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jason-neal / companion_simulations

Simulating combined host+companion spectra, and fitting to observed crires spectra.
MIT License
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Scheduled biweekly dependency update for week 17 #47

Closed pyup-bot closed 6 years ago

pyup-bot commented 6 years ago

Update astropy from 3.0.1 to 3.0.2.

Changelog ### 3.0.2 ``` ================== Bug Fixes --------- astropy.config ^^^^^^^^^^^^^^ astropy.constants ^^^^^^^^^^^^^^^^^ astropy.convolution ^^^^^^^^^^^^^^^^^^^ astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Computing a 3D separation between two ``SkyCoord`` objects (with the ``separation_3d`` method) now works with or without velocity data attached to the objects. [7387] astropy.cosmology ^^^^^^^^^^^^^^^^^ astropy.extern ^^^^^^^^^^^^^^ astropy.io.ascii ^^^^^^^^^^^^^^^^ astropy.io.fits ^^^^^^^^^^^^^^^ astropy.io.misc ^^^^^^^^^^^^^^^ astropy.io.registry ^^^^^^^^^^^^^^^^^^^ astropy.io.votable ^^^^^^^^^^^^^^^^^^ - Fix validate with xmllint=True. [7255, 7283] astropy.modeling ^^^^^^^^^^^^^^^^ - ``FittingWithOutlierRemoval`` now handles model sets, as long as the underlying fitter supports masked values. [7199] - Remove assumption that ``model_set_axis == 0`` for 2D models in ``LinearLSQFitter``. [7317, 7199] - Fix the shape of the outputs when a model set is evaluated with ``model_set_axis=False`` . [7317] - Fix behaviour of certain models with units, by making certain unit-related attributes readonly. [7210] - Add a ``Multiply`` model which preseves unit through evaluate, unlike ``Scale`` which is dimensionless. [7210] astropy.nddata ^^^^^^^^^^^^^^ astropy.samp ^^^^^^^^^^^^ astropy.stats ^^^^^^^^^^^^^ - Accept a tuple for the ``axis`` parameter in ``sigma_clip``, like the underlying ``numpy`` functions and some other functions in ``stats``. [7199] astropy.table ^^^^^^^^^^^^^ astropy.tests ^^^^^^^^^^^^^ - The function ``quantity_allclose`` was moved to the ``units`` package with the new, shorter name ``allclose``. This eliminates a runtime dependency on ``pytest`` which was causing issues for some affiliated packages. The old import will continue to work but may be deprecated in the future. [7252] astropy.time ^^^^^^^^^^^^ astropy.units ^^^^^^^^^^^^^ - ``u.quantity_input`` no longer errors if the return annotation for a function is ``None``. [7336] - Added a units-aware ``allclose`` function (this was previously available in the ``tests`` module as ``quantity_allclose``). To complement ``allclose``, a new ``isclose`` function is also added and backported. [7252] astropy.utils ^^^^^^^^^^^^^ astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ astropy.wcs ^^^^^^^^^^^ ```
Links - PyPI: https://pypi.org/project/astropy - Changelog: https://pyup.io/changelogs/astropy/ - Homepage: http://astropy.org

Update numba from 0.37.0 to 0.38.0.

