CVS commit: pkgsrc/math/py-xarray

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Sat Apr 11 13:47:08 UTC 2020

Modified Files:
        pkgsrc/math/py-xarray: Makefile PLIST distinfo

Log Message:
py-xarray: updated to 0.15.1

v0.15.1:
This release brings many new features such as :py:meth:`Dataset.weighted` methods for weighted array
reductions, a new jupyter repr by default, and the start of units integration with pint. There's also
the usual batch of usability improvements, documentation additions, and bug fixes.

Breaking changes
- Raise an error when assigning to the ``.values`` or ``.data`` attribute of
  dimension coordinates i.e. ``IndexVariable`` objects. This has been broken since
  v0.12.0. Please use :py:meth:`DataArray.assign_coords` or :py:meth:`Dataset.assign_coords`
  instead.

New Features
- Weighted array reductions are now supported via the new :py:meth:`DataArray.weighted`
  and :py:meth:`Dataset.weighted` methods. See :ref:`comput.weighted`.
- The new jupyter notebook repr (``Dataset._repr_html_`` and
  ``DataArray._repr_html_``) (introduced in 0.14.1) is now on by default. To
  disable, use ``xarray.set_options(display_style="text")``.
- Added support for :py:class:`pandas.DatetimeIndex`-style rounding of
  ``cftime.datetime`` objects directly via a :py:class:`CFTimeIndex` or via the
  :py:class:`~core.accessor_dt.DatetimeAccessor`.
- Support new h5netcdf backend keyword `phony_dims` (available from h5netcdf
  v0.8.0 for :py:class:`~xarray.backends.H5NetCDFStore`.
- Add partial support for unit aware arrays with pint.
- :py:meth:`Dataset.groupby` and :py:meth:`DataArray.groupby` now raise a
  `TypeError` on multiple string arguments. Receiving multiple string arguments
  often means a user is attempting to pass multiple dimensions as separate
  arguments and should instead pass a single list of dimensions.
- :py:func:`map_blocks` can now apply functions that add new unindexed dimensions.
- An ellipsis (``...``) is now supported in the ``dims`` argument of
  :py:meth:`Dataset.stack` and :py:meth:`DataArray.stack`, meaning all
  unlisted dimensions, similar to its meaning in :py:meth:`DataArray.transpose`.
- :py:meth:`Dataset.where` and :py:meth:`DataArray.where` accept a lambda as a
  first argument, which is then called on the input; replicating pandas' behavior.
- ``skipna`` is available in :py:meth:`Dataset.quantile`, :py:meth:`DataArray.quantile`,
  :py:meth:`core.groupby.DatasetGroupBy.quantile`, :py:meth:`core.groupby.DataArrayGroupBy.quantile`

Bug fixes
- Fix :py:meth:`Dataset.interp` when indexing array shares coordinates with the
  indexed variable
- Fix recombination of groups in :py:meth:`Dataset.groupby` and
  :py:meth:`DataArray.groupby` when performing an operation that changes the
  size of the groups along the grouped dimension. By `Eric Jansen
  <https://github.com/ej81>`_.
- Fix use of multi-index with categorical values
- Fix alignment with ``join="override"`` when some dimensions are unindexed.
- Fix :py:meth:`Dataset.swap_dims` and :py:meth:`DataArray.swap_dims` producing
  index with name reflecting the previous dimension name instead of the new one
- Use ``dask_array_type`` instead of ``dask_array.Array`` for type
  checking.
- :py:func:`concat` can now handle coordinate variables only present in one of
  the objects to be concatenated when ``coords="different"``.
- xarray now respects the over, under and bad colors if set on a provided colormap.
- :py:func:`coarsen` now respects ``xr.set_options(keep_attrs=True)``
  to preserve attributes. :py:meth:`Dataset.coarsen` accepts a keyword
  argument ``keep_attrs`` to change this setting.
  :pull:`3801`) By `Andrew Thomas <https://github.com/amcnicho>`_.
- Delete associated indexes when deleting coordinate variables.
- Fix :py:meth:`xarray.core.dataset.Dataset.to_zarr` when using `append_dim` and `group`
  simultaneously.
- Fix html repr on :py:class:`Dataset` with non-string keys

Documentation
- Fix documentation of :py:class:`DataArray` removing the deprecated mention
  that when omitted, `dims` are inferred from a `coords`-dict.
- Improve the :py:func:`where` docstring.
- Update the installation instructions: only explicitly list recommended dependencies

