jason-neal / companion_simulations

Simulating combined host+companion spectra, and fitting to observed crires spectra.
MIT License
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Scheduled monthly dependency update for October #72

Closed pyup-bot closed 5 years ago

pyup-bot commented 5 years ago

Update ephem from 3.7.6.0 to 3.7.7.0.

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Links - PyPI: https://pypi.org/project/ephem - Homepage: http://rhodesmill.org/pyephem/

Update joblib from 0.13.2 to 0.14.0.

Changelog ### 0.14.0 ``` -------------- - Improved the load balancing between workers to avoid stranglers caused by an excessively large batch size when the task duration is varying significantly (because of the combined use of ``joblib.Parallel`` and ``joblib.Memory`` with a partially warmed cache for instance). https://github.com/joblib/joblib/pull/899 - Add official support for Python 3.8: fixed protocol number in `Hasher` and updated tests. - Fix a deadlock when using the dask backend (when scattering large numpy arrays). https://github.com/joblib/joblib/pull/914 - Warn users that they should never use `joblib.load` with files from untrusted sources. Fix security related API change introduced in numpy 1.6.3 that would prevent using joblib with recent numpy versions. https://github.com/joblib/joblib/pull/879 - Upgrade to cloudpickle 1.1.1 that add supports for the upcoming Python 3.8 release among other things. https://github.com/joblib/joblib/pull/878 - Fix semaphore availability checker to avoid spawning resource trackers on module import. https://github.com/joblib/joblib/pull/893 - Fix the oversubscription protection to only protect against nested `Parallel` calls. This allows `joblib` to be run in background threads. https://github.com/joblib/joblib/pull/934 - Fix `ValueError` (negative dimensions) when pickling large numpy arrays on Windows. https://github.com/joblib/joblib/pull/920 - Upgrade to loky 2.6.0 that add supports for the setting environment variables in child before loading any module. https://github.com/joblib/joblib/pull/940 - Fix the oversubscription protection for native libraries using threadpools (OpenBLAS, MKL, Blis and OpenMP runtimes). The maximal number of threads is can now be set in children using the ``inner_max_num_threads`` in ``parallel_backend``. It defaults to ``cpu_count() // n_jobs``. https://github.com/joblib/joblib/pull/940 ```
Links - PyPI: https://pypi.org/project/joblib - Changelog: https://pyup.io/changelogs/joblib/ - Docs: https://joblib.readthedocs.io

Update numba from 0.45.0 to 0.45.1.

Changelog ### 0.45.1 ``` -------------- This patch release addresses some regressions reported in the 0.45.0 release and ```
Links - PyPI: https://pypi.org/project/numba - Changelog: https://pyup.io/changelogs/numba/ - Repo: http://numba.github.com

Update numpy from 1.17.0 to 1.17.2.

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Links - PyPI: https://pypi.org/project/numpy - Homepage: https://www.numpy.org

Update multiprocess from 0.70.8 to 0.70.9.

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Links - PyPI: https://pypi.org/project/multiprocess - Changelog: https://pyup.io/changelogs/multiprocess/ - Repo: https://github.com/uqfoundation/multiprocess/releases/download/multiprocess-0.70.9/multiprocess-0.70.9.tar.gz - Homepage: https://pypi.org/project/multiprocess

Update pandas from 0.25.0 to 0.25.1.

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

Update scipy from 1.3.0 to 1.3.1.

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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 sqlalchemy from 1.3.6 to 1.3.8.

