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jason-neal / companion_simulations

Simulating combined host+companion spectra, and fitting to observed crires spectra.
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Scheduled monthly dependency update for February #75

Closed pyup-bot closed 4 years ago

pyup-bot commented 4 years ago

Update astropy from 3.2.3 to 4.0.

Changelog ### 4.0 ``` ================ New Features ------------ astropy.config ^^^^^^^^^^^^^^ - The config and cache directories and the name of the config file are now customizable. This allows affiliated packages to put their configuration files in locations other than ``CONFIG_DIR/.astropy/``. [8237] astropy.constants ^^^^^^^^^^^^^^^^^ - The version of constants can be specified via ScienceState in a way that ``constants`` and ``units`` will be consistent. [8517] - Default constants now use CODATA 2018 and IAU 2015 definitions. [8761] - Constants can be pickled and unpickled. [9377] astropy.convolution ^^^^^^^^^^^^^^^^^^^ - Fixed a bug [9168] where having a kernel defined using unitless astropy quantity objects would result in a crash [9300] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Changed ``coordinates.solar_system_ephemeris`` to also accept local files as input. The ephemeris can now be selected by either keyword (e.g. 'jpl', 'de430'), URL or file path. [8767] - Added a ``cylindrical`` property to ``SkyCoord`` for shorthand access to a ``CylindricalRepresentation`` of the coordinate, as is already available for other common representations. [8857] - The default parameters for the ``Galactocentric`` frame are now controlled by a ``ScienceState`` subclass, ``galactocentric_frame_defaults``. New parameter sets will be added to this object periodically to keep up with ever-improved measurements of the solar position and motion. [9346] - Coordinate frame classes can now have multiple aliases by assigning a list of aliases to the class variable ``name``. Any of the aliases can be used for attribute-style access or as the target of ``tranform_to()`` calls. [8834] - Passing a NaN to ``Distance`` no longer raises a warning. [9598] astropy.cosmology ^^^^^^^^^^^^^^^^^ - The pre-publication Planck 2018 cosmological parameters are included as the ``Planck2018_arXiv_v2`` object. Please note that the values are preliminary, and when the paper is accepted a final version will be included as ``Planck18``. [8111] astropy.extern ^^^^^^^^^^^^^^ - Remove the bundled ``six`` module. [8315] astropy.io.ascii ^^^^^^^^^^^^^^^^ - Removed incorrect warnings on ``Overflow`` when reading in ``FloatType`` 0.0 with ``use_fast_converter``; synchronised ``IntType`` ``Overflow`` warning messages. [9082] astropy.io.misc ^^^^^^^^^^^^^^^ - Eliminate deprecated compatibility mode when writing ``Table`` metadata to HDF5 format. [8899] - Add support for orthogonal polynomial models to ASDF. [9107] astropy.io.fits ^^^^^^^^^^^^^^^ - Changed the ``fitscheck`` and ``fitsdiff`` script to use the ``argparse`` module instead of ``optparse``. [9148] - Allow writing of ``Table`` objects with ``Time`` columns that are also table indices to FITS files. [8077] astropy.io.registry ^^^^^^^^^^^^^^^^^^^ astropy.io.votable ^^^^^^^^^^^^^^^^^^ - Support VOTable version 1.4. The main addition is the new element, TIMESYS, which allows defining of metadata for temporal coordinates much like COOSYS defines metadata for celestial coordinates. [9475] astropy.logger ^^^^^^^^^^^^^^ - Added a configuration option to specify the text encoding of the log file, with the default behavior being the platform-preferred encoding. [9203] astropy.modeling ^^^^^^^^^^^^^^^^ - Major rework of modeling internals. See modeling documentation for details. `<https://docs.astropy.org/en/latest/modeling/changes_for_4.html>`_ . [8769] - Significant reorganization of the documentation. [9078, 9171] - Add ``Tabular1D.inverse`` [9083] - ``Model.rename`` was changed to add the ability to rename ``Model.inputs`` and ``Model.outputs``. [9220] - New function ``fix_inputs`` to generate new models from others by fixing specific inputs variable values to constants. [9135] - ``inputs`` and ``outputs`` are now model instance attributes, and ``n_inputs`` and ``n_outputs`` are class attributes. Backwards compatible default values of ``inputs`` and ``outputs`` are generated. ``Model.inputs`` and ``Model.outputs`` are now settable which allows renaming them on per user case. [9298] - Add a new model representing a sequence of rotations in 3D around an arbitrary number of axes. [9369] - Add many of the numpy ufunc functions as models. [9401] - Add ``BlackBody`` model. Deprecate ``BlackBody1D`` model and ``blackbody_nu`` and ``blackbody_lambda`` functions. [9282] - Add ``Drude1D`` model. [9452] - Added analytical King model (KingProjectedAnalytic1D) [9084] - Added Exponential1D and Logarithmic1D models [9351] astropy.nddata ^^^^^^^^^^^^^^ - Add a way for technically invalid but unambiguous units in a fits header to be parsed by ``CCDData``. [9397] - ``NDData`` now only accepts WCS objects which implement either the high, or low level APE 14 WCS API. All WCS objects are converted to a high level WCS object, so ``NDData.wcs`` now always returns a high level APE 14 object. Not all array slices are valid for wcs objects, so some slicing operations which used to work may now fail. [9067] astropy.samp ^^^^^^^^^^^^ astropy.stats ^^^^^^^^^^^^^ - The ``biweight_location``, ``biweight_scale``, and ``biweight_midvariance`` functions now allow for the ``axis`` keyword to be a tuple of integers. [9309] - Added an ``ignore_nan`` option to the ``biweight_location``, ``biweight_scale``, and ``biweight_midvariance`` functions. [9457] - A numpy ``MaskedArray`` can now be input to the ``biweight_location``, ``biweight_scale``, and ``biweight_midvariance`` functions. [9466] - Removed the warning related to p0 in the Bayesian blocks algorithm. The caveat related to p0 is described in the docstring for ``Events``. [9567] astropy.table ^^^^^^^^^^^^^ - Improved the implementation of ``Table.replace_column()`` to provide a speed-up of 5 to 10 times for wide tables. The method can now accept any input which convertible to a column of the correct length, not just ``Column`` subclasses.[8902] - Improved the implementation of ``Table.add_column()`` to provide a speed-up of 2 to 10 (or more) when adding a column to tables, with increasing benefit as the number of columns increases. The method can now accept any input which is convertible to a column of the correct length, not just ``Column`` subclasses. [8933] - Changed the implementation of ``Table.add_columns()`` to use the new ``Table.add_column()`` method. In most cases the performance is similar or slightly faster to the previous implemenation. [8933] - ``MaskedColumn.data`` will now return a plain ``MaskedArray`` rather than the previous (unintended) ``masked_BaseColumn``. [8855] - Added depth-wise stacking ``dstack()`` in higher level table operation. It help will in stacking table column depth-wise. [8939] - Added a new table equality method ``values_equal()`` which allows comparison table values to another table, list, or value, and returns an element-by-element equality table. [9068] - Added new ``join_type='cartesian'`` option to the ``join`` operation. [9288] - Allow adding a table column as a list of mixin-type objects, for instance ``t['q'] = [1 * u.m, 2 * u.m]``. [9165] - Allow table ``join()`` using any sortable key column (e.g. Time), not just ndarray subclasses. A column is considered sortable if there is a ``<column>.info.get_sortable_arrays()`` method that is implemented. [9340] - Added ``Table.iterrows()`` for making row-wise iteration faster. [8969] - Allow table to be initialized with a list of dict where the dict keys are not the same in every row. The table column names are the set of all keys found in the input data, and any missing key/value pairs are turned into missing data in the table. [9425] - Prevent unnecessary ERFA warnings when indexing by ``Time`` columns. [9545] - Added support for sorting tables which contain non-mutable mixin columns (like ``SkyCoord``) for which in-place item update is not allowed. [9549] - Ensured that inserting ``np.ma.masked`` (or any other value with a mask) into a ``MaskedColumn`` causes a masked entry to be inserted. [9623] - Fixed a bug that caused an exception when initializing a ``MaskedColumn`` from another ``MaskedColumn`` that has a structured dtype. [9651] astropy.tests ^^^^^^^^^^^^^ - The plugin that handles the custom header in the test output has been moved to the ``pytest-astropy-header plugin`` package. See the README at https://github.com/astropy/pytest-astropy-header for information about using this new plugin. [9214] astropy.time ^^^^^^^^^^^^ - Added a new time format ``ymdhms`` for representing times via year, month, day, hour, minute, and second attributes. [7644] - ``TimeDelta`` gained a ``to_value`` method, so that it becomes easier to use it wherever a ``Quantity`` with units of time could be used. [8762] - Made scalar ``Time`` and ``TimeDelta`` objects hashable based on JD, time scale, and location attributes. [8912] - Improved error message when bad input is used to initialize a ``Time`` or ``TimeDelta`` object and the format is specified. [9296] - Allow numeric time formats to be initialized with numpy ``longdouble``, ``Decimal`` instances, and strings. One can select just one of these using ``in_subfmt``. The output can be similarly set using ``out_subfmt``. [9361] - Introduce a new ``.to_value()`` method for ``Time`` (and adjusted the existing method for ``TimeDelta``) so that one can get values in a given ``format`` and possible ``subfmt`` (e.g., ``to_value('mjd', 'str')``. [9361] - Prevent unecessary ERFA warnings when sorting ``Time`` objects. [9545] astropy.timeseries ^^^^^^^^^^^^^^^^^^ - Addig ``epoch_phase``, ``wrap_phase`` and ``normalize_phase`` keywords to ``TimeSeries.fold()`` to control the phase of the epoch and to return normalized phase rather than time for the folded TimeSeries. [9455] astropy.uncertainty ^^^^^^^^^^^^^^^^^^^ - ``Distribution`` was rewritten such that it deals better with subclasses. As a result, Quantity distributions now behave correctly with ``to`` methods yielding new distributions of the kind expected for the starting distribution, and ``to_value`` yielding ``NdarrayDistribution`` instances. [9429, 9442] - The ``pdf_*`` properties that were used to calculate statistical properties of ``Distrubution`` instances were changed into methods. This allows one to pass parameters such as ``ddof`` to ``pdf_std`` and ``pdf_var`` (which generally should equal 1 instead of the default 0), and reflects that these are fairly involved calcuations, not just "properties". [9613] astropy.units ^^^^^^^^^^^^^ - Support for unicode parsing. Supported at the moment are superscripts, Ohm, Ångström, and the micro-sign. [9348] - Accept non-unit type annotations in quantity_input. [8984] - For numpy 1.17 and later, the new ``__array_function__`` protocol is used to ensure that all top-level numpy functions interact properly with ``Quantity``, preserving units also in operations like ``np.concatenate``. [8808] - Add equivalencies for surface brightness units to spectral_density. [9282] astropy.utils ^^^^^^^^^^^^^ - ``astropy.utils.data.download_file`` and ``astropy.utils.data.get_readable_fileobj`` now provides an ``http_headers`` keyword to pass in specific request headers for the download. It also now defaults to providing ``User-Agent: Astropy`` and ``Accept: */*`` headers. The default ``User-Agent`` value can be set with a new ``astropy.data.conf.default_http_user_agent`` configuration item. [9508, 9564] - Added a new ``astropy.utils.misc.unbroadcast`` function which can be used to return the smallest array that can be broadcasted back to the initial array. [9209] - The specific IERS Earth rotation parameter table used for time and coordinate transformations can now be set, either in a context or per session, using ``astropy.utils.iers.earth_rotation_table``. [9244] - Added ``export_cache`` and ``import_cache`` to permit transporting downloaded data to machines with no Internet connection. Several new functions are available to investigate the cache contents; e.g., ``check_download_cache`` can be used to confirm that the persistent cache has not become damaged. [9182] - A new ``astropy.utils.iers.LeapSeconds`` class has been added to track leap seconds. [9365] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Added a new ``time_support`` context manager/function for making it easy to plot and format ``Time`` objects in Matplotlib. [8782] - Added support for plotting any WCS compliant with the generalized (APE 14) WCS API with WCSAxes. [8885, 9098] - Improved display of information when inspecting ``WCSAxes.coords``. [9098] - Improved error checking for the ``slices=`` argument to ``WCSAxes``. [9098] - Added support for more solar frames in WCSAxes. [9275] - Add support for one dimensional plots to ``WCSAxes``. [9266] - Add a ``get_format_unit`` to ``wcsaxes.CoordinateHelper``. [9392] - ``WCSAxes`` now, by default, sets a default label for plot axes which is the WCS physical type (and unit) for that axis. This can be disabled using the ``coords[i].set_auto_axislabel(False)`` or by explicitly setting an axis label. [9392] - Fixed the display of tick labels when plotting all sky images that have a coord_wrap less than 360. [9542] astropy.wcs ^^^^^^^^^^^ - Added a ``astropy.wcs.wcsapi.pixel_to_pixel`` function that can be used to transform pixel coordinates in one dataset with a WCS to pixel coordinates in another dataset with a different WCS. This function is designed to be efficient when the input arrays are broadcasted views of smaller arrays. [9209] - Added a ``local_partial_pixel_derivatives`` function that can be used to determine a matrix of partial derivatives of each world coordinate with respect to each pixel coordinate. [9392] - Updated wcslib to v6.4. [9125] - Improved the ``SlicedLowLevelWCS`` class in ``astropy.wcs.wcsapi`` to avoid storing chains of nested ``SlicedLowLevelWCS`` objects when applying multiple slicing operations in turn. [9210] - Added a ``wcs_info_str`` function to ``astropy.wcs.wcsapi`` to show a summary of an APE-14-compliant WCS as a string. [8546, 9207] - Added two new optional attributes to the APE 14 low-level WCS: ``pixel_axis_names`` and ``world_axis_names``. [9156] - Updated the WCS class to now correctly take and return ``Time`` objects in the high-level APE 14 API (e.g. ``pixel_to_world``. [9376] - ``SlicedLowLevelWCS`` now raises ``IndexError`` rather than ``ValueError`` on an invalid slice. [9067] - Added ``fit_wcs_from_points`` function to ``astropy.wcs.utils``. Fits a WCS object to set of matched detector/sky coordinates. [9469] - Fix various bugs in ``SlicedLowLevelWCS`` when the WCS being sliced was one dimensional. [9693] API Changes ----------- astropy.config ^^^^^^^^^^^^^^ astropy.constants ^^^^^^^^^^^^^^^^^ - Deprecated ``set_enabled_constants`` context manager. Use ``astropy.physical_constants`` and ``astropy.astronomical_constants``. [9025] astropy.convolution ^^^^^^^^^^^^^^^^^^^ - Removed the deprecated keyword argument ``interpolate_nan`` from ``convolve_fft``. [9356] - Removed the