Changelog ### 0.38.0 ``` -------------- Following on from the bug fix focus of the last release, this release swings back towards the addition of new features and usability improvements based on community feedback. This release is comparatively large! Three key features/ changes to note are: * Numba (via llvmlite) is now backed by LLVM 6.0, general vectorization is improved as a result. A significant long standing LLVM bug that was causing corruption was also found and fixed. * Further considerable improvements in vectorization are made available as Numba now supports Intel's short vector math library (SVML). Try it out with `conda install -c numba icc_rt`. * CUDA 8.0 is now the minimum supported CUDA version. Other highlights include: * Bug fixes to `parallel=True` have enabled more vectorization opportunities when using the ParallelAccelerator technology. * Much effort has gone into improving error reporting and the general usability of Numba. This includes highlighted error messages and performance tips documentation. Try it out with `conda install colorama`. * A number of new NumPy functions are supported, `np.convolve`, `np.correlate` `np.reshape`, `np.transpose`, `np.permutation`, `np.real`, `np.imag`, and `np.searchsorted` now supports the`side` kwarg. Further, `np.argsort` now supports the `kind` kwarg with `quicksort` and `mergesort` available. * The Numba extension API has gained the ability operate more easily with functions from Cython modules through the use of `numba.extending.get_cython_function_address` to obtain function addresses for direct use in `ctypes.CFUNCTYPE`. * Numba now allows the passing of jitted functions (and containers of jitted functions) as arguments to other jitted functions. * The CUDA functionality has gained support for a larger selection of bit manipulation intrinsics, also SELP, and has had a number of bugs fixed. * Initial work to support the PPC64LE platform has been added, full support is however waiting on the LLVM 6.0.1 release as it contains critical patches not present in 6.0.0. It is hoped that any remaining issues will be fixed in the next release. * The capacity for advanced users/compiler engineers to define their own compilation pipelines. Enhancements: * PR 2660: Support bools from cffi in nopython. * PR 2741: Enhance error message for undefined variables. * PR 2744: Add diagnostic error message to test suite discovery failure. * PR 2748: Added Intel SVML optimizations as opt-out choice working by default * PR 2762: Support transpose with axes arguments. * PR 2777: Add support for np.correlate and np.convolve * PR 2779: Implement np.random.permutation * PR 2801: Passing jitted functions as args * PR 2802: Support np.real() and np.imag() * PR 2807: Expose `import_cython_function` * PR 2821: Add kwarg 'side' to np.searchsorted * PR 2822: Adds stable argsort * PR 2832: Fixups for llvmlite 0.23/llvm 6 * PR 2836: Support `index` method on tuples * PR 2839: Support for np.transpose and np.reshape. * PR 2843: Custom pipeline * PR 2847: Replace signed array access indices in unsiged prange loop body * PR 2859: Add support for improved error reporting. * PR 2880: This adds a github issue template. * PR 2881: Build recipe to clone Intel ICC runtime. * PR 2882: Update TravisCI to test SVML * PR 2893: Add reference to the data buffer in array.ctypes object * PR 2895: Move to CUDA 8.0 Fixes: * PR 2737: Fix 2007 (part 1). Empty array handling in np.linalg. * PR 2738: Fix install_requires to allow pip getting pre-release version * PR 2740: Fix 2208. Generate better error message. * PR 2765: Fix Bit-ness * PR 2780: PowerPC reference counting memory fences * PR 2805: Fix six imports. * PR 2813: Fix 2812: gufunc scalar output bug. * PR 2814: Fix the build post 2727 * PR 2831: Attempt to fix 2473 * PR 2842: Fix issue with test discovery and broken CUDA drivers. * PR 2850: Add rtsys init guard and test. * PR 2852: Skip vectorization test with targets that are not x86 * PR 2856: Prevent printing to stdout in `test_extending.py` * PR 2864: Correct C code to prevent compiler warnings. * PR 2889: Attempt to fix 2386. * PR 2891: Removed test skipping for inspect_cfg * PR 2898: Add guard to parallel test on unsupported platforms * PR 2907: Update change log for PPC64LE LLVM dependency. * PR 2911: Move build requirement to llvmlite>=0.23.0dev0 * PR 2912: Fix random permutation test. * PR 2914: Fix MD list syntax in issue template. Documentation Updates: * PR 2739: Explicitly state default value of error_model in docstring * PR 2803: DOC: parallel vectorize requires signatures * PR 2829: Add Python 2.7 EOL plan to docs * PR 2838: Use automatic numbering syntax in list. * PR 2877: Add performance tips documentation. * PR 2883: Fix 2872: update rng doc about thread/fork-safety * PR 2908: Add missing link and ref to docs. * PR 2909: Tiny typo correction ParallelAccelerator enhancements/fixes: * PR 2727: Changes to enable vectorization in ParallelAccelerator. * PR 2816: Array analysis for transpose with arbitrary arguments * PR 2874: Fix dead code eliminator not to remove a call with side-effect * PR 2886: Fix ParallelAccelerator arrayexpr repr CUDA enhancements: * PR 2734: More Constants From cuda.h * PR 2767: Add len(..) Support to DeviceNDArray * PR 2778: Add More Device Array API Functions to CUDA Simulator * PR 2824: Add CUDA Primitives for Population Count * PR 2835: Emit selp Instructions to Avoid Branching * PR 2867: Full support for CUDA device attributes CUDA fixes: * PR 2768: Don't Compile Code on Every Assignment * PR 2878: Fixes a Win64 issue with the test in Pr/2865 Contributors: The following people contributed to this release. * Abutalib Aghayev * Alex Olivas * Anton Malakhov * Dong-hee Na * Ehsan Totoni (core dev) * John Zwinck * Josh Wilson * Kelsey Jordahl * Nick White * Olexa Bilaniuk * Rik-de-Kort * Siu Kwan Lam (core dev) * Stan Seibert (core dev) * Stuart Archibald (core dev) * Thomas Arildsen * Todd A. Anderson (core dev) ```
Links - PyPI: https://pypi.org/project/numba - Changelog: https://pyup.io/changelogs/numba/ - Repo: http://numba.github.com

