------------------------------------------------------------------
So far, ``np.polyfit`` used a non-standard factor in the scaling of the the
covariance matrix. Namely, rather than using the standard ``chisq/(M-N)``, it
scaled it with ``chisq/(M-N-2)`` where M is the number of data points and N is the
number of parameters.  This scaling is inconsistent with other fitting programs
such as e.g. ``scipy.optimize.curve_fit`` and was changed to ``chisq/(M-N)``.

``maximum`` and ``minimum`` no longer emit warnings
---------------------------------------------------
As part of code introduced in 1.10,  ``float32`` and ``float64`` set invalid
float status when a Nan is encountered in `numpy.maximum` and `numpy.minimum`,
when using SSE2 semantics. This caused a `RuntimeWarning` to sometimes be
emitted. In 1.15 we fixed the inconsistencies which caused the warnings to
become more conspicuous. Now no warnings will be emitted.

Umath and multiarray c-extension modules merged into a single module
--------------------------------------------------------------------
The two modules were merged, according to `NEP 15`_. Previously `np.core.umath`
and `np.core.multiarray` were seperate c-extension modules. They are now python
wrappers to the single `np.core/_multiarray_math` c-extension module.

.. _`NEP 15` : http://www.numpy.org/neps/nep-0015-merge-multiarray-umath.html

``getfield`` validity checks extended
-------------------------------------
`numpy.ndarray.getfield` now checks the dtype and offset arguments to prevent
accessing invalid memory locations.

NumPy functions now support overrides with ``__array_function__``
-----------------------------------------------------------------
NumPy has a new experimental mechanism for overriding the implementation of
almost all NumPy functions on non-NumPy arrays by defining an
``__array_function__`` method, as described in `NEP 18`_.

This feature is not yet been enabled by default, but has been released to
facilitate experimentation by potential users. See the NEP for details on
setting the appropriate environment variable. We expect the NumPy 1.17 release
will enable overrides by default, which will also be more performant due to a
new implementation written in C.

.. _`NEP 18` : http://www.numpy.org/neps/nep-0018-array-function-protocol.html

Arrays based off readonly buffers cannot be set ``writeable``
-------------------------------------------------------------
We now disallow setting the ``writeable`` flag True on arrays created
from ``fromstring(readonly-buffer)``.


==========================

1.15.4

==========================

This is a bugfix release for bugs and regressions reported following the 1.15.3
release.  The Python versions supported by this release are 2.7, 3.4-3.7. The
wheels are linked with OpenBLAS v0.3.0, which should fix some of the linalg
problems reported for NumPy 1.14.

Compatibility Note
==================

The NumPy 1.15.x OS X wheels released on PyPI no longer contain 32-bit
binaries.  That will also be the case in future releases. See
`11625 <https://github.com/numpy/numpy/issues/11625>`__ for the related
discussion.  Those needing 32-bit support should look elsewhere or build
from source.

Contributors
============

A total of 4 people contributed to this release.  People with a "+" by their
names contributed a patch for the first time.

* Charles Harris
* Matti Picus
* Sebastian Berg
* bbbbbbbbba +

Pull requests merged
====================

A total of 4 pull requests were merged for this release.

* `12296 <https://github.com/numpy/numpy/pull/12296>`__: BUG: Dealloc cached buffer info
* `12297 <https://github.com/numpy/numpy/pull/12297>`__: BUG: Fix fill value in masked array '==' and '!=' ops.
* `12307 <https://github.com/numpy/numpy/pull/12307>`__: DOC: Correct the default value of `optimize` in `numpy.einsum`
* `12320 <https://github.com/numpy/numpy/pull/12320>`__: REL: Prepare for the NumPy 1.15.4 release


==========================

1.15.3

==========================

This is a bugfix release for bugs and regressions reported following the 1.15.2
release.  The Python versions supported by this release are 2.7, 3.4-3.7. The
wheels are linked with OpenBLAS v0.3.0, which should fix some of the linalg
problems reported for NumPy 1.14.

Compatibility Note
==================

The NumPy 1.15.x OS X wheels released on PyPI no longer contain 32-bit
binaries.  That will also be the case in future releases. See
`11625 <https://github.com/numpy/numpy/issues/11625>`__ for the related
discussion.  Those needing 32-bit support should look elsewhere or build
from source.

Contributors
============

A total of 7 people contributed to this release.  People with a "+" by their
names contributed a patch for the first time.

* Allan Haldane
* Charles Harris
* Jeroen Demeyer
* Kevin Sheppard
* Matthew Bowden +
* Matti Picus
* Tyler Reddy

Pull requests merged
====================

A total of 12 pull requests were merged for this release.