Changelog ### 1.3.8 ``` :released: August 27, 2019 .. change:: :tags: bug, orm :tickets: 4823 Fixed bug where :class:`.Load` objects were not pickleable due to mapper/relationship state in the internal context dictionary. These objects are now converted to picklable using similar techniques as that of other elements within the loader option system that have long been serializable. .. change:: :tags: bug, postgresql :tickets: 4623 Revised the approach for the just added support for the psycopg2 "execute_values()" feature added in 1.3.7 for :ticket:`4623`. The approach relied upon a regular expression that would fail to match for a more complex INSERT statement such as one which had subqueries involved. The new approach matches exactly the string that was rendered as the VALUES clause. .. change:: :tags: usecase, orm :tickets: 4285 Added support for the use of an :class:`.Enum` datatype using Python pep-435 enumeration objects as values for use as a primary key column mapped by the ORM. As these values are not inherently sortable, as required by the ORM for primary keys, a new :attr:`.TypeEngine.sort_key_function` attribute is added to the typing system which allows any SQL type to implement a sorting for Python objects of its type which is consulted by the unit of work. The :class:`.Enum` type then defines this using the database value of a given enumeration. The sorting scheme can be also be redefined by passing a callable to the :paramref:`.Enum.sort_key_function` parameter. Pull request courtesy Nicolas Caniart. .. change:: :tags: bug, engine :tickets: 4807 Fixed an issue whereby if the dialect "initialize" process which occurs on first connect would encounter an unexpected exception, the initialize process would fail to complete and then no longer attempt on subsequent connection attempts, leaving the dialect in an un-initialized, or partially initialized state, within the scope of parameters that need to be established based on inspection of a live connection. The "invoke once" logic in the event system has been reworked to accommodate for this occurrence using new, private API features that establish an "exec once" hook that will continue to allow the initializer to fire off on subsequent connections, until it completes without raising an exception. This does not impact the behavior of the existing ``once=True`` flag within the event system. .. change:: :tags: bug, sqlite, reflection :tickets: 4810 Fixed bug where a FOREIGN KEY that was set up to refer to the parent table by table name only without the column names would not correctly be reflected as far as setting up the "referred columns", since SQLite's PRAGMA does not report on these columns if they weren't given explicitly. For some reason this was harcoded to assume the name of the local column, which might work for some cases but is not correct. The new approach reflects the primary key of the referred table and uses the constraint columns list as the referred columns list, if the remote column(s) aren't present in the reflected pragma directly. .. change:: :tags: bug, postgresql :tickets: 4822 Fixed bug where Postgresql operators such as :meth:`.postgresql.ARRAY.Comparator.contains` and :meth:`.postgresql.ARRAY.Comparator.contained_by` would fail to function correctly for non-integer values when used against a :class:`.postgresql.array` object, due to an erroneous assert statement. .. change:: :tags: feature, engine :tickets: 4815 Added new parameter :paramref:`.create_engine.hide_parameters` which when set to True will cause SQL parameters to no longer be logged, nor rendered in the string representation of a :class:`.StatementError` object. .. change:: :tags: usecase, postgresql :tickets: 4824 Added support for reflection of CHECK constraints that include the special PostgreSQL qualifier "NOT VALID", which can be present for CHECK constraints that were added to an exsiting table with the directive that they not be applied to existing data in the table. The PostgreSQL dictionary for CHECK constraints as returned by :meth:`.Inspector.get_check_constraints` may include an additional entry ``dialect_options`` which within will contain an entry ``"not_valid": True`` if this symbol is detected. Pull request courtesy Bill Finn. .. changelog:: ``` ### 1.3.7 ``` :released: August 14, 2019 .. change:: :tags: bug, sql :tickets: 4778 Fixed issue where :class:`.Index` object which contained a mixture of functional expressions which were not resolvable to a particular column, in combination with string-based column names, would fail to initialize its internal state correctly leading to failures during DDL compilation. .. change:: :tags: bug, sqlite :tickets: 4798 The dialects that support json are supposed to take arguments ``json_serializer`` and ``json_deserializer`` at the create_engine() level, however the SQLite dialect calls them ``_json_serilizer`` and ``_json_deserilalizer``. The names have been corrected, the old names are accepted with a change warning, and these parameters are now documented as :paramref:`.create_engine.json_serializer` and :paramref:`.create_engine.json_deserializer`. .. change:: :tags: bug, mysql :tickets: 4804 The MySQL dialects will emit "SET NAMES" at the start of a connection when charset is given to the MySQL driver, to appease an apparent behavior observed in MySQL 8.0 that raises a collation error when a UNION includes string columns unioned against columns of the form CAST(NULL AS CHAR(..)), which is what SQLAlchemy's polymorphic_union function does. The issue seems to have affected PyMySQL for at least a year, however has recently appeared as of mysqlclient 1.4.4 based on changes in how this DBAPI creates a connection. As the presence of this directive impacts three separate MySQL charset settings which each have intricate effects based on their presense, SQLAlchemy will now emit the directive on new connections to ensure correct behavior. .. change:: :tags: usecase, postgresql :tickets: 4623 Added new dialect flag for the psycopg2 dialect, ``executemany_mode`` which supersedes the previous experimental ``use_batch_mode`` flag. ``executemany_mode`` supports both the "execute batch" and "execute values" functions provided by psycopg2, the latter which is used for compiled :func:`.insert` constructs. Pull request courtesy Yuval Dinari. .. seealso:: :ref:`psycopg2_executemany_mode` .. change:: :tags: bug, sql :tickets: 4787 Fixed bug where :meth:`.TypeEngine.column_expression` method would not be applied to subsequent SELECT statements inside of a UNION or other :class:`.CompoundSelect`, even though the SELECT statements are rendered at the topmost level of the statement. New logic now differentiates between rendering the column expression, which is needed for all SELECTs in the list, vs. gathering the returned data type for the result row, which is needed only for the first SELECT. .. change:: :tags: bug, sqlite :tickets: 4793 Fixed bug where usage of "PRAGMA table_info" in SQLite dialect meant that reflection features to detect for table existence, list of table columns, and list of foreign keys, would default to any table in any attached database, when no schema name was given and the table did not exist in the base schema. The fix explicitly runs PRAGMA for the 'main' schema and then the 'temp' schema if the 'main' returned no rows, to maintain the behavior of tables + temp tables in the "no schema" namespace, attached tables only in the "schema" namespace. .. change:: :tags: bug, sql :tickets: 4780 Fixed issue where internal cloning of SELECT constructs could lead to a key error if the copy of the SELECT changed its state such that its list of columns changed. This was observed to be occurring in some ORM scenarios which may be unique to 1.3 and above, so is partially a regression fix. .. change:: :tags: bug, orm :tickets: 4777 Fixed regression caused by new selectinload for many-to-one logic where a primaryjoin condition not based on real foreign keys would cause KeyError if a related object did not exist for a given key value on the parent object. .. change:: :tags: usecase, mysql :tickets: 4783 Added reserved words ARRAY and MEMBER to the MySQL reserved words list, as MySQL 8.0 has now made these reserved. .. change:: :tags: bug, events :tickets: 4794 Fixed issue in event system where using the ``once=True`` flag with dynamically generated listener functions would cause event registration of future events to fail if those listener functions were garbage collected after they were used, due to an assumption that a listened function is strongly referenced. The "once" wrapped is now modified to strongly reference the inner function persistently, and documentation is updated that using "once" does not imply automatic de-registration of listener functions. .. change:: :tags: bug, mysql :tickets: 4751 Added another fix for an upstream MySQL 8 issue where a case sensitive table name is reported incorrectly in foreign key constraint reflection, this is an extension of the fix first added for :ticket:`4344` which affects a case sensitive column name. The new issue occurs through MySQL 8.0.17, so the general logic of the 88718 fix remains in place. .. seealso:: https://bugs.mysql.com/bug.php?id=96365 - upstream bug .. change:: :tags: usecase, mssql :tickets: 4782 Added new :func:`.mssql.try_cast` construct for SQL Server which emits "TRY_CAST" syntax. Pull request courtesy Leonel Atencio. .. change:: :tags: bug, orm :tickets: 4803 Fixed bug where using :meth:`.Query.first` or a slice expression in conjunction with a query that has an expression based "offset" applied would raise TypeError, due to an "or" conditional against "offset" that did not expect it to be a SQL expression as opposed to an integer or None. .. changelog:: ```
Links - PyPI: https://pypi.org/project/sqlalchemy - Changelog: https://pyup.io/changelogs/sqlalchemy/ - Homepage: http://www.sqlalchemy.org

