Closed pyup-bot closed 5 years ago
coveralls
commented
5 years ago Coverage remained the same at 55.948% when pulling 2777b9571a9fd3d06e5ec5fb5b1b409050ce0ba4 on pyup/scheduled-update-2019-01-01 into d190800968019066c05c32ad8afcaf6786ec9c0b on develop.
coveralls
commented
5 years ago Coverage remained the same at 55.948% when pulling 2777b9571a9fd3d06e5ec5fb5b1b409050ce0ba4 on pyup/scheduled-update-2019-01-01 into d190800968019066c05c32ad8afcaf6786ec9c0b on develop.
pyup-bot
commented
5 years ago Closing this in favor of #63
Update astropy from 3.0.4 to 3.1.1.
Changelog
### 3.1.1 ``` ================== Bug fixes --------- astropy.config ^^^^^^^^^^^^^^ astropy.constants ^^^^^^^^^^^^^^^^^ astropy.convolution ^^^^^^^^^^^^^^^^^^^ astropy.coordinates ^^^^^^^^^^^^^^^^^^^ astropy.cosmology ^^^^^^^^^^^^^^^^^ astropy.extern ^^^^^^^^^^^^^^ astropy.io.ascii ^^^^^^^^^^^^^^^^ - Fix error when writing out empty table. [8279] astropy.io.misc ^^^^^^^^^^^^^^^ astropy.io.fits ^^^^^^^^^^^^^^^ - ``fitsdiff --ignore-hdus`` now prints input filenames in the diff report instead of ``<HDUList object at 0x1150f9778>``. [8295] astropy.io.registry ^^^^^^^^^^^^^^^^^^^ astropy.io.votable ^^^^^^^^^^^^^^^^^^ astropy.modeling ^^^^^^^^^^^^^^^^ astropy.nddata ^^^^^^^^^^^^^^ astropy.samp ^^^^^^^^^^^^ astropy.stats ^^^^^^^^^^^^^ astropy.table ^^^^^^^^^^^^^ astropy.tests ^^^^^^^^^^^^^ astropy.time ^^^^^^^^^^^^ astropy.uncertainty ^^^^^^^^^^^^^^^^^^^ astropy.units ^^^^^^^^^^^^^ - Ensure correctness of units when raising to a negative power. [8263] - Fix ``with_H0`` equivalency to use the correct direction of conversion. [8292] - Add support for ``np.matmul`` as a ``ufunc`` (new in numpy 1.16). [8264] astropy.utils ^^^^^^^^^^^^^ astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ astropy.wcs ^^^^^^^^^^^ Other Changes and Additions --------------------------- ``` ### 3.1 ``` ================ New Features ------------ astropy.convolution ^^^^^^^^^^^^^^^^^^^ - ``convolve`` now accepts any array-like input, not just ``numpy.ndarray`` or lists. [7303] - ``convolve`` Now raises AstropyUserWarning if nan_treatment='interpolate' and preserve_nan=False and NaN values are present post convolution. [8088] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - The ``SkyCoord.from_name`` constructor now has the ability to create coordinate objects by parsing object catalogue names that have embedded J-coordinates. [7830] - The new function ``make_transform_graph_docs`` can be used to create a docstring graph from a custom ``TransformGraph`` object. [7135] - ``KDTree`` for catalog matching is now built with sliding midpoint rule rather than standard. In code, this means setting ``compact_nodes=False`` and ``balanced_tree=False`` in ``cKDTree``. The sliding midpoint rule is much more suitable for catalog matching, and results in 1000x speedup in some cases. [7324] - Additional information about a site loaded from the Astropy sites registry is now available in ``EarthLocation.info.meta``. [7857] - Added a ``concatenate_representations`` function to combine coordinate representation data and any associated differentials. [7922] - ``BaseCoordinateFrame`` will now check for a method named ``_astropy_repr_in_frame`` when constructing the string forms of attributes. Allowing any class to control how ``BaseCoordinateFrame`` represents it when it is an attribute of a frame. [7745] - Some rarely-changed attributes of frame classes are now cached, resulting in speedups (up to 50% in some cases) when creating new scalar frame or ``SkyCoord`` objects. [7949, 5952] - Added a ``directional_offset_by`` method to ``SkyCoord`` that computes a new coordinate given a coordinate, position angle, and angular separation [5727] astropy.cosmology ^^^^^^^^^^^^^^^^^ - The default cosmology has been changed from ``WMAP9`` to ``Planck15``. [8123] - Distance calculations with ``LambaCDM`` with no radiation (T_CMB0=0) are now 20x faster by using elliptic integrals for non-flat cases. [7155] - Distance calculations with ``FlatLambaCDM`` with no radiation (T_CMB0=0) are now 20x faster by using the hypergeometric function solution for this special case. [7087] - Age calculations with ``FlatLambdaCDM`` with no radiation (Tcmb0=0) are now 1000x faster by using analytic solutions instead of integrating. [7117] astropy.io.ascii ^^^^^^^^^^^^^^^^ - Latex reader now ignores ``\toprule``, ``\midrule``, and ``\bottomrule`` commands. [7349] - Added the RST (Restructured-text) table format and the fast version of the RDB reader to the set of formats that are guessed by default. [5578] - The read trace (used primarily for debugging) now includes guess argument sets that were skipped entirely e.g. for not supporting user-supplied kwargs. All guesses thus removed from ``filtered_guess_kwargs`` are now listed as "Disabled" at the beginning of the trace. [5578] - Emit a warning when reading an ECSV file without specifying the ``format`` and without PyYAML installed. Previously this silently fell through to parsing as a basic format file and the file metadata was lost. [7580] - Optionally allow writing masked columns to ECSV with the mask explicitly specified as a separate column instead of marking masked elements with "" (empty string). This allows handling the case of a masked string column with "" data rows. [7481] astropy.io.misc ^^^^^^^^^^^^^^^ - Added support for saving all representation classes and many coordinate frames to the asdf format. [7079] - Added support for saving models with units to the asdf format. [7237] - Added a new ``character_as_bytes`` keyword to the HDF5 Table reading function to control whether byte string columns in the HDF5 file are left as bytes or converted to unicode. The default is to read as bytes (``character_as_bytes=True``). [7024, 8017] astropy.io.fits ^^^^^^^^^^^^^^^ - ``HDUList.pop()`` now accepts string and tuple extension name specifications. [7236] - Add an ``ignore_hdus`` keyword to ``FITSDiff`` to allow ignoring HDUs by NAME when diffing two FITS files [7538] - Optionally allow writing masked columns to FITS with the mask explicitly specified as a separate column instead of using the FITS standard of certain embedded null values (``NaN`` for float, ``TNULL`` for integers). This can be used to work around limitations in the FITS standard. [7481] - All time coordinates can now be written to and read from FITS binary tables, including those with vectorized locations. [7430] - The ``fitsheader`` command line tool now supports a ``dfits+fitsort`` mode, and the dotted notation for keywords (e.g. ``ESO.INS.ID``). [7240] - Fall back to reading arrays using mode='denywrite' if mode='readonly' fails when using memory-mapping. This solves cases on some platforms when the available address space was less than the file size (even when using memory mapping). [7926] astropy.modeling ^^^^^^^^^^^^^^^^ - Add a ``Multiply`` model which preserves unit through evaluate, unlike ``Scale`` which is dimensionless. [7210] - Add a ``uses_quantity`` property to ``Model`` which allows introspection of if the ``Model`` can accept ``Quantity`` objects. [7417] - Add a ``separability_matrix`` function