Scheduled monthly dependency update for November

[pyup-bot]

Update astropy from 3.2.1 to 3.2.3.

Changelog

3.2.3

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

Other Changes and Additions
---------------------------

- Updated IERS A URLs due to USNO prolonged maintenance. [9443]

3.2.2

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

Bug fixes
---------

astropy.convolution
^^^^^^^^^^^^^^^^^^^

- Fixed a bug in ``discretize_oversample_1D/2D()`` from
``astropy.convolution.utils``, which might occasionally introduce unexpected
oversampling grid dimensions due to a numerical precision issue. [9293]

- Fixed a bug [9168] where having a kernel defined using unitless astropy
quantity objects would result in a crash [9300]

astropy.coordinates
^^^^^^^^^^^^^^^^^^^

- Fix concatenation of representations for cases where the units were different.
[8877]

- Check for NaN values in catalog and match coordinates before building and
querying the ``KDTree`` for coordinate matching. [9007]

- Fix sky coordinate matching when a dimensionless distance is provided. [9008]

- Raise a faster and more meaningful error message when differential data units
are not compatible with a containing representation's units. [9064]

- Changed the timescale in ICRS to CIRS from 'tdb' to 'tt' conversion and
vice-versa, as the erfa function that gets called in the process, pnm06a
accepts time in TT. [9079]

astropy.io.ascii
^^^^^^^^^^^^^^^^

- Fixed the fast reader when used in parallel and with the multiprocessing
'spawn' method (which is the default on MacOS X with Python 3.8 and later),
and enable parallel fast reader on Windows. [8853]

astropy.io.fits
^^^^^^^^^^^^^^^

- Fixes bug where an invalid TRPOS<n> keyword was being generated for FITS
time column when no location was available. [8784]

- Fixed a wrong exception when converting a Table with a unit that is not FITS
compliant and not convertible to a string using ``format='fits'``. [8906]

- Fixed an issue with A3DTABLE extension that could not be read. [9012]

- Fixed the update of the header when creating GroupsHDU from data. [9216]

astropy.nddata
^^^^^^^^^^^^^^

- Fix to ``add_array``, which now accepts ``array_small`` having dimensions
equal to ``array_large``, instead of only allowing smaller sizes of
arrays. [9118]

astropy.stats
^^^^^^^^^^^^^

- Fixed ``median_absolute_deviation`` for the case where ``ignore_nan=True``
and an input masked array contained both NaNs and infs. [9307]

astropy.table
^^^^^^^^^^^^^

- Comparisons between ``Column`` instances and ``Quantity`` will now
correctly take into account the unit (as was already the case for
regular operations such as addition). [8904]

astropy.time
^^^^^^^^^^^^

- Allow ``Time`` to be initialized with an empty value for all formats. [8854]

- Fixed a troubling bug in which ``Time`` could loose precision, with deviations
of 300 ns. [9328]

astropy.timeseries
^^^^^^^^^^^^^^^^^^

- Fixed handling of ``Quantity`` input data for all methods of
``LombScarge.false_alarm_probabilty``. [9246]

astropy.units
^^^^^^^^^^^^^

- Allow conversion of ``Column`` with logarithmic units to a suitable
``Quantity`` subclass if ``subok=True``. [9188]

- Ensured that we simplify powers to smaller denominators if that is
consistent within rounding precision. [9267]

- Ensured that the powers shown in a unit's repr are always correct,
not oversimplified. [9267]

astropy.utils
^^^^^^^^^^^^^

- Fixed ``find_api_page`` access by using custom request headers and HTTPS
when version is specified. [9032]

- Make ``download_file`` (and by extension ``get_readable_fileobj`` and others)
check the size of downloaded files against the size claimed by the server.
[9302]

- Fix ``find_current_module`` so that it works properly if astropy is being used
inside a bundle such as that produced by PyInstaller. [8845]

