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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 November #84

Closed pyup-bot closed 3 years ago

pyup-bot commented 4 years ago

Update astropy from 3.2.3 to 4.1.

Changelog ### 4.1 ``` ================ New Features ------------ astropy.config ^^^^^^^^^^^^^^ - Add new function ``generate_config`` to generate the configuration file and include it in the documentation. [10148] - ``ConfigNamespace.__iter__`` and ``ConfigNamespace.keys`` now yield ``ConfigItem`` names defined within it. Similarly, ``items`` and ``values`` would yield like a Python dictionary would. [10139] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Added a new ``SpectralCoord`` class that can be used to define spectral coordinates and transform them between different velocity frames. [10185] - Angle parsing now supports ``cardinal direction`` in the cases where angles are initialized as ``string`` instances. eg ``"17°53'27"W"``.[9859] - Allow in-place modification of array-valued ``Frame`` and ``SkyCoord`` objects. This provides limited support for updating coordinate data values from another coordinate object of the same class and equivalent frame attributes. [9857] - Added a robust equality operator for comparing ``SkyCoord``, frame, and representation objects. A comparison like ``sc1 == sc2`` will now return a boolean or boolean array where the objects are strictly equal in all relevant frame attributes and coordinate representation values. [10154] - Added the True Equator Mean Equinox (TEME) frame. [10149] - The ``Galactocentric`` frame will now use the "latest" parameter definitions by default. This currently corresponds to the values defined in v4.0, but will change with future releases. [10238] - The ``SkyCoord.from_name()`` and Sesame name resolving functionality now is able to cache results locally and will do so by default. [9162] - Allow in-place modification of array-valued ``Representation`` and ``Differential`` objects, including of representations with attached differentials. [10210] astropy.io.ascii ^^^^^^^^^^^^^^^^ - Functional Units can now be processed in CDS-tables. [9971] - Allow reading in ASCII tables which have duplicate column names. [9939] - Fixed failure of ASCII ``fast_reader`` to handle ``names``, ``include_names``, ``exclude_names`` arguments for ``RDB`` formatted tables. Homogenised checks and exceptions for invalid ``names`` arguments. Improved performance when parsing "wide" tables with many columns. [10306] - Added type validation of key arguments in calls to ``io.ascii.read()`` and ``io.ascii.write()`` functions. [10005] astropy.io.misc ^^^^^^^^^^^^^^^ - Added serialization of parameter constraints fixed and bounds. [10082] - Added 'functional_models.py' and 'physical_models.py' to asdf/tags/transform, with to allow serialization of all functional and physical models. [10028, 10293] - Fix ASDF serialization of circular model inverses, and remove explicit calls to ``asdf.yamlutil`` functions that became unnecessary in asdf 2.6.0. [10189, 10384] astropy.io.fits ^^^^^^^^^^^^^^^ - Added support for writing Dask arrays to disk efficiently for ``ImageHDU`` and ``PrimaryHDU``. [9742] - Add HDU name and ver to FITSDiff report where appropriate [10197] astropy.io.votable ^^^^^^^^^^^^^^^^^^ - New ``exceptions.conf.max_warnings`` configuration item to control the number of times a type of warning appears before being suppressed. [10152] - No longer ignore attributes whose values were specified as empty strings. [10583] astropy.modeling ^^^^^^^^^^^^^^^^ - Added Plummer1D model to ``functional_models``. [9896] - Added ``UnitsMapping`` model and ``Model.coerce_units`` to support units on otherwise unitless models. [9936] - Added ``domain`` and ``window`` attributes to ``repr`` and ``str``. Fixed bug with ``_format_repr`` in core.py. [9941] - Polynomial attributes ``domain`` and ``window`` are now tuples of size 2 and are validated. `repr` and `print` show only their non-default values. [10145] - Added ``replace_submodel()`` method to ``CompoundModel`` to modify an existing instance. [10176] - Delay construction of ``CompoundModel`` inverse until property is accessed, to support ASDF deserialization of circular inverses in component models. [10384] astropy.nddata ^^^^^^^^^^^^^^ - Added support in the ``bitmask`` module for using mnemonic bit flag names when specifying the bit flags to be used or ignored when converting a bit field to a boolean. [10095, 10208] - Added ``reshape_as_blocks`` function to reshape a data array into blocks, which is useful to efficiently apply functions on block subsets of the data instead of using loops. The reshaped array is a view of the input data array. [10214] - Added a ``cache`` keyword option to allow caching for ``CCDData.read`` if filename is a URL. [10265] astropy.table ^^^^^^^^^^^^^ - Added ability to specify a custom matching function for table joins. In particular this makes it possible to do cross-match table joins on ``SkyCoord``, ``Quantity``, or standard columns, where column entries within a specified distance are considered to be matched. [10169] - Added ``units`` and ``descriptions`` keyword arguments to the Table object initialization and ``Table.read()`` methods. This allows directly setting the ``unit`` and ``description`` for the table columns at the time of creating or reading the table. [9671] - Make table ``Row`` work as mappings, by adding ``.keys()`` and ``.values()`` methods. With this ``**row`` becomes possible, as does, more simply, turning a ``Row`` into a dictionary with ``dict(row)``. [9712] - Added two new ``Table`` methods ``.items()`` and ``.values()``, which return respectively ``tbl.columns.items()`` (iterator over name, column tuples) and ``tbl.columns.values()`` (list of columns) for a ``Table`` object ``tbl``. [9780] - Added new ``Table`` method ``.round()``, which rounds numeric columns to the specified number of decimals. [9862] - Updated ``to_pandas()`` and ``from_pandas()`` to use and support Pandas nullable integer data type for masked integer data. [9541] - The HDF5 writer, ``write_table_hdf5()``, now allows passing through additional keyword arguments to the ``h5py.Group.create_dataset()``. [9602] - Added capability to add custom table attributes to a ``Table`` subclass. These attributes are persistent and can be set during table creation. [10097] - Added support for ``SkyCoord`` mixin columns in ``dstack``, ``vstack`` and ``insert_row`` functions. [9857] - Added support for coordinate ``Representation`` and ``Differential`` mixin columns. [10210] astropy.time ^^^^^^^^^^^^ - Added a new time format ``unix_tai`` which is essentially Unix time but with leap seconds included. More precisely, this is the number of seconds since ``1970-01-01 00:00:08 TAI`` and corresponds to the ``CLOCK_TAI`` clock available on some linux platforms. [10081] - Improve initialization time by a factor of four when creating a scalar ``Time`` object in a format like ``unix`` or ``cxcsec`` (time delta from a reference epoch time). [10406] astropy.units ^^^^^^^^^^^^^ - Added ``torr`` pressure unit. [9787] - Added the ``equal_nan`` keyword argument to ``isclose`` and ``allclose``, and updated the docstrings. [9849] - Added ``Rankine`` temperature unit. [9916] - Added integrated flux unit conversion to ``spectral_density`` equivalency. [10015] - Changed ``pixel_scale`` equivalency to allow scales defined in any unit. [10123] - The ``quantity_input`` decorator now optionally allows passing through numeric values or numpy arrays with numeric dtypes to arguments where ``dimensionless_unscaled`` is an allowed unit. [10232] astropy.utils ^^^^^^^^^^^^^ - Added a new ``MetaAttribute`` class to support easily adding custom attributes to a subclass of classes like ``Table`` or ``NDData`` that have a ``meta`` attribute. [10097] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Added ``invalid`` keyword to ``SqrtStretch``, ``LogStretch``, ``PowerStretch``, and ``ImageNormalize`` classes and the ``simple_norm`` function. This keyword is used to replace generated NaN values. [10182] - Fixed an issue where ticks were sometimes not drawn at the edges of a spherical projection on a WCSAxes. [10442] astropy.wcs ^^^^^^^^^^^ - WCS objects with a spectral axis will now return ``SpectralCoord`` objects when calling ``pixel_to_world`` instead of ``Quantity``, and can now take either ``Quantity`` or ``SpectralCoord`` as input to ``pixel_to_world``. [10185] - Implemented support for the ``-TAB`` algorithm (WCS Paper III). [9641] - Added