deprecated keyword argument ``stddev`` from ``Gaussian2DKernel``. [9356] - Deprecated and renamed ``MexicanHat1DKernel`` and ``MexicanHat2DKernel`` to ``RickerWavelet1DKernel`` and ``RickerWavelet2DKernel``. [9445] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Removed the ``recommended_units`` attribute from Representations; it was deprecated since 3.0. [8892] - Removed the deprecated frame attribute classes, ``FrameAttribute``, ``TimeFrameAttribute``, ``QuantityFrameAttribute``,``CartesianRepresentationFrameAttribute``; deprecated since 3.0. [9326] - Removed ``longitude`` and ``latitude`` attributes from ``EarthLocation``; deprecated since 2.0. [9326] - The ``DifferentialAttribute`` for frame classes now passes through any input to the ``allowed_classes`` if only one allowed class is specified, i.e. this now allows passing a quantity in for frame attributes that use ``DifferentialAttribute``. [9325] - Removed the deprecated ``galcen_ra`` and ``galcen_dec`` attributes from the ``Galactocentric`` frame. [9346] astropy.cosmology ^^^^^^^^^^^^^^^^^ astropy.extern ^^^^^^^^^^^^^^ astropy.io.ascii ^^^^^^^^^^^^^^^^ - Masked column handling has changed, see ``astropy.table`` entry below. [8789] astropy.io.misc ^^^^^^^^^^^^^^^ - Masked column handling has changed, see ``astropy.table`` entry below. [8789] - Removed deprecated ``usecPickle`` kwarg from ``fnunpickle`` and ``fnpickle``. [8890] astropy.io.fits ^^^^^^^^^^^^^^^ - Masked column handling has changed, see ``astropy.table`` entry below. [8789] - ``io.fits.Header`` has been made safe for subclasses for copying and slicing. As a result of this change, the private subclass ``CompImageHeader`` now always should be passed an explicit ``image_header``. [9229] - Removed the deprecated ``tolerance`` option in ``fitsdiff`` and ``io.fits.diff`` classes. [9520] - Removed deprecated keyword arguments for ``CompImageHDU``: ``compressionType``, ``tileSize``, ``hcompScale``, ``hcompSmooth``, ``quantizeLevel``. [9520] astropy.io.registry ^^^^^^^^^^^^^^^^^^^ astropy.io.votable ^^^^^^^^^^^^^^^^^^ - Changed ``pedantic`` argument to ``verify`` and change it to have three string-based options (``ignore``, ``warn``, and ``exception``) instead of just being a boolean. In addition, changed default to ``ignore``, which means that warnings will not be shown by default when loading VO tables. [8715] astropy.modeling ^^^^^^^^^^^^^^^^ - Eliminates support for compound classes (but not compound instances!) [8769] - Slicing compound models more restrictive. [8769] - Shape of parameters now includes n_models as dimension. [8769] - Parameter instances now hold values instead of models. [8769] - Compound model parameters now share instance and value with constituent models. [8769] - No longer possible to assign slices of parameter values to model parameters attribute (it is possible to replace it with a complete array). [8769] - Many private attributes and methods have changed (see documentation). [8769] - The deprecated ``rotations.rotation_matrix_from_angle`` was removed. [9363] - Deprecated and renamed ``MexicanHat1D`` and ``MexicanHat2D`` to ``RickerWavelet1D`` and ``RickerWavelet2D``. [9445] - Deprecated ``modeling.utils.ExpressionTree``. [9576] astropy.nddata ^^^^^^^^^^^^^^ astropy.samp ^^^^^^^^^^^^ astropy.stats ^^^^^^^^^^^^^ - Removed the ``iters`` keyword from sigma clipping stats functions. [8948] - Renamed the ``a`` parameter to ``data`` in biweight stat functions. [8948] - Renamed the ``a`` parameter to ``data`` in ``median_absolute_deviation``. [9011] - Renamed the ``conflevel`` keyword to ``confidence_level`` in ``poisson_conf_interval``. Usage of ``conflevel`` now issues ``AstropyDeprecationWarning``. [9408] - Renamed the ``conf`` keyword to ``confidence_level`` in ``binom_conf_interval`` and ``binned_binom_proportion``. Usage of ``conf`` now issues ``AstropyDeprecationWarning``. [9408] - Renamed the ``conf_lvl`` keyword to ``confidence_level`` in ``jackknife_stats``. Usage of ``conf_lvl`` now issues ``AstropyDeprecationWarning``. [9408] astropy.table ^^^^^^^^^^^^^ - The handling of masked columns in the ``Table`` class has changed in a way that may impact program behavior. Now a ``Table`` with ``masked=False`` may contain both ``Column`` and ``MaskedColumn`` objects, and adding a masked column or row to a table no longer "upgrades" the table and columns to masked. This means that tables with masked data which are read via ``Table.read()`` will now always have ``masked=False``, though specific columns will be masked as needed. Two new table properties ``has_masked_columns`` and ``has_masked_values`` were added. See the ``Masking change in astropy 4.0`` section within `<https://docs.astropy.org/en/latest/table/masking.html>`_ for details. [8789] - Table operation functions such as ``join``, ``vstack``, ``hstack``, etc now always return a table with ``masked=False``, though the individual columns may be masked as necessary. [8957] - Changed implementation of ``Table.add_column()`` and ``Table.add_columns()`` methods. Now it is possible add any object(s) which can be converted or broadcasted to a valid column for the table. ``Table.__setitem__`` now just calls ``add_column``. - Changed default table configuration setting ``replace_warnings`` from ``['slice']`` to ``[]``. This removes the default warning when replacing a table column that is a slice of another column. [9144] - Removed the non-public method ``astropy.table.np_utils.recarray_fromrecords``. [9165] astropy.tests ^^^^^^^^^^^^^ - In addition to ``DeprecationWarning``, now ``FutureWarning`` and ``ImportWarning`` would also be turned into exceptions. [8506] - ``warnings_to_ignore_by_pyver`` option in ``enable_deprecations_as_exceptions()`` has changed. Please refer to API documentation. [8506] - Default settings for ``warnings_to_ignore_by_pyver`` are updated to remove very old warnings that are no longer relevant and to add a new warning caused by ``pytest-doctestplus``. [8506] astropy.time ^^^^^^^^^^^^ - ``Time.get_ut1_utc`` now uses the auto-updated ``IERS_Auto`` by default, instead of the bundled ``IERS_B`` file. [9226] - Time formats that do not use ``val2`` now raise ValueError instead of silently ignoring a provided value. [9373] - Custom time formats can now accept floating-point types with extended precision. Existing time formats raise exceptions rather than discarding extended precision through conversion to ordinary floating-point. [9368] - Time formats (implemented in subclasses of ``TimeFormat``) now have their input and output routines more thoroughly validated, making it more difficult to create damaged ``Time`` objects. [9375] - The ``TimeDelta.to_value()`` method now can also take the ``format`` name as its argument, in which case the value will be calculated using the ``TimeFormat`` machinery. For this case, one can also pass a ``subfmt`` argument to retrieve the value in another form than ``float``. [9361] astropy.timeseries ^^^^^^^^^^^^^^^^^^ - Keyword ``midpoint_epoch`` is renamed to ``epoch_time``. [9455] astropy.uncertainty ^^^^^^^^^^^^^^^^^^^ - ``Distribution`` was rewritten such that it deals better with subclasses. As a result, Quantity distributions now behave correctly with ``to`` methods yielding new distributions of the kind expected for the starting distribution, and ``to_value`` yielding ``NdarrayDistribution`` instances. [9442] astropy.units ^^^^^^^^^^^^^ - For consistency with ``ndarray``, scalar ``Quantity.value`` will now return a numpy scalar rather than a python one. This should help keep track of precision better, but may lead to unexpected results for the rare cases where numpy scalars behave