Update tqdm from 4.32.2 to 4.36.1.

Changelog ### 4.36.0 ``` - expose more custom format params - potential thread safety fix (548) - update submodule architecture (198 -> 800) + backward-compatibility + expose `utils` + rename `main` -> `cli` + add/fix tests + fix minor cached var optimisation + `gui` partial upgrade (790) + `notebook` upgrade (790) * support `{bar}` in `bar_format` (594) * inherit methods including `set_*(refresh)` (740 -> 741) + ready for `contrib` releases (252) - support custom `bar_format` with unknown `total` - fix `tqdm_notebook` red block on explicit `file=None` (791) - update notebook to fully support custom `bar_format` (594, 649) - misc tidy + warnings + linting + update submodule contribution guide (252) + parallel `(py)make test` + fix Zenodo metadata - update documentation + `pandas`, `notebook`, `gui` (245) + indentation + update multiprocessing and multithreading examples (796) ``` ### 4.35.0 ``` - add `{bar}` format specifier (623 -> 799) + `[width][type]` - add tests and documentation - update performance tests ``` ### 4.34.0 ``` - add `leave=None` convenience option for `leave = position == 0` - ensure nested completed bars respect `leave=True` (230) - ensure nested bars are cleared before being moved up (795) - support both ` ` and `=` syntax for CLI options (761 -> 774) - misc documentation updates (778, 782) - fix/update tests - update GitHub docker package deployment ``` ### 4.33.0 ``` - fix `pandas==0.25` API change (780) - add contributor badges (`sourcerer`) - fix py26 travis CI - metadata fixes + `.zenodo.json` + `CODEOWNERS` - GitHub package registry docker deployment - minor linting - documentation updates (773) ```
Links - PyPI: https://pypi.org/project/tqdm - Changelog: https://pyup.io/changelogs/tqdm/ - Repo: https://github.com/tqdm/tqdm

Update hypothesis from 4.32.2 to 4.37.0.

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

Update pytest from 5.0.1 to 5.2.0.

Changelog ### 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. - `5523 <https://github.com/pytest-dev/pytest/issues/5523>`_: Fixed using multiple short options together in the command-line (for example ``-vs``) in Python 3.8+. - `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 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
pyup-bot commented 5 years ago

Closing this in favor of #73