an ``_as_mpl_axes`` method to the ``HightLevelWCSWrapper`` class. [10138] - Add .upper() to ctype or ctype names to wcsapi/fitwcs.py to mitigate bugs from unintended lower/upper case issues [10557] API Changes ----------- astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - The equality operator for comparing ``SkyCoord``, frame, and representation objects was changed. A comparison like ``sc1 == sc2`` was previously equivalent to ``sc1 is sc2``. It will now return a boolean or boolean array where the objects are strictly equal in all relevant frame attributes and coordinate representation values. If the objects have different frame attributes or representation types then an exception will be raised. [10154] - SkyCoord.radial_velocity_correction now allows you to pass an obstime directly when the SkyCoord also has an obstime set. In this situation, the position of the SkyCoord has space motion applied to correct to the passed obstime. This allows mm/s radial velocity precision for objects with large space motion. [10094] - For consistency with other astropy classes, coordinate ``Representations`` and ``Differentials`` can now be initialized with an instance of their own class if that instance is passed in as the first argument. [10210] astropy.io.ascii ^^^^^^^^^^^^^^^^ - Changed the behavior when reading a table where both the ``names`` argument is provided (to specify the output column names) and the ``converters`` argument is provided (to specify column conversion functions). Previously the ``converters`` dict names referred to the *input* table column names, but now they refer to the *output* table column names. [9739] astropy.io.votable ^^^^^^^^^^^^^^^^^^ - For FIELDs with datatype="char", store the values as strings instead of bytes. [9505] astropy.table ^^^^^^^^^^^^^ - ``Table.from_pandas`` now supports a ``units`` dictionary as argument to pass units for columns in the ``DataFrame``. [9472] astropy.time ^^^^^^^^^^^^ - Require that ``in_subfmt`` and ``out_subfmt`` properties of a ``Time`` object have allowed values at the time of being set, either when creating the object or when setting those properties on an existing ``Time`` instance. Previously the validation of those properties was not strictly enforced. [9868] astropy.utils ^^^^^^^^^^^^^ - Changed the exception raised by ``get_readable_fileobj`` on missing compression modules (for ``bz2`` or ``lzma``/``xz`` support) to ``ModuleNotFoundError``, consistent with ``io.fits`` file handlers. [9761] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Deprecated the ``imshow_only_kwargs`` keyword in ``imshow_norm``. [9915] - Non-finite input values are now automatically excluded in ``HistEqStretch`` and ``InvertedHistEqStretch``. [10177] - The ``PowerDistStretch`` and ``InvertedPowerDistStretch`` ``a`` value is restricted to be ``a >= 0`` in addition to ``a != 1``. [10177] - The ``PowerStretch``, ``LogStretch``, and ``InvertedLogStretch`` ``a`` value is restricted to be ``a > 0``. [10177] - The ``AsinhStretch`` and ``SinhStretch`` ``a`` value is restricted to be ``0 < a <= 1``. [10177] Bug Fixes --------- astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Fix a bug where for light deflection by the Sun it was always assumed that the source was at infinite distance, which in the (rare and) absolute worst-case scenario could lead to errors up to 3 arcsec. [10666] astropy.io.votable ^^^^^^^^^^^^^^^^^^ - For FIELDs with datatype="char", store the values as strings instead of bytes. [9505] astropy.modeling ^^^^^^^^^^^^^^^^ - Fixed an issue of ``Model.render`` when the input ``out`` datatype is not float64. [10542] astropy.table ^^^^^^^^^^^^^ - Fix a bug that prevented ``Time`` columns from being used to sort a table. [10824] astropy.wcs ^^^^^^^^^^^ - WCS objects with a spectral axis will now return ``SpectralCoord`` objects when calling ``pixel_to_world`` instead of ``Quantity`` (note that ``SpectralCoord`` is a sub-class of ``Quantity``). [10185] - Add .upper() to ctype or ctype names to wcsapi/fitwcs.py to mitigate bugs from unintended lower/upper case issues [10557] - Added bounds to ``fit_wcs_from_points`` to ensure CRPIX is on input image. [10346] Other Changes and Additions --------------------------- - The way in which users can specify