Pygeoprocessing

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* Removing the ``numpy<2`` constraint for requirements.txt that should have
been included in the 2.4.5 release. https://github.com/natcap/pygeoprocessing/issues/396
* Handling GDAL-based ``RuntimeError``s raised during ``pygeoprocessing.reproject_vector``.
https://github.com/natcap/pygeoprocessing/issues/409

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* Updating for numpy 2.0 API changes. Pygeoprocessing is now compatible with
numpy 2.0 and later. https://github.com/natcap/pygeoprocessing/issues/396

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* Our github actions for building python distributions now use
`actions/setup-pythonv5`, which uses node 20.
https://github.com/natcap/pygeoprocessing/issues/384
* ``warp_raster`` and ``build_overviews`` no longer raise a ``ValueError`` if
called with an invalid resampling algorithm. We now fall back to the
underlying GDAL functions' error messages.
https://github.com/natcap/pygeoprocessing/issues/387
* Implementing decaying flow accumulation for D8 routing.
https://github.com/natcap/pygeoprocessing/issues/386
* Updated to Cython 3.
* Dropped support for Python 3.7.
* Enabled GDAL exceptions (``gdal.UseExceptions``) throughout pygeoprocessing.
This is done with a context manager so should not affect other code or
libraries. https://github.com/natcap/pygeoprocessing/issues/391

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* Wheels for python 3.12 are now built during our github actions runs.
https://github.com/natcap/pygeoprocessing/issues/381
* ``get_gis_type`` can accept a path to a remote file, allowing the GDAL driver
to open it if the driver supports the protocol.
https://github.com/natcap/pygeoprocessing/issues/375
* If running on a SLURM system (identified by the presence of ``SLURM*``
environment variables), the GDAL cache max is checked against the amount of
memory available on the compute node. If GDAL may exceed the available slurm
memory, a warning is issued or logged.
https://github.com/natcap/pygeoprocessing/issues/361
* Fixed an issue in ``extract_strahler_streams_d8`` where a nodata pixel
could be mistakenly treated as a stream seed point, ultimately creating
a stream feature with no geometry.
https://github.com/natcap/pygeoprocessing/issues/361
* Improved ``align_and_resize_raster_stack`` so that rasterization of a vector
mask only happens once, regardless of the number of rasters in the stack.
In addition, the created mask raster's path may be defined by the caller so
that it persists across calls to ``align_and_resize_raster_stack``.
https://github.com/natcap/pygeoprocessing/issues/366
* Improved ``warp_raster`` to allow for a pre-defined mask raster to be
provided instead of a vector. If both are provided, the mask raster alone is
used. The new mask raster must have the same dimensions and geotransform as
the output warped raster. https://github.com/natcap/pygeoprocessing/issues/366
* Fixed a bug in ``zonal_statistics`` where the wrong number of disjoint
polygon sets were being reported in the logs.
https://github.com/natcap/pygeoprocessing/issues/368
* Pygeoprocessing is now tested against python 3.12.
https://github.com/natcap/pygeoprocessing/issues/355

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* Fixed an issue where MFD flow direction was producing many nodata holes given
a large-enough DEM. These nodata holes would then propagate to flow
accumulation and stream extraction, producing very disjointed stream
networks. https://github.com/natcap/pygeoprocessing/issues/350
* Improved progress logging in MFD flow direction, MFD flow accumulation, MFD
stream extraction to prevent integer overflows in percentages and improve
the readability of log messages. https://github.com/natcap/pygeoprocessing/issues/246
* Fixed an issue introduced in 2.4.1 where ``zonal_statistics`` results could
vary depending on the bounding boxes of the disjoint polygon sets calculated
from the input vector.
* Added a new function, ``pygeoprocessing.align_bbox``, which pads a bounding
box to align with the grid of a given geotransform.
* Added support for int64 and uint64 (GDAL 3.5+)
https://github.com/natcap/pygeoprocessing/issues/352
* Added support for signed bytes (GDAL 3.7+)
https://github.com/natcap/pygeoprocessing/issues/329
* Fixed a bug where ``calculate_slope`` did not work as expected when the DEM
raster's nodata value is NaN (https://github.com/natcap/pygeoprocessing/issues/352)

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* The ``pygeoprocessing`` package metadata has been updated to use
``importlib.metadata`` (python >= 3.8) or ``importlib_metadata``
(python < 3.8) for retrieving the package version, in keeping with
recommendations from ``setuptools_scm``. The dependency
``importlib_metadata`` is now required for installs on python < 3.8.
* Fixed another memory leak in ``pygeoprocessing.raster_calculator``, where
shared memory objects under certain circumstances were not being unlinked at
the end of the function, resulting in excess memory usage and a warning
during the shutdown of the python process.
https://github.com/natcap/pygeoprocessing/issues/247
* Added a new function, ``pygeoprocessing.array_equals_nodata``, which returns
a boolean array indicating which elements have nodata. It handles integer,
float, and ``nan`` comparison, and the case where the nodata value is `None`.
* Standardized the approach used in ``warp_raster`` and
``create_raster_from_bounding_box`` for determining the dimensions of the
target raster given a target bounding box and pixel sizes.
https://github.com/natcap/pygeoprocessing/issues/321
* ``pygeoprocessing.routing.delineate_watersheds_d8`` now handles the case
where the input flow direction raster does not have a defined spatial
reference. https://github.com/natcap/pygeoprocessing/issues/254
* Updating internal documentation describing TauDEM flow directions, and adding
for how to convert from a flow direction raster from what TauDEM expects to
what pygeoprocessing expects.
https://github.com/natcap/pygeoprocessing/issues/255
* Users may now specify the overview level to use when calling ``warp_raster``.
By default, ``pygeoprocessing`` will use the base layer.
https://github.com/natcap/pygeoprocessing/issues/326
* Fixed a bug across ``pygeoprocessing`` where some valid resampling methods
would throw an exception because they were not recognized. This was only
happening when ``pygeoprocessing`` was installed alongside GDAL < 3.4.
* Fixing an issue with ``pygeoprocessing.multiprocessing.raster_calculator``
where the function would raise an Exception when the target raster path was
provided as a filename only, not within a directory, even though the parent
directory could be inferred. https://github.com/natcap/pygeoprocessing/issues/313
* Fixing a bug where the statistics worker in
``pygeoprocessing.raster_calculator`` may return a complex value. This is
only an issue when pygeoprocessing is compiled against Cython 3.0.0 and
later. https://github.com/natcap/pygeoprocessing/issues/342
* Added the new function ``pygeoprocessing.raster_map``, a higher-level version
of ``raster_calculator``. https://github.com/natcap/pygeoprocessing/issues/235