Scheduled monthly dependency update for November

Update astropy from 3.0.4 to 3.0.5.

Changelog

### 3.0.5 ``` ================== Bug Fixes --------- astropy.config ^^^^^^^^^^^^^^ astropy.constants ^^^^^^^^^^^^^^^^^ astropy.convolution ^^^^^^^^^^^^^^^^^^^ astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Fixed bug in which consecutive ``StaticMatrixTransform``'s in a frame transform path would be combined in the incorrect order. [7707] astropy.cosmology ^^^^^^^^^^^^^^^^^ astropy.extern ^^^^^^^^^^^^^^ astropy.io.ascii ^^^^^^^^^^^^^^^^ astropy.io.fits ^^^^^^^^^^^^^^^ astropy.io.misc ^^^^^^^^^^^^^^^ astropy.io.registry ^^^^^^^^^^^^^^^^^^^ astropy.io.votable ^^^^^^^^^^^^^^^^^^ astropy.modeling ^^^^^^^^^^^^^^^^ astropy.nddata ^^^^^^^^^^^^^^ astropy.samp ^^^^^^^^^^^^ astropy.stats ^^^^^^^^^^^^^ astropy.table ^^^^^^^^^^^^^ astropy.tests ^^^^^^^^^^^^^ - Fixing bug that doctests were not picked up from the narrative documentation when tests were run for all modules. [7767] astropy.time ^^^^^^^^^^^^ astropy.units ^^^^^^^^^^^^^ astropy.utils ^^^^^^^^^^^^^ astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ astropy.wcs ^^^^^^^^^^^ Other Changes and Additions --------------------------- ```

Links

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

Update matplotlib from 3.0.0 to 3.0.1.

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Links

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

Update numba from 0.40.0 to 0.40.1.

Changelog

### 0.40.1 ``` -------------- This is a PyPI-only patch release to ensure that PyPI wheels can enable the TBB threading backend, and to disable the OpenMP backend in the wheels. Limitations of manylinux1 and variation in user environments can cause segfaults when OpenMP is enabled on wheel builds. Note that this release has no functional changes for users who obtained Numba 0.40.0 via conda. Patches: * PR 3338: Accidentally left Anton off contributor list for 0.40.0 * PR 3374: Disable OpenMP in wheel building * PR 3376: Update 0.40.1 changelog and docs on OpenMP backend ```

Links

- PyPI: https://pypi.org/project/numba - Changelog: https://pyup.io/changelogs/numba/ - Repo: http://numba.github.com

Update numpy from 1.15.2 to 1.15.3.

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Links

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

Update multiprocess from 0.70.6 to 0.70.6.1.

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

Links

- PyPI: https://pypi.org/project/multiprocess - Changelog: https://pyup.io/changelogs/multiprocess/ - Homepage: https://pypi.org/project/multiprocess

Update sqlalchemy from 1.2.12 to 1.2.13.

Changelog

### 1.2.13 ``` :released: October 31, 2018 .. change:: :tags: bug, postgresql :tickets: 4337 Added support for the :class:`.aggregate_order_by` function to receive multiple ORDER BY elements, previously only a single element was accepted. .. change:: :tags: bug, mysql :tickets: 4348 Added word ``function`` to the list of reserved words for MySQL, which is now a keyword in MySQL 8.0 .. change:: :tags: feature, sql :versions: 1.3.0b1 Refactored :class:`.SQLCompiler` to expose a :meth:`.SQLCompiler.group_by_clause` method similar to the :meth:`.SQLCompiler.order_by_clause` and :meth:`.SQLCompiler.limit_clause` methods, which can be overridden by dialects to customize how GROUP BY renders. Pull request courtesy Samuel Chou. .. change:: :tags: bug, misc Fixed issue where part of the utility language helper internals was passing the wrong kind of argument to the Python ``__import__`` builtin as the list of modules to be imported. The issue produced no symptoms within the core library but could cause issues with external applications that redefine the ``__import__`` builtin or otherwise instrument it. Pull request courtesy Joe Urciuoli. .. change:: :tags: bug, orm :tickets: 4349 Fixed bug where "dynamic" loader needs to explicitly set the "secondary" table in the FROM clause of the query, to suit the case where the secondary is a join object that is otherwise not pulled into the query from its columns alone. .. change:: :tags: bug, orm, declarative :tickets: 4350 Fixed regression caused by :ticket:`4326` in version 1.2.12 where using :class:`.declared_attr` with a mixin in conjunction with :func:`.orm.synonym` would fail to map the synonym properly to an inherited subclass. .. change:: :tags: bug, misc, py3k :tickets: 4339 Fixed additional warnings generated by Python 3.7 due to changes in the organization of the Python ``collections`` and ``collections.abc`` packages. Previous ``collections`` warnings were fixed in version 1.2.11. Pull request courtesy xtreak. .. change:: :tags: bug, ext Added missing ``.index()`` method to list-based association collections in the association proxy extension. .. change:: :tags: bug, mysql :tickets: 4344 Added a workaround for a MySQL bug 88718 introduced in the 8.0 series, where the reflection of a foreign key constraint is not reporting the correct case sensitivity for the referred column, leading to errors during use of the reflected constraint such as when using the automap extension. The workaround emits an additional query to the information_schema tables in order to retrieve the correct case sensitive name. .. change:: :tags: bug, sql :tickets: 4341 Fixed bug where the :paramref:`.Enum.create_constraint` flag on the :class:`.Enum` datatype would not be propagated to copies of the type, which affects use cases such as declarative mixins and abstract bases. .. change:: :tags: bug, orm, declarative :tickets: 4352 The column conflict resolution technique discussed at :ref:`declarative_column_conflicts` is now functional for a :class:`.Column` that is also a primary key column. Previously, a check for primary key columns declared on a single-inheritance subclass would occur before the column copy were allowed to pass. .. changelog:: ```