which returns the correlation matrix of inputs and outputs. [7803] - Fixed compatibility of ``JointFitter`` with the latest version of Numpy. [7984] - Add ``prior`` and ``posterior`` constraints to modeling parameters. These are not used by any current fitters, but are provided to allow user code to experiment with Bayesian fitters. [7558] astropy.nddata ^^^^^^^^^^^^^^ - ``NDUncertainty`` objects now have a ``quantity`` attribute for simple conversion to quantities. [7704] - Add a ``bitmask`` module that provides functions for manipulating bitmasks and data quality (DQ) arrays. [7944] astropy.stats ^^^^^^^^^^^^^ - Add an ``astropy.stats.bls`` module with an implementation of the "box least squares" periodogram that is commonly used for discovering transiting exoplanets and eclipsing binaries. [7391] astropy.table ^^^^^^^^^^^^^ - Added support for full use of ``Time`` mixin column for join, hstack, and vstack table operations. [6888] - Added a new table index engine, ``SCEngine``, based on the Sorted Containers package. [7574] - Add a new keyword argument ``serialize_method`` to ``Table.write`` to control how ``Time`` and ``MaskedColumn`` columns are written. [7481] - Allow mixin columns to be used in table ``group`` and ``unique`` functions. This applies to both the key columns and the other data columns. [7712] - Added support for stacking ``Column``, mixin column (e.g. ``Quantity``, ``Time``) or column-like objects. [7674] - Added support for inserting a row into a Table that has ``Time`` or ``TimeDelta`` column(s). [7897] astropy.tests ^^^^^^^^^^^^^ - Added an option ``--readonly`` to the test command to change the permissions on the temporary installation location to read-only. [7598] astropy.time ^^^^^^^^^^^^ - Allow array-valued ``Time`` object to be modified in place. [6028] - Added support for missing values (masking) to the ``Time`` class. [6028] - Added supper for a 'local' time scale (for free-running clocks, etc.), and round-tripping to the corresponding FITS time scale. [7122] - Added `datetime.timedelta` format class for ``TimeDelta``. [7441] - Added ``strftime`` and ``strptime`` methods to ``Time`` class. These methods are similar to those in the Python standard library `time` package and provide flexible input and output formatting. [7323] - Added ``datetime64`` format to the ``Time`` class to support working with ``numpy.datetime64`` dtype arrays. [7361] - Add fractional second support for ``strftime`` and ``strptime`` methods of ``Time`` class. [7705] - Added an ``insert`` method to allow inserting one or more values into a ``Time`` or ``TimeDelta`` object. [7897] - Remove timescale from string version of FITS format time string. The timescale is not part of the FITS standard and should not be included. This change may cause some compatibility issues for code that relies on round-tripping a FITS format string with a timescale. Strings generated from previous versions of this package are still understood but a DeprecationWarning will be issued. [7870] astropy.uncertainty ^^^^^^^^^^^^^^^^^^^ - This sub-package was added as a "preview" (i.e. API unstable), containing the ``Distribution`` class and associated convenience functions. [6945] astropy.units ^^^^^^^^^^^^^ - Add complex numbers support for ``Quantity._repr_latex_``. [7676] - Add ``thermodynamic_temperature`` equivalency to convert between Jy/beam and "thermodynamic temperature" for cosmology. [7054] - Add millibar unit. [7863] - Add maggy and nanomaggy unit, as well as associated ``zero_point_flux`` equivalency. [7891] - ``AB`` and ``ST`` are now enabled by default, and have alternate names ``ABflux`` and ``STflux``. [7891] - Added ``littleh`` unit and associated ``with_H0`` equivalency. [7970] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Added ``imshow_norm`` function, which combines imshow and creation of a ``ImageNormalize`` object. [7785] astropy.visualization.wcsaxes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Add support for setting ``set_separator(None)`` in WCSAxes to use default separators. [7570] - Added two keyword argument options to ``CoordinateHelper.set_format_unit``: ``decimal`` can be used to specify whether to use decimal formatting for the labels (by default this is False for degrees and hours and True otherwise), and ``show_decimal_unit`` can be used to determine whether the units should be shown for decimal labels. [7318] - Added documentation for ``transform=`` and ``coord_meta=``. [7698] - Allow ``coord_meta=`` to optionally include ``format_unit=``. [7848] - Add support for more rcParams related to the grid, ticks, and labels, and should work with most built-in Matplotlib styles. [7961] - Improved rendering of outward-facing ticks. [7961] - Add support for ``tick_params`` (which is a standard Matplotlib function/method) on both the ``WCSAxes`` class and the individual ``CoordinateHelper`` classes. Note that this is provided for compatibility with Matplotlib syntax users may be familiar with, but it is not the preferred way to change settings. Instead, methods such as ``set_ticks`` should be preferred. [7969] - Moved the argument ``exclude_overlapping`` from ``set_ticks`` to ``set_ticklabel``. [7969] - Added a ``pad=`` argument to ``set_ticklabel`` to provide a way to control the padding between ticks and tick labels. [7969] - Added support for setting the tick direction in ``set_ticks`` using the ``direction=`` keyword argument. [7969] astropy.wcs ^^^^^^^^^^^ - Map ITRS frames to terrestrial WCS coordinates. This will make it possible to use WCSAxes to make figures that combine both celestial and terrestrial features. An example is plotting the coordinates of an astronomical transient over an all- sky satellite image to illustrate the position relative to the Earth at the time of the event. The ITRS frame is identified with WCSs that use the ``TLON-`` and ``TLAT-`` coordinate types. There are several examples of WCSs where this syntax is used to describe terrestrial coordinate systems: Section 7.4.1 of `WCS in FITS "Paper II" <http://adsabs.harvard.edu/abs/2002A%26A...395.1077C>`_ and the `WCSTools documentation <http://tdc-www.harvard.edu/software/wcstools/wcstools.multiwcs.html>`_. [6990] - Added the abstract base class for the low-level WCS API described in APE 14 (https://doi.org/10.5281/zenodo.1188875). [7325] - Add ``WCS.contains()`` function to check if the WCS footprint contains a given sky coordinate. [7273] - Added the abstract base class for the high-level WCS API described in APE 14 (https://doi.org/10.5281/zenodo.1188875). [7325] - Added the high-level wrapper class for low-level WCS objects as described in APE 14 (https://doi.org/10.5281/zenodo.1188875). [7326] - Added a new property ``WCS.has_distortion``. [7326] - Deprecated ``_naxis1`` and ``_naxis2`` in favor of ``pixel_shape``. [7973] - Added compatibility to wcslib version 6. [8093] API Changes ----------- astropy.convolution ^^^^^^^^^^^^^^^^^^^ - ``kernel`` can now be a tuple. [7561] - Not technically an API changes, however, the doc string indicated that ``boundary=None`` was the default when actually it