Pygeoprocessing

------------------
* Adding explicit support for Python 3.9 and testing on Python 3.9.
* Fixed an issue in ``create_raster_from_vector_extents`` that would cause a
confusing exception to be raised if there was no geometry in the vector.
Now raises a ``ValueError`` with a helpful error message.
* Changed parameters in ``convolve_2d`` to allow API to set
``ignore_nodata_and_edges=True`` while ``mask_nodata=False`` and updated
docstring to indicate this is useful in cases such as filling nodata holes
in missing datasets. Additionally added a logger ``debug`` message to note
this "unusual" setting of these parameters in case of accidental usage
which could be noted during development.
* Fixed issue in zonal statistics that could cause the aggregate vector to be
locked due to a dereferencing race condition. This was present in some
cases with a flaky unit test but could have been seen in practice if the
vector was deleted immediately after the call to ``zonal_statistics``.
* Fixed issue in ``routing.fill_pits`` that used a numerical "is close" test
when determining if two pixels were at equal height. In the case of
hydrological pitfilling, pixels must be exactly equal height to be
considered a plateau otherwise a drain into or out of the pixel is
resolved. Testing is close allowed a hydrological pit to remain since it
was "close" to the same height as a draining pixel.
* Added a D8 Strahler order stream extraction function at
``pygeoprocessing.extract_strahler_streams_d8``. Creates segmented
geometric lines which correspond to streams on the landscape.
* Added a D8 subwatershed calculation function at
``pygeoprocessing.calculate_subwatershed_boundary``. Creates subwatersheds
that are segmented at the junctions of the streams created by
``pygeoprocessing.extract_strahler_streams_d8``.
* Removing all instances of ``__swig_destroy__`` to prevent multiprocessing
memory corruption.
* Exposing a ``use_shared_memory`` flag on ``raster_calculator`` to allow
a user to use shared memory objects when calculating statistics. This
feature is only available for Python >= 3.8. If available, this
feature creates a significant runtime improvement but can be unstable
in multiprocessing configurations. For this reason it is set to
``False`` as the default value.
* Added a ``max_timeout`` parameter to ``convolve_2d`` and
``raster_calculator`` to allow the user to specify the maximum amount of
time to wait for worker threads to terminate. In normal operation these
threads should terminate in a short amount of time but are generously
timed with the ``pygeoprocessing._MAX_TIMEOUT`` parameter. This parameter
allows a user to tune in cases that may involve significant latency such
as in a heavy multiprocess environment.
* Added a ``pygeoprocessing.routing.detect_outlets`` function that creates a
vector with points placed on the center of the pixels in a D8 or MFD flow
direction raster that are outlet pixels. The vector has additional metadata
about the (i, j) locations of the pixel in raster coordinate space.
* Replacing ``merge_rasters`` with ``stitch_rasters`` that can take an
arbitrary list of raster path bands and stitch them into an existing raster
of same or different projection. Additional functionality to preserve
area variant values when stitching from a linear meters projection to
WGS84. Useful when the units of the base raster are in "units per pixel"
rather than "units per area".
* Added a ``max_pixel_fill_count`` parameter to ``routing.fill_pits`` to
guard against pitfilling large natural depression. Defaults to 500.
* Fixed an issue in ``align_and_resize_raster_stack`` that would ignore
the bounds of a feature in a mask vector if the
``"mask_vector_where_filter"`` clause was invoked and instead only
considered the entire bounds of the vector.
* Fixed an issue with ``convolve_2d`` that allowed output rasters to be
created without a defined nodata value.
* Fixed a LOGGER message bug that occurred in ``zonal_statistics``.
* Fixed an issue in ``distance_to_channel_mfd`` that would generate a raster
with distances to the edge of the raster even if there was no channel. Now
generates nodata so it is consistent with ``distance_to_channel_d8``.
* The ``convolve_2d`` function now raises a ValueError if either the signal
or kernel raster has a row based blocksize since this could result in
very long runtimes due to gdal cache thrashing.
* Fixed an issue that would cause a ``convolve_2d`` worker to crash if the
integrating kernel was not a float and also ``normalize_kernel=True``
thus causing the entire function call to deadlock.
* Added a check on ``transform_bounding_box`` to ensure the target bounding
box's coordinates were finite. This guards against cases where a transform
into another coordinate system creates a degenerate bounding box.
Previously the function would silently return non-finite coordinates.
* Fixing issue when calculating histogram for floating point rasters the
logging progress percent would be incorrectly calculated.