differently than python ones (e.g., taking the square root of a negative number). [8876] - Removed the ``magnitude_zero_points`` module, which was deprecated in favour of ``astropy.units.photometric`` since 3.1. [9353] - ``EquivalentUnitsList`` now has a ``_repr_html_`` method to output a HTML table on a call to ``find_equivalent_units`` in Jupyter notebooks. [9495] astropy.utils ^^^^^^^^^^^^^ - ``download_file`` and related functions now accept a list of fallback sources, and they are able to update the cache at the user's request. [9182] - Allow ``astropy.utils.console.ProgressBarOrSpinner.map`` and ``.map_unordered`` to take an argument ``multiprocessing_start_method`` to control how subprocesses are started; the different methods (``fork``, ``spawn``, and ``forkserver``) have different implications in terms of security, efficiency, and behavioural anomalies. The option is useful in particular for cross-platform testing because Windows supports only ``spawn`` while Linux defaults to ``fork``. [9182] - All operations that act on the astropy download cache now take an argument ``pkgname`` that allows one to specify which package's cache to use. [8237, 9182] - Removed deprecated ``funcsigs`` and ``futures`` from ``astropy.utils.compat``. [8909] - Removed the deprecated ``astropy.utils.compat.numpy`` module. [8910] - Deprecated ``InheritDocstrings`` as it is natively supported by Sphinx 1.7 or higher. [8881] - Deprecated ``astropy.utils.timer`` module, which has been moved to ``astroquery.utils.timer`` and will be part of ``astroquery`` 0.4.0. [9038] - Deprecated ``astropy.utils.misc.set_locale`` function, as it is meant for internal use only. [9471] - The implementation of ``data_info.DataInfo`` has changed (for a considerable performance boost). Generally, this should not affect simple subclasses, but because the class now uses ``__slots__`` any attributes on the class have to be explicitly given a slot. [8998] - ``IERS`` tables now use ``nan`` to mark missing values (rather than ``1e20``). [9226] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - The default ``clip`` value is now ``False`` in ``ImageNormalize``. [9478] - The default ``clip`` value is now ``False`` in ``simple_norm``. [9698] - Infinite values are now excluded when calculating limits in ``ManualInterval`` and ``MinMaxInterval``. They were already excluded in all other interval classes. [9480] astropy.wcs ^^^^^^^^^^^ Bug Fixes --------- astropy.config ^^^^^^^^^^^^^^ astropy.constants ^^^^^^^^^^^^^^^^^ astropy.convolution ^^^^^^^^^^^^^^^^^^^ astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - The ``QuantityAttribute`` class now supports a None default value if a unit is specified. [9345] - When ``Representation`` classes with the same name are defined, this no longer leads to a ``ValueError``, but instead to a warning and the removal of both from the name registry (i.e., one either has to use the class itself to set, e.g., ``representation_type``, or refer to the class by its fully qualified name). [8561] astropy.cosmology ^^^^^^^^^^^^^^^^^ astropy.extern ^^^^^^^^^^^^^^ astropy.io.ascii ^^^^^^^^^^^^^^^^ astropy.io.misc ^^^^^^^^^^^^^^^ astropy.io.fits ^^^^^^^^^^^^^^^ - Implemented skip (after warning) of header cards with reserved keywords in ``table_to_hdu``. [9390] - Add ``AstropyDeprecationWarning`` to ``read_table_fits`` when ``hdu=`` is selected, but does not match single present table HDU. [9512] astropy.io.registry ^^^^^^^^^^^^^^^^^^^ astropy.io.votable ^^^^^^^^^^^^^^^^^^ - Address issue 8995 by ignoring BINARY2 null mask bits for string values on parsing a VOTable. In this way, the reader should never create masked values for string types. [9057] - Corrected a spurious warning issued for the ``value`` attribute of the ``<OPTION>`` element in VOTable, as well as a test that erroneously treated the warning as acceptable. [9470] astropy.modeling ^^^^^^^^^^^^^^^^ astropy.nddata ^^^^^^^^^^^^^^ - ``Cutout2D`` will now get the WCS from its first argument if that argument has with WCS property. [9492] - ``overlap_slices`` will now raise a ``ValueError`` if the input position contains any non-finite values (e.g. NaN or inf). [9648] astropy.samp ^^^^^^^^^^^^ astropy.stats ^^^^^^^^^^^^^ - Fixed a bug where ``bayesian_blocks`` returned a single edge. [8560] - Fixed input data type validation for ``bayesian_blocks`` to work int arrays. [9513] astropy.table ^^^^^^^^^^^^^ - Fix bug where adding a column consisting of a list of masked arrays was dropping the masks. [9048] - ``Quantity`` columns with custom units can now round-trip via FITS tables, as long as the custom unit is enabled during reading (otherwise, the unit will become an ``UnrecognizedUnit``). [9015] - Fix bug where string values could be truncated when inserting into a ``Column`` or ``MaskedColumn``, or when adding or inserting a row containing string values. [9559] astropy.tests ^^^^^^^^^^^^^ astropy.time ^^^^^^^^^^^^ - Fix bug when ``Time`` object is created with only masked elements. [9624] astropy.timeseries ^^^^^^^^^^^^^^^^^^ astropy.uncertainty ^^^^^^^^^^^^^^^^^^^ astropy.units ^^^^^^^^^^^^^ - Ensure that output from test functions of and comparisons between quantities can be stored into pre-allocated output arrays (using ``out=array``) [9273] astropy.utils ^^^^^^^^^^^^^ - For the default ``IERS_Auto`` table, which combines IERS A and B values, the IERS nutation parameters "dX_2000A" and "dY_2000A" are now also taken from the actual IERS B file rather than from the B values stored in the IERS A file. Any differences should be negligible for any practical application, but this may help exactly reproducing results. [9237] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Calling ``WCSAxes.set_axis_off()`` now correctly turns off drawing the Axes. [9411] - Fix incorrect transformation behavior in ``WCSAxes.plot_coord`` and correctly handle when input coordinates are not already in spherical representations. [8927] - Fixed ``ImageNormalize`` so that when it is intialized without ``data`` it will still use the input ``interval`` class. [9698] - Fixed ``ImageNormalize`` to handle input data with non-finite values. [9698] astropy.wcs ^^^^^^^^^^^ - Fix incorrect value returned by ``wcsapi.HighLevelWCSWrapper.axis_correlation_matrix``. [9554] - ``FITSWCSAPIMixin`` now returns tuples not lists from ``pixel_to_world`` and ``world_to_pixel``. [9678] - Fix NaN-masking of world coordinates when some but not all of the coordinates were flagged as invalid by WCSLIB. This occurred for example with WCS with >2 dimensions where two of the dimensions were celestial coordinates and pixel coordinates ouside of the 'sky' were converted to world coordinates - previously all world coordinates were masked even if uncorrelated with the celestial axes, but this is no longer the case. [9688] Other Changes and Additions --------------------------- - Versions of Python <3.6 are no longer supported. [8955] - Matplotlib 2.1 and later is now required. [8787] - Versions of Numpy <1.16 are no longer supported. [9292] - Updated the bundled CFITSIO library to 3.470. See ``cextern/cfitsio/docs/changes.txt`` for additional information. [9233] - The bundled ERFA was updated to version 1.6.0 (based on SOFA 20190722). This includes a fix that avoids precision loss for negative JDs. [9323] - The leap seconds in the bundled ERFA library are now updated automatically. [9365] - The default server for the IERS data files has been updated to reflect long-term downtime of the canonical USNO server. [9487, 9508] ```
Links - PyPI: https://pypi.org/project/astropy - Changelog: https://pyup.io/changelogs/astropy/ - Homepage: http://astropy.org