is ``boundary='fill'``. The doc string has been corrected, however, someone may interpret this as an API change not realising that nothing has actually changed. [7293] - ``interpolate_replace_nans()`` can no longer accept the keyword argument ``preserve_nan``. It is explicitly set to ``False``. [8088] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Fixed ``astropy.coordinates.concatenate`` to include velocity data in the concatenation. [7922] - Changed the name of the single argument to ``Frame.realize_frame()`` from the (incorrect) ``representation_type`` to ``data``. [7923] - Negative parallaxes passed to ``Distance()`` now raise an error by default (``allow_negative=False``), or are converted to NaN values with a warning (``allow_negative=True``). [7988] - Negating a ``SphericalRepresentation`` object now changes the angular coordinates (by rotating 180º) instead of negating the distance. [7988] - Creation of new frames now generally creates copies of frame attributes, rather than inconsistently either copying or making references. [8204] - The frame class method ``is_equivalent_frame`` now checks for equality of components to determine if a frame is the same when it has frame attributes that are representations, rather than checking if they are the same object. [8218] astropy.io.ascii ^^^^^^^^^^^^^^^^ - If a fast reader is explicitly selected (e.g. ``fast_reader='force'``) and options which are incompatible with the fast reader are provided (e.g. ``quotechar=''``) then now a ``ParameterError`` exception will be raised. [5578] - The fast readers will now raise ``InconsistentTableError`` instead of ``CParserError`` if the number of data and header columns do not match. [5578] - Changed a number of ``ValueError`` exceptions to ``InconsistentTableError`` in places where the exception is related to parsing a table which is inconsistent with the specified table format. Note that ``InconsistentTableError`` inherits from ``ValueError`` so no user code changes are required. [7425] astropy.io.fits ^^^^^^^^^^^^^^^ - The ``fits.table_to_hdu()`` function will translate any column ``format`` attributes to a TDISPn format string, if possible, and store it as a TDISPn keyword in the ``HDU`` header. [7226] astropy.modeling ^^^^^^^^^^^^^^^^ - Change the order of the return values from ``FittingWithOutlierRemoval``, such that ``fitted_model`` comes first, for consistency with other fitters. For the second value, return only a boolean outlier ``mask``, instead of the previous ``MaskedArray`` (which included a copy of the input data that was both redundant and inadvertently corrupted at masked points). Return a consistent type for the second value when ``niter=0``. [7407] - Set the minimum value for the ``bolometric_flux`` parameter of the ``BlackBody1D`` model to zero. [7045] astropy.nddata ^^^^^^^^^^^^^^ - Add two new uncertainty classes, ``astropy.nddata.VarianceUncertainty`` and ``astropy.nddata.InverseVariance``. [6971] astropy.stats ^^^^^^^^^^^^^ - String values can now be used for the ``cenfunc`` and ``stdfunc`` keywords in the ``SigmaClip`` class and ``sigma_clip`` and ``sigma_clipped_stats`` functions. [7478] - The ``SigmaClip`` class and ``sigma_clip`` and ``sigma_clipped_stats`` functions now have a ``masked`` keyword, which can be used to return either a masked array (default) or an ndarray with the min/max values. [7478] - The ``iters`` keyword has been renamed (and deprecated) to ``maxiters`` in the ``SigmaClip`` class and ``sigma_clip`` and ``sigma_clipped_stats`` functions. [7478] astropy.table ^^^^^^^^^^^^^ - ``Table.read()`` on a FITS binary table file will convert any TDISPn header keywords to a Python formatting string when possible, and store it in the column ``format`` attribute. [7226] - No values provided to stack will now raise ``ValueError`` rather than ``TypeError``. [7674] astropy.tests ^^^^^^^^^^^^^ - ``from astropy.tests.helper import *`` no longer includes ``quantity_allclose``. However, ``from astropy.tests.helper import quantity_allclose`` would still work. [7381] - ``warnings_to_ignore_by_pyver`` option in ``enable_deprecations_as_exceptions()`` now takes ``None`` as key. Any deprecation message that is mapped to ``None`` will be ignored regardless of the Python version. [7790] astropy.time ^^^^^^^^^^^^ - Added the ability to use ``local`` as time scale in ``Time`` and ``TimeDelta``. [6487] - Comparisons, addition, and subtraction of ``Time`` instances with non-time instances will now return ``NotImplemented`` rather than raise the ``Time``-specific ``OperandTypeError``. This will generally lead to a regular ``TypeError``. As a result, ``OperandTypeError`` now only occurs if the operation is between ``Time`` instances of incompatible type or scale. [7584] astropy.units ^^^^^^^^^^^^^ - In ``UnitBase.compose()``, if a sequence (list|tuple) is passed in to ``units``, the default for ``include_prefix_units`` is set to `True`, so that no units get ignored. [6957] - Negative parallaxes are now converted to NaN values when using the ``parallax`` equivalency. [7988] astropy.utils ^^^^^^^^^^^^^ - ``InheritDocstrings`` now also works on class properties. [7166] - ``diff_values()``, ``report_diff_values()``, and ``where_not_allclose()`` utility functions are moved from ``astropy.io.fits.diff``. [7444] - ``invalidate_caches()`` has been removed from the ``astropy.utils.compat`` namespace, use it directly from ``importlib``. [7872] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - In ``ImageNormalize``, the default for ``clip`` is set to ``True``. [7800] - Changed ``AsymmetricPercentileInterval`` and ``MinMaxInterval`` to ignore NaN values in arrays. [7360] - Automatically default to using ``grid_type='contours'`` in WCSAxes when using a custom ``Transform`` object if the transform has no inverse. [7847] Performance Improvements ------------------------ - Reduced import time by more cautious use of the standard library. [7647] astropy.convolution ^^^^^^^^^^^^^^^^^^^ - Major performance overhaul to ``convolve()``. [7293] - ``convolve()``: Boundaries ``fill``, ``extend``, and ``wrap`` now use a single implementation that pads the image with the correct boundary values before convolving. The runtimes of these three were significantly skewed. They now have equivalent runtimes that are also faster than before due to performant contiguous memory access. However, this does increase the memory footprint as an entire new image array is required plus that needed for the padded region.