Internal Changes
- Remove the internal ``import_seaborn`` function which handled the deprecation of
  the ``seaborn.apionly`` entry point
- Don't test pint integration in combination with datetime objects.
- Change test_open_mfdataset_list_attr to only run with dask installed
- Preserve the ability to index with ``method="nearest"`` with a
  :py:class:`CFTimeIndex` with pandas versions greater than 1.0.1
- Greater flexibility and improved test coverage of subtracting various types
  of objects from a :py:class:`CFTimeIndex`. By `Spencer Clark
  <https://github.com/spencerkclark>`_.
- Update Azure CI MacOS image, given pending removal.
- Remove xfails for scipy 1.0.1 for tests that append to netCDF files
- Remove conversion to :py:class:`pandas.Panel`, given its removal in pandas
  in favor of xarray's objects.

v0.15.0:
This release brings many improvements to xarray's documentation: our examples are now binderized notebooks (`click here 
<https://mybinder.org/v2/gh/pydata/xarray/master?urlpath=lab/tree/doc/examples/weather-data.ipynb>`_)
and we have new example notebooks from our SciPy 2019 sprint (many thanks to our contributors!).

This release also features many API improvements such as a new
:py:class:`~core.accessor_dt.TimedeltaAccessor` and support for :py:class:`CFTimeIndex` in
:py:meth:`~DataArray.interpolate_na`); as well as many bug fixes.

Breaking changes
- Bumped minimum tested versions for dependencies:
  - numpy 1.15
  - pandas 0.25
  - dask 2.2
  - distributed 2.2
  - scipy 1.3

- Remove ``compat`` and ``encoding`` kwargs from ``DataArray``, which
  have been deprecated since 0.12.
  Instead, specify the ``encoding`` kwarg when writing to disk or set
  the :py:attr:`DataArray.encoding` attribute directly.
- :py:func:`xarray.dot`, :py:meth:`DataArray.dot`, and the ``@`` operator now
  use ``align="inner"`` (except when ``xarray.set_options(arithmetic_join="exact")``;

New Features
- Implement :py:meth:`DataArray.pad` and :py:meth:`Dataset.pad`.
- :py:meth:`DataArray.sel` and :py:meth:`Dataset.sel` now support :py:class:`pandas.CategoricalIndex`.
- Support using an existing, opened h5netcdf ``File`` with
  :py:class:`~xarray.backends.H5NetCDFStore`. This permits creating an
  :py:class:`~xarray.Dataset` from a h5netcdf ``File`` that has been opened
  using other means
- Implement ``median`` and ``nanmedian`` for dask arrays. This works by rechunking
  to a single chunk along all reduction axes.
- :py:func:`~xarray.concat` now preserves attributes from the first Variable.
- :py:meth:`Dataset.quantile`, :py:meth:`DataArray.quantile` and ``GroupBy.quantile``
  now work with dask Variables.
- Added the ``count`` reduction method to both :py:class:`~core.rolling.DatasetCoarsen`
  and :py:class:`~core.rolling.DataArrayCoarsen` objects.
- Add ``meta`` kwarg to :py:func:`~xarray.apply_ufunc`;
  this is passed on to :py:func:`dask.array.blockwise`.
- Add ``attrs_file`` option in :py:func:`~xarray.open_mfdataset` to choose the
  source file for global attributes in a multi-file dataset
  :pull:`3498`). By `Julien Seguinot <https://github.com/juseg>`_.
- :py:meth:`Dataset.swap_dims` and :py:meth:`DataArray.swap_dims`
  now allow swapping to dimension names that don't exist yet.
- Extend :py:class:`~core.accessor_dt.DatetimeAccessor` properties
  and support ``.dt`` accessor for timedeltas
  via :py:class:`~core.accessor_dt.TimedeltaAccessor`
- Improvements to interpolating along time axes
  - Support :py:class:`CFTimeIndex` in :py:meth:`DataArray.interpolate_na`
  - define 1970-01-01 as the default offset for the interpolation index for both
    :py:class:`pandas.DatetimeIndex` and :py:class:`CFTimeIndex`,
  - use microseconds in the conversion from timedelta objects to floats to avoid
    overflow errors.