Update numpy from 1.14.2 to 1.14.3.

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

Update scipy from 1.0.0 to 1.0.1.

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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 1.2.5 to 1.2.7.

Changelog ### 1.2.7 ``` :released: April 20, 2018 .. change:: :tags: bug, orm :tickets: 4228 Fixed regression in 1.2 within sharded query feature where the new "identity_token" element was not being correctly considered within the scope of a lazy load operation, when searching the identity map for a related many-to-one element. The new behavior will allow for making use of the "id_chooser" in order to determine the best identity key to retrieve from the identity map. In order to achieve this, some refactoring of 1.2's "identity_token" approach has made some slight changes to the implementation of ``ShardedQuery`` which should be noted for other derivations of this class. .. change:: :tags: bug, postgresql :tickets: 4229 Fixed bug where the special "not equals" operator for the Postgresql "range" datatypes such as DATERANGE would fail to render "IS NOT NULL" when compared to the Python ``None`` value. .. change:: :tags: bug, mssql :tickets: 4234 :versions: 1.3.0b1 Fixed 1.2 regression caused by :ticket:`4060` where the query used to reflect SQL Server cross-schema foreign keys was limiting the criteria incorrectly. .. change:: :tags: bug, oracle :versions: 1.3.0b1 The Oracle NUMBER datatype is reflected as INTEGER if the precision is NULL and the scale is zero, as this is how INTEGER values come back when reflected from Oracle's tables. Pull request courtesy Kent Bower. .. change:: :tags: feature, postgresql :tickets: 4160 :versions: 1.3.0b1 Added new PG type :class:`.postgresql.REGCLASS` which assists in casting table names to OID values. Pull request courtesy Sebastian Bank. .. change:: :tags: bug, sql :tickets: 4231 :versions: 1.3.0b1 Fixed issue where the compilation of an INSERT statement with the "literal_binds" option that also uses an explicit sequence and "inline" generation, as on Postgresql and Oracle, would fail to accommodate the extra keyword argument within the sequence processing routine. .. change:: :tags: bug, orm :tickets: 4241 Fixed issue in single-inheritance loading where the use of an aliased entity against a single-inheritance subclass in conjunction with the :meth:`.Query.select_from` method would cause the SQL to be rendered with the unaliased table mixed in to the query, causing a cartesian product. In particular this was affecting the new "selectin" loader when used against a single-inheritance subclass. .. changelog:: ``` ### 1.2.6 ``` :released: March 30, 2018 .. change:: :tags: bug, mssql :tickets: 4227 :versions: 1.3.0b1 Adjusted the SQL Server version detection for pyodbc to only allow for numeric tokens, filtering out non-integers, since the dialect does tuple- numeric comparisons with this value. This is normally true for all known SQL Server / pyodbc drivers in any case. .. change:: :tags: feature, postgresql :versions: 1.3.0b1 Added support for "PARTITION BY" in Postgresql table definitions, using "postgresql_partition_by". Pull request courtesy Vsevolod Solovyov. .. change:: :tags: bug, sql :tickets: 4204 :versions: 1.3.0b1 Fixed a regression that occurred from the previous fix to :ticket:`4204` in version 1.2.5, where a CTE that refers to