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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 monthly dependency update for June #79

Closed pyup-bot closed 4 years ago

pyup-bot commented 4 years ago

Update astropy from 3.2.3 to 4.0.1.post1.

Changelog ### 4.0.1 ``` ================== Bug fixes --------- astropy.config ^^^^^^^^^^^^^^ - Fixed a bug where importing a development version of a package that uses ``astropy`` configuration system can result in a ``~/.astropy/config/package..cfg`` file. [9975] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Fixed a bug where a vestigal trace of a frame class could persist in the transformation graph even after the removal of all transformations involving that frame class. [9815] - Fixed a bug with ``TransformGraph.remove_transform()`` when the "from" and "to" frame classes are not explicitly specified. [9815] - Read-only longitudes can now be passed in to ``EarthLocation`` even if they include angles outside of the range of -180 to 180 degrees. [9900] - SkyCoord.radial_velocity_correction no longer raises an Exception when space motion information is present on the SkyCoord. [9980] astropy.io ^^^^^^^^^^ - Fixed a bug that prevented the unified I/O infrastructure from working with datasets that are represented by directories rather than files. [9866] astropy.io.ascii ^^^^^^^^^^^^^^^^ - Fixed a bug in the ``fast_reader`` C parsers incorrectly returning entries of isolated positive/negative signs as ``float`` instead of ``str``. [9918] - Fixed a segmentation fault in the ``fast_reader`` C parsers when parsing an invalid file with ``guess=True`` and the file contains inconsistent column numbers in combination with a quoted field; e.g., ``"1 2\n 3 4 '5'"``. [9923] - Magnitude, decibel, and dex can now be stored in ``ecsv`` files. [9933] astropy.io.misc ^^^^^^^^^^^^^^^ - Magnitude, decibel, and dex can now be stored in ``hdf5`` files. [9933] - Fixed serialization of polynomial models to include non default values of domain and window values. [9956, 9961] - Fixed a bug which affected overwriting tables within ``hdf5`` files. Overwriting an existing path with associated column meta data now also overwrites the meta data associated with the table. [9950] - Fixed serialization of Time objects with location under time-1.0.0 ASDF schema. [9983] astropy.io.fits ^^^^^^^^^^^^^^^ - Fix regression with ``GroupsHDU`` which needs to modify the header to handle invalid headers, and fix accesing ``.data`` for empty HDU. [9711, 9934] - Fix ``fitsdiff`` when its arguments are directories that contain other directories. [9711] - Fix writing noncontiguous data to a compressed HDU. [9958] - Added verification of ``disp`` (``TDISP``) keyword to ``fits.Column`` and extended tests for ``TFORM`` and ``TDISP`` validation. [9978] - Fix checksum verification to process all HDUs instead of only the first one because of the lazy loading feature. [10012] - Allow passing ``output_verify`` to ``.close`` when using the context manager. [10030] - Prevent instantiation of ``PrimaryHDU`` and ``ImageHDU`` with a scalar. [10041] - Fix column access by attribute with FITS_rec: columns with scaling or columns from ASCII tables where not properly converted when accessed by attribute name. [10069] astropy.io.misc ^^^^^^^^^^^^^^^ - Magnitude, decibel, and dex can now be stored in ``hdf5`` files. [9933] - Fixed serialization of polynomial models to include non default values of domain and window values. [9956, 9961] - Fixed a bug which affected overwriting tables within ``hdf5`` files. Overwriting an existing path with associated column meta data now also overwrites the meta data associated with the table. [9950] - Fixed serialization of Time objects with location under time-1.0.0 ASDF schema. [9983] astropy.modeling ^^^^^^^^^^^^^^^^ - Fixed a bug in setting default values of parameters of orthonormal polynomials when constructing a model set. [9987] astropy.table ^^^^^^^^^^^^^ - Fixed bug in ``Table.reverse`` for tables that contain non-mutable mixin columns (like ``SkyCoord``) for which in-place item update is not allowed. [9839] - Tables containing Magnitude, decibel, and dex columns can now be saved to ``ecsv`` files. [9933] - Fixed bug where adding or inserting a row fails on a table with an index defined on a column that is not the first one. [10027] - Ensured that ``table.show_in_browser`` also worked for mixin columns like ``Time`` and ``SkyCoord``. [10068] astropy.time ^^^^^^^^^^^^ - Fix inaccuracy when converting between TimeDelta and datetime.timedelta. [9679] - Fixed exception when changing ``format`` in the case when ``out_subfmt`` is defined and is incompatible with the new