Bug fixes
- Applying a user-defined function that adds new dimensions using :py:func:`apply_ufunc`
  and ``vectorize=True`` now works with ``dask > 2.0``.
- Fix :py:meth:`~xarray.combine_by_coords` to allow for combining incomplete
  hypercubes of Datasets
- Fix :py:func:`~xarray.combine_by_coords` when combining cftime coordinates
  which span long time intervals
- Fix plotting with transposed 2D non-dimensional coordinates.
- :py:meth:`plot.FacetGrid.set_titles` can now replace existing row titles of a
  :py:class:`~xarray.plot.FacetGrid` plot. In addition :py:class:`~xarray.plot.FacetGrid` gained
  two new attributes: :py:attr:`~xarray.plot.FacetGrid.col_labels` and
  :py:attr:`~xarray.plot.FacetGrid.row_labels` contain :py:class:`matplotlib.text.Text` handles for both column and
  row labels. These can be used to manually change the labels.
- Fix issue with Dask-backed datasets raising a ``KeyError`` on some computations involving :py:func:`map_blocks`
- Ensure :py:meth:`Dataset.quantile`, :py:meth:`DataArray.quantile` issue the correct error
  when ``q`` is out of bounds
- Fix regression in xarray 0.14.1 that prevented encoding times with certain
  ``dtype``, ``_FillValue``, and ``missing_value`` encodings
- Raise an error when trying to use :py:meth:`Dataset.rename_dims` to
  rename to an existing name
- :py:meth:`Dataset.rename`, :py:meth:`DataArray.rename` now check for conflicts with
  MultiIndex level names.
- :py:meth:`Dataset.merge` no longer fails when passed a :py:class:`DataArray` instead of a :py:class:`Dataset`.
- Fix a regression in :py:meth:`Dataset.drop`: allow passing any
  iterable when dropping variables
- Fixed errors emitted by ``mypy --strict`` in modules that import xarray.
- Allow plotting of binned coordinates on the y axis in :py:meth:`plot.line`
  and :py:meth:`plot.step` plots
- setuptools is now marked as a dependency of xarray

Documentation
- Switch doc examples to use `nbsphinx <https://nbsphinx.readthedocs.io>`_ and replace
  ``sphinx_gallery`` scripts with Jupyter notebooks.
- Added :doc:`example notebook <examples/ROMS_ocean_model>` demonstrating use of xarray with
  Regional Ocean Modeling System (ROMS) ocean hydrodynamic model output.
- Added :doc:`example notebook <examples/ERA5-GRIB-example>` demonstrating the visualization of
  ERA5 GRIB data.
  `Stephan Siemen <https://github.com/StephanSiemen>`_.
- Added examples for :py:meth:`DataArray.quantile`, :py:meth:`Dataset.quantile` and
  ``GroupBy.quantile``.
- Add new :doc:`example notebook <examples/apply_ufunc_vectorize_1d>` example notebook demonstrating
  vectorization of a 1D function using :py:func:`apply_ufunc` , dask and numba.
- Added example for :py:func:`~xarray.map_blocks`.

Internal Changes
- Make sure dask names change when rechunking by different chunk sizes. Conversely, make sure they
  stay the same when rechunking by the same chunk size.
- 2x to 5x speed boost (on small arrays) for :py:meth:`Dataset.isel`,
  :py:meth:`DataArray.isel`, and :py:meth:`DataArray.__getitem__` when indexing by int,
  slice, list of int, scalar ndarray, or 1-dimensional ndarray.
- Removed internal method ``Dataset._from_vars_and_coord_names``,
  which was dominated by ``Dataset._construct_direct``.
- Replaced versioneer with setuptools-scm. Moved contents of setup.py to setup.cfg.
  Removed pytest-runner from setup.py, as per deprecation notice on the pytest-runner
  project.
- Use of isort is now enforced by CI.


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/math/py-xarray/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/py-xarray/PLIST \
    pkgsrc/math/py-xarray/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/py-xarray/Makefile
diff -u pkgsrc/math/py-xarray/Makefile:1.2 pkgsrc/math/py-xarray/Makefile:1.3
--- pkgsrc/math/py-xarray/Makefile:1.2  Sat Sep 21 21:10:49 2019
+++ pkgsrc/math/py-xarray/Makefile      Sat Apr 11 13:47:08 2020
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.2 2019/09/21 21:10:49 minskim Exp $
+# $NetBSD: Makefile,v 1.3 2020/04/11 13:47:08 adam Exp $
 
-DISTNAME=      xarray-0.13.0
+DISTNAME=      xarray-0.15.1
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-CATEGORIES=    math
+CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=x/xarray/}
 
 MAINTAINER=    jihbed.research%gmail.com@localhost
@@ -12,10 +12,11 @@ LICENSE=    apache-2.0
 
 DEPENDS+=      ${PYPKGPREFIX}-numpy>=1.0:../../math/py-numpy
 DEPENDS+=      ${PYPKGPREFIX}-pandas>=0.18.1:../../math/py-pandas
-
-PYTHON_VERSIONS_INCOMPATIBLE=  27      # py-pandads
+DEPENDS+=      ${PYPKGPREFIX}-setuptools>=41.2:../../devel/py-setuptools
 
 USE_LANGUAGES= # none
 
+PYTHON_VERSIONS_INCOMPATIBLE=  27      # py-pandads
+
 .include "../../lang/python/egg.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/math/py-xarray/PLIST
diff -u pkgsrc/math/py-xarray/PLIST:1.1 pkgsrc/math/py-xarray/PLIST:1.2
--- pkgsrc/math/py-xarray/PLIST:1.1     Sat Sep 21 18:14:21 2019
+++ pkgsrc/math/py-xarray/PLIST Sat Apr 11 13:47:08 2020
@@ -1,15 +1,13 @@
-@comment $NetBSD: PLIST,v 1.1 2019/09/21 18:14:21 minskim Exp $
+@comment $NetBSD: PLIST,v 1.2 2020/04/11 13:47:08 adam Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
 ${PYSITELIB}/${EGG_INFODIR}/requires.txt
 ${PYSITELIB}/${EGG_INFODIR}/top_level.txt
 ${PYSITELIB}/xarray/__init__.py
 ${PYSITELIB}/xarray/__init__.pyc
 ${PYSITELIB}/xarray/__init__.pyo
-${PYSITELIB}/xarray/_version.py
-${PYSITELIB}/xarray/_version.pyc
-${PYSITELIB}/xarray/_version.pyo
 ${PYSITELIB}/xarray/backends/__init__.py
 ${PYSITELIB}/xarray/backends/__init__.pyc
 ${PYSITELIB}/xarray/backends/__init__.pyo
@@ -139,6 +137,9 @@ ${PYSITELIB}/xarray/core/extensions.pyo
 ${PYSITELIB}/xarray/core/formatting.py
 ${PYSITELIB}/xarray/core/formatting.pyc
 ${PYSITELIB}/xarray/core/formatting.pyo
+${PYSITELIB}/xarray/core/formatting_html.py
+${PYSITELIB}/xarray/core/formatting_html.pyc
+${PYSITELIB}/xarray/core/formatting_html.pyo
 ${PYSITELIB}/xarray/core/groupby.py
 ${PYSITELIB}/xarray/core/groupby.pyc
 ${PYSITELIB}/xarray/core/groupby.pyo
@@ -169,6 +170,9 @@ ${PYSITELIB}/xarray/core/ops.pyo
 ${PYSITELIB}/xarray/core/options.py
 ${PYSITELIB}/xarray/core/options.pyc
 ${PYSITELIB}/xarray/core/options.pyo
+${PYSITELIB}/xarray/core/parallel.py
+${PYSITELIB}/xarray/core/parallel.pyc
+${PYSITELIB}/xarray/core/parallel.pyo
 ${PYSITELIB}/xarray/core/pdcompat.py
 ${PYSITELIB}/xarray/core/pdcompat.pyc
 ${PYSITELIB}/xarray/core/pdcompat.pyo
@@ -193,6 +197,9 @@ ${PYSITELIB}/xarray/core/utils.pyo
 ${PYSITELIB}/xarray/core/variable.py
 ${PYSITELIB}/xarray/core/variable.pyc
 ${PYSITELIB}/xarray/core/variable.pyo
+${PYSITELIB}/xarray/core/weighted.py
+${PYSITELIB}/xarray/core/weighted.pyc
+${PYSITELIB}/xarray/core/weighted.pyo
 ${PYSITELIB}/xarray/plot/__init__.py
 ${PYSITELIB}/xarray/plot/__init__.pyc
 ${PYSITELIB}/xarray/plot/__init__.pyo
@@ -209,6 +216,8 @@ ${PYSITELIB}/xarray/plot/utils.py
 ${PYSITELIB}/xarray/plot/utils.pyc
 ${PYSITELIB}/xarray/plot/utils.pyo
 ${PYSITELIB}/xarray/py.typed
+${PYSITELIB}/xarray/static/css/style.css
+${PYSITELIB}/xarray/static/html/icons-svg-inline.html
 ${PYSITELIB}/xarray/testing.py
 ${PYSITELIB}/xarray/testing.pyc
 ${PYSITELIB}/xarray/testing.pyo
@@ -299,6 +308,9 @@ ${PYSITELIB}/xarray/tests/test_extension
 ${PYSITELIB}/xarray/tests/test_formatting.py
 ${PYSITELIB}/xarray/tests/test_formatting.pyc
 ${PYSITELIB}/xarray/tests/test_formatting.pyo
+${PYSITELIB}/xarray/tests/test_formatting_html.py
+${PYSITELIB}/xarray/tests/test_formatting_html.pyc
+${PYSITELIB}/xarray/tests/test_formatting_html.pyo
 ${PYSITELIB}/xarray/tests/test_groupby.py
 ${PYSITELIB}/xarray/tests/test_groupby.pyc
 ${PYSITELIB}/xarray/tests/test_groupby.pyo
@@ -338,12 +350,18 @@ ${PYSITELIB}/xarray/tests/test_tutorial.
 ${PYSITELIB}/xarray/tests/test_ufuncs.py
 ${PYSITELIB}/xarray/tests/test_ufuncs.pyc
 ${PYSITELIB}/xarray/tests/test_ufuncs.pyo
+${PYSITELIB}/xarray/tests/test_units.py
+${PYSITELIB}/xarray/tests/test_units.pyc
+${PYSITELIB}/xarray/tests/test_units.pyo
 ${PYSITELIB}/xarray/tests/test_utils.py
 ${PYSITELIB}/xarray/tests/test_utils.pyc
 ${PYSITELIB}/xarray/tests/test_utils.pyo
 ${PYSITELIB}/xarray/tests/test_variable.py
 ${PYSITELIB}/xarray/tests/test_variable.pyc
 ${PYSITELIB}/xarray/tests/test_variable.pyo
+${PYSITELIB}/xarray/tests/test_weighted.py
+${PYSITELIB}/xarray/tests/test_weighted.pyc
+${PYSITELIB}/xarray/tests/test_weighted.pyo
 ${PYSITELIB}/xarray/tutorial.py
 ${PYSITELIB}/xarray/tutorial.pyc
 ${PYSITELIB}/xarray/tutorial.pyo
@@ -353,6 +371,6 @@ ${PYSITELIB}/xarray/ufuncs.pyo
 ${PYSITELIB}/xarray/util/__init__.py
 ${PYSITELIB}/xarray/util/__init__.pyc
 ${PYSITELIB}/xarray/util/__init__.pyo
+${PYSITELIB}/xarray/util/print_versions.py
 ${PYSITELIB}/xarray/util/print_versions.pyc
 ${PYSITELIB}/xarray/util/print_versions.pyo
-${PYSITELIB}/xarray/util/print_versions.py
Index: pkgsrc/math/py-xarray/distinfo
diff -u pkgsrc/math/py-xarray/distinfo:1.1 pkgsrc/math/py-xarray/distinfo:1.2
--- pkgsrc/math/py-xarray/distinfo:1.1  Sat Sep 21 18:14:21 2019
+++ pkgsrc/math/py-xarray/distinfo      Sat Apr 11 13:47:08 2020
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2019/09/21 18:14:21 minskim Exp $
+$NetBSD: distinfo,v 1.2 2020/04/11 13:47:08 adam Exp $
 
-SHA1 (xarray-0.13.0.tar.gz) = 99a1feb68499c2954e3e407f6d382a9ca0eec23b
-RMD160 (xarray-0.13.0.tar.gz) = ac1dd2421efed8f0a4ef0ab2c4e7f30551ef2e88
-SHA512 (xarray-0.13.0.tar.gz) = 09f25e5ec06c1ff904ad24a01d24de719aa4903d214115ce1d5bbab21b0acc6b9374845da728495aaf67984cbf06b9d93dd5035cf25ec5c918977be707b3898d
-Size (xarray-0.13.0.tar.gz) = 1821280 bytes
+SHA1 (xarray-0.15.1.tar.gz) = 40efe1711499dab9d2c47c32721eca416a75b30f
+RMD160 (xarray-0.15.1.tar.gz) = 215db3e091b5d6712390116a4006cda7fbab226b
+SHA512 (xarray-0.15.1.tar.gz) = 8a2d7e9173c51c65ffe856fa83df730e0e7de9777726c6d6e8f7f4edcc512b3a980c7dc854c19d3bc4bec50e815ad776bd433a5750680f2851a2b0b1f505ea14
+Size (xarray-0.15.1.tar.gz) = 1934184 bytes