Update matplotlib from 3.1.1 to 3.1.2.

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

Update joblib from 0.14.0 to 0.14.1.

Changelog ### 0.14.1 ``` -------------- - Configure the loky workers' environment to mitigate oversubsription with nested multi-threaded code in the following case: - allow for a suitable number of threads for numba (``NUMBA_NUM_THREADS``); - enable Interprocess Communication for scheduler coordination when the nested code uses Threading Building Blocks (TBB) (``ENABLE_IPC=1``) https://github.com/joblib/joblib/pull/951 - Fix a regression where the loky backend was not reusing previously spawned workers. https://github.com/joblib/joblib/pull/968 - Revert https://github.com/joblib/joblib/pull/847 to avoid using `pkg_resources` that introduced a performance regression under Windows: https://github.com/joblib/joblib/issues/965 ```
Links - PyPI: https://pypi.org/project/joblib - Changelog: https://pyup.io/changelogs/joblib/ - Docs: https://joblib.readthedocs.io

Update numba from 0.46.0 to 0.48.0.

Changelog ### 0.48.0 ``` ----------------------------- This release is particularly small as it was present to catch anything that missed the 0.47.0 deadline (the deadline deliberately coincided with the end of support for Python 2.7). The next release will be considerably larger. The core changes in this release are dominated by the start of the clean up needed for the end of Python 2.7 support, improvements to the CUDA target and support for numerous additional unicode string methods. Enhancements from user contributed PRs (with thanks!): * Brian Wignall fixed more spelling typos in 4998. * Denis Smirnov added support for string methods ``capitalize`` (4823), ``casefold`` (4824), ``swapcase`` (4825), ``rsplit`` (4834), ``partition`` (4845) and ``splitlines`` (4849). * Elena Totmenina extended support for string methods ``startswith`` (4867) and added ``endswith`` (4868). * Eric Wieser made ``type_callable`` return the decorated function itself in 4760 * Ethan Pronovost added support for ``np.argwhere`` in 4617 * Graham Markall contributed a large number of CUDA enhancements and fixes, namely: * 5068: Remove Python 3.4 backports from utils * 4975: Make ``device_array_like`` create contiguous arrays (Fixes 4832) * 5023: Don't launch ForAll kernels with 0 elements (Fixes 5017) * 5016: Fix various issues in CUDA library search (Fixes 4979) * 5014: Enable use of records and bools for shared memory, remove ddt, add additional transpose tests * 4964: Fix 4628: Add more appropriate typing for CUDA device arrays * 5007: test_consuming_strides: Keep dev array alive * 4997: State that CUDA Toolkit 8.0 required in docs * James Bourbeau added the Python 3.8 classifier to setup.py in 5027. * John Kirkham added a clarification to the ``__cuda_array_interface__`` documentation in 5049. * Leo Fang Fixed an indexing problem in ``dummyarray`` in 5012. * Marcel Bargull fixed a build and test issue for Python 3.8 in 5029. * Maria Rubtsov added support for string methods ``isdecimal`` (4842), ``isdigit`` (4843), ``isnumeric`` (4844) and ``replace`` (4865). General Enhancements: * PR 4760: Make type_callable return the decorated function * PR 5010: merge string prs This merge PR included the following: * PR 4823: Implement str.capitalize() based on CPython * PR 4824: Implement str.casefold() based on CPython * PR 4825: Implement str.swapcase() based on CPython * PR 4834: Implement str.rsplit() based on CPython * PR 4842: Implement str.isdecimal * PR 4843: Implement str.isdigit * PR 4844: Implement str.isnumeric * PR 4845: Implement str.partition() based on CPython * PR 4849: Implement str.splitlines() based on CPython * PR 4865: Implement str.replace * PR 4867: Functionality extension str.startswith() based on CPython * PR 4868: Add functionality for str.endswith() * PR 5039: Disable help messages. * PR 4617: Add coverage for ``np.argwhere`` Fixes: * PR 4724: Only use lives (and not aliases) to create post parfor live set. * PR 4998: Fix more spelling typos * PR 5024: Propagate semantic constants ahead of static rewrites. * PR 5027: Add Python 3.8 classifier to setup.py * PR 5046: Update setup.py and buildscripts for dependency requirements * PR 5053: Convert from arrays to names in define() and don't invalidate for multiple consistent defines. * PR 5058: Permit mixed int types in wrap_index * PR 5078: Catch the use of global typed-list in JITed functions * PR 5092: Fix 5087, bug in bytecode analysis. CUDA Enhancements/Fixes: * PR 4964: Fix 4628: Add more appropriate typing for CUDA device arrays * PR 4975: Make ``device_array_like`` create contiguous arrays (Fixes 4832) * PR 4997: State that CUDA Toolkit 8.0 required in docs * PR 5007: test_consuming_strides: Keep dev array alive * PR 5012: Fix IndexError when accessing the "-1" element of dummyarray * PR 5014: Enable use of records and bools for shared memory, remove ddt, add additional transpose tests * PR 5016: Fix various issues in CUDA library search (Fixes 4979) * PR 5023: Don't launch ForAll kernels with 0 elements (Fixes 5017) * PR 5068: Remove Python 3.4 backports from utils Documentation Updates: * PR 5049: Clarify what dictionary means * PR 5062: Update docs for updated version requirements * PR 5090: Update deprecation notices for 0.48.0 CI updates: * PR 5029: Install optional dependencies for Python 3.8 tests * PR 5040: Drop Py2.7 and Py3.5 from public CI * PR 5048: Fix CI py38 Authors: * Brian Wignall * Denis Smirnov * Elena Totmenina * Eric Wieser * Ethan Pronovost * Graham Markall * James Bourbeau * John Kirkham * Leo Fang * Marcel Bargull * Maria Rubtsov * Siu Kwan Lam (core dev) * Stan Seibert (core dev) * Stuart Archibald (core dev) * Todd A. Anderson (core dev) * Valentin Haenel (core dev) ``` ### 0.47.0 ``` ----------------------------- This release expands the capability of Numba in a number of important areas and is also significant as it is the last major point release with support for Python 2 and Python 3.5 included. The next release (0.48.0) will be for Python ```
Links - PyPI: https://pypi.org/project/numba - Changelog: https://pyup.io/changelogs/numba/ - Repo: http://numba.github.com

Update numpy from 1.17.3 to 1.18.1.

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

Update pandas from 0.25.3 to 1.0.0.

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

Update scipy from 1.3.1 to 1.4.1.