[7293] - ``convolve()``: Core computation ported from Cython to C. Several optimization techniques have been implemented to achieve performance gains, e.g. compiler hoisting, and vectorization, etc. Compiler optimization level ``-O2`` required for hoisting and ``-O3`` for vectorization. [7293] - ``convolve()``: ``nan_treatment=‘interpolate’`` was slow to compute irrespective of whether any NaN values exist within the array. The input array is now checked for NaN values and interpolation is disabled if non are found. This is a significant performance boost for arrays without NaN values. [7293] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Sped up creating SkyCoord objects by a factor of ~2 in some cases. [7615] - Sped up getting xyz vectors from ``CartesianRepresentation`` (which is used a lot internally). [7638] - Sped up transformations and some representation methods by replacing python code with (compiled) ``erfa`` ufuncs. [7639] - Sped up adding differential (velocity) data to representations by a factor of ~20, which improves the speed of frame and SkyCoord initialization. [7924] - Refactored ``SkyCoord`` initializer to improve performance and code clarity. [7958] - Sped up initialization of ``Longitude`` by ~40%. [7616] astropy.stats ^^^^^^^^^^^^^ - The ``SigmaClip`` class and ``sigma_clip`` and ``sigma_clipped_stats`` functions are now significantly faster. [7478] - A Cython implementation for `astropy.stats.kuiper_two` and a vectorized implementation for `astropy.stats.kuiper_false_positive_probability` have been added, speeding up both functions. [8104] astropy.units ^^^^^^^^^^^^^ - Sped up creating new composite units, and raising units to some power [7549, 7649] - Sped up Unit.to when target unit is the same as the original unit. [7643] - Lazy-load ``scipy.special`` to shorten ``astropy.units`` import time. [7636] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Significantly sped up drawing of contours in WCSAxes. [7568] Bug Fixes --------- astropy.convolution ^^^^^^^^^^^^^^^^^^^ - Fixed bug in ``convolve_fft`` where masked input was copied with ``numpy.asarray`` instead of ``numpy.asanyarray``. ``numpy.asarray`` removes the mask subclass causing ``numpy.ma.ismasked(input)`` to fail, causing ``convolve_fft`` to ignore all masked input. [8137] - Remove function side-effects of input data from ``convolve_fft``. It was possible for input data to remain modified if particular exceptions were raised. [8152] astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - ``EarthLocation.of_address`` now uses the OpenStreetMap geocoding API by default to retrieve coordinates, with the Google API (which now requires an API key) as an option. [7918] - Fixed a bug that caused frame objects with NaN distances to have NaN sky positions, even if valid sky coordinates were specified. [7988] - Fixed ``represent_as()`` to not round-trip through cartesian if the same representation class as the instance is passed in. [7988] astropy.io.ascii ^^^^^^^^^^^^^^^^ - Fixed a problem when ``guess=True`` that ``fast_reader`` options could be dropped after the first fast reader class was tried. [5578] - Units in CDS-formatted tables are now parsed correctly by the units module. [7348] astropy.io.misc ^^^^^^^^^^^^^^^ - Fixed bug when writing a table with masked columns to HDF5. Previously the mask was being silently dropped. If the ``serialize_meta`` option is enabled the data mask will now be written as an additional column and the masked columns will round-trip correctly. [7481] - Fixed a bug where writing to HDF5 failed for for tables with columns of unicode strings. Now those columns are first encoded to UTF-8 and written as byte strings. [7024, 8017] - Fixed a bug with serializing the bounding_box of models initialized with ``Quantities`` . [8052] astropy.io.fits ^^^^^^^^^^^^^^^ - Added support for ``copy.copy`` and ``copy.deepcopy`` for ``HDUList``. [7218] - Override ``HDUList.copy()`` to return a shallow HDUList instance. [7218] astropy.modeling ^^^^^^^^^^^^^^^^ - Fix behaviour of certain models with units, by making certain unit-related attributes readonly. [7210] - Fixed an issue with validating a ``bounding_box`` whose items are ``Quantities``. [8052] - Fix ``Moffat1D`` and ``Moffat2D`` derivatives. [8108] astropy.nddata ^^^^^^^^^^^^^^ - Fixed rounding behavior in ``overlap_slices`` for even-sized small arrays. [7859] - Added support for pickling ``NDData`` instances that have an uncertainty. [7383] astropy.stats ^^^^^^^^^^^^^ - Fix errors in ``kuiper_false_positive_probability``. [7975] astropy.tests ^^^^^^^^^^^^^ - Fixing bug that prevented to run the doctests on only a single rst documentation file rather than all of them. [8055] astropy.time ^^^^^^^^^^^^ - Fix a bug when setting a ``TimeDelta`` array item with plain float value(s). This was always interpreted as a JD (day) value regardless of the ``TimeDelta`` format. [7990] astropy.units ^^^^^^^^^^^^^ - To simplify fast creation of ``Quantity`` instances from arrays, one can now write ``array << unit`` (equivalent to ``Quantity(array, unit, copy=False)``). If ``array`` is already a ``Quantity``, this will convert the quantity to the requested units; in-place conversion can be done with ``quantity <<= unit``. [7734] astropy.utils ^^^^^^^^^^^^^ - Fixed a bug due to which ``report_diff_values()`` was reporting incorrect number of differences when comparing two ``numpy.ndarray``. [7470] - The download progress bar is now only displayed in terminals, to avoid polluting piped output. [7577] - Ignore URL mirror caching when there is no internet. [8163] astropy.visualization ^^^^^^^^^^^^^^^^^^^^^ - Right ascension coordinates are now shown in hours by default, and the ``set_format_unit`` method on ``CoordinateHelper`` now works correctly with angle coordinates. [7215] Other Changes and Additions --------------------------- - The documentation build now uses the Sphinx configuration from sphinx-astropy rather than from astropy-helpers. [7139] - Versions of Numpy <1.13 are no longer supported. [7058] - Running tests now suppresses the output of the installation stage by default, to allow easier viewing of the test results. To re-enable the output as before, use ``python setup.py test --verbose-install``. [7512] - The ERFA functions are now wrapped in ufuncs instead of custom C code, leading to some speed improvements, and setting the stage for allowing overrides with ``__array_ufunc__``. [7502] - Updated the bundled CFITSIO library to 3.450. See ``cextern/cfitsio/docs/changes.txt`` for additional information. [8014] - The ``representation`` keywords in coordinate frames are now deprecated in favor of the ``representation_type`` keywords (which are less ambiguously named). [8119] ``` ### 3.0.5 ``` ================== Bug Fixes --------- astropy.coordinates ^^^^^^^^^^^^^^^^^^^ - Fixed bug in which consecutive ``StaticMatrixTransform``'s in a frame transform path would be combined in the incorrect order. [7707] astropy.tests ^^^^^^^^^^^^^ - Fixing bug that doctests were not picked up from the narrative documentation when tests were run for all modules. [7767] ```Links
- PyPI: https://pypi.org/project/astropy - Changelog: https://pyup.io/changelogs/astropy/ - Homepage: http://astropy.orgUpdate matplotlib from 3.0.0 to 3.0.2.
Changelog
Links
- PyPI: https://pypi.org/project/matplotlib - Changelog: https://pyup.io/changelogs/matplotlib/ - Homepage: http://matplotlib.orgUpdate joblib from 0.12.5 to 0.13.0.
The bot wasn't able to find a changelog for this release. Got an idea?
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- PyPI: https://pypi.org/project/joblib - Changelog: https://pyup.io/changelogs/joblib/ - Docs: https://joblib.readthedocs.ioUpdate numba from 0.40.0 to 0.42.0.