whether to build astropy against existing installations of C libraries rather than the bundled one has changed, and should now be done via environment variables rather than setup.py flags (e.g. --use-system-erfa). The available variables are ``ASTROPY_USE_SYSTEM_CFITSIO``, ``ASTROPY_USE_SYSTEM_ERFA``, ``ASTROPY_USE_SYSTEM_EXPAT``, ``ASTROPY_USE_SYSTEM_WCSLIB``, and ``ASTROPY_USE_SYSTEM_ALL``. These should be set to ``1`` to build against the system libraries. [9730] - The infrastructure of the package has been updated in line with the APE 17 roadmap (https://github.com/astropy/astropy-APEs/blob/master/APE17.rst). The main changes are that the ``python setup.py test`` and ``python setup.py build_docs`` commands will no longer work. The easiest way to replicate these commands is to install the tox (https://tox.readthedocs.io) package and run ``tox -e test`` and ``tox -e build_docs``. It is also possible to run pytest and sphinx directly. Other significant changes include switching to setuptools_scm to manage the version number, and adding a ``pyproject.toml`` to opt in to isolated builds as described in PEP 517/518. [9726] - Bundled ``expat`` is updated to version 2.2.9. [10038] - Increase minimum asdf version to 2.6.0. [10189] - The bundled version of PLY was updated to 3.11. [10258] - Removed dependency on scikit-image. [10214] - Added ``optimize=True`` flag to calls of ``yacc.yacc`` (as already done for ``lex.lex``) to allow running in ``python -OO`` session without raising an exception in ``astropy.units.format``. [10379] ``` ### 4.0.4 ``` ================== Bug Fixes --------- astropy.config ^^^^^^^^^^^^^^ astropy.constants ^^^^^^^^^^^^^^^^^ astropy.convolution ^^^^^^^^^^^^^^^^^^^ astropy.coordinates ^^^^^^^^^^^^^^^^^^^ astropy.cosmology ^^^^^^^^^^^^^^^^^ astropy.extern ^^^^^^^^^^^^^^ astropy.io.ascii ^^^^^^^^^^^^^^^^ - Partially fixed a performance issue when reading in parallel mode. Parallel reading currently has substantially worse performance than the default serial reading, so we now ignore the parallel option and fall back to serial reading. [10880] astropy.io.fits ^^^^^^^^^^^^^^^ astropy.io.misc ^^^^^^^^^^^^^^^ astropy.io.registry ^^^^^^^^^^^^^^^^^^^ astropy.io.votable ^^^^^^^^^^^^^^^^^^ astropy.modeling ^^^^^^^^^^^^^^^^ astropy.nddata ^^^^^^^^^^^^^^ astropy.samp ^^^^^^^^^^^^ astropy.stats ^^^^^^^^^^^^^ astropy.table ^^^^^^^^^^^^^ astropy.tests ^^^^^^^^^^^^^ astropy.time ^^^^^^^^^^^^ - Fix a problem with the ``plot_date`` format for matplotlib >= 3.3 caused by a change in the matplotlib plot date default reference epoch in that release. [10876] astropy.timeseries ^^^^^^^^^^^^^^^^^^ astropy.uncertainty ^^^^^^^^^^^^^^^^^^^ astropy.units ^^^^^^^^^^^^^ astropy.utils ^^^^^^^^^^^^^ astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ astropy.wcs ^^^^^^^^^^^ Other Changes and Additions --------------------------- ``` ### 4.0.3 ``` ================== Bug Fixes --------- astropy.table ^^^^^^^^^^^^^ - Fixed a small bug where initializing an empty ``Column`` with a structured dtype with a length and a shape failed to give the requested dtype. [10819] Other Changes and Additions --------------------------- - Fixed installation of the source distribution with pip<19. [10837, 10852] ``` ### 4.0.2 ``` ================== New Features ------------ astropy.utils ^^^^^^^^^^^^^ - ``astropy.utils.data.download_file`` now supports FTPS/FTP over TLS. [9964] - ``astropy.utils.data`` now uses a lock-free mechanism for caching. This new mechanism uses a new cache layout and so ignores caches created using earlier mechanisms (which were causing lockups on clusters). The two cache formats can coexist but do not share any files. [10437] - ``astropy.utils.data`` now ignores the config item ``astropy.utils.data.conf.download_cache_lock_attempts`` since no locking is done. [10437] - ``astropy.utils.data.download_file`` and related functions now interpret the parameter or config file setting ``timeout=0`` to mean they should make no attempt to download files. [10437] - ``astropy.utils.import_file_to_cache`` now accepts a keyword-only argument ``replace``, defaulting to True, to determine whether it should replace existing files in the cache, in a way as close to atomic as possible. [10437] - ``astropy.utils.data.download_file`` and