itself after the :meth:`.CTE.alias` method has been called would not refer to iself correctly. .. change:: :tags: bug, engine :tickets: 4225 :versions: 1.3.0b1 Fixed bug in connection pool where a connection could be present in the pool without all of its "connect" event handlers called, if a previous "connect" handler threw an exception; note that the dialects themselves have connect handlers that emit SQL, such as those which set transaction isolation, which can fail if the database is in a non-available state, but still allows a connection. The connection is now invalidated first if any of the connect handlers fail. .. change:: :tags: bug, oracle :tickets: 4211 :versions: 1.3.0b1 The minimum cx_Oracle version supported is 5.2 (June 2015). Previously, the dialect asserted against version 5.0 but as of 1.2.2 we are using some symbols that did not appear until 5.2. .. change:: :tags: bug, declarative :tickets: 4221 Removed a warning that would be emitted when calling upon ``__table_args__``, ``__mapper_args__`` as named with a ``declared_attr`` method, when called from a non-mapped declarative mixin. Calling these directly is documented as the approach to use when one is overidding one of these methods on a mapped class. The warning still emits for regular attribute names. .. change:: :tags: bug, orm :tickets: 4215 :versions: 1.3.0b1 Fixed bug where using :meth:`.Mutable.associate_with` or :meth:`.Mutable.as_mutable` in conjunction with a class that has non- primary mappers set up with alternatively-named attributes would produce an attribute error. Since non-primary mappers are not used for persistence, the mutable extension now excludes non-primary mappers from its instrumentation steps. .. changelog:: ```
Links - PyPI: https://pypi.org/project/sqlalchemy - Changelog: https://pyup.io/changelogs/sqlalchemy/ - Homepage: http://www.sqlalchemy.org

Update tqdm from 4.19.8 to 4.23.1.

Changelog ### 4.23.1 ``` - fix `AttributeError`s (546) + `pos` on initialisation (323, 510 -> 544) + `fp` on `write()` (383) - fix py34 CI - update documentation ``` ### 4.23.0 ``` - Fix `disable=True` where`iterable` has no `len()` and is not `None` (539) - Add `ncols` to specify `tqdm_notebook` bar width (276 -> 292) - allow custom `pandas` `total` (364 -> 535) - Add `progress_apply` for `pandas.(Series|DataFrame).(rolling|expanding)` (530 -> 537) - unit tests, pep8 tidy - `postfix` non-`dict` documentation note ``` ### 4.22.0 ``` - allow direct non-string assignment to `postfix` member (lists, dicts, etc) (382 -> 534) - documentation updates - unit tests ``` ### 4.21.0 ``` - fix 532 `write()` with manual `position` + more robust free position finding - add `TqdmWarning` base class - fix GUI `__del__()` + add `TqdmExperimentalWarning` - add, tidy & fix unit tests - documentation + wiki release notes + update contributors + fix `7zx` example ``` ### 4.20.0 ``` - `pandas` wrapper: remove `*args` and add better `total` handling (244, 299, 322, 366 -> 524) - document windows unicode know issues (454) - suppress `RuntimeError: Set changed size during iteration` -> `TqdmSynchronisationWarning` (481) ``` ### 4.19.9 ``` - fix monitor thread termination and update tests (527) ```
Links - PyPI: https://pypi.org/project/tqdm - Changelog: https://pyup.io/changelogs/tqdm/ - Repo: https://github.com/tqdm/tqdm/issues

Update codacy-coverage from 1.3.10 to 1.3.11.