Links

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

Update tqdm from 4.25.0 to 4.28.1.

Changelog

### 4.28.0 ``` - remove installation of man pages by default (460, 628) - CLI:add `--manpath` option (629) - documentation additions and fixes ``` ### 4.27.0 ``` - fix `str.isnumeric` 605 - fix `WeakSet` `KeyError` 548, 553, 596 -> 607 - stop `tqdm_notebook` description truncation 582 -> 599 - include `unit_scale` for `rate` 608 - add `auto` -> nowarning `autonotebook` - add better postfix numeric formatting 621 - minor refactoring 609 -> 616 - update documentation - add unit tests - fix py26 CI ``` ### 4.26.0 ``` - fix `smoothing` (566 -> 601) - `pandas` updates + address the `FutureWarning` in `pandas`, drop `pandas` test in py34, add in py37 (603) + support `pandas` `axis='index' or 'columns'` (570) - minor documentation updates (597, 600, 606) + developer notes ```

Links

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

Update hypothesis from 3.74.0 to 3.82.1.

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

Links

- PyPI: https://pypi.org/project/hypothesis - Repo: https://github.com/HypothesisWorks/hypothesis/tree/master/hypothesis-python

Update pytest from 3.8.1 to 3.9.3.

Changelog

### 3.9.3 ``` ========================= Bug Fixes --------- - `4174 <https://github.com/pytest-dev/pytest/issues/4174>`_: Fix "ValueError: Plugin already registered" with conftest plugins via symlink. - `4181 <https://github.com/pytest-dev/pytest/issues/4181>`_: Handle race condition between creation and deletion of temporary folders. - `4221 <https://github.com/pytest-dev/pytest/issues/4221>`_: Fix bug where the warning summary at the end of the test session was not showing the test where the warning was originated. - `4243 <https://github.com/pytest-dev/pytest/issues/4243>`_: Fix regression when ``stacklevel`` for warnings was passed as positional argument on python2. Improved Documentation ---------------------- - `3851 <https://github.com/pytest-dev/pytest/issues/3851>`_: Add reference to ``empty_parameter_set_mark`` ini option in documentation of ``pytest.mark.parametrize`` Trivial/Internal Changes ------------------------ - `4028 <https://github.com/pytest-dev/pytest/issues/4028>`_: Revert patching of ``sys.breakpointhook`` since it appears to do nothing. - `4233 <https://github.com/pytest-dev/pytest/issues/4233>`_: Apply an import sorter (``reorder-python-imports``) to the codebase. - `4248 <https://github.com/pytest-dev/pytest/issues/4248>`_: Remove use of unnecessary compat shim, six.binary_type ``` ### 3.9.2 ``` ========================= Bug Fixes --------- - `2909 <https://github.com/pytest-dev/pytest/issues/2909>`_: Improve error message when a recursive dependency between fixtures is detected. - `3340 <https://github.com/pytest-dev/pytest/issues/3340>`_: Fix logging messages not shown in hooks ``pytest_sessionstart()`` and ``pytest_sessionfinish()``. - `3533 <https://github.com/pytest-dev/pytest/issues/3533>`_: Fix unescaped XML raw objects in JUnit report for skipped tests - `3691 <https://github.com/pytest-dev/pytest/issues/3691>`_: Python 2: safely format warning message about passing unicode strings to ``warnings.warn``, which may cause surprising ``MemoryError`` exception when monkey patching ``warnings.warn`` itself. - `4026 <https://github.com/pytest-dev/pytest/issues/4026>`_: Improve error message when it is not possible to determine a function's signature. - `4177 <https://github.com/pytest-dev/pytest/issues/4177>`_: Pin ``setuptools>=40.0`` to support ``py_modules`` in ``setup.cfg`` - `4179 <https://github.com/pytest-dev/pytest/issues/4179>`_: Restore the tmpdir behaviour of symlinking the current test run. - `4192 <https://github.com/pytest-dev/pytest/issues/4192>`_: Fix filename reported by ``warnings.warn`` when using ``recwarn`` under python2. ``` ### 3.9.1 ``` ========================= Features -------- - `4159 <https://github.com/pytest-dev/pytest/issues/4159>`_: For test-suites containing test classes, the information about the subclassed module is now output only if a higher verbosity level is specified (at least "-vv"). ``` ### 3.9.0 ``` ========================================================================= Deprecations ------------ - `3616 <https://github.com/pytest-dev/pytest/issues/3616>`_: The