- Fix path to renamed classes, which previously included duplicate path/module
information under certain circumstances. [8845]

astropy.visualization
^^^^^^^^^^^^^^^^^^^^^

- Silence numpy runtime warnings in ``WCSAxes`` when drawing grids. [8882]

astropy.wcs
^^^^^^^^^^^

- Fixed equality test between ``cunit`` where the first element was equal but
the following elements differed. [9154]

- Fixed a crash while loading a WCS from headers containing duplicate SIP
keywords. [8893]

- Fixed a possible buffer overflow when using too large negative indices for
``cunit`` or ``ctype`` [9151]

- Fixed reference counting in ``WCSBase.__init__`` [9166]

- Fix ``SlicedLowLevelWCS`` ``world_to_pixel_values`` and
``pixel_to_world_values`` when inputs need broadcasting to the same shape.
(i.e. when one input is sliced out) [9250]

- Fixed a bug that caused ``WCS.array_shape``, ``WCS.pixel_shape`` and
``WCS.pixel_bounds`` to be incorrect after using ``WCS.sub``. [9095]


Other Changes and Additions
---------------------------

- Fixed a bug that caused files outside of the astropy module directory to be
included as package data, resulting in some cases in errors when doing
repeated builds. [9039]

Links

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

Update numpy from 1.17.0 to 1.17.3.

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

Links

• PyPI: https://pypi.org/project/numpy
• Homepage: https://www.numpy.org

Update scipy from 1.3.0 to 1.3.1.

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

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 hypothesis from 4.32.2 to 4.42.5.

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

Links

• PyPI: https://pypi.org/project/hypothesis
• Changelog: https://pyup.io/changelogs/hypothesis/
• Repo: https://github.com/HypothesisWorks/hypothesis/tree/master/hypothesis-python

Update pre-commit from 1.17.0 to 1.20.0.

Changelog

1.20.0

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

Features
- Allow building newer versions of `ruby`.
 - 1193 issue by choffee.
 - 1195 PR by choffee.
- Bump versions reported in `pre-commit sample-config`.
 - 1197 PR by asottile.

Fixes
- Fix rare race condition with multiple concurrent first-time runs.
 - 1192 issue by raholler.
 - 1196 PR by asottile.

1.19.0

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

Features
- Allow `--hook-type` to be specified multiple times.
 - example: `pre-commit install --hook-type pre-commit --hook-type pre-push`
 - 1139 issue by MaxymVlasov.
 - 1145 PR by asottile.
- Include more version information in crash logs.
 - 1142 by marqueewinq.
- Hook colors are now passed through on platforms which support `pty`.
 - 1169 by asottile.
- pre-commit now  uses `importlib.metadata` directly when running in python 3.8
 - 1176 by asottile.
- Normalize paths to forward slash separators on windows.
 - makes it easier to match paths with `files:` regex
 - avoids some quoting bugs in shell-based hooks
 - 1173 issue by steigenTI.
 - 1179 PR by asottile.

Fixes
- Remove some extra newlines from error messages.
 - 1148 by asottile.
- When a hook is not executable it now reports `not executable` instead of
`not found`.
 - 1159 issue by nixjdm.
 - 1161 PR by WillKoehrsen.
- Fix interleaving of stdout / stderr in hooks.
 - 1168 by asottile.
- Fix python environment `healthy()` check when current working directory
contains modules which shadow standard library names.
 - issue by vwhsu92.
 - 1185 PR by asottile.

Updating
- Regexes handling both backslashes and forward slashes for directory
separators now only need to handle forward slashes.

1.18.3

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

Fixes
- Fix `node_modules` plugin installation on windows
 - 1123 issue by henryykt.
 - 1122 PR by henryykt.

1.18.2

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

Fixes
- Make default python lookup more deterministic to avoid redundant installs
 - 1117 PR by scop.

1.18.1

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

Fixes
- Fix installation of `rust` hooks with new `cargo`
 - 1112 issue by zimbatm.
 - 1113 PR by zimbatm.