related functions now treat ``http://example.com`` and ``http://example.com/`` as equivalent. [10631] astropy.wcs ^^^^^^^^^^^ - The new auxiliary WCS parameters added in WCSLIB 7.1 are now exposed as the ``aux`` attribute of ``Wcsprm``. [10333] - Updated bundled version of ``WCSLIB`` to v7.3. [10433] Bug fixes --------- astropy.config ^^^^^^^^^^^^^^ - Added an extra fallback to ``os.expanduser('~')`` when trying to find the user home directory. [10570] astropy.constants ^^^^^^^^^^^^^^^^^ - Corrected definition of parsec to 648 000 / pi AU following IAU 2015 B2 [10569] astropy.convolution ^^^^^^^^^^^^^^^^^^^ - Fixed a bug where a float-typed integers in the argument ``x_range`` of ``astropy.convolution.utils.discretize_oversample_1D`` (and the 2D version as well) fails because it uses ``numpy.linspace``, which requires an ``int``. [10696] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Ensure that for size-1 array ``SkyCoord`` and coordinate frames the attributes also properly become scalars when indexed with 0. [10113] - Fixed a bug where ``SkyCoord.separation()`` and ``SkyCoord.separation_3d`` were not accepting a frame object. [10332] - Ensure that the ``lon`` values in ``SkyOffsetFrame`` are wrapped correctly at 180 degree regardless of how the underlying data is represented. [10163] - Fixed an error in the obliquity of the ecliptic when transforming to/from the ``*TrueEcliptic`` coordinate frames. The error would primarily result in an inaccuracy in the ecliptic latitude on the order of arcseconds. [10129] - Fixed an error in the computation of the location of solar system bodies where the Earth location of the observer was ignored during the correction for light travel time. [10292] - Ensure that coordinates with proper motion that are transformed to other coordinate frames still can be represented properly. [10276] - Improve the error message given when trying to get a cartesian representation for coordinates that have both proper motion and radial velocity, but no distance. [10276] - Fixed an error where ``SkyCoord.apply_space_motion`` would return incorrect results when no distance is set and proper motion is high. [10296] - Make the parsing of angles thread-safe so that ``Angle`` can be used in Python multithreading. [10556] - Fixed reporting of ``EarthLocation.info`` which previously raised an exception. [10592] astropy.io.ascii ^^^^^^^^^^^^^^^^ - Fixed a bug with the C ``fast_reader`` not correctly parsing newlines when ``delimiter`` was also set to ``\n`` or ``\r``; ensured consistent handling of input strings without newline characters. [9929] astropy.io.fits ^^^^^^^^^^^^^^^ - Fix integer formats of ``TFORMn=Iw`` columns in ASCII tables to correctly read values exceeding int32 - setting int16, int32 or int64 according to ``w``. [9901] - Fix unclosed memory-mapped FITS files in ``FITSDiff`` when difference found. [10159] - Fix crash when reading an invalid table file. [10171] - Fix duplication issue when setting a keyword ending with space. [10482] - Fix ResourceWarning with ``fits.writeto`` and ``pathlib.Path`` object. [10599] - Fix repr for commentary cards and strip spaces for commentary keywords. [10640] - Fix compilation of cfitsio with Xcode 12. [10772] - Fix handling of 1-dimensional arrays with a single element in ``BinTableHDU`` [10768] astropy.io.misc ^^^^^^^^^^^^^^^ - Fix id URL in ``baseframe-1.0.0`` ASDF schema. [10223] - Write keys to ASDF only if the value is present, to account for a change in behavior in asdf 2.8. [10674] astropy.io.registry ^^^^^^^^^^^^^^^^^^^ - Fix ``Table.(read|write).help`` when reader or writer has no docstring. [10460] astropy.io.votable ^^^^^^^^^^^^^^^^^^ - Fixed parsing failure of VOTable with no fields. When detecting a non-empty table with no fields, the following warning/exception is issued: E25 "No FIELDs are defined; DATA section will be ignored." [10192] astropy.modeling ^^^^^^^^^^^^^^^^ - Fixed a problem with mapping ``input_units`` and ``return_units`` of a ``CompoundModel`` to the units of the constituent models. [10158] - Removed hard-coded names of inputs and outputs. [10174] - Fixed a problem where slicing a ``CompoundModel`` by name will crash if there ``fix_inputs`` operators are present. [10224] - Removed a limitation of fitting of data with units with compound models without units when the expression involves operators other than addition and subtraction. [10415] - Fixed a problem with fitting ``Linear1D`` and ``Planar2D`` in model sets. [10623] - Fixed reported module name of ``math_functions`` model classes. [10694] - Fixed reported module name of ``tabular`` model classes. [10709] - Do not create new ``math_functions`` models for ufuncs that are only aliases (divide and mod). [10697] - Fix calculation of the ``Moffat2D`` derivative with respect to gamma. [10784] astropy.stats ^^^^^^^^^^^^^ - Fixed an API regression where ``SigmaClip.