format. [9812] - Fixed exceptions in ``Time.to_value()``: when supplying any ``subfmt`` argument for string-based formats like 'iso', and for ``subfmt='long'`` for the formats 'byear', 'jyear', and 'decimalyear'. [9812] - Fixed bug where the location attribute was lost when creating a new ``Time`` object from an existing ``Time`` or list of ``Time`` objects. [9969] - Fixed a bug where an exception occurred when creating a ``Time`` object if the ``val1`` argument was a regular double and the ``val2`` argument was a ``longdouble``. [10034] astropy.timeseries ^^^^^^^^^^^^^^^^^^ - Fixed issue with reference time for the ``transit_time`` parameter returned by the ``BoxLeastSquares`` periodogram. Now, the ``transit_time`` will be within the range of the input data and arbitrary time offsets/zero points no longer affect results. [10013] astropy.units ^^^^^^^^^^^^^ - Fix for ``quantity_input`` annotation raising an exception on iterable types that don't define a general ``__contains__`` for checking if ``None`` is contained (e.g. Enum as of python3.8), by instead checking for instance of Sequence. [9948] - Fix for ``u.Quantity`` not taking into account ``ndmin`` if constructed from another ``u.Quantity`` instance with different but convertible unit [10066] astropy.utils ^^^^^^^^^^^^^ - Fixed ``deprecated_renamed_argument`` not passing in user value to deprecated keyword when the keyword has no new name. [9981] - Fixed ``deprecated_renamed_argument`` not issuing a deprecation warning when deprecated keyword without new name is passed in as positional argument. [9985] - Fixed detection of read-only filesystems in the caching code. [10007] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Fixed bug from matplotlib >=3.1 where an empty Quantity array is sent for unit conversion as an empty list. [9848] - Fix bug in ``ZScaleInterval`` to return the array minimum and maximum when there are less then ``min_npixels`` in the input array. [9913] - Fix a bug in simplifying axis labels that affected non-rectangular frames. [8004, 9991] Other Changes and Additions --------------------------- - Increase minimum asdf version to 2.5.2. [9996, 9819] - Updated wcslib to v7.2. [10021] ``` ### 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.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.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/v4.0.x/modeling/changes_for_4.html>`_ . [8769] - 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. [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.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. Currently supported 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.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.extern ^^^^^^^^^^^^^^ - Remove the bundled ``six`` module. [8315] 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.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] - Deprecated ``BlackBody1D`` model and ``blackbody_nu`` and ``blackbody_lambda`` functions. [9282] - 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.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/v4.0.x/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``. [8933] - 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] Bug Fixes --------- astropy.convolution ^^^^^^^^^^^^^^^^^^^ - Fixed ``nan_treatment='interpolate'`` option to ``convolve_fft`` to properly take into account ``fill_value``. [8122] 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.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.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.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.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.time ^^^^^^^^^^^^ - Fix bug when ``Time`` object is created with only masked elements. [9624] - Fix inaccuracy when converting between TimeDelta and datetime.timedelta. [9679] 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] - 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] - The default WCS to celestial frame mapping for world coordinate systems that specify ``TLON`` and ``TLAT`` coordinates will now return an ITRS frame with the representation class set to ``SphericalRepresentation``. This fixes a bug that caused ``WCS.pixel_to_world`` to raise an error for such world coordinate systems. [9609] - ``FITSWCSAPIMixin`` now returns tuples not lists from ``pixel_to_world`` and ``world_to_pixel``. [9678] 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 1.7.0. This is based on SOFA 20190722. This includes a fix to avoid precision loss for negative JDs, and also includes additional routines to allow updates to the leap-second table. [9323, 9734] - 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 3.2.1.