1.18.0

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

Features
- Use the current running executable if it matches the requested
`language_version`
 - 1062 PR by asottile.
- Print the stage when a hook is not found
 - 1078 issue by madkinsz.
 - 1079 PR by madkinsz.
- `pre-commit autoupdate` now supports non-`master` default branches
 - 1089 PR by asottile.
- Add `pre-commit init-templatedir` which makes it easier to automatically
enable `pre-commit` in cloned repositories.
 - 1084 issue by ssbarnea.
 - 1090 PR by asottile.
 - 1107 PR by asottile.
- pre-commit's color can be controlled using
`PRE_COMMIT_COLOR={auto,always,never}`
 - 1073 issue by saper.
 - 1092 PR by geieredgar.
 - 1098 PR by geieredgar.
- pre-commit's color can now be disabled using `TERM=dumb`
 - 1073 issue by saper.
 - 1103 PR by asottile.
- pre-commit now supports `docker` based hooks on windows
 - 1072 by cz-fish.
 - 1093 PR by geieredgar.

Fixes
- Fix shallow clone
 - 1077 PR by asottile.
- Fix autoupdate version flip flop when using shallow cloning
 - 1076 issue by mxr.
 - 1088 PR by asottile.
- Fix autoupdate when the current revision is invalid
 - 1088 PR by asottile.

Misc.
- Replace development instructions with `tox --devenv ...`
 - 1032 issue by yoavcaspi.
 - 1067 PR by asottile.

Links

• PyPI: https://pypi.org/project/pre-commit
• Changelog: https://pyup.io/changelogs/pre-commit/
• Repo: https://github.com/pre-commit/pre-commit

Update pytest from 5.0.1 to 5.2.2.

Changelog

5.2.2

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

Bug Fixes
---------

- `5206 <https://github.com/pytest-dev/pytest/issues/5206>`_: Fix ``--nf`` to not forget about known nodeids with partial test selection.


- `5906 <https://github.com/pytest-dev/pytest/issues/5906>`_: Fix crash with ``KeyboardInterrupt`` during ``--setup-show``.


- `5946 <https://github.com/pytest-dev/pytest/issues/5946>`_: Fixed issue when parametrizing fixtures with numpy arrays (and possibly other sequence-like types).


- `6044 <https://github.com/pytest-dev/pytest/issues/6044>`_: Properly ignore ``FileNotFoundError`` exceptions when trying to remove old temporary directories,
for instance when multiple processes try to remove the same directory (common with ``pytest-xdist``
for example).

5.2.1

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

Bug Fixes
---------

- `5902 <https://github.com/pytest-dev/pytest/issues/5902>`_: Fix warnings about deprecated ``cmp`` attribute in ``attrs>=19.2``.

5.2.0

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

Deprecations
------------

- `1682 <https://github.com/pytest-dev/pytest/issues/1682>`_: Passing arguments to pytest.fixture() as positional arguments is deprecated - pass them
as a keyword argument instead.



Features
--------

- `1682 <https://github.com/pytest-dev/pytest/issues/1682>`_: The ``scope`` parameter of ``pytest.fixture`` can now be a callable that receives
the fixture name and the ``config`` object as keyword-only parameters.
See `the docs <https://docs.pytest.org/en/latest/fixture.htmldynamic-scope>`__ for more information.


- `5764 <https://github.com/pytest-dev/pytest/issues/5764>`_: New behavior of the ``--pastebin`` option: failures to connect to the pastebin server are reported, without failing the pytest run



Bug Fixes
---------

- `5806 <https://github.com/pytest-dev/pytest/issues/5806>`_: Fix "lexer" being used when uploading to bpaste.net from ``--pastebin`` to "text".


- `5884 <https://github.com/pytest-dev/pytest/issues/5884>`_: Fix ``--setup-only`` and ``--setup-show`` for custom pytest items.



Trivial/Internal Changes
------------------------

- `5056 <https://github.com/pytest-dev/pytest/issues/5056>`_: The HelpFormatter uses ``py.io.get_terminal_width`` for better width detection.

5.1.3

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

Bug Fixes
---------

- `5807 <https://github.com/pytest-dev/pytest/issues/5807>`_: Fix pypy3.6 (nightly) on windows.