Changelog ### 1.4.1 ``` compared to `1.4.0`. Importantly, it aims to fix a problem where an older version of `pybind11` may cause a segmentation fault when imported alongside incompatible libraries. Authors ======= * Ralf Gommers * Tyler Reddy ``` ### 1.4.0 ``` many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with ``python -Wd`` and check for ``DeprecationWarning`` s). Our development attention will now shift to bug-fix releases on the 1.4.x branch, and on adding new features on the master branch. This release requires Python 3.5+ and NumPy `>=1.13.3` (for Python 3.5, 3.6), `>=1.14.5` (for Python 3.7), `>= 1.17.3` (for Python 3.8) For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. Highlights of this release --------------------------- - a new submodule, `scipy.fft`, now supersedes `scipy.fftpack`; this means support for ``long double`` transforms, faster multi-dimensional transforms, improved algorithm time complexity, release of the global intepreter lock, and control over threading behavior - support for ``pydata/sparse`` arrays in `scipy.sparse.linalg` - substantial improvement to the documentation and functionality of several `scipy.special` functions, and some new additions - the generalized inverse Gaussian distribution has been added to `scipy.stats` - an implementation of the Edmonds-Karp algorithm in `scipy.sparse.csgraph.maximum_flow` - `scipy.spatial.SphericalVoronoi` now supports n-dimensional input, has linear memory complexity, improved performance, and supports single-hemisphere generators New features ============ Infrastructure ---------------- Documentation can now be built with ``runtests.py --doc`` A ``Dockerfile`` is now available in the ``scipy/scipy-dev`` repository to facilitate getting started with SciPy development. `scipy.constants` improvements -------------------------------- `scipy.constants` has been updated with the CODATA 2018 constants. `scipy.fft` added ------------------- `scipy.fft` is a new submodule that supersedes the `scipy.fftpack` submodule. For the most part, this is a drop-in replacement for ``numpy.fft`` and `scipy.fftpack` alike. With some important differences, `scipy.fft`: - uses NumPy's conventions for real transforms (``rfft``). This means the return value is a complex array, half the size of the full ``fft`` output. This is different from the output of ``fftpack`` which returned a real array representing complex components packed together. - the inverse real to real transforms (``idct`` and ``idst``) are normalized for ``norm=None`` in thesame way as ``ifft``. This means the identity ``idct(dct(x)) == x`` is now ``True`` for all norm modes. - does not include the convolutions or pseudo-differential operators from ``fftpack``. This submodule is based on the ``pypocketfft`` library, developed by the author of ``pocketfft`` which was recently adopted by NumPy as well. ``pypocketfft`` offers a number of advantages over fortran ``FFTPACK``: - support for long double (``np.longfloat``) precision transforms. - faster multi-dimensional transforms using vectorisation - Bluestein’s algorithm removes the worst-case ``O(n^2)`` complexity of ``FFTPACK`` - the global interpreter lock (``GIL``) is released during transforms - optional multithreading of multi-dimensional transforms via the ``workers`` argument Note that `scipy.fftpack` has not been deprecated and will continue to be maintained but is now considered legacy. New code is recommended to use `scipy.fft` instead, where possible. `scipy.fftpack` improvements -------------------------------- `scipy.fftpack` now uses pypocketfft to perform its FFTs, offering the same speed and accuracy benefits listed for scipy.fft above but without the improved API. `scipy.integrate` improvements -------------------------------- The function `scipy.integrate.solve_ivp` now has an ``args`` argument. This allows the user-defined functions passed to the function to have additional parameters without having to create wrapper functions or lambda expressions for them. `scipy.integrate.solve_ivp` can now return a ``y_events`` attribute representing the solution of the ODE at event times New ``OdeSolver`` is implemented --- ``DOP853``. This is a high-order explicit Runge-Kutta method originally implemented in Fortran. Now we provide a pure Python implementation usable through ``solve_ivp`` with all its features. `scipy.integrate.quad` provides better user feedback when break points are specified with a weighted integrand. `scipy.integrate.quad_vec` is now available for general purpose integration of vector-valued functions `scipy.interpolate` improvements ---------------------------------- `scipy.interpolate.pade` now handles complex input data gracefully `scipy.interpolate.Rbf` can now interpolate multi-dimensional functions `scipy.io` improvements ------------------------- `scipy.io.wavfile.read` can now read data from a `WAV` file that has a malformed header, similar to other modern `WAV` file parsers `scipy.io.FortranFile` now has an expanded set of available ``Exception`` classes for handling poorly-formatted files `scipy.linalg` improvements ----------------------------- The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct results for complex-valued matrices. Before this, the function only returned correct values for real-valued matrices. New boolean keyword argument ``check_finite`` for `scipy.linalg.norm`; whether to check that the input matrix contains only finite numbers. Disabling may give a performance gain, but may result in problems (crashes, non-termination) if the inputs do contain infinities or NaNs. `scipy.linalg.solve_triangular` has improved performance for a C-ordered triangular matrix ``LAPACK`` wrappers have been added for ``?geequ``, ``?geequb``, ``?syequb``, and ``?heequb`` Some performance improvements may be observed due to an internal optimization in operations involving LAPACK routines via ``_compute_lwork``. This is particularly true for operations on small arrays. Block ``QR`` wrappers are now available in `scipy.linalg.lapack` `scipy.ndimage` improvements ------------------------------ `scipy.optimize` improvements -------------------------------- It is now possible to use linear and non-linear constraints with `scipy.optimize.differential_evolution`. `scipy.optimize.linear_sum_assignment` has been re-written in C++ to improve performance, and now allows input costs to be infinite. A ``ScalarFunction.fun_and_grad`` method was added for convenient simultaneous retrieval of a function and gradient evaluation `scipy.optimize.minimize` ``BFGS`` method has improved performance by avoiding duplicate evaluations in some cases Better user feedback is provided when an objective function returns an array instead of a scalar. `scipy.signal` improvements ----------------------------- Added a new function to calculate convolution using the overlap-add method, named `scipy.signal.oaconvolve`. Like `scipy.signal.fftconvolve`, this function supports specifying dimensions along which to do the convolution. `scipy.signal.cwt` now supports complex wavelets. The implementation of ``choose_conv_method`` has been updated to reflect the new FFT implementation. In addition, the performance has been significantly improved (with rather drastic improvements in edge cases). The function ``upfirdn`` now has a ``mode`` keyword argument that can be used to select the signal extension mode used at the signal boundaries. These modes are also available for use in ``resample_poly`` via a newly added ``padtype`` argument. `scipy.signal.sosfilt` now benefits from Cython code for improved performance `scipy.signal.resample` should be more efficient by leveraging ``rfft`` when possible `scipy.sparse` improvements ------------------------------- It is now possible to use the LOBPCG method in `scipy.sparse.linalg.svds`. `scipy.sparse.linalg.LinearOperator` now supports the operation ``rmatmat`` for adjoint matrix-matrix multiplication, in addition to ``rmatvec``. Multiple stability updates enable float32 support in the LOBPCG eigenvalue solver for symmetric and Hermitian eigenvalues problems in ``scipy.sparse.linalg.lobpcg``. A solver for the maximum flow problem has been added as `scipy.sparse.csgraph.maximum_flow`. `scipy.sparse.csgraph.maximum_bipartite_matching` now allows non-square inputs, no longer requires a perfect matching to exist, and has improved performance. `scipy.sparse.lil_matrix` conversions now perform better in some scenarios Basic support is available for ``pydata/sparse`` arrays in `scipy.sparse.linalg` `scipy.sparse.linalg.spsolve_triangular` now supports the ``unit_diagonal`` argument to improve call signature similarity with its dense counterpart, `scipy.linalg.solve_triangular` ``assertAlmostEqual`` may now be used with sparse matrices, which have added support for ``__round__`` `scipy.spatial` improvements ------------------------------ The bundled Qhull library was upgraded to version 2019.1, fixing several issues. Scipy-specific patches are no longer applied to it. `scipy.spatial.SphericalVoronoi` now has linear memory complexity, improved performance, and supports single-hemisphere generators. Support has also been added for handling generators that lie on a great circle arc (geodesic input) and for generators in n-dimensions. `scipy.spatial.transform.Rotation` now includes functions for calculation of a mean rotation, generation of the 3D rotation groups, and reduction of rotations with rotational symmetries. `scipy.spatial.transform.Slerp` is now callable with a scalar argument `scipy.spatial.voronoi_plot_2d` now supports furthest site Voronoi diagrams `scipy.spatial.Delaunay` and `scipy.spatial.Voronoi` now have attributes for tracking whether they are furthest site diagrams `scipy.special` improvements ------------------------------ The Voigt profile has been added as `scipy.special.voigt_profile`. A real dispatch has been added for the Wright Omega function (`scipy.special.wrightomega`). The analytic continuation of the Riemann zeta function has been added. (The Riemann zeta function is the one-argument variant of `scipy.special.zeta`.) The complete elliptic integral of the first kind (`scipy.special.ellipk`) is now available in `scipy.special.cython_special`. The accuracy of `scipy.special.hyp1f1` for real arguments has been improved. The documentation of many functions has been improved. `scipy.stats` improvements ---------------------------- `scipy.stats.multiscale_graphcorr` added as an independence test that operates on high dimensional and nonlinear data sets. It has higher statistical power than other `scipy.stats` tests while being the only one that operates on multivariate data. The generalized inverse Gaussian distribution (`scipy.stats.geninvgauss`) has been added. It is now possible to efficiently reuse `scipy.stats.binned_statistic_dd` with new values by providing the result of a previous call to the function. `scipy.stats.hmean` now handles input with zeros more gracefully. The beta-binomial distribution is now available in `scipy.stats.betabinom`. `scipy.stats.zscore`, `scipy.stats.circmean`, `scipy.stats.circstd`, and `scipy.stats.circvar` now support the ``nan_policy`` argument for enhanced handling of ``NaN`` values `scipy.stats.entropy` now accepts an ``axis`` argument `scipy.stats.gaussian_kde.resample` now accepts a ``seed`` argument to empower reproducibility `scipy.stats.multiscale_graphcorr` has been added for calculation of the multiscale graph correlation (MGC) test statistic `scipy.stats.kendalltau` performance has improved, especially for large inputs, due to improved cache usage `scipy.stats.truncnorm` distribution has been rewritten to support much wider tails Deprecated features =================== `scipy` deprecations ----------------------- Support for NumPy functions exposed via the root SciPy namespace is deprecated and will be removed in 2.0.0. For example, if you use ``scipy.rand`` or ``scipy.diag``, you should change your code to directly use ``numpy.random.default_rng`` or ``numpy.diag``, respectively. They remain available in the currently continuing Scipy 1.x release series. The exception to this rule is using ``scipy.fft`` as a function -- :mod:`scipy.fft` is now meant to be used only as a module, so the ability to call ``scipy.fft(...)`` will be removed in SciPy 1.5.0. In `scipy.spatial.Rotation` methods ``from_dcm``, ``as_dcm`` were renamed to ``from_matrix``, ``as_matrix`` respectively. The old names will be removed in SciPy 1.6.0. Backwards incompatible changes ============================== `scipy.special` changes ----------------------------- The deprecated functions ``hyp2f0``, ``hyp1f2``, and ``hyp3f0`` have been removed. The deprecated function ``bessel_diff_formula`` has been removed. The function ``i0`` is no longer registered with ``numpy.dual``, so that ``numpy.dual.i0`` will unconditionally refer to the NumPy version regardless of whether `scipy.special` is imported. The function ``expn`` has been changed to return ``nan`` outside of its domain of definition (``x, n < 0``) instead of ``inf``. `scipy.sparse` changes ----------------------------- Sparse matrix reshape now raises an error if shape is not two-dimensional, rather than guessing what was meant. The behavior is now the same as before SciPy 1.1.0. `scipy.spatial` changes -------------------------- The default behavior of the ``match_vectors`` method of `scipy.spatial.transform.Rotation` was changed for input vectors that are not normalized and not of equal lengths. Previously, such vectors would be normalized within the method. Now, the calculated rotation takes the vector length into account, longer vectors will have a larger weight. For more details, see https://github.com/scipy/scipy/issues/10968. `scipy.signal` changes ------------------------- `scipy.signal.resample` behavior for length-1 signal inputs has been fixed to output a constant (DC) value rather than an impulse, consistent with the assumption of signal periodicity in the FFT method. `scipy.signal.cwt` now performs complex conjugation and time-reversal of wavelet data, which is a backwards-incompatible bugfix for time-asymmetric wavelets. `scipy.stats` changes ------------------------ `scipy.stats.loguniform` added with better documentation as (an alias for ``scipy.stats.reciprocal``). ``loguniform`` generates random variables that are equally likely in the log space; e.g., ``1``, ``10`` and ``100`` are all equally likely if ``loguniform(10 ** 0, 10 ** 2).rvs()`` is used. Other changes ============= The ``LSODA`` method of `scipy.integrate.solve_ivp` now correctly detects stiff problems. `scipy.spatial.cKDTree` now accepts and correctly handles empty input data `scipy.stats.binned_statistic_dd` now calculates the standard deviation statistic in a numerically stable way. `scipy.stats.binned_statistic_dd` now throws an error if the input data contains either ``np.nan`` or ``np.inf``. Similarly, in `scipy.stats` now all continuous distributions' ``.fit()`` methods throw an error if the input data contain any instance of either ``np.nan`` or ``np.inf``. Authors ======= * endolith * Abhinav + * Anne Archibald * ashwinpathak20nov1996 + * Danilo Augusto + * Nelson Auner + * aypiggott + * Christoph Baumgarten * Peter Bell * Sebastian Berg * Arman Bilge + * Benedikt Boecking + * Christoph Boeddeker + * Daniel Bunting * Evgeni Burovski * Angeline Burrell + * Angeline G. Burrell + * CJ Carey * Carlos Ramos Carreño + * Mak Sze Chun + * Malayaja Chutani + * Christian Clauss + * Jonathan Conroy + * Stephen P Cook + * Dylan Cutler + * Anirudh Dagar + * Aidan Dang + * dankleeman + * Brandon David + * Tyler Dawson + * Dieter Werthmüller * Joe Driscoll + * Jakub Dyczek + * Dávid Bodnár * Fletcher Easton + * Stefan Endres * etienne + * Johann Faouzi * Yu Feng * Isuru Fernando + * Matthew H Flamm * Martin Gauch + * Gabriel Gerlero + * Ralf Gommers * Chris Gorgolewski + * Domen Gorjup + * Edouard Goudenhoofdt + * Jan Gwinner + * Maja Gwozdz + * Matt Haberland * hadshirt + * Pierre Haessig + * David Hagen * Charles Harris * Gina Helfrich + * Alex Henrie + * Francisco J. Hernandez Heras + * Andreas Hilboll * Lindsey Hiltner * Thomas Hisch * Min ho Kim + * Gert-Ludwig Ingold * jakobjakobson13 + * Todd Jennings * He Jia * Muhammad Firmansyah Kasim + * Andrew Knyazev + * Holger Kohr + * Mateusz Konieczny + * Krzysztof Pióro + * Philipp Lang + * Peter Mahler Larsen + * Eric Larson * Antony Lee * Gregory R. Lee * Chelsea Liu + * Jesse Livezey * Peter Lysakovski + * Jason Manley + * Michael Marien + * Nikolay Mayorov * G. D. McBain + * Sam McCormack + * Melissa Weber Mendonça + * Kevin Michel + * mikeWShef + * Sturla Molden * Eric Moore * Peyton Murray + * Andrew Nelson * Clement Ng + * Juan Nunez-Iglesias * Renee Otten + * Kellie Ottoboni + * Ayappan P * Sambit Panda + * Tapasweni Pathak + * Oleksandr Pavlyk * Fabian Pedregosa * Petar Mlinarić * Matti Picus * Marcel Plch + * Christoph Pohl + * Ilhan Polat * Siddhesh Poyarekar + * Ioannis Prapas + * James Alan Preiss + * Yisheng Qiu + * Eric Quintero * Bharat Raghunathan + * Tyler Reddy * Joscha Reimer * Antonio Horta Ribeiro * Lucas Roberts * rtshort + * Josua Sassen * Kevin Sheppard * Scott Sievert * Leo Singer * Kai Striega * Søren Fuglede Jørgensen * tborisow + * Étienne Tremblay + * tuxcell + * Miguel de Val-Borro * Andrew Valentine + * Hugo van Kemenade * Paul van Mulbregt * Sebastiano Vigna * Pauli Virtanen * Dany Vohl + * Ben Walsh + * Huize Wang + * Warren Weckesser * Anreas Weh + * Joseph Weston + * Adrian Wijaya + * Timothy Willard + * Josh Wilson * Kentaro Yamamoto + * Dave Zbarsky + A total of 141 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete. ``` ### 1.3.3 ``` compared to `1.3.2`. In particular, a test suite issue involving multiprocessing was fixed for Windows and Python `3.8` on macOS. Wheels were also updated to place `msvcp140.dll` at the appropriate location, which was previously causing issues. Authors ======= Ilhan Polat Tyler Reddy Ralf Gommers ``` ### 1.3.2 ``` SciPy `1.3.2` is a bug-fix and maintenance release that adds support for Python `3.8`. Authors ===== * CJ Carey * Dany Vohl * Martin Gauch + * Ralf Gommers * Matt Haberland * Eric Larson * Nikolay Mayorov * Sam McCormack + * Andrew Nelson * Tyler Reddy * Pauli Virtanen * Huize Wang + * Warren Weckesser * Joseph Weston + A total of 14 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete. ```
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 1.3.10 to 1.3.13.

