Pygeoprocessing

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* A new submodule, ``pygeoprocessing.kernels`` has been added to facilitate the
creation of kernel rasters needed for calls to
``pygeoprocessing.convolve_2d``. Functions for creating common decay kernels
have been added, along with functions to facilitate the creation of
distance-based kernels using a user-defined function
(``pygeoprocessing.create_kernel``) and to facilitate the creation of kernels
using custom 2D numpy arrays, such as those commonly used in image processing
(``pygeoprocessing.kernel_from_numpy_array``).
https://github.com/natcap/pygeoprocessing/issues/268
* Logging across functions in ``pygeoprocessing.geoprocessing`` now correctly
reports the function that it's being called from rather than ``<lambda>``.
https://github.com/natcap/pygeoprocessing/issues/300
* The function ``pygeoprocessing.reproject_vector`` now accepts an optional
parameter ``layer_name`` to allow the target vector layer name to be defined
by the user. If the user does not provide a ``layer_name``, the layer name
will be copied from the source vector.
https://github.com/natcap/pygeoprocessing/issues/301
* Implement the proposed new function ``pygeoprocessing.raster_reduce``, a
wrapper around ``pygeoprocessing.iterblocks``
(https://github.com/natcap/pygeoprocessing/issues/285)
* Nodata value checking in ``pygeoprocessing.routing`` now correctly handles
comparison of ``nan`` values. This is explicitly tested in
``pygeoprocessing.routing.fill_pits``, but should also improve the
experience of other routing functions as well.
https://github.com/natcap/pygeoprocessing/issues/248
* Added a function to build overviews for a raster,
``pygeoprocessing.build_overviews``. Related to this,
``pygeoprocessing.get_raster_info()`` now includes an ``'overviews'`` key
listing the pixel dimensions of each overview layer in a raster.
https://github.com/natcap/pygeoprocessing/issues/280
* Added a D8 stream extraction function at
``pygeoprocessing.routing.extract_streams_d8`` which takes a D8 flow
accumulation raster and a flow accumulation threshold, setting all pixels
with accumulation above that threshold to 1 and all other valid pixels to 0.
https://github.com/natcap/pygeoprocessing/issues/272
* Adding a new function, ``pygeoprocessing.create_raster_from_bounding_box``,
that enables the creation of a new raster from a bounding box.
https://github.com/natcap/pygeoprocessing/issues/276
* Win32 wheels of PyGeoprocessing are no longer created through our GitHub
Actions workflows and will no longer be produced or distributed as part of
our release checklist. For details (and metrics!) see:
https://github.com/natcap/pygeoprocessing/issues/232

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* ``pygeoprocessing.calculate_disjoint_polygon_set`` now offers an optional
parameter, ``geometries_may_touch`` for cases where geometries are known to
have intersecting boundaries but nonintersecting interiors.
https://github.com/natcap/pygeoprocessing/issues/269
* Pygeoprocessing is now tested against Python 3.11.
* Adding the target filename to progress logging in
``pygeoprocessing.raster_calculator``.
* ``pygeoprocessing.zonal_statistics`` will now optionally include a count of
the number of pixels per value encountered under each polygon. A warning
will be logged when invoked on floating-point rasters, as using this on
continuous rasters can result in excessive memory consumption. To use this
feature, set ``include_value_counts=True`` when calling ``zonal_statistics``.
* ``pygeoprocessing.get_gis_type`` will now raise a ``ValueError`` if the file
cannot be opened as ``gdal.OF_RASTER`` or ``gdal.OF_VECTOR``.
https://github.com/natcap/pygeoprocessing/issues/244
* Fixing an error message in ``convolve_2d`` when the signal or kernel is a
row based blocksize. https://github.com/natcap/pygeoprocessing/issues/228.

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* Fixing an issue with imports at the ``pygeoprocessing`` module level that was
causing linters like PyLint and IDE command-completion programs like JEDI-vim
to not be able to identify the attributes of the ``pygeoprocessing`` module
namespace.
* Reducing the amount of memory used by
``pygeoprocessing.new_raster_from_base`` when filling an array with values to
only as much memory as is needed for the datatype.
* Fixing a memory leak in ``pygeoprocessing.raster_calculator`` where
shared memory objects were being inadvertently created when they should not
have been and then they were not subsequently destroyed.
* ``calculate_disjoint_polygon_set`` will now skip over empty geometries.
Previously, the presence of empty geometries would cause an error to be
raised.
* Fixed a ``DeprecationWarning`` in ``calculate_disjoint_polygon_set`` caused
by the use of a deprecated logging ``warn`` method.

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* Post-release due to corrupted sdist released on Github and PyPI. The sdist
for 2.3.3 failed to install. The wheels were unaffected. No code changes.

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* Fixing a bug in ``shapely_geometry_to_vector`` where a feature name mismatch
between the ``fields`` and ``attribute_list`` inputs would silently pass
under most circumstances. Now an informative ``ValueError`` is raised.
* Testing against Python 3.10.
* Pinned ``numpy`` versions in ``pyproject.toml`` to the lowest compatible
version for each supported python version. This prevents issues when
``pygeoprocessing`` is used in an environment with a lower numpy version
than it was built with (https://github.com/cython/cython/issues/4452).

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* Restore functionality in ``reclassify_raster`` that allows for nodata
values to be reclassified. This was accidentally removed in 2.3.1.