- `5811 <https://github.com/pytest-dev/pytest/issues/5811>`_: Handle ``--fulltrace`` correctly with ``pytest.raises``.


- `5819 <https://github.com/pytest-dev/pytest/issues/5819>`_: Windows: Fix regression with conftest whose qualified name contains uppercase
characters (introduced by 5792).

5.1.2

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

Bug Fixes
---------

- `2270 <https://github.com/pytest-dev/pytest/issues/2270>`_: Fixed ``self`` reference in function-scoped fixtures defined plugin classes: previously ``self``
would be a reference to a *test* class, not the *plugin* class.


- `570 <https://github.com/pytest-dev/pytest/issues/570>`_: Fixed long standing issue where fixture scope was not respected when indirect fixtures were used during
parametrization.


- `5782 <https://github.com/pytest-dev/pytest/issues/5782>`_: Fix decoding error when printing an error response from ``--pastebin``.


- `5786 <https://github.com/pytest-dev/pytest/issues/5786>`_: Chained exceptions in test and collection reports are now correctly serialized, allowing plugins like
``pytest-xdist`` to display them properly.


- `5792 <https://github.com/pytest-dev/pytest/issues/5792>`_: Windows: Fix error that occurs in certain circumstances when loading
``conftest.py`` from a working directory that has casing other than the one stored
in the filesystem (e.g., ``c:\test`` instead of ``C:\test``).

5.1.1

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

Bug Fixes
---------

- `5751 <https://github.com/pytest-dev/pytest/issues/5751>`_: Fixed ``TypeError`` when importing pytest on Python 3.5.0 and 3.5.1.

5.1.0

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

Removals
--------

- `5180 <https://github.com/pytest-dev/pytest/issues/5180>`_: As per our policy, the following features have been deprecated in the 4.X series and are now
removed:

* ``Request.getfuncargvalue``: use ``Request.getfixturevalue`` instead.

* ``pytest.raises`` and ``pytest.warns`` no longer support strings as the second argument.

* ``message`` parameter of ``pytest.raises``.

* ``pytest.raises``, ``pytest.warns`` and ``ParameterSet.param`` now use native keyword-only
 syntax. This might change the exception message from previous versions, but they still raise
 ``TypeError`` on unknown keyword arguments as before.

* ``pytest.config`` global variable.

* ``tmpdir_factory.ensuretemp`` method.

* ``pytest_logwarning`` hook.

* ``RemovedInPytest4Warning`` warning type.

* ``request`` is now a reserved name for fixtures.


For more information consult
`Deprecations and Removals <https://docs.pytest.org/en/latest/deprecations.html>`__ in the docs.


- `5565 <https://github.com/pytest-dev/pytest/issues/5565>`_: Removed unused support code for `unittest2 <https://pypi.org/project/unittest2/>`__.

The ``unittest2`` backport module is no longer
necessary since Python 3.3+, and the small amount of code in pytest to support it also doesn't seem
to be used: after removed, all tests still pass unchanged.

Although our policy is to introduce a deprecation period before removing any features or support
for third party libraries, because this code is apparently not used
at all (even if ``unittest2`` is used by a test suite executed by pytest), it was decided to
remove it in this release.

If you experience a regression because of this, please
`file an issue <https://github.com/pytest-dev/pytest/issues/new>`__.


- `5615 <https://github.com/pytest-dev/pytest/issues/5615>`_: ``pytest.fail``, ``pytest.xfail`` and ``pytest.skip`` no longer support bytes for the message argument.

This was supported for Python 2 where it was tempting to use ``"message"``
instead of ``u"message"``.

Python 3 code is unlikely to pass ``bytes`` to these functions. If you do,
please decode it to an ``str`` beforehand.



Features
--------

- `5564 <https://github.com/pytest-dev/pytest/issues/5564>`_: New ``Config.invocation_args`` attribute containing the unchanged arguments passed to ``pytest.main()``.