Changelog ### 1.3.13 ``` :released: January 22, 2020 .. change:: :tags: bug, postgresql :tickets: 5039 Fixed issue where the PostgreSQL dialect would fail to parse a reflected CHECK constraint that was a boolean-valued function (as opposed to a boolean-valued expression). .. change:: :tags: bug, ext :tickets: 5086 Fixed bug in sqlalchemy.ext.serializer where a unique :class:`.BindParameter` object could conflict with itself if it were present in the mapping itself, as well as the filter condition of the query, as one side would be used against the non-deserialized version and the other side would use the deserialized version. Logic is added to :class:`.BindParameter` similar to its "clone" method which will uniquify the parameter name upon deserialize so that it doesn't conflict with its original. .. change:: :tags: usecase, sql :tickets: 5079 A function created using :class:`.GenericFunction` can now specify that the name of the function should be rendered with or without quotes by assigning the :class:`.quoted_name` construct to the .name element of the object. Prior to 1.3.4, quoting was never applied to function names, and some quoting was introduced in :ticket:`4467` but no means to force quoting for a mixed case name was available. Additionally, the :class:`.quoted_name` construct when used as the name will properly register its lowercase name in the function registry so that the name continues to be available via the ``func.`` registry. .. seealso:: :class:`.GenericFunction` .. change:: :tags: bug, engine :tickets: 5048 Fixed issue where the collection of value processors on a :class:`.Compiled` object would be mutated when "expanding IN" parameters were used with a datatype that has bind value processors; in particular, this would mean that when using statement caching and/or baked queries, the same compiled._bind_processors collection would be mutated concurrently. Since these processors are the same function for a given bind parameter namespace every time, there was no actual negative effect of this issue, however, the execution of a :class:`.Compiled` object should never be causing any changes in its state, especially given that they are intended to be thread-safe and reusable once fully constructed. .. change:: :tags: tests, postgresql :tickets: 5057 Improved detection of two phase transactions requirement for the PostgreSQL database by testing that max_prepared_transactions is set to a value greater than 0. Pull request courtesy Federico Caselli. .. change:: :tags: bug, orm, engine :tickets: 5056, 5050, 5071 Added test support and repaired a wide variety of unnecessary reference cycles created for short-lived objects, mostly in the area of ORM queries. Thanks much to Carson Ip for the help on this. .. change:: :tags: orm, bug :tickets: 5107 Fixed regression in loader options introduced in 1.3.0b3 via :ticket:`4468` where the ability to create a loader option using :meth:`.PropComparator.of_type` targeting an aliased entity that is an inheriting subclass of the entity which the preceding relationship refers to would fail to produce a matching path. See also :ticket:`5082` fixed in this same release which involves a similar kind of issue. .. change:: :tags: bug, tests :tickets: 4946 Fixed a few test failures which would occur on Windows due to SQLite file locking issues, as well as some timing issues in connection pool related tests; pull request courtesy Federico Caselli. .. change:: :tags: orm, bug :tickets: 5082 Fixed regression in joined eager loading introduced in 1.3.0b3 via :ticket:`4468` where the ability to create a joined option across a :func:`.with_polymorphic` into a polymorphic subclass using :meth:`.RelationshipProperty.of_type` and then further along regular mapped relationships would fail as the polymorphic subclass would not add itself to the load path in a way that could be located by the loader strategy. A tweak has been made to resolve this scenario. .. change:: :tags: performance, orm Identified a performance issue in the system by which a join is constructed based on a mapped relationship. The clause adaption system would be used for the majority of join expressions including in the common case where no adaptation is needed. The conditions under which this adaptation occur have been refined so that average non-aliased joins along a simple relationship without a "secondary" table use about 70% less function calls. .. change:: :tags: usecase, postgresql :tickets: 5040 Added support for prefixes to the :class:`.CTE` construct, to allow support for Postgresql 12 "MATERIALIZED" and "NOT MATERIALIZED" phrases. Pull request courtesy Marat Sharafutdinov. .. seealso:: :meth:`.HasCTE.cte` .. change:: :tags: bug, mssql :tickets: 5045 Fixed issue where a timezone-aware ``datetime`` value being converted to string for use as a parameter value of a :class:`.mssql.DATETIMEOFFSET` column was omitting the fractional seconds. .. change:: :tags: bug, orm :tickets: 5068 Repaired a warning in the ORM flush process that was not covered by test coverage when deleting objects that use the "version_id" feature. This warning is generally unreachable unless using a dialect that sets the "supports_sane_rowcount" flag to False, which is not typically the case however is possible for some MySQL configurations as well as older Firebird drivers, and likely some third party dialects. .. change:: :tags: bug, orm :tickets: 5065 Fixed bug where usage of joined eager loading woul
pyup-bot commented 4 years ago

Closing this in favor of #76