Changelog ### 3.2.1 ``` This is the first bugfix release of the 3.2.x series. This release contains several critical bug-fixes: - fix `Quiver.set_UVC` calls with scalar inputs - fix `bezier.get_parallels` failure from floating point rounding errors - fix markers specified as tuples (polygons, stars, or asterisks) - fix saving PNGs to file objects in some places - fix saving figures using the nbAgg/notebook backend - fix saving with tight layout using the PGF backend - fix setting custom datapath in rcParams (note: it is still deprecated) - fix various issues running setup.py in non-CI environments - fix xpdf distiller - various minor bug and documentation fixes ``` ### 3.2.0rc1 ``` This is the first release candidate from Matplotlib 3.2 ```
Links - PyPI: https://pypi.org/project/matplotlib - Changelog: https://pyup.io/changelogs/matplotlib/ - Homepage: https://matplotlib.org

Update ephem from 3.7.7.0 to 3.7.7.1.

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

Update joblib from 0.14.0 to 0.15.1.

Changelog ### 0.15.1 ``` -------------- - Make joblib work on Python 3 installation that do not ship with the lzma package in their standard library. ``` ### 0.15.0 ``` -------------- - Drop support for Python 2 and Python 3.5. All objects in ``joblib.my_exceptions`` and ``joblib.format_stack`` are now deprecated and will be removed in joblib 0.16. Note that no deprecation warning will be raised for these objects Python < 3.7. https://github.com/joblib/joblib/pull/1018 - Fix many bugs related to the temporary files and folder generated when automatically memory mapping large numpy arrays for efficient inter-process communication. In particular, this would cause `PermissionError` exceptions to be raised under Windows and large leaked files in `/dev/shm` under Linux in case of crash. https://github.com/joblib/joblib/pull/966 - Make the dask backend collect results as soon as they complete leading to a performance improvement: https://github.com/joblib/joblib/pull/1025 - Fix the number of jobs reported by ``effective_n_jobs`` when ``n_jobs=None`` called in a parallel backend context. https://github.com/joblib/joblib/pull/985 - Upgraded vendored cloupickle to 1.4.1 and loky to 2.8.0. This allows for Parallel calls of dynamically defined functions with type annotations in particular. ``` ### 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 0.49.1.

Changelog ### 0.49.1 ``` ---------------------------- This is a bugfix release for 0.49.0, it fixes some residual issues with SSA form, a critical bug in the branch pruning logic and a number of other smaller issues: * PR 5587: Fixed 5586 Threading Implementation Typos * PR 5592: Fixes 5583 Remove references to cffi_support from docs and examples * PR 5614: Fix invalid type in resolve for comparison expr in parfors. * PR 5624: Fix erroneous rewrite of predicate to bit const on prune. * PR 5627: Fixes 5623, SSA local def scan based on invalid equality assumption. * PR 5629: Fixes naming error in array_exprs * PR 5630: Fix 5570. Incorrect race variable detection due to SSA naming. * PR 5638: Make literal_unroll function work as a freevar. * PR 5648: Unset the memory manager after EMM Plugin tests * PR 5651: Fix some SSA issues * PR 5652: Pin to sphinx=2.4.4 to avoid problem with C declaration * PR 5658: Fix unifying undefined first class function types issue * PR 5669: Update example in 5m guide WRT SSA type stability. * PR 5676: Restore ``numba.types`` as public API Authors: * Graham Markall * Juan Manuel Cruz Martinez * Pearu Peterson * Sean Law * Stuart Archibald (core dev) * Siu Kwan Lam (core dev) ``` ### 0.49.0 ``` ----------------------------- This release is very large in terms of code changes. Large scale removal of unsupported Python and NumPy versions has taken place along with a significant amount of refactoring to simplify the Numba code base to make it easier for contributors. Numba's intermediate representation has also undergone some important changes to solve a number of long standing issues. In addition some new features have been added and a large number of bugs have been fixed! IMPORTANT: In this release Numba's internals have moved about a lot. A backwards compatibility "shim" is provided for this release so as to not immediately break projects using Numba's internals. If a module is imported from a moved location the shim will issue a deprecation warning and suggest how to update the import statement for the new location. The shim will be removed in 0.50.0! Highlights of core feature changes include: * Removal of all Python 2 related code and also updating the minimum supported Python version to 3.6, the minimum supported NumPy version to 1.15 and the minimum supported SciPy version to 1.0. (Stuart Archibald). * Refactoring of the Numba code base. The code is now organised into submodules by functionality. This cleans up Numba's top level namespace. (Stuart Archibald). * Introduction of an ``ir.Del`` free static single assignment form for Numba's intermediate representation (Siu Kwan Lam and Stuart Archibald). * An OpenMP-like thread masking API has been added for use with code using the parallel CPU backends (Aaron Meurer and Stuart Archibald). * For the CUDA target, all kernel launches now require a configuration, this preventing accidental launches of kernels with the old default of a single thread in a single block. The hard-coded autotuner is also now removed, such tuning is deferred to CUDA API calls that provide the same functionality (Graham Markall). * The CUDA target also gained an External Memory Management plugin interface to allow Numba to use another CUDA-aware library for all memory allocations and deallocations (Graham Markall). * The Numba Typed List container gained support for construction from iterables (Valentin Haenel). * Experimental support was added for first-class function types (Pearu Peterson). Enhancements from user contributed PRs (with thanks!): * Aaron Meurer added support for thread masking at runtime in 4615. * Andreas Sodeur fixed a long standing bug that was preventing ``cProfile`` from working with Numba JIT compiled functions in 4476. * Arik Funke fixed error messages in ``test_array_reductions`` (5278), fixed an issue with test discovery (5239), made it so the documentation would build again on windows (5453) and fixed a nested list problem in the docs in 5489. * Antonio Russo fixed a SyntaxWarning in 5252. * Eric Wieser added support for inferring the types of object arrays (5348) and iterating over 2D arrays (5115), also fixed some compiler warnings due to missing (void) in 5222. Also helped improved the "shim" and associated warnings in 5485, 5488, 5498 and partly 5532. * Ethan Pronovost fixed a problem with the shim erroneously warning for jitclass use in 5454 and also prevented illegal return values in jitclass ``__init__`` in 5505. * Gabriel Majeri added SciPy 2019 talks to the docs in 5106. * Graham Markall changed the Numba HTML documentation theme to resolve a number of long standing issues in 5346. Also contributed were a large number of CUDA enhancements and fixes, namely: * 5519: CUDA: Silence the test suite - Fix 4809, remove autojit, delete prints * 5443: Fix 5196: Docs: assert in CUDA only enabled for debug * 5436: Fix 5408: test_set_registers_57 fails on Maxwell * 5423: Fix 5421: Add notes on printing in CUDA kernels * 5400: Fix 4954, and some other small CUDA testsuite fixes * 5328: NBEP 7: External Memory Management Plugin Interface * 5144: Fix 4875: Make 2655 test with debug expect to pass * 5323: Document lifetime semantics of CUDA Array Interface * 5061: Prevent kernel launch with no configuration, remove autotuner * 5099: Fix 5073: Slices of dynamic shared memory all alias * 5136: CUDA: Enable asynchronous operations on the default stream * 5085: Support other itemsizes with view * 5059: Docs: Explain how to use Memcheck with Numba, fixups in CUDA documentation * 4957: Add notes on overwriting gufunc inputs to docs * Greg Jennings fixed an issue with ``np.random.choice`` not acknowledging the RNG seed correctly in 3897/5310. * Guilherme Leobas added support for ``np.isnat`` in 5293. * Henry Schreiner made the llvmlite requirements more explicit in requirements.txt in 5150. * Ivan Butygin helped fix an issue with parfors sequential lowering in 5114/5250. * Jacques Gaudin fixed a bug for Python >= 3.8 in ``numba -s`` in 5548. * Jim Pivarski added some hints for debugging entry points in 5280. * John Kirkham added ``numpy.dtype`` coercion for the ``dtype`` argument to CUDA device arrays in 5252. * Leo Fang added a list of libraries that support ``__cuda_array_interface__`` in 5104. * Lucio Fernandez-Arjona added ``getitem`` for the NumPy record type when the index is a ``StringLiteral`` type in 5182 and improved the documentation rendering via additions to the TOC and removal of numbering in 5450. * Mads R. B. Kristensen fixed an issue with ``__cuda_array_interface__`` not requiring the context in 5189. * Marcin Tolysz added support for nested modules in AOT compilation in 5174. * Mike Williams fixed some issues with NumPy records and ``getitem`` in the CUDA simulator in 5343. * Pearu Peterson added experimental support for first-class function types in 5287 (and fixes in 5459, 5473/5429, and 5557). * Ravi Teja Gutta added support for ``np.flip`` in 4376/5313. * Rohit Sanjay fixed an issue with type refinement for unicode input supplied to typed-list ``extend()`` (5295) and fixed unicode ``.strip()`` to strip all whitespace characters in 5213. * Vladimir Lukyanov fixed an awkward bug in ``typed.dict`` in 5361, added a fix to ensure the LLVM and assembly dumps are highlighted correctly in 5357 and implemented a Numba IR Lexer and added highlighting to Numba IR dumps in 5333. * hdf fixed an issue with the ``boundscheck`` flag in the CUDA jit target in 5257. General Enhancements: * PR 4615: Allow masking threads out at runtime * PR 4798: Add branch pruning based on raw predicates. * PR 5115: Add support for iterating over 2D arrays * PR 5117: Implement ord()/chr() * PR 5122: Remove Python 2. * PR 5127: Calling convention adaptor for boxer/unboxer to call jitcode * PR 5151: implement None-typed typed-list * PR 5174: Nested modules https://github.com/numba/numba/issues/4739 * PR 5182: Add getitem for Record type when index is StringLiteral * PR 5185: extract code-gen utilities from closures * PR 5197: Refactor Numba, part I * PR 5210: Remove more unsupported Python versions from build tooling. * PR 5212: Adds support for viewing the CFG of the ELF disassembly. * PR 5227: Immutable typed-list * PR 5231: Added support for ``np.asarray`` to be used with ``numba.typed.List`` * PR 5235: Added property ``dtype`` to ``numba.typed.List`` * PR 5272: Refactor parfor: split up ParforPass * PR 5281: Make IR ir.Del free until legalized. * PR 5287: First-class function type * PR 5293: np.isnat * PR 5294: Create typed-list from iterable * PR 5295: refine typed-list on unicode input to extend * PR 5296: Refactor parfor: better exception from passes * PR 5308: Provide ``numba.extending.is_jitted`` * PR 5320: refactor array_analysis * PR 5325: Let literal_unroll accept types.Named*Tuple * PR 5330: refactor common operation in parfor lowering into a new util * PR 5333: Add: highlight Numba IR dump * PR 5342: Support for tuples passed to parfors. * PR 5348: Add support for inferring the types of object arrays * PR 5351: SSA again * PR 5352: Add shim to accommodate refactoring. * PR 5356: implement allocated parameter in njit * PR 5369: Make test ordering more consistent across feature availability * PR 5428: Wip/deprecate jitclass location * PR 5441: Additional changes to first class function * PR 5455: Move to llvmlite 0.32.