- `5576 <https://github.com/pytest-dev/pytest/issues/5576>`_: New `NUMBER <https://docs.pytest.org/en/latest/doctest.htmlusing-doctest-options>`__
option for doctests to ignore irrelevant differences in floating-point numbers.
Inspired by Sébastien Boisgérault's `numtest <https://github.com/boisgera/numtest>`__
extension for doctest.



Improvements
------------

- `5471 <https://github.com/pytest-dev/pytest/issues/5471>`_: JUnit XML now includes a timestamp and hostname in the testsuite tag.


- `5707 <https://github.com/pytest-dev/pytest/issues/5707>`_: Time taken to run the test suite now includes a human-readable representation when it takes over
60 seconds, for example::

   ===== 2 failed in 102.70s (0:01:42) =====



Bug Fixes
---------

- `4344 <https://github.com/pytest-dev/pytest/issues/4344>`_: Fix RuntimeError/StopIteration when trying to collect package with "__init__.py" only.


- `5115 <https://github.com/pytest-dev/pytest/issues/5115>`_: Warnings issued during ``pytest_configure`` are explicitly not treated as errors, even if configured as such, because it otherwise completely breaks pytest.


- `5477 <https://github.com/pytest-dev/pytest/issues/5477>`_: The XML file produced by ``--junitxml`` now correctly contain a ``<testsuites>`` root element.


- `5524 <https://github.com/pytest-dev/pytest/issues/5524>`_: Fix issue where ``tmp_path`` and ``tmpdir`` would not remove directories containing files marked as read-only,
which could lead to pytest crashing when executed a second time with the ``--basetemp`` option.


- `5537 <https://github.com/pytest-dev/pytest/issues/5537>`_: Replace ``importlib_metadata`` backport with ``importlib.metadata`` from the
standard library on Python 3.8+.


- `5578 <https://github.com/pytest-dev/pytest/issues/5578>`_: Improve type checking for some exception-raising functions (``pytest.xfail``, ``pytest.skip``, etc)
so they provide better error messages when users meant to use marks (for example ``pytest.xfail``
instead of ``pytest.mark.xfail``).


- `5606 <https://github.com/pytest-dev/pytest/issues/5606>`_: Fixed internal error when test functions were patched with objects that cannot be compared
for truth values against others, like ``numpy`` arrays.


- `5634 <https://github.com/pytest-dev/pytest/issues/5634>`_: ``pytest.exit`` is now correctly handled in ``unittest`` cases.
This makes ``unittest`` cases handle ``quit`` from pytest's pdb correctly.


- `5650 <https://github.com/pytest-dev/pytest/issues/5650>`_: Improved output when parsing an ini configuration file fails.


- `5701 <https://github.com/pytest-dev/pytest/issues/5701>`_: Fix collection of ``staticmethod`` objects defined with ``functools.partial``.


- `5734 <https://github.com/pytest-dev/pytest/issues/5734>`_: Skip async generator test functions, and update the warning message to refer to ``async def`` functions.



Improved Documentation
----------------------

- `5669 <https://github.com/pytest-dev/pytest/issues/5669>`_: Add docstring for ``Testdir.copy_example``.



Trivial/Internal Changes
------------------------

- `5095 <https://github.com/pytest-dev/pytest/issues/5095>`_: XML files of the ``xunit2`` family are now validated against the schema by pytest's own test suite
to avoid future regressions.


- `5516 <https://github.com/pytest-dev/pytest/issues/5516>`_: Cache node splitting function which can improve collection performance in very large test suites.


- `5603 <https://github.com/pytest-dev/pytest/issues/5603>`_: Simplified internal ``SafeRepr`` class and removed some dead code.


- `5664 <https://github.com/pytest-dev/pytest/issues/5664>`_: When invoking pytest's own testsuite with ``PYTHONDONTWRITEBYTECODE=1``,
the ``test_xfail_handling`` test no longer fails.


- `5684 <https://github.com/pytest-dev/pytest/issues/5684>`_: Replace manual handling of ``OSError.errno`` in the codebase by new ``OSError`` subclasses (``PermissionError``, ``FileNotFoundError``, etc.).