Changelog
### 0.42.0 ``` -------------- In this release the major features are: - The capability to launch and attach the GDB debugger from within a jitted function. - The upgrading of LLVM to version 7.0.0. We added a draft of the project roadmap to the developer manual. The roadmap is for informational purposes only as priorities and resources may change. Here are some enhancements from contributed PRs: - 3532. Daniel Wennberg improved the ``cuda.{pinned, mapped}`` API so that the associated memory is released immediately at the exit of the context manager. - 3531. Dimitri Vorona enabled the inlining of jitclass methods. - 3516. Simon Perkins added the support for passing numpy dtypes (i.e. ``np.dtype("int32")``) and their type constructor (i.e. ``np.int32``) into a jitted function. - 3509. Rob Ennis added support for ``np.corrcoef``. A regression issue (3554, 3461) relating to making an empty slice in parallel mode is resolved by 3558. General Enhancements: * PR 3392: Launch and attach gdb directly from Numba. * PR 3437: Changes to accommodate LLVM 7.0.x * PR 3509: Support for np.corrcoef * PR 3516: Typeof dtype values * PR 3520: Fix stencil ignoring cval if out kwarg supplied. * PR 3531: Fix jitclass method inlining and avoid unnecessary increfs * PR 3538: Avoid future C-level assertion error due to invalid visibility * PR 3543: Avoid implementation error being hidden by the try-except * PR 3544: Add `long_running` test flag and feature to exclude tests. * PR 3549: ParallelAccelerator caching improvements * PR 3558: Fixes array analysis for inplace binary operators. * PR 3566: Skip alignment tests on armv7l. * PR 3567: Fix unifying literal types in namedtuple * PR 3576: Add special copy routine for NumPy out arrays * PR 3577: Fix example and docs typos for `objmode` context manager. reorder statements. * PR 3580: Use alias information when determining whether it is safe to * PR 3583: Use `ir.unknown_loc` for unknown `Loc`, as 3390 with tests * PR 3587: Fix llvm.memset usage changes in llvm7 * PR 3596: Fix Array Analysis for Global Namedtuples * PR 3597: Warn users if threading backend init unsafe. * PR 3605: Add guard for writing to read only arrays from ufunc calls * PR 3606: Improve the accuracy of error message wording for undefined type. * PR 3611: gdb test guard needs to ack ptrace permissions * PR 3616: Skip gdb tests on ARM. CUDA Enhancements: * PR 3532: Unregister temporarily pinned host arrays at once * PR 3552: Handle broadcast arrays correctly in host->device transfer. * PR 3578: Align cuda and cuda simulator kwarg names. Documentation Updates: * PR 3545: Fix njit description in 5 min guide * PR 3570: Minor documentation fixes for numba.cuda * PR 3581: Fixing minor typo in `reference/types.rst` * PR 3594: Changing `stencil` docs to correctly reflect `func_or_mode` param * PR 3617: Draft roadmap as of Dec 2018 Contributors: * Aaron Critchley * Daniel Wennberg * Dimitri Vorona * Dominik Stańczak * Ehsan Totoni (core dev) * Iskander Sharipov * Rob Ennis * Simon Muller * Simon Perkins * Siu Kwan Lam (core dev) * Stan Seibert (core dev) * Stuart Archibald (core dev) * Todd A. Anderson (core dev) ``` ### 0.41.0 ``` -------------- This release adds the following major features: * Diagnostics showing the optimizations done by ParallelAccelerator * Support for profiling Numba-compiled functions in Intel VTune * Additional NumPy functions: partition, nancumsum, nancumprod, ediff1d, cov, conj, conjugate, tri, tril, triu * Initial support for Python 3 Unicode strings General Enhancements: * PR 1968: armv7 support * PR 2983: invert mapping b/w binop operators and the operator module 2297 * PR 3160: First attempt at parallel diagnostics * PR 3307: Adding NUMBA_ENABLE_PROFILING envvar, enabling jit event * PR 3320: Support for np.partition * PR 3324: Support for np.nancumsum and np.nancumprod * PR 3325: Add location information to exceptions. * PR 3337: Support for np.ediff1d * PR 3345: Support for np.cov * PR 3348: Support user pipeline class in with lifting * PR 3363: string support * PR 3373: Improve error message for empty imprecise lists. * PR 3375: Enable overload(operator.getitem) * PR 3402: Support negative indexing in tuple. * PR 3414: Refactor Const type * PR 3416: Optimized usage of alloca out of the loop * PR 3424: Updates for llvmlite 0.26 * PR 3462: Add support for `np.conj/np.conjugate`. * PR 3480: np.tri, np.tril, np.triu - default optional args * PR 3481: Permit dtype argument as sole kwarg in np.eye CUDA Enhancements: * PR 3399: Add max_registers Option to cuda.jit Continuous Integration / Testing: * PR 3303: CI with Azure Pipelines * PR 3309: Workaround race condition with apt * PR 3371: Fix issues with Azure Pipelines * PR 3362: Fix 3360: `RuntimeWarning: 'numba.runtests' found in sys.modules` * PR 3374: Disable openmp in wheel building * PR 3404: Azure Pipelines templates * PR 3419: Fix cuda tests and error reporting in test discovery * PR 3491: Prevent faulthandler installation on armv7l * PR 3493: Fix CUDA test that used negative indexing behaviour that's fixed. * PR 3495: Start Flake8 checking of Numba source Fixes: * PR 2950: Fix dispatcher to only consider contiguous-ness. * PR 3124: Fix 3119, raise for 0d arrays in reductions * PR 3228: Reduce redundant module linking * PR 3329: Fix AOT on windows. * PR 3335: Fix memory management of __cuda_array_interface__ views. * PR 3340: Fix typo in error name. * PR 3365: Fix the default unboxing logic * PR 3367: Allow non-global reference to objmode() context-manager * PR 3381: Fix global reference in objmode for dynamically created function * PR 3382: CUDA_ERROR_MISALIGNED_ADDRESS Using Multiple Const Arrays * PR 3384: Correctly handle very old versions of colorama * PR 3394: Add 32bit package guard for non-32bit installs * PR 3397: Fix with-objmode warning * PR 3403 Fix label offset in call inline after parfor pass * PR 3429: Fixes raising of user defined exceptions for exec(<string>). * PR 3432: Fix error due to function naming in CI in py2.7 * PR 3444: Fixed TBB's single thread execution and test added for 3440 * PR 3449: Allow matching non-array objects in find_callname() * PR 3455: Change getiter and iternext to not be pure. Resolves 3425 * PR 3467: Make ir.UndefinedType singleton class. * PR 3478: Fix np.random.shuffle sideeffect * PR 3487: Raise unsupported for kwargs given to `print()` * PR 3488: Remove dead script. * PR 3498: Fix stencil support for boolean as return type * PR 3511: Fix handling make_function literals (regression of 3414) * PR 3514: Add missing unicode != unicode * PR 3527: Fix complex math sqrt implementation for large -ve values * PR 3530: This adds arg an check for the pattern supplied to Parfors. * PR 3536: Sets list dtor linkage to `linkonce_odr` to fix visibility in AOT Documentation Updates: * PR 3316: Update 0.40 changelog with additional PRs * PR 3318: Tweak spacing to avoid search box wrapping onto second line * PR 3321: Add note about memory leaks with exceptions to docs. Fixes 3263 * PR 3322: Add FAQ on CUDA + fork issue. Fixes 3315. * PR 3343: Update docs for argsort, kind kwarg partially supported. * PR 3357: Added mention of njit in 5minguide.rst * PR 3434: Fix parallel reduction example in docs. * PR 3452: Fix broken link and mark up problem. * PR 3484: Size Numba logo in docs in em units. Fixes 3313 * PR 3502: just two typos * PR 3506: Document string support * PR 3513: Documentation for parallel diagnostics. * PR 3526: Fix 5 min guide with respect to njit decl Contributors: * Alex Ford * Andreas Sodeur * Anton Malakhov * Daniel Stender * Ehsan Totoni (core dev) * Henry Schreiner * Marcel Bargull * Matt Cooper * Nick White * Nicolas Hug * rjenc29 * Siu Kwan Lam (core dev) * Stan Seibert (core dev) * Stuart Archibald (core dev) * Todd A. Anderson (core dev) ``` ### 0.40.1 ``` -------------- This is a PyPI-only patch release to ensure that PyPI wheels can enable the TBB threading backend, and to disable the OpenMP backend in the wheels. Limitations of manylinux1 and variation in user environments can cause segfaults when OpenMP is enabled on wheel builds. Note that this release has no functional changes for users who obtained Numba 0.40.0 via conda. Patches: * PR 3338: Accidentally left Anton off contributor list for 0.40.0 * PR 3374: Disable OpenMP in wheel building * PR 3376: Update 0.40.1 changelog and docs on OpenMP backend ```Links
- PyPI: https://pypi.org/project/numba - Changelog: https://pyup.io/changelogs/numba/ - Repo: http://numba.github.comUpdate numpy from 1.15.2 to 1.15.4.