following accesses have been documented as deprecated for years, but are now actually emitting deprecation warnings. * Access of ``Module``, ``Function``, ``Class``, ``Instance``, ``File`` and ``Item`` through ``Node`` instances. Now users will this warning:: usage of Function.Module is deprecated, please use pytest.Module instead Users should just ``import pytest`` and access those objects using the ``pytest`` module. * ``request.cached_setup``, this was the precursor of the setup/teardown mechanism available to fixtures. You can consult `funcarg comparison section in the docs <https://docs.pytest.org/en/latest/funcarg_compare.html>`_. * Using objects named ``"Class"`` as a way to customize the type of nodes that are collected in ``Collector`` subclasses has been deprecated. Users instead should use ``pytest_collect_make_item`` to customize node types during collection. This issue should affect only advanced plugins who create new collection types, so if you see this warning message please contact the authors so they can change the code. * The warning that produces the message below has changed to ``RemovedInPytest4Warning``:: getfuncargvalue is deprecated, use getfixturevalue - `3988 <https://github.com/pytest-dev/pytest/issues/3988>`_: Add a Deprecation warning for pytest.ensuretemp as it was deprecated since a while. Features -------- - `2293 <https://github.com/pytest-dev/pytest/issues/2293>`_: Improve usage errors messages by hiding internal details which can be distracting and noisy. This has the side effect that some error conditions that previously raised generic errors (such as ``ValueError`` for unregistered marks) are now raising ``Failed`` exceptions. - `3332 <https://github.com/pytest-dev/pytest/issues/3332>`_: Improve the error displayed when a ``conftest.py`` file could not be imported. In order to implement this, a new ``chain`` parameter was added to ``ExceptionInfo.getrepr`` to show or hide chained tracebacks in Python 3 (defaults to ``True``). - `3849 <https://github.com/pytest-dev/pytest/issues/3849>`_: Add ``empty_parameter_set_mark=fail_at_collect`` ini option for raising an exception when parametrize collects an empty set. - `3964 <https://github.com/pytest-dev/pytest/issues/3964>`_: Log messages generated in the collection phase are shown when live-logging is enabled and/or when they are logged to a file. - `3985 <https://github.com/pytest-dev/pytest/issues/3985>`_: Introduce ``tmp_path`` as a fixture providing a Path object. - `4013 <https://github.com/pytest-dev/pytest/issues/4013>`_: Deprecation warnings are now shown even if you customize the warnings filters yourself. In the previous version any customization would override pytest's filters and deprecation warnings would fall back to being hidden by default. - `4073 <https://github.com/pytest-dev/pytest/issues/4073>`_: Allow specification of timeout for ``Testdir.runpytest_subprocess()`` and ``Testdir.run()``. - `4098 <https://github.com/pytest-dev/pytest/issues/4098>`_: Add returncode argument to pytest.exit() to exit pytest with a specific return code. - `4102 <https://github.com/pytest-dev/pytest/issues/4102>`_: Reimplement ``pytest.deprecated_call`` using ``pytest.warns`` so it supports the ``match='...'`` keyword argument. This has the side effect that ``pytest.deprecated_call`` now raises ``pytest.fail.Exception`` instead of ``AssertionError``. - `4149 <https://github.com/pytest-dev/pytest/issues/4149>`_: Require setuptools>=30.3 and move most of the metadata to ``setup.cfg``. Bug Fixes --------- - `2535 <https://github.com/pytest-dev/pytest/issues/2535>`_: Improve error message when test functions of ``unittest.TestCase`` subclasses use a parametrized fixture. - `3057 <https://github.com/pytest-dev/pytest/issues/3057>`_: ``request.fixturenames`` now correctly returns the name of fixtures created by ``request.getfixturevalue()``. - `3946 <https://github.com/pytest-dev/pytest/issues/3946>`_: Warning filters passed as command line options using ``-W`` now take precedence over filters defined in ``ini`` configuration files. - `4066 <https://github.com/pytest-dev/pytest/issues/4066>`_: Fix source reindenting by using ``textwrap.dedent`` directly. - `4102 <https://github.com/pytest-dev/pytest/issues/4102>`_: ``pytest.warn`` will capture previously-warned warnings in