__call__`` would convert masked elements to ``nan`` and upcast the dtype to ``float64`` in its output ``MaskedArray`` when using the ``axis`` parameter along with the defaults ``masked=True`` and ``copy=True``. [10610] - Fixed an issue where fully masked ``MaskedArray`` input to ``sigma_clipped_stats`` gave incorrect results. [10099] - Fixed an issue where ``sigma_clip`` and ``SigmaClip.__call__`` would return a masked array instead of a ``ndarray`` when ``masked=False`` and the input was a full-masked ``MaskedArray``. [10099] - Fixed bug with ``funcs.poisson_conf_interval`` where an integer for N with ``interval='kraft-burrows-nousek'`` would throw an error with mpmath backend. [10427] - Fixed bug in ``funcs.poisson_conf_interval`` with ``interval='kraft-burrows-nousek'`` where certain combinations of source and background count numbers led to ``ValueError`` due to the choice of starting value for numerical optimization. [10618] astropy.table ^^^^^^^^^^^^^ - Fixed a bug when writing a table with mixin columns to FITS, ECSV or HDF5. If one of the data attributes of the mixin (e.g. ``skycoord.ra``) had the same name as one of the table column names (``ra``), the column (``ra``) would be dropped when reading the table back. [10222] - Fixed a bug when sorting an indexed table on the indexed column after first sorting on another column. [10103] - Fixed a bug in table argsort when called with ``reverse=True`` for an indexed table. [10103] - Fixed a performance regression introduced in 9048 when initializing a table from Python lists. Also fixed incorrect behavior (for data types other than float) when those lists contain ``np.ma.masked`` elements to indicate masked data. [10636] - Avoid modifying ``.meta`` when serializing columns to FITS. [10485] - Avoid crash when reading a FITS table that contains mixin info and PyYAML is missing. [10485] astropy.time ^^^^^^^^^^^^ - Ensure that for size-1 array ``Time``, the location also properly becomes a scalar when indexed with 0. [10113] astropy.units ^^^^^^^^^^^^^ - Refined test_parallax to resolve difference between 2012 and 2015 definitions. [10569] astropy.utils ^^^^^^^^^^^^^ - The default IERS server has been updated to use the FTPS server hosted by CDDIS. [9964] - Fixed memory allocation on 64-bit systems within ``xml.iterparse`` [10076] - Fix case where ``None`` could be used in a numerical computation. [10126] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Fixed a bug where the ``ImageNormalize`` ``clip`` keyword was ignored when used with calling the object on data. [10098] - Fixed a bug where ``axes.xlabel``/``axes.ylabel`` where not correctly set nor returned on an ``EllipticalFrame`` class ``WCSAxes`` plot. [10446] astropy.wcs ^^^^^^^^^^^ - Handled WCS 360 -> 0 deg crossover in ``fit_wcs_from_points`` [10155] - Do not issue ``DATREF`` warning when ``MJDREF`` has default value. [10440] - Fixed a bug due to which ``naxis`` argument was ignored if ``header`` was supplied during the initialization of a WCS object. [10532] Other Changes and Additions --------------------------- - Improved the speed of sorting a large ``Table`` on a single column by a factor of around 5. [10103] - Ensure that astropy can be used inside Application bundles built with pyinstaller. [8795] - Updated the bundled CFITSIO library to 3.49. See ``cextern/cfitsio/docs/changes.txt`` for additional information. [10256, 10665] - ``extract_array`` raises a ``ValueError`` if the data type of the input array is inconsistent with the ``fill_value``. [10602] ``` ### 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
pyup-bot commented 3 years ago

Closing this in favor of #85