Changelog
### 1.15.4 ``` ========================== This is a bugfix release for bugs and regressions reported following the 1.15.3 release. The Python versions supported by this release are 2.7, 3.4-3.7. The wheels are linked with OpenBLAS v0.3.0, which should fix some of the linalg problems reported for NumPy 1.14. Compatibility Note ================== The NumPy 1.15.x OS X wheels released on PyPI no longer contain 32-bit binaries. That will also be the case in future releases. See `11625 <https://github.com/numpy/numpy/issues/11625>`__ for the related discussion. Those needing 32-bit support should look elsewhere or build from source. Contributors ============ A total of 4 people contributed to this release. People with a "+" by their names contributed a patch for the first time. * Charles Harris * Matti Picus * Sebastian Berg * bbbbbbbbba + Pull requests merged ==================== A total of 4 pull requests were merged for this release. * `12296 <https://github.com/numpy/numpy/pull/12296>`__: BUG: Dealloc cached buffer info * `12297 <https://github.com/numpy/numpy/pull/12297>`__: BUG: Fix fill value in masked array '==' and '!=' ops. * `12307 <https://github.com/numpy/numpy/pull/12307>`__: DOC: Correct the default value of `optimize` in `numpy.einsum` * `12320 <https://github.com/numpy/numpy/pull/12320>`__: REL: Prepare for the NumPy 1.15.4 release ========================== ``` ### 1.15.3 ``` ========================== This is a bugfix release for bugs and regressions reported following the 1.15.2 release. The Python versions supported by this release are 2.7, 3.4-3.7. The wheels are linked with OpenBLAS v0.3.0, which should fix some of the linalg problems reported for NumPy 1.14. Compatibility Note ================== The NumPy 1.15.x OS X wheels released on PyPI no longer contain 32-bit binaries. That will also be the case in future releases. See `11625 <https://github.com/numpy/numpy/issues/11625>`__ for the related discussion. Those needing 32-bit support should look elsewhere or build from source. Contributors ============ A total of 7 people contributed to this release. People with a "+" by their names contributed a patch for the first time. * Allan Haldane * Charles Harris * Jeroen Demeyer * Kevin Sheppard * Matthew Bowden + * Matti Picus * Tyler Reddy Pull requests merged ==================== A total of 12 pull requests were merged for this release. * `12080 <https://github.com/numpy/numpy/pull/12080>`__: MAINT: Blacklist some MSVC complex functions. * `12083 <https://github.com/numpy/numpy/pull/12083>`__: TST: Add azure CI testing to 1.15.x branch. * `12084 <https://github.com/numpy/numpy/pull/12084>`__: BUG: test_path() now uses Path.resolve() * `12085 <https://github.com/numpy/numpy/pull/12085>`__: TST, MAINT: Fix some failing tests on azure-pipelines mac and... * `12187 <https://github.com/numpy/numpy/pull/12187>`__: BUG: Fix memory leak in mapping.c * `12188 <https://github.com/numpy/numpy/pull/12188>`__: BUG: Allow boolean subtract in histogram * `12189 <https://github.com/numpy/numpy/pull/12189>`__: BUG: Fix in-place permutation * `12190 <https://github.com/numpy/numpy/pull/12190>`__: BUG: limit default for get_num_build_jobs() to 8 * `12191 <https://github.com/numpy/numpy/pull/12191>`__: BUG: OBJECT_to_* should check for errors * `12192 <https://github.com/numpy/numpy/pull/12192>`__: DOC: Prepare for NumPy 1.15.3 release. * `12237 <https://github.com/numpy/numpy/pull/12237>`__: BUG: Fix MaskedArray fill_value type conversion. * `12238 <https://github.com/numpy/numpy/pull/12238>`__: TST: Backport azure-pipeline testing fixes for Mac ========================== ```Links
- PyPI: https://pypi.org/project/numpy - Changelog: https://pyup.io/changelogs/numpy/ - Homepage: http://www.numpy.orgUpdate multiprocess from 0.70.6 to 0.70.6.1.
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Links
- PyPI: https://pypi.org/project/multiprocess - Changelog: https://pyup.io/changelogs/multiprocess/ - Homepage: https://pypi.org/project/multiprocessUpdate scipy from 1.1.0 to 1.2.0.
Changelog
### 1.2.0 ``` many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with ``python -Wd`` and check for ``DeprecationWarning`` s). Our development attention will now shift to bug-fix releases on the 1.2.x branch, and on adding new features on the master branch. This release requires Python 2.7 or 3.4+ and NumPy 1.8.2 or greater. **Note**: This will be the last SciPy release to support Python 2.7. Consequently, the 1.2.x series will be a long term support (LTS) release; we will backport bug fixes until 1 Jan 2020. For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. Highlights of this release -------------------------- - 1-D root finding improvements with a new solver, ``toms748``, and a new unified interface, ``root_scalar`` - New ``dual_annealing`` optimization method that combines stochastic and local deterministic searching - A new optimization algorithm, ``shgo`` (simplicial homology global optimization) for derivative free optimization problems - A new category of quaternion-based transformations are available in `scipy.spatial.transform` New features ============ `scipy.ndimage` improvements -------------------------------- Proper spline coefficient calculations have been added for the ``mirror``, ``wrap``, and ``reflect`` modes of `scipy.ndimage.rotate` `scipy.fftpack` improvements -------------------------------- DCT-IV, DST-IV, DCT-I, and DST-I orthonormalization are now supported in `scipy.fftpack`. `scipy.interpolate` improvements -------------------------------- `scipy.interpolate.pade` now accepts a new argument for the order of the numerator `scipy.cluster` improvements ---------------------------- `scipy.cluster.vq.kmeans2` gained a new initialization method, kmeans++. `scipy.special` improvements ---------------------------- The function ``softmax`` was added to `scipy.special`. `scipy.optimize` improvements ----------------------------- The one-dimensional nonlinear solvers have been given a unified interface `scipy.optimize.root_scalar`, similar to the `scipy.optimize.root` interface for multi-dimensional solvers. ``scipy.optimize.root_scalar(f, bracket=[a ,b], method="brenth")`` is equivalent to ``scipy.optimize.brenth(f, a ,b)``. If no ``method`` is specified, an appropriate one will be selected based upon the bracket and the number of derivatives available. The so-called Algorithm 748 of Alefeld, Potra and Shi for root-finding within an enclosing interval has been added as `scipy.optimize.toms748`. This provides guaranteed convergence to a root with convergence rate per function evaluation of approximately 1.65 (for sufficiently well-behaved functions.) ``differential_evolution`` now has the ``updating`` and ``workers`` keywords. The first chooses between continuous updating of the best solution vector (the default), or once per generation. Continuous updating can lead to faster convergence. The ``workers`` keyword accepts an ``int`` or map-like callable, and parallelises the solver (having the side effect of updating once per generation). Supplying an ``int`` evaluates the trial solutions in N parallel parts. Supplying a map-like callable allows other parallelisation approaches (such as ``mpi4py``, or ``joblib``) to be used. ``dual_annealing`` (and ``shgo`` below) is a powerful new general purpose global optizimation (GO) algorithm. ``dual_annealing`` uses two annealing processes to accelerate the convergence towards the global minimum of an objective mathematical function. The first annealing process controls the stochastic Markov chain searching and the second annealing process controls the deterministic minimization. So, dual annealing is a hybrid method that takes advantage of stochastic and local deterministic searching in an efficient way. ``shgo`` (simplicial homology global optimization) is a similar algorithm appropriate for solving black box and derivative free optimization (DFO) problems. The algorithm generally converges to the global solution in finite time. The convergence holds for non-linear inequality and equality constraints. In addition to returning a global minimum, the algorithm also returns any other global and local minima found after every iteration. This makes it useful for exploring the solutions in a domain. `scipy.optimize.newton` can now accept a scalar or an array ``MINPACK`` usage is now thread-safe, such that ``MINPACK`` + callbacks may be used on multiple threads. `scipy.signal` improvements --------------------------- Digital filter design functions now include a parameter to specify the sampling rate. Previously, digital