Python 2. Previously they were never raised. - `4108 <https://github.com/pytest-dev/pytest/issues/4108>`_: Resolve symbolic links for args. This fixes running ``pytest tests/test_foo.py::test_bar``, where ``tests`` is a symlink to ``project/app/tests``: previously ``project/app/conftest.py`` would be ignored for fixtures then. - `4132 <https://github.com/pytest-dev/pytest/issues/4132>`_: Fix duplicate printing of internal errors when using ``--pdb``. - `4135 <https://github.com/pytest-dev/pytest/issues/4135>`_: pathlib based tmpdir cleanup now correctly handles symlinks in the folder. - `4152 <https://github.com/pytest-dev/pytest/issues/4152>`_: Display the filename when encountering ``SyntaxWarning``. Improved Documentation ---------------------- - `3713 <https://github.com/pytest-dev/pytest/issues/3713>`_: Update usefixtures documentation to clarify that it can't be used with fixture functions. - `4058 <https://github.com/pytest-dev/pytest/issues/4058>`_: Update fixture documentation to specify that a fixture can be invoked twice in the scope it's defined for. - `4064 <https://github.com/pytest-dev/pytest/issues/4064>`_: According to unittest.rst, setUpModule and tearDownModule were not implemented, but it turns out they are. So updated the documentation for unittest. - `4151 <https://github.com/pytest-dev/pytest/issues/4151>`_: Add tempir testing example to CONTRIBUTING.rst guide Trivial/Internal Changes ------------------------ - `2293 <https://github.com/pytest-dev/pytest/issues/2293>`_: The internal ``MarkerError`` exception has been removed. - `3988 <https://github.com/pytest-dev/pytest/issues/3988>`_: Port the implementation of tmpdir to pathlib. - `4063 <https://github.com/pytest-dev/pytest/issues/4063>`_: Exclude 0.00 second entries from ``--duration`` output unless ``-vv`` is passed on the command-line. - `4093 <https://github.com/pytest-dev/pytest/issues/4093>`_: Fixed formatting of string literals in internal tests. ``` ### 3.8.2 ``` ========================= Deprecations and Removals ------------------------- - `4036 <https://github.com/pytest-dev/pytest/issues/4036>`_: The ``item`` parameter of ``pytest_warning_captured`` hook is now documented as deprecated. We realized only after the ``3.8`` release that this parameter is incompatible with ``pytest-xdist``. Our policy is to not deprecate features during bugfix releases, but in this case we believe it makes sense as we are only documenting it as deprecated, without issuing warnings which might potentially break test suites. This will get the word out that hook implementers should not use this parameter at all. In a future release ``item`` will always be ``None`` and will emit a proper warning when a hook implementation makes use of it. Bug Fixes --------- - `3539 <https://github.com/pytest-dev/pytest/issues/3539>`_: Fix reload on assertion rewritten modules. - `4034 <https://github.com/pytest-dev/pytest/issues/4034>`_: The ``.user_properties`` attribute of ``TestReport`` objects is a list of (name, value) tuples, but could sometimes be instantiated as a tuple of tuples. It is now always a list. - `4039 <https://github.com/pytest-dev/pytest/issues/4039>`_: No longer issue warnings about using ``pytest_plugins`` in non-top-level directories when using ``--pyargs``: the current ``--pyargs`` mechanism is not reliable and might give false negatives. - `4040 <https://github.com/pytest-dev/pytest/issues/4040>`_: Exclude empty reports for passed tests when ``-rP`` option is used. - `4051 <https://github.com/pytest-dev/pytest/issues/4051>`_: Improve error message when an invalid Python expression is passed to the ``-m`` option. - `4056 <https://github.com/pytest-dev/pytest/issues/4056>`_: ``MonkeyPatch.setenv`` and ``MonkeyPatch.delenv`` issue a warning if the environment variable name is not ``str`` on Python 2. In Python 2, adding ``unicode`` keys to ``os.environ`` causes problems with ``subprocess`` (and possible other modules), making this a subtle bug specially susceptible when used with ``from __future__ import unicode_literals``. Improved Documentation ---------------------- - `3928 <https://github.com/pytest-dev/pytest/issues/3928>`_: Add possible values for fixture scope to docs. ```

Links

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

jason-neal / companion_simulations