Links

• PyPI: https://pypi.org/project/pytest
• Changelog: https://pyup.io/changelogs/pytest/
• Homepage: https://docs.pytest.org/en/latest/

Update pytest-cov from 2.7.1 to 2.8.1.

Changelog

2.8.1

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

* Fixed `348 <https://github.com/pytest-dev/pytest-cov/issues/348>`_ -
regression when only certain reports (html or xml) are used then ``--cov-fail-under`` always fails.

2.8.0

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

* Fixed ``RecursionError`` that can occur when using
`cleanup_on_signal <https://pytest-cov.readthedocs.io/en/latest/subprocess-support.htmlif-you-got-custom-signal-handling>`__ or
`cleanup_on_sigterm <https://pytest-cov.readthedocs.io/en/latest/subprocess-support.htmlif-you-got-custom-signal-handling>`__.
See: `294 <https://github.com/pytest-dev/pytest-cov/issues/294>`_.
The 2.7.x releases of pytest-cov should be considered broken regarding aforementioned cleanup API.
* Added compatibility with future xdist release that deprecates some internals
(match pytest-xdist master/worker terminology).
Contributed by Thomas Grainger in `321 <https://github.com/pytest-dev/pytest-cov/pull/321>`_
* Fixed breakage that occurs when multiple reporting options are used.
Contributed by Thomas Grainger in `338 <https://github.com/pytest-dev/pytest-cov/pull/338>`_.
* Changed internals to use a stub instead of ``os.devnull``.
Contributed by Thomas Grainger in `332 <https://github.com/pytest-dev/pytest-cov/pull/332>`_.
* Added support for Coverage 5.0.
Contributed by Ned Batchelder in `319 <https://github.com/pytest-dev/pytest-cov/pull/319>`_.
* Added support for float values in ``--cov-fail-under``.
Contributed by Martín Gaitán in `311 <https://github.com/pytest-dev/pytest-cov/pull/311>`_.
* Various documentation fixes. Contributed by
Juanjo Bazán,
Andrew Murray and
Albert Tugushev in
`298 <https://github.com/pytest-dev/pytest-cov/pull/298>`_,
`299 <https://github.com/pytest-dev/pytest-cov/pull/299>`_ and
`307 <https://github.com/pytest-dev/pytest-cov/pull/307>`_.
* Various testing improvements. Contributed by
Ned Batchelder,
Daniel Hahler,
Ionel Cristian Mărieș and
Hugo van Kemenade in
`313 <https://github.com/pytest-dev/pytest-cov/pull/313>`_,
`314 <https://github.com/pytest-dev/pytest-cov/pull/314>`_,
`315 <https://github.com/pytest-dev/pytest-cov/pull/315>`_,
`316 <https://github.com/pytest-dev/pytest-cov/pull/316>`_,
`325 <https://github.com/pytest-dev/pytest-cov/pull/325>`_,
`326 <https://github.com/pytest-dev/pytest-cov/pull/326>`_,
`334 <https://github.com/pytest-dev/pytest-cov/pull/334>`_ and
`335 <https://github.com/pytest-dev/pytest-cov/pull/335>`_.
* Added the ``--cov-context`` CLI options that enables coverage contexts. Only works with coverage 5.0+.
Contributed by Ned Batchelder in `345 <https://github.com/pytest-dev/pytest-cov/pull/345>`_.

Links

• PyPI: https://pypi.org/project/pytest-cov
• Changelog: https://pyup.io/changelogs/pytest-cov/
• Repo: https://github.com/pytest-dev/pytest-cov

Update python-coveralls from 2.9.2 to 2.9.3.

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

Links

• PyPI: https://pypi.org/project/python-coveralls
• Changelog: https://pyup.io/changelogs/python-coveralls/
• Repo: http://github.com/z4r/python-coveralls

[coveralls]

Coverage remained the same at 95.331% when pulling 61a0174 on pyup/scheduled-update-2019-11-01 into 75b270f on develop.