* `12080 <https://github.com/numpy/numpy/pull/12080>`__: MAINT: Blacklist some MSVC complex functions.
* `12083 <https://github.com/numpy/numpy/pull/12083>`__: TST: Add azure CI testing to 1.15.x branch.
* `12084 <https://github.com/numpy/numpy/pull/12084>`__: BUG: test_path() now uses Path.resolve()
* `12085 <https://github.com/numpy/numpy/pull/12085>`__: TST, MAINT: Fix some failing tests on azure-pipelines mac and...
* `12187 <https://github.com/numpy/numpy/pull/12187>`__: BUG: Fix memory leak in mapping.c
* `12188 <https://github.com/numpy/numpy/pull/12188>`__: BUG: Allow boolean subtract in histogram
* `12189 <https://github.com/numpy/numpy/pull/12189>`__: BUG: Fix in-place permutation
* `12190 <https://github.com/numpy/numpy/pull/12190>`__: BUG: limit default for get_num_build_jobs() to 8
* `12191 <https://github.com/numpy/numpy/pull/12191>`__: BUG: OBJECT_to_* should check for errors
* `12192 <https://github.com/numpy/numpy/pull/12192>`__: DOC: Prepare for NumPy 1.15.3 release.
* `12237 <https://github.com/numpy/numpy/pull/12237>`__: BUG: Fix MaskedArray fill_value type conversion.
* `12238 <https://github.com/numpy/numpy/pull/12238>`__: TST: Backport azure-pipeline testing fixes for Mac


=========================

Links

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

Update pandas from 0.23.4 to 0.24.2.

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

Links

• PyPI: https://pypi.org/project/pandas
• Homepage: http://pandas.pydata.org

Update pyfaidx from 0.5.4.2 to 0.5.5.2.

Changelog

0.5.5.1

- Added better exceptions for files that do not contain any valid sequences (144)

0.5.5

- Added proper BGZF support, fixing 131. Note: this fix requires code present in Biopython 1.73, which is not yet released. If you need this functionality in the mean time, install the biopython development version
- Enhancement to `faidx` script: allow -v to be specified alongside -g (142). Thanks daler!

Links

• PyPI: https://pypi.org/project/pyfaidx
• Changelog: https://pyup.io/changelogs/pyfaidx/
• Homepage: http://mattshirley.com
• Docs: https://pythonhosted.org/pyfaidx/

Update pyparsing from 2.2.1 to 2.4.0.

Changelog

2.4.0

---------------------------
- Well, it looks like the API change that was introduced in 2.3.1 was more
drastic than expected, so for a friendlier forward upgrade path, this
release:
. Bumps the current version number to 2.4.0, to reflect this
 incompatible change.
. Adds a pyparsing.__compat__ object for specifying compatibility with
 future breaking changes.
. Conditionalizes the API-breaking behavior, based on the value
 pyparsing.__compat__.collect_all_And_tokens.  By default, this value
 will be set to True, reflecting the new bugfixed behavior. To set this
 value to False, add to your code:

     import pyparsing
     pyparsing.__compat__.collect_all_And_tokens = False

. User code that is dependent on the pre-bugfix behavior can restore
 it by setting this value to False.

In 2.5 and later versions, the conditional code will be removed and
setting the flag to True or False in these later versions will have no
effect.

- Updated unitTests.py and simple_unit_tests.py to be compatible with
"python setup.py test". To run tests using setup, do:

   python setup.py test
   python setup.py test -s unitTests.suite
   python setup.py test -s simple_unit_tests.suite

Prompted by issue 83 and PR submitted by bdragon28, thanks.

- Fixed bug in runTests handling '\n' literals in quoted strings.

- Added tag_body attribute to the start tag expressions generated by
makeHTMLTags, so that you can avoid using SkipTo to roll your own
tag body expression:

   a, aEnd = pp.makeHTMLTags('a')
   link = a + a.tag_body("displayed_text") + aEnd
   for t in s.searchString(html_page):
       print(t.displayed_text, '->', t.startA.href)

- indentedBlock failure handling was improved; PR submitted by TMiguelT,
thanks!

- Address Py2 incompatibility in simpleUnitTests, plus explain() and
Forward str() cleanup; PRs graciously provided by eswald.

- Fixed docstring with embedded '\w', which creates SyntaxWarnings in
Py3.8, issue 80.

- Examples:

- Added example parser for rosettacode.org tutorial compiler.

- Added example to show how an HTML table can be parsed into a
 collection of Python lists or dicts, one per row.

- Updated SimpleSQL.py example to handle nested selects, reworked
 'where' expression to use infixNotation.

- Added include_preprocessor.py, similar to macroExpander.py.

- Examples using makeHTMLTags use new tag_body expression when
 retrieving a tag's body text.

- Updated examples that are runnable as unit tests:

     python setup.py test -s examples.antlr_grammar_tests
     python setup.py test -s examples.test_bibparse

2.3.1

-----------------------------
- POSSIBLE API CHANGE: this release fixes a bug when results names were
attached to a MatchFirst or Or object containing an And object.
Previously, a results name on an And object within an enclosing MatchFirst
or Or could return just the first token in the And. Now, all the tokens
matched by the And are correctly returned. This may result in subtle
changes in the tokens returned if you have this condition in your pyparsing
scripts.

- New staticmethod ParseException.explain() to help diagnose parse exceptions
by showing the failing input line and the trace of ParserElements in
the parser leading up to the exception. explain() returns a multiline
string listing each element by name. (This is still an experimental
method, and the method signature and format of the returned string may
evolve over the next few releases.)

Example:
      define a parser to parse an integer followed by an
      alphabetic word

[pyup-bot]

Closing this in favor of #42