filters could only be specified using normalized frequency, but different functions used different scales (e.g. 0 to 1 for ``butter`` vs 0 to π for ``freqz``), leading to errors and confusion. With the ``fs`` parameter, ordinary frequencies can now be entered directly into functions, with the normalization handled internally. ``find_peaks`` and related functions no longer raise an exception if the properties of a peak have unexpected values (e.g. a prominence of 0). A ``PeakPropertyWarning`` is given instead. The new keyword argument ``plateau_size`` was added to ``find_peaks``. ``plateau_size`` may be used to select peaks based on the length of the flat top of a peak. ``welch()`` and ``csd()`` methods in `scipy.signal` now support calculation of a median average PSD, using ``average='mean'`` keyword `scipy.sparse` improvements --------------------------- The `scipy.sparse.bsr_matrix.tocsr` method is now implemented directly instead of converting via COO format, and the `scipy.sparse.bsr_matrix.tocsc` method is now also routed via CSR conversion instead of COO. The efficiency of both conversions is now improved. The issue where SuperLU or UMFPACK solvers crashed on matrices with non-canonical format in `scipy.sparse.linalg` was fixed. The solver wrapper canonicalizes the matrix if necessary before calling the SuperLU or UMFPACK solver. The ``largest`` option of `scipy.sparse.linalg.lobpcg()` was fixed to have a correct (and expected) behavior. The order of the eigenvalues was made consistent with the ARPACK solver (``eigs()``), i.e. ascending for the smallest eigenvalues, and descending for the largest eigenvalues. The `scipy.sparse.random` function is now faster and also supports integer and complex values by passing the appropriate value to the ``dtype`` argument. `scipy.spatial` improvements ---------------------------- The function `scipy.spatial.distance.jaccard` was modified to return 0 instead of ``np.nan`` when two all-zero vectors are compared. Support for the Jensen Shannon distance, the square-root of the divergence, has been added under `scipy.spatial.distance.jensenshannon` An optional keyword was added to the function `scipy.spatial.cKDTree.query_ball_point()` to sort or not sort the returned indices. Not sorting the indices can speed up calls. A new category of quaternion-based transformations are available in `scipy.spatial.transform`, including spherical linear interpolation of rotations (``Slerp``), conversions to and from quaternions, Euler angles, and general rotation and inversion capabilities (`spatial.transform.Rotation`), and uniform random sampling of 3D rotations (`spatial.transform.Rotation.random`). `scipy.stats` improvements -------------------------- The Yeo-Johnson power transformation is now supported (``yeojohnson``, ``yeojohnson_llf``, ``yeojohnson_normmax``, ``yeojohnson_normplot``). Unlike the Box-Cox transformation, the Yeo-Johnson transformation can accept negative values. Added a general method to sample random variates based on the density only, in the new function ``rvs_ratio_uniforms``. The Yule-Simon distribution (``yulesimon``) was added -- this is a new discrete probability distribution. ``stats`` and ``mstats`` now have access to a new regression method, ``siegelslopes``, a robust linear regression algorithm `scipy.stats.gaussian_kde` now has the ability to deal with weighted samples, and should have a modest improvement in performance Levy Stable Parameter Estimation, PDF, and CDF calculations are now supported for `scipy.stats.levy_stable`. The Brunner-Munzel test is now available as ``brunnermunzel`` in ``stats`` and ``mstats`` `scipy.linalg` improvements -------------------------- `scipy.linalg.lapack` now exposes the LAPACK routines using the Rectangular Full Packed storage (RFP) for upper triangular, lower triangular, symmetric, or Hermitian matrices; the upper trapezoidal fat matrix RZ decomposition routines are now available as well. Deprecated features =================== The functions ``hyp2f0``, ``hyp1f2`` and ``hyp3f0`` in ``scipy.special`` have been deprecated. Backwards incompatible changes ============================== LAPACK version 3.4.0 or later is now required. Building with Apple Accelerate is no longer supported. The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct results for all angles. Before this, the function only returned correct values for those angles which were greater than pi/4. Support for the Bento build system has been removed. Bento has not been maintained for several years, and did not have good Python 3 or wheel support, hence it was time to remove it. The required signature of `scipy.optimize.lingprog` ``method=simplex`` callback function has changed. Before iteration begins, the simplex solver first converts the problem into a standard form that does not, in general, have the same variables or constraints as the problem defined by the user. Previously, the simplex solver would pass a user-specified callback function several separate arguments, such as the current solution vector ``xk``, corresponding to this standard form problem. Unfortunately, the relationship between the standard form problem and the user-defined problem was not documented, limiting the utility of the information passed to the callback function. In addition to numerous bug fix changes, the simplex solver now passes a user-specified callback function a single ``OptimizeResult`` object containing information that corresponds directly to the user-defined problem. In future releases, this ``OptimizeResult`` object may be expanded to include additional information, such as variables corresponding to the standard-form problem and information concerning the relationship between the standard-form and user-defined problems. The implementation of `scipy.sparse.random` has changed, and this affects the numerical values returned for both ``sparse.random`` and ``sparse.rand`` for some matrix shapes and a given seed. `scipy.optimize.newton` will no longer use Halley's method in cases where it negatively impacts convergence Other changes ============= Authors ======= * endolith * luzpaz * Hameer Abbasi + * akahard2dj + * Anton Akhmerov * Joseph Albert * alexthomas93 + * ashish + * atpage + * Blair Azzopardi + * Yoshiki Vázquez Baeza * Bence Bagi + * Christoph Baumgarten * Lucas Bellomo + * BH4 + * Aditya Bharti * Max Bolingbroke * François Boulogne * Ward Bradt + * Matthew Brett * Evgeni Burovski * Rafał Byczek + * Alfredo Canziani + * CJ Carey * Lucía Cheung + * Poom Chiarawongse + * Jeanne Choo + * Robert Cimrman * Graham Clenaghan + * cynthia-rempel + * Johannes Damp + * Jaime Fernandez del Rio * Dowon + * emmi474 + * Stefan Endres + * Thomas Etherington + * Alex Fikl + * fo40225 + * Joseph Fox-Rabinovitz * Lars G * Abhinav Gautam + * Stiaan Gerber + * C.A.M. Gerlach + * Ralf Gommers * Todd Goodall * Lars Grueter + * Sylvain Gubian + * Matt Haberland * David Hagen * Will Handley + * Charles Harris * Ian Henriksen * Thomas Hisch + * Theodore Hu * Michael Hudson-Doyle + * Nicolas Hug + * jakirkham + * Jakob Jakobson + * James + * Jan Schlüter * jeanpauphilet + * josephmernst + * Kai + * Kai-Striega + * kalash04 + * Toshiki Kataoka + * Konrad0 + * Tom Krauss + * Johannes Kulick * Lars Grüter + * Eric Larson * Denis Laxalde * Will Lee + * Katrin Leinweber + * Yin Li + * P. L. Lim + * Jesse Livezey + * Duncan Macleod + * MatthewFlamm + * Nikolay Mayorov * Mike McClurg + * Christian Meyer + * Mark Mikofski * Naoto Mizuno + * mohmmadd + * Nathan Musoke * Anju Geetha Nair + * Andrew Nelson * Ayappan P + * Nick Papior * Haesun Park + * Ronny Pfannschmidt + * pijyoi + * Ilhan Polat * Anthony Polloreno + * Ted Pudlik * puenka * Eric Quintero * Pradeep Reddy Raamana + * Vyas Ramasubramani + * Ramon Viñas + * Tyler Reddy * Joscha Reimer * Antonio H Ribeiro * richardjgowers + * Rob + * robbystk + * Lucas Roberts + * rohan + * Joaquin Derrac Rus + * Josua Sassen + * Bruce Sharpe + * Max Shinn + * Scott Sievert * Sourav Singh * Strahinja Lukić + * Kai Striega + * Shinya SUZUKI + * Mike Toews + * Piotr Uchwat * Miguel de Val-Borro + * Nicky van Foreest * Paul van Mulbregt * Gael Varoquaux * Pauli Virtanen * Stefan van der Walt * Warren Weckesser * Joshua Wharton + * Bernhard M. Wiedemann + * Eric Wieser * Josh Wilson * Tony Xiang + * Roman Yurchak + * Roy Zywina + A total of 137 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete. ```Links
- PyPI: https://pypi.org/project/scipy - Changelog: https://pyup.io/changelogs/scipy/ - Repo: https://github.com/scipy/scipy/releases - Homepage: https://www.scipy.orgUpdate sqlalchemy from 1.2.12 to 1.2.15.