------------------
* ``pygeoprocessing.warp_raster`` now raises a ``ValueError`` when an invalid
resampling method is provided.
* Fixed bug in ``pygeoprocessing.warp_raster`` that would not properly handle
GDAL Byte type signing when masking warped raster with a vector.
* Fixed issue in ``convolve_2d`` that would cause excessive memory use
leading to out of memory errors.
* Fixed issue in ``convolve_2d`` that could lead to a file removal race
condition and raise a ``FileNotFoundException`` when ignoring nodata
regions.

------------------
* Fixed a critical bug introduced in 2.1.0 that generated invalid results in
`convolve_2d` for any raster larger than 256x256.
* Added an optional parameter, ``target_layer_name`` to
``pygeoprocessing.routing.delineate_watersheds_d8`` for cases where a
caller would like to define the output layer name.

------------------
* Modified ``pygeoprocessing.numpy_array_to_raster`` to take boolean arrays.
* Modified ``pygeoprocessing.convolve_2d`` to guard against nonsensical queries
to both ``ignore_nodata_and_edges=True`` but also ``mask_nodata=False``.
A query of this combination now raises a ``ValueError`` to guard against
programmer error.
* Added a custom exception class ``ReclassificationMissingValuesError`` to
``pygeoprocessing``. ``pygeoprocessing.reclassify_raster`` raises this
exception instead of ``ValueError`` when a raster pixel value is not
represented in ``value_map``. This custom exception provides a list of
missing raster pixel values in a ``missing_values`` attribute that allows
the caller access to the pixel values that are missing through a Python type
rather than indirectly through an error message.
* Correcting the docstring for ``pygeoprocessing.numpy_array_to_raster`` to
specify that the ``pixel_size`` parameter must be a tuple or list, not an
int.
* ``pygeoprocessing.routing.delineate_watersheds_d8`` now has an optional
parameter ``write_diagnostic_vector``. When ``True``, this parameter will
cause a new vector per outflow feature to be created in the ``working_dir``.
This parameter defaults to ``False``. This is a change from prior behavior,
when the diagnostic vectors were always created, which could occupy a lot of
computational time under large outflow geometries.
* Added a ``pygeoprocessing.multiprocessing.raster_calculator`` function which
matches the API and results of ``pygeoprocessing.raster_calculator`` but uses
multiple processing cores to compute raster calculation blocks.
when the diagnostic vectors were always created, which could occupy
significant computational time under large outflow geometries.
* Minor performance improvement to ``pygeoprocessing.convolve_2d`` by
preventing a pre-processing step that initialized temporary rasters with zero
values as well as added asynchronous work distribution for kernel/signal
block processing.
* Modified logging message for ``pygeoprocessing.new_raster_from_base`` when
filling a raster such that an informative error message is printed with
context as to the function, file, status, and value being filled.

------------------
* Adding Python 3.8 support and dropping Python 3.6 support.
* Adding GDAL 3 support and dropping GDAL 2 support. The only non-backwards
compatible issue in GDAL 2 to GDAL 3 is the need to handle Axis Ordering with
osr.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER) because of
https://trac.osgeo.org/gdal/wiki/rfc73_proj6_wkt2_srsbarn#Axisorderissues?.
Since Axis ordering now matters for Geographic CRS the expected order is
Lat,Lon but we use osr.OAMS_TRADITIONAL_GIS_ORDER to swap to Lon,Lat.
* Using osr.CreateCoordinateTransformation() instