search

jason-neal / companion_simulations

Simulating combined host+companion spectra, and fitting to observed crires spectra.
MIT License
2 stars 0 forks source link

Scheduled monthly dependency update for October #83

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 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 bundled version of ``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 3.3.2.

Changelog ### 3.3.2 ``` This is the second bugfix release of the 3.3.x series. This release contains several critical bug-fixes: * fix `Axis` scale on twinned `Axes` * fix auto-close of `Figure`s in nbagg * fix automatic title placement if `Axes` is off the `Figure` * fix autoranging of log scales with barstacked histogram * fix extra redraws when using `Button` or `TextBox` widgets * fix imshow with `LogNorm` and large vmin/vmax ranges * fix plotting Pandas `DataFrame` with string `MultiIndex` * fix `scatter` with `marker=''` * fix `scatter3d` color/linewidth re-projection * fix state of mode buttons in TkAgg backends * include license files in built distribution * reduce Visual C++ runtime requirements on Windows ``` ### 3.3.1 ``` This is the first bugfix release of the 3.3.x series. This release contains several critical bug-fixes: * fix docstring import issues when running Python with optimization * fix `hist` with categorical data, such as with Pandas * fix install on BSD systems * fix nbagg compatibility with Chrome 84+ * fix ordering of scatter marker size in 3D plots * fix performance regression when plotting `Path`s * fix reading from URL in `imread` * fix several regressions with new date epoch handling * fix some bad constrained and tight layout interactions with colorbars * fix use of customized toolbars in TkAgg and WXAgg backends ``` ### 3.3.0 ``` Highlights of this release include: - Provisional API for composing semantic axes layouts from text or nested lists - New Axes.sharex, Axes.sharey methods - Turbo colormap - colors.BoundaryNorm supports extend keyword argument - Text color for legend labels - Pcolor and Pcolormesh now accept shading='nearest' and 'auto' - Allow tick formatters to be set with str or function inputs - New Axes.axline method - Dates use a modern epoch - Improved font weight detection - Axes3D no longer distorts the 3D plot to match the 2D aspect ratio - More consistent toolbar behavior across backends - Toolbar icons are now styled for dark themes - Cursor text now uses a number of significant digits matching pointing precision - Functions to compute a Path's size - savefig() gained a backend keyword argument - Saving SVG now supports adding metadata - Saving PDF metadata via PGF now consistent with PDF backend - NbAgg and WebAgg no longer use jQuery & jQuery UI For the full details please see the [What's New](https://matplotlib.org/3.3.0/users/whats_new.html) and [API changes](https://matplotlib.org/3.3.0/api/api_changes.html) in the documentation. ``` ### 3.2.2 ``` This is the second bugfix release of the 3.2.x series. This release contains several critical bug-fixes: - support fractional HiDPI scaling with Qt backends - support new Python and fix syntax errors in legacy Python - support new Qt 5 and fix support for Qt 4 - fix animation writer fallback - fix figure resizing - fix handling of large arcs - fix issues with tight layout - fix saving figures after closing windows or under certain size conditions - fix scatter when specifying a single color - fix several memory leaks - fix unexpected autoscaling behavior - fix various issues with usetex - various minor bug and documentation fixes ``` ### 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.

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

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

Update joblib from 0.14.0 to 0.16.0.

Changelog ### 0.16.0 ``` -------------- - Fix a problem in the constructors of of Parallel backends classes that inherit from the `AutoBatchingMixin` that prevented the dask backend to properly batch short tasks. https://github.com/joblib/joblib/pull/1062 - Fix a problem in the way the joblib dask backend batches calls that would badly interact with the dask callable pickling cache and lead to wrong results or errors. https://github.com/joblib/joblib/pull/1055 - Prevent a dask.distributed bug from surfacing in joblib's dask backend during nested Parallel calls (due to joblib's auto-scattering feature) https://github.com/joblib/joblib/pull/1061 - Workaround for a race condition after Parallel calls with the dask backend that would cause low level warnings from asyncio coroutines: https://github.com/joblib/joblib/pull/1078 ``` ### 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 0.51.2.

Changelog ### 0.51.2 ``` ---------------------------------- This is a bugfix release for 0.51.1. It fixes a critical performance bug in the CFG back edge computation algorithm that leads to exponential time complexity arising in compilation for use cases with certain pathological properties. * PR 6195: PR 6187 Continue. Don't visit already checked successors Authors: * Graham Markall * Siu Kwan Lam (core dev) ``` ### 0.51.1 ``` -------------------------------- This is a bugfix release for 0.51.0, it fixes a critical bug in caching, another critical bug in the CUDA target initialisation sequence and also fixes some compile time performance regressions: * PR 6141: Fix 6130 objmode cache segfault * PR 6146: Fix compilation slowdown due to controlflow analysis * PR 6147: CUDA: Don't make a runtime call on import * PR 6153: Fix for 6151. Make UnicodeCharSeq into str for comparison. * PR 6168: Fix Issue 6167: Failure in test_cuda_submodules Authors: * Graham Markall * Siu Kwan Lam (core dev) * Stuart Archibald (core dev) ``` ### 0.51.0 ``` -------------------------------- This release continues to add new features to Numba and also contains a significant number of bug fixes and stability improvements. Highlights of core feature changes include: * The compilation chain is now based on LLVM 10 (Valentin Haenel). * Numba has internally switched to prefer non-literal types over literal ones so as to reduce function over-specialisation, this with view of speeding up compile times (Siu Kwan Lam). * On the CUDA target: Support for CUDA Toolkit 11, Ampere, and Compute Capability 8.0; Printing of ``SASS`` code for kernels; Callbacks to Python functions can be inserted into CUDA streams, and streams are async awaitable; Atomic ``nanmin`` and ``nanmax`` functions are added; Fixes for various miscompilations and segfaults. (mostly Graham Markall; call backs on streams by Peter Würtz). Intel also kindly sponsored research and development that lead to some exciting new features: * Support for heterogeneous immutable lists and heterogeneous immutable string key dictionaries. Also optional initial/construction value capturing for all lists and dictionaries containing literal values (Stuart Archibald). * A new pass-by-reference mutable structure extension type ``StructRef`` (Siu Kwan Lam). * Object mode blocks are now cacheable, with the side effect of numerous bug fixes and performance improvements in caching. This also permits caching of functions defined in closures (Siu Kwan Lam). Deprecations to note: To align with other targets, the ``argtypes`` and ``restypes`` kwargs to ``cuda.jit`` are now deprecated, the ``bind`` kwarg is also deprecated. Further the ``target`` kwarg to the ``numba.jit`` decorator family is deprecated. General Enhancements: * PR 5463: Add str(int) impl * PR 5526: Impl. np.asarray(literal) * PR 5619: Add support for multi-output ufuncs * PR 5711: Division with timedelta input * PR 5763: Support minlength argument to np.bincount * PR 5779: Return zero array from np.dot when the arguments are empty. * PR 5796: Add implementation for np.positive * PR 5849: Setitem for records when index is StringLiteral, including literal unroll * PR 5856: Add support for conversion of inplace_binop to parfor. * PR 5893: Allocate 1D iteration space one at a time for more even distribution. * PR 5922: Reduce objmode and unpickling overhead * PR 5944: re-enable OpenMP in wheels * PR 5946: Implement literal dictionaries and lists. * PR 5956: Update numba_sysinfo.py * PR 5978: Add structref as a mutable struct that is pass-by-ref * PR 5980: Deprecate target kwarg for numba.jit. * PR 6058: Add prefer_literal option to overload API Fixes: * PR 5674: Fix 3955. Allow `with objmode` to be cached * PR 5724: Initialize process lock lazily to prevent multiprocessing issue * PR 5783: Make np.divide and np.remainder code more similar * PR 5808: Fix 5665 Block jit(nopython=True, forceobj=True) and suppress njit(forceobj=True) * PR 5834: Fix the is operator on Ellipsis * PR 5838: Ensure ``Dispatcher.__eq__`` always returns a bool * PR 5841: cleanup: Use PythonAPI.bool_from_bool in more places * PR 5862: Do not leak loop iteration variables into the numba.np.npyimpl namespace * PR 5869: Update repomap * PR 5879: Fix erroneous input mutation in linalg routines * PR 5882: Type check function in jit decorator * PR 5925: Use np.inf and -np.inf for max and min float values respectively. * PR 5935: Fix default arguments with multiprocessing * PR 5952: Fix "Internal error ... local variable 'errstr' referenced before assignment during BoundFunction(...)" * PR 5962: Fix SVML tests with LLVM 10 and AVX512 * PR 5972: fix flake8 for numba/runtests.py * PR 5995: Update setup.py with new llvmlite versions * PR 5996: Set lower bound for llvmlite to 0.33 * PR 6004: Fix problem in branch pruning with LiteralStrKeyDict * PR 6017: Fixing up numba_do_raise * PR 6028: Fix 6023 * PR 6031: Continue 5821 * PR 6035: Fix overspecialize of literal * PR 6046: Fixes statement reordering bug in maximize fusion step. * PR 6056: Fix issue on invalid inlining of non-empty build_list by inline_arraycall * PR 6057: fix aarch64/python_3.8 failure on master * PR 6070: Fix overspecialized containers * PR 6071: Remove f-strings in setup.py * PR 6072: Fix for 6005 * PR 6073: Fixes invalid C prototype in helper function. * PR 6078: Duplicate NumPy's PyArray_DescrCheck macro * PR 6081: Fix issue with cross drive use and relpath. * PR 6083: Fix bug in initial value unify. * PR 6087: remove invalid sanity check from randrange tests * PR 6089: Fix invalid reference to TypingError * PR 6097: Add function code and closure bytes into cache key * PR 6099: Restrict upper limit of TBB version due to ABI changes. * PR 6101: Restrict lower limit of icc_rt version due to assumed SVML bug. * PR 6107: Fix and test 6095 * PR 6109: Fixes an issue reported in 6094 * PR 6111: Decouple LiteralList and LiteralStrKeyDict from tuple * PR 6116: Fix 6102. Problem with non-unique label. CUDA Enhancements/Fixes: * PR 5359: Remove special-casing of 0d arrays * PR 5709: CUDA: Refactoring of cuda.jit and kernel / dispatcher abstractions * PR 5732: CUDA Docs: document ``forall`` method of kernels * PR 5745: CUDA stream callbacks and async awaitable streams * PR 5761: Add implmentation for int types for isnan and isinf for CUDA * PR 5819: Add support for CUDA 11 and Ampere / CC 8.0 * PR 5826: CUDA: Add function to get SASS for kernels * PR 5846: CUDA: Allow disabling NVVM optimizations, and fix debug issues * PR 5851: CUDA EMM enhancements - add default get_ipc_handle implementation, skip a test conditionally * PR 5852: CUDA: Fix ``cuda.test()`` * PR 5857: CUDA docs: Add notes on resetting the EMM plugin * PR 5859: CUDA: Fix reduce docs and style improvements * PR 6016: Fixes change of list spelling in a cuda test. * PR 6020: CUDA: Fix 5820, adding atomic nanmin / nanmax * PR 6030: CUDA: Don't optimize IR before sending it to NVVM * PR 6052: Fix dtype for atomic_add_double testsuite * PR 6080: CUDA: Prevent auto-upgrade of atomic intrinsics * PR 6123: Fix 6121 Documentation Updates: * PR 5782: Host docs on Read the Docs * PR 5830: doc: Mention that caching uses pickle * PR 5963: Fix broken link to numpy ufunc signature docs * PR 5975: restructure communication section * PR 5981: Document bounds-checking behavior in python deviations page * PR 5993: Docs for structref * PR 6008: Small fix so bullet points are rendered by sphinx * PR 6013: emphasize cuda kernel functions are asynchronous * PR 6036: Update deprecation doc from numba.errors to numba.core.errors * PR 6062: Change references to numba.pydata.org to https CI updates: * PR 5850: Updates the "New Issue" behaviour to better redirect users. * PR 5940: Add discourse badge * PR 5960: Setting mypy on CI Enhancements from user contributed PRs (with thanks!): * Aisha Tammy added the ability to switch off TBB support at compile time in 5821 (continued in 6031 by Stuart Archibald). * Alexander Stiebing fixed a reference before assignment bug in 5952. * Alexey Kozlov fixed a bug in tuple getitem for literals in 6028. * Andrew Eckart updated the repomap in 5869, added support for Read the Docs in 5782, fixed a bug in the ``np.dot`` implementation to correctly handle empty arrays in 5779 and added support for ``minlength`` to ``np.bincount`` in 5763. * ``bitsisbits`` updated ``numba_sysinfo.py`` to handle HSA agents correctly in 5956. * Daichi Suzuo Fixed a bug in the threading backend initialisation sequence such that it is now correctly a lazy lock in 5724. * Eric Wieser contributed a number of patches, particularly in enhancing and improving the ``ufunc`` capabilities: * 5359: Remove special-casing of 0d arrays * 5834: Fix the is operator on Ellipsis * 5619: Add support for multi-output ufuncs * 5841: cleanup: Use PythonAPI.bool_from_bool in more places * 5862: Do not leak loop iteration variables into the numba.np.npyimpl namespace * 5838: Ensure ``Dispatcher.__eq__`` always returns a bool * 5830: doc: Mention that caching uses pickle * 5783: Make np.divide and np.remainder code more similar * Ethan Pronovost added a guard to prevent the common mistake of applying a jit decorator to the same function twice in 5881. * Graham Markall contributed many patches to the CUDA target, as follows: * 6052: Fix dtype for atomic_add_double tests * 6030: CUDA: Don't optimize IR before sending it to NVVM * 5846: CUDA: Allow disabling NVVM optimizations, and fix debug issues * 5826: CUDA: Add function to get SASS for kernels * 5851: CUDA EMM enhancements - add default get_ipc_handle implementation, skip a test conditionally * 5709: CUDA: Refactoring of cuda.jit and kernel / dispatcher abstractions * 5819: Add support for CUDA 11 and Ampere / CC 8.0 * 6020: CUDA: Fix 5820, adding atomic nanmin / nanmax * 5857: CUDA docs: Add notes on resetting the EMM plugin * 5859: CUDA: Fix reduce docs and style improvements * 5852: CUDA: Fix ``cuda.test()`` * 5732: CUDA Docs: document ``forall`` method of kernels * Guilherme Leobas added support for ``str(int)`` in 5463 and ``np.asarray(literal value) in 5526. * Hameer Abbasi deprecated the ``target`` kwarg for ``numba.jit`` in 5980. * Hannes Pahl added a badge to the Numba github page linking to the new discourse forum in 5940 and also fixed a bug that permitted illegal combinations of flags to be passed into ``jit`` in 5808. * Kayran Schmidt emphasized that CUDA kernel functions are asynchronous in the documentation in 6013. * Leonardo Uieda fixed a broken link to the NumPy ufunc signature docs in 5963. * Lucio Fernandez-Arjona added mypy to CI and started adding type annotations to the code base in 5960, also fixed a (de)serialization problem on the dispatcher in 5935, improved the undefined variable error message in 5876, added support for division with timedelta input in 5711 and implemented ``setitem`` for records when the index is a ``StringLiteral`` in 5849. * Ludovic Tiako documented Numba's bounds-checking behavior in the python deviations page in 5981. * Matt Roeschke changed all ``http`` references ``https`` in 6062. * ``niteya-shah`` implemented ``isnan`` and ``isinf`` for integer types on the CUDA target in 5761 and implemented ``np.positive`` in 5796. * Peter Würtz added CUDA stream callbacks and async awaitable streams in 5745. * ``rht`` fixed an invalid import referred to in the deprecation documentation in 6036. * Sergey Pokhodenko updated the SVML tests for LLVM 10 in 5962. * Shyam Saladi fixed a Sphinx rendering bug in 6008. Authors: * Aisha Tammy * Alexander Stiebing * Alexey Kozlov * Andrew Eckart * ``bitsisbits`` * Daichi Suzuo * Eric Wieser * Ethan Pronovost * Graham Markall * Guilherme Leobas * Hameer Abbasi * Hannes Pahl * Kayran Schmidt * Kozlov, Alexey * Leonardo Uieda * Lucio Fernandez-Arjona * Ludovic Tiako * Matt Roeschke * ``niteya-shah`` * Peter Würtz * Sergey Pokhodenko * Shyam Saladi * ``rht`` * Siu Kwan Lam (core dev) * Stuart Archibald (core dev) * Todd A. Anderson (core dev) * Valentin Haenel (core dev) ``` ### 0.50.1 ``` ----------------------------- This is a bugfix release for 0.50.0, it fixes a critical bug in error reporting and a number of other smaller issues: * PR 5861: Added except for possible Windows get_terminal_size exception * PR 5876: Improve undefined variable error message * PR 5884: Update the deprecation notices for 0.50.1 * PR 5889: Fixes literally not forcing re-dispatch for inline='always' * PR 5912: Fix bad attr access on certain typing templates breaking exceptions. * PR 5918: Fix cuda test due to 5876 Authors: * ``pepping_dore`` * Lucio Fernandez-Arjona * Siu Kwan Lam (core dev) * Stuart Archibald (core dev) ``` ### 0.50.0 ``` ----------------------------- This is a more usual release in comparison to the others that have been made in the last six months. It comprises the result of a number of maintenance tasks along with some new features and a lot of bug fixes. Highlights of core feature changes include: * The compilation chain is now based on LLVM 9. * The error handling and reporting system has been improved to reduce the size of error messages, and also improve quality and specificity. * The CUDA target has more stream constructors available and a new function for compiling to PTX without linking and loading the code to a device. Further, the macro-based system for describing CUDA threads and blocks has been replaced with standard typing and lowering implementations, for improved debugging and extensibility. IMPORTANT: The backwards compatibility shim, that was present in 0.49.x to accommodate the refactoring of Numba's internals, has been removed. If a module is imported from a moved location an ``ImportError`` will occur. General Enhancements: * PR 5060: Enables np.sum for timedelta64 * PR 5225: Adjust interpreter to make conditionals predicates via bool() call. * PR 5506: Jitclass static methods * PR 5580: Revert shim * PR 5591: Fix 5525 Add figure for total memory to ``numba -s`` output. * PR 5616: Simplify the ufunc kernel registration * PR 5617: Remove /examples from the Numba repo. * PR 5673: Fix inliners to run all passes on IR and clean up correctly. * PR 5700: Make it easier to understand type inference: add SSA dump, use for ``DEBUG_TYPEINFER`` * PR 5702: Fixes for LLVM 9 * PR 5722: Improve error messages. * PR 5758: Support NumPy 1.18 Fixes: * PR 5390: add error handling for lookup_module * PR 5464: Jitclass drops annotations to avoid error * PR 5478: Fix 5471. Issue with omitted type not recognized as literal value. * PR 5517: Fix numba.typed.List extend for singleton and empty iterable * PR 5549: Check type getitem * PR 5568: Add skip to entrypoint test on windows * PR 5581: Revert 5568 * PR 5602: Fix segfault caused by pop from numba.typed.List * PR 5645: Fix SSA redundant CFG computation * PR 5686: Fix issue with SSA not minimal * PR 5689: Fix bug in unified_function_type (issue 5685) * PR 5694: Skip part of slice array analysis if any part is not analyzable. * PR 5697: Fix usedef issue with parfor loopnest variables. * PR 5705: A fix for cases where SSA looks like a reduction variable. * PR 5714: Fix bug in test * PR 5717: Initialise Numba extensions ahead of any compilation starting. * PR 5721: Fix array iterator layout. * PR 5738: Unbreak master on buildfarm * PR 5757: Force LLVM to use ZMM registers for vectorization. * PR 5764: fix flake8 errors * PR 5768: Interval example: fix import * PR 5781: Moving record array examples to a test module * PR 5791: Fix up no cgroups problem * PR 5795: Restore refct removal pass and make it strict * PR 5807: Skip failing test on POWER8 due to PPC CTR Loop problem. * PR 5812: Fix side issue from 5792, overload inliner cached IR being mutated. * PR 5815: Pin llvmlite to 0.33 * PR 5833: Fixes the source location appearing incorrectly in error messages. CUDA Enhancements/Fixes: * PR 5347: CUDA: Provide more stream constructors * PR 5388: CUDA: Fix OOB write in test_round{f4,f8} * PR 5437: Fix 5429: Exception using ``.get_ipc_handle(...)`` on array from ``as_cuda_array(...)`` * PR 5481: CUDA: Replace macros with typing and lowering implementations * PR 5556: CUDA: Make atomic semantics match Python / NumPy, and fix 5458 * PR 5558: CUDA: Only release primary ctx if retained * PR 5561: CUDA: Add function for compiling to PTX (+ other small fixes) * PR 5573: CUDA: Skip tests under cuda-memcheck that hang it * PR 5578: Implement math.modf for CUDA target * PR 5704: CUDA Eager compilation: Fix max_registers kwarg * PR 5718: CUDA lib path tests: unset CUDA_PATH when CUDA_HOME unset * PR 5800: Fix LLVM 9 IR for NVVM * PR 5803: CUDA Update expected error messages to fix 5797 Documentation Updates: * PR 5546: DOC: Add documentation about cost model to inlining notes. * PR 5653: Update doc with respect to try-finally case Enhancements from user contributed PRs (with thanks!): * Elias Kuthe fixed in issue with imports in the Interval example in 5768 * Eric Wieser Simplified the ufunc kernel registration mechanism in 5616 * Ethan Pronovost patched a problem with ``__annotations__`` in ``jitclass`` in 5464, fixed a bug that lead to infinite loops in Numba's ``Type.__getitem__`` in 5549, fixed a bug in ``np.arange`` testing in 5714 and added support for ``staticmethod`` to ``jitclass`` in 5506. * Gabriele Gemmi implemented ``math.modf`` for the CUDA target in 5578 * Graham Markall contributed many patches, largely to the CUDA target, as follows: * 5347: CUDA: Provide more stream constructors * 5388: CUDA: Fix OOB write in test_round{f4,f8} * 5437: Fix 5429: Exception using ``.get_ipc_handle(...)`` on array from ``as_cuda_array(...)`` * 5481: CUDA: Replace macros with typing and lowering implementations * 5556: CUDA: Make atomic semantics match Python / NumPy, and fix 5458 * 5558: CUDA: Only release primary ctx if retained * 5561: CUDA: Add function for compiling to PTX (+ other small fixes) * 5573: CUDA: Skip tests under cuda-memcheck that hang it * 5648: Unset the memory manager after EMM Plugin tests * 5700: Make it easier to understand type inference: add SSA dump, use for ``DEBUG_TYPEINFER`` * 5704: CUDA Eager compilation: Fix max_registers kwarg * 5718: CUDA lib path tests: unset CUDA_PATH when CUDA_HOME unset * 5800: Fix LLVM 9 IR for NVVM * 5803: CUDA Update expected error messages to fix 5797 * Guilherme Leobas updated the documentation surrounding try-finally in 5653 * Hameer Abbasi added documentation about the cost model to the notes on inlining in 5546 * Jacques Gaudin rewrote ``numba -s`` to produce and consume a dictionary of output about the current system in 5591 * James Bourbeau Updated min/argmin
pyup-bot commented 3 years ago

Closing this in favor of #84