Changelog
### 1.2.15 ``` :released: December 11, 2018 .. change:: :tags: bug, orm :tickets: 4367 Fixed bug where the ORM annotations could be incorrect for the primaryjoin/secondaryjoin a relationship if one used the pattern ``ForeignKey(SomeClass.id)`` in the declarative mappings. This pattern would leak undesired annotations into the join conditions which can break aliasing operations done within :class:`.Query` that are not supposed to impact elements in that join condition. These annotations are now removed up front if present. .. change:: :tags: bug, orm, declarative :tickets: 4374 A warning is emitted in the case that a :func:`.column` object is applied to a declarative class, as it seems likely this intended to be a :class:`.Column` object. .. change:: :tags: bug, orm :tickets: 4366 In continuing with a similar theme as that of very recent :ticket:`4349`, repaired issue with :meth:`.RelationshipProperty.Comparator.any` and :meth:`.RelationshipProperty.Comparator.has` where the "secondary" selectable needs to be explicitly part of the FROM clause in the EXISTS subquery to suit the case where this "secondary" is a :class:`.Join` object. .. change:: :tags: bug, orm :tickets: 4363 Fixed regression caused by :ticket:`4349` where adding the "secondary" table to the FROM clause for a dynamic loader would affect the ability of the :class:`.Query` to make a subsequent join to another entity. The fix adds the primary entity as the first element of the FROM list since :meth:`.Query.join` wants to jump from that. Version 1.3 will have a more comprehensive solution to this problem as well (:ticket:`4365`). .. change:: :tags: bug, orm :tickests: 4400 Fixed bug where chaining of mapper options using :meth:`.RelationshipProperty.of_type` in conjunction with a chained option that refers to an attribute name by string only would fail to locate the attribute. .. change:: :tag: feature, mysql :tickets: 4381 Added support for the ``write_timeout`` flag accepted by mysqlclient and pymysql to be passed in the URL string. .. change:: :tag: bug, postgresql :tickets: 4377, 4380 Fixed issue where reflection of a PostgreSQL domain that is expressed as an array would fail to be recognized. Pull request courtesy Jakub Synowiec. .. changelog:: ``` ### 1.2.14 ``` :released: November 10, 2018 .. change:: :tags: bug, orm :tickets: 4357 Fixed bug in :meth:`.Session.bulk_update_mappings` where alternate mapped attribute names would result in the primary key column of the UPDATE statement being included in the SET clause, as well as the WHERE clause; while usually harmless, for SQL Server this can raise an error due to the IDENTITY column. This is a continuation of the same bug that was fixed in :ticket:`3849`, where testing was insufficient to catch this additional flaw. .. change:: :tags: bug, mysql :tickets: 4361 Fixed regression caused by :ticket:`4344` released in 1.2.13, where the fix for MySQL 8.0's case sensitivity problem with referenced column names when reflecting foreign key referents is worked around using the ``information_schema.columns`` view. The workaround was failing on OSX / ``lower_case_table_names=2`` which produces non-matching casing for the ``information_schema.columns`` vs. that of ``SHOW CREATE TABLE``, so in case-insensitive SQL modes case-insensitive matching is now used. .. change:: :tags: bug, orm :tickets: 4347 Fixed a minor performance issue which could in some cases add unnecessary overhead to result fetching, involving the use of ORM columns and entities that include those same columns at the same time within a query. The issue has to do with hash / eq overhead when referring to the column in different ways. .. changelog:: ``` ### 1.2.13 ``` :released: October 31, 2018 .. change:: :tags: bug, postgresql :tickets: 4337 Added support for the :class:`.aggregate_order_by` function to receive multiple ORDER BY elements, previously only a single element was accepted. .. change:: :tags: bug, mysql :tickets: 4348 Added word ``function`` to the list of reserved words for MySQL, which is now a keyword in MySQL 8.0 .. change:: :tags: feature, sql :versions: 1.3.0b1 Refactored :class:`.SQLCompiler` to expose a :meth:`.SQLCompiler.group_by_clause` method similar to the :meth:`.SQLCompiler.order_by_clause` and :meth:`.SQLCompiler.limit_clause` methods, which can be overridden by dialects to customize how GROUP BY renders. Pull request courtesy Samuel Chou. .. change:: :tags: bug, misc Fixed issue where part of the utility language helper internals was passing the wrong kind of argument to the Python ``__import__`` builtin as the list of modules to be imported. The issue produced no symptoms within the core library but could cause issues with external applications that redefine the ``__import__`` builtin or otherwise instrument it. Pull request courtesy Joe Urciuoli. .. change:: :tags: bug, orm :tickets: 4349 Fixed bug where "dynamic" loader needs to explicitly set the "secondary" table in the FROM clause of the query, to suit the case where the secondary is a join object that is otherwise not pulled into the query from its columns alone. .. change:: :tags: bug, orm, declarative :tickets: 4350 Fixed regression caused by :ticket:`4326` in version 1.2.12 where using :class:`.declared_attr` with a mixin in conjunction with :func:`.orm.synonym` would fail to map the synonym properly to an inherited subclass. .. change:: :tags: bug, misc, py3k :tickets: 4339 Fixed additional warnings generated by Python 3.7 due to changes in the organization of the Python ``collections`` and ``collections.abc`` packages. Previous ``collections`` warnings were fixed in version 1.2.11. Pull request courtesy xtreak. .. change:: :tags: bug, ext Added missing ``.index()`` method to list-based association collections in the association proxy extension. .. change:: :tags: bug, mysql :tickets: 4344 Added a workaround for a MySQL bug 88718 introduced in the 8.0 series, where the reflection of a foreign key constraint is not reporting the correct case sensitivity for the referred column, leading to errors during use of the reflected constraint such as when using the automap extension. The workaround emits an additional query to the information_schema tables in order to retrieve the correct case sensitive name. .. change:: :tags: bug, sql :tickets: 4341 Fixed bug where the :paramref:`.Enum.create_constraint` flag on the :class:`.Enum` datatype would not be propagated to copies of the type, which affects use cases such as declarative mixins and abstract bases. .. change:: :tags: bug, orm, declarative :tickets: 4352 The column conflict resolution technique discussed at :ref:`declarative_column_conflicts` is now functional for a :class:`.Column` that is also a primary key column. Previously, a check for primary key columns declared on a single-inheritance subclass would occur before the column copy were allowed to pass. .. changelog:: ```Links
- PyPI: https://pypi.org/project/sqlalchemy - Changelog: https://pyup.io/changelogs/sqlalchemy/ - Homepage: http://www.sqlalchemy.orgUpdate tqdm from 4.25.0 to 4.28.1.
Changelog
### 4.28.0 ``` - remove installation of man pages by defaul