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Links - PyPI: https://pypi.org/project/codacy-coverage - Changelog: https://pyup.io/changelogs/codacy-coverage/ - Repo: https://github.com/codacy/python-codacy-coverage

Update hypothesis from 3.50.2 to 3.56.5.

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Links - PyPI: https://pypi.org/project/hypothesis - Repo: https://github.com/HypothesisWorks/hypothesis/issues

Update pytest from 3.4.2 to 3.5.1.

Changelog ### 3.5.0 ``` ========================= Deprecations and Removals ------------------------- - ``record_xml_property`` fixture is now deprecated in favor of the more generic ``record_property``. (`2770 <https://github.com/pytest-dev/pytest/issues/2770>`_) - Defining ``pytest_plugins`` is now deprecated in non-top-level conftest.py files, because they "leak" to the entire directory tree. (`3084 <https://github.com/pytest-dev/pytest/issues/3084>`_) Features -------- - New ``--show-capture`` command-line option that allows to specify how to display captured output when tests fail: ``no``, ``stdout``, ``stderr``, ``log`` or ``all`` (the default). (`1478 <https://github.com/pytest-dev/pytest/issues/1478>`_) - New ``--rootdir`` command-line option to override the rules for discovering the root directory. See `customize <https://docs.pytest.org/en/latest/customize.html>`_ in the documentation for details. (`1642 <https://github.com/pytest-dev/pytest/issues/1642>`_) - Fixtures are now instantiated based on their scopes, with higher-scoped fixtures (such as ``session``) being instantiated first than lower-scoped fixtures (such as ``function``). The relative order of fixtures of the same scope is kept unchanged, based in their declaration order and their dependencies. (`2405 <https://github.com/pytest-dev/pytest/issues/2405>`_) - ``record_xml_property`` renamed to ``record_property`` and is now compatible with xdist, markers and any reporter. ``record_xml_property`` name is now deprecated. (`2770 <https://github.com/pytest-dev/pytest/issues/2770>`_) - New ``--nf``, ``--new-first`` options: run new tests first followed by the rest of the tests, in both cases tests are also sorted by the file modified time, with more recent files coming first. (`3034 <https://github.com/pytest-dev/pytest/issues/3034>`_) - New ``--last-failed-no-failures`` command-line option that allows to specify the behavior of the cache plugin's --last-failed`` feature when no tests failed in the last run (or no cache was found): ``none`` or ``all`` (the default). (`3139 <https://github.com/pytest-dev/pytest/issues/3139>`_) - New ``--doctest-continue-on-failure`` command-line option to enable doctests to show multiple failures for each snippet, instead of stopping at the first failure. (`3149 <https://github.com/pytest-dev/pytest/issues/3149>`_) - Captured log messages are added to the ``<system-out>`` tag in the generated junit xml file if the ``junit_logging`` ini option is set to ``system-out``. If the value of this ini option is ``system-err`, the logs are written to ``<system-err>``. The default value for ``junit_logging`` is ``no``, meaning captured logs are not written to the output file. (`3156 <https://github.com/pytest-dev/pytest/issues/3156>`_) - Allow the logging plugin to handle ``pytest_runtest_logstart`` and ``pytest_runtest_logfinish`` hooks when live logs are enabled. (`3189 <https://github.com/pytest-dev/pytest/issues/3189>`_) - Passing `--log-cli-level` in the command-line now automatically activates