* * PR 5457: implement repr for untyped lists Fixes: * PR 4476: Another attempt at fixing frame injection in the dispatcher tracing path * PR 4942: Prevent some parfor aliasing. Rename copied function var to prevent recursive type locking. * PR 5092: Fix 5087 * PR 5150: More explicit llvmlite requirement in requirements.txt * PR 5172: fix version spec for llvmlite * PR 5176: Normalize kws going into fold_arguments. * PR 5183: pass 'inline' explicitly to overload * PR 5193: Fix CI failure due to missing files when installed * PR 5213: Fix ``.strip()`` to strip all whitespace characters * PR 5216: Fix namedtuple mistreated by dispatcher as simple tuple * PR 5222: Fix compiler warnings due to missing (void) * PR 5232: Fixes a bad import that breaks master * PR 5239: fix test discovery for unittest * PR 5247: Continue PR 5126 * PR 5250: Part fix/5098 * PR 5252: Trivially fix SyntaxWarning * PR 5276: Add prange variant to has_no_side_effect. * PR 5278: fix error messages in test_array_reductions * PR 5310: PR 3897 continued * PR 5313: Continues PR 4376 * PR 5318: Remove AUTHORS file reference from MANIFEST.in * PR 5327: Add warning if FNV hashing is found as the default for CPython. * PR 5338: Remove refcount pruning pass * PR 5345: Disable test failing due to removed pass. * PR 5357: Small fix to have llvm and asm highlighted properly * PR 5361: 5081 typed.dict * PR 5431: Add tolerance to numba extension module entrypoints. * PR 5432: Fix code causing compiler warnings. * PR 5445: Remove undefined variable * PR 5454: Don't warn for numba.experimental.jitclass * PR 5459: Fixes issue 5448 * PR 5480: Fix for 5477, literal_unroll KeyError searching for getitems * PR 5485: Show the offending module in "no direct replacement" error message * PR 5488: Add missing ``numba.config`` shim * PR 5495: Fix missing null initializer for variable after phi strip * PR 5498: Make the shim deprecation warnings work on python 3.6 too * PR 5505: Better error message if __init__ returns value * PR 5527: Attempt to fix 5518 * PR 5529: PR 5473 continued * PR 5532: Make ``numba.<mod>`` available without an import * PR 5542: Fixes RC2 module shim bug * PR 5548: Fix 5537 Removed reference to ``platform.linux_distribution`` * PR 5555: Fix 5515 by reverting changes to ArrayAnalysis * PR 5557: First-class function call cannot use keyword arguments * PR 5569: Fix RewriteConstGetitems not registering calltype for new expr * PR 5571: Pin down llvmlite requirement CUDA Enhancements/Fixes: * PR 5061: Prevent kernel launch with no configuration, remove autotuner * PR 5085: Support other itemsizes with view * PR 5099: Fix 5073: Slices of dynamic shared memory all alias * PR 5104: Add a list of libraries that support __cuda_array_interface__ * PR 5136: CUDA: Enable asynchronous operations on the default stream * PR 5144: Fix 4875: Make 2655 test with debug expect to pass * PR 5189: __cuda_array_interface__ not requiring context * PR 5253: Coerce ``dtype`` to ``numpy.dtype`` * PR 5257: boundscheck fix * PR 5319: Make user facing error string use abs path not rel. * PR 5323: Document lifetime semantics of CUDA Array Interface * PR 5328: NBEP 7: External Memory Management Plugin Interface * PR 5343: Fix cuda spoof * PR 5400: Fix 4954, and some other small CUDA testsuite fixes * PR 5436: Fix 5408: test_set_registers_57 fails on Maxwell * PR 5519: CUDA: Silence the test suite - Fix 4809, remove autojit, delete prints Documentation Updates: * PR 4957: Add notes on overwriting gufunc inputs to docs * PR 5059: Docs: Explain how to use Memcheck with Numba, fixups in CUDA documentation * PR 5106: Add SciPy 2019 talks to docs * PR 5147: Update master for 0.48.0 updates * PR 5155: Explain what inlining at Numba IR level will do * PR 5161: Fix README.rst formatting * PR 5207: Remove AUTHORS list * PR 5249: fix target path for See also * PR 5262: fix typo in inlining docs * PR 5270: fix 'see also' in typeddict docs * PR 5280: Added some hints for debugging entry points. * PR 5297: Update docs with intro to {g,}ufuncs. * PR 5326: Update installation docs with OpenMP requirements. * PR 5346: Docs: use sphinx_rtd_theme * PR 5366: Remove reference to Python 2.7 in install check output * PR 5423: Fix 5421: Add notes on printing in CUDA kernels * PR 5438: Update package deps for doc building. * PR 5440: Bump deprecation notices. * PR 5443: Fix 5196: Docs: assert in CUDA only enabled for debug * PR 5450: Docs: remove numbers and add titles to TOC * PR 5453: fix building docs on windows * PR 5489: docs: fix rendering of nested bulleted list CI updates: * PR 5314: Update the image used in Azure CI for OSX. * PR 5360: Remove Travis CI badge. Authors: * Aaron Meurer * Andreas Sodeur * Antonio Russo * Arik Funke * Eric Wieser * Ethan Pronovost * Gabriel Majeri * Graham Markall * Greg Jennings * Guilherme Leobas * hdf * Henry Schreiner * Ivan Butygin * Jacques Gaudin * Jim Pivarski * John Kirkham * Leo Fang * Lucio Fernandez-Arjona * Mads R. B. Kristensen * Marcin Tolysz * Mike Williams * Pearu Peterson * Ravi Teja Gutta * Rohit Sanjay * Siu Kwan Lam (core dev) * Stan Seibert (core dev) * Stuart Archibald (core dev) * Todd A. Anderson (core dev) * Valentin Haenel (core dev) * Vladimir Lukyanov ``` ### 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 1.18.4.

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

Update pandas from 0.25.3 to 1.0.4.

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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.cons
pyup-bot commented 4 years ago

Closing this in favor of #80