live logging. (`3190 <https://github.com/pytest-dev/pytest/issues/3190>`_) - Add command line option ``--deselect`` to allow deselection of individual tests at collection time. (`3198 <https://github.com/pytest-dev/pytest/issues/3198>`_) - Captured logs are printed before entering pdb. (`3204 <https://github.com/pytest-dev/pytest/issues/3204>`_) - Deselected item count is now shown before tests are run, e.g. ``collected X items / Y deselected``. (`3213 <https://github.com/pytest-dev/pytest/issues/3213>`_) - The builtin module ``platform`` is now available for use in expressions in ``pytest.mark``. (`3236 <https://github.com/pytest-dev/pytest/issues/3236>`_) - The *short test summary info* section now is displayed after tracebacks and warnings in the terminal. (`3255 <https://github.com/pytest-dev/pytest/issues/3255>`_) - New ``--verbosity`` flag to set verbosity level explicitly. (`3296 <https://github.com/pytest-dev/pytest/issues/3296>`_) - ``pytest.approx`` now accepts comparing a numpy array with a scalar. (`3312 <https://github.com/pytest-dev/pytest/issues/3312>`_) Bug Fixes --------- - Suppress ``IOError`` when closing the temporary file used for capturing streams in Python 2.7. (`2370 <https://github.com/pytest-dev/pytest/issues/2370>`_) - Fixed ``clear()`` method on ``caplog`` fixture which cleared ``records``, but not the ``text`` property. (`3297 <https://github.com/pytest-dev/pytest/issues/3297>`_) - During test collection, when stdin is not allowed to be read, the ``DontReadFromStdin`` object still allow itself to be iterable and resolved to an iterator without crashing. (`3314 <https://github.com/pytest-dev/pytest/issues/3314>`_) Improved Documentation ---------------------- - Added a `reference <https://docs.pytest.org/en/latest/reference.html>`_ page to the docs. (`1713 <https://github.com/pytest-dev/pytest/issues/1713>`_) Trivial/Internal Changes ------------------------ - Change minimum requirement of ``attrs`` to ``17.4.0``. (`3228 <https://github.com/pytest-dev/pytest/issues/3228>`_) - Renamed example directories so all tests pass when ran from the base directory. (`3245 <https://github.com/pytest-dev/pytest/issues/3245>`_) - Internal ``mark.py`` module has been turned into a package. (`3250 <https://github.com/pytest-dev/pytest/issues/3250>`_) - ``pytest`` now depends on the `more-itertools <https://github.com/erikrose/more-itertools>`_ package. (`3265 <https://github.com/pytest-dev/pytest/issues/3265>`_) - Added warning when ``[pytest]`` section is used in a ``.cfg`` file passed with ``-c`` (`3268 <https://github.com/pytest-dev/pytest/issues/3268>`_) - ``nodeids`` can now be passed explicitly to ``FSCollector`` and ``Node`` constructors. (`3291 <https://github.com/pytest-dev/pytest/issues/3291>`_) - Internal refactoring of ``FormattedExcinfo`` to use ``attrs`` facilities and remove old support code for legacy Python versions. (`3292 <https://github.com/pytest-dev/pytest/issues/3292>`_) - Refactoring to unify how verbosity is handled internally. (`3296 <https://github.com/pytest-dev/pytest/issues/3296>`_) - Internal refactoring to better integrate with argparse. (`3304 <https://github.com/pytest-dev/pytest/issues/3304>`_) - Fix a python example when calling a fixture in doc/en/usage.rst (`3308 <https://github.com/pytest-dev/pytest/issues/3308>`_) ```
Links - PyPI: https://pypi.org/project/pytest - Changelog: https://pyup.io/changelogs/pytest/ - Repo: https://github.com/pytest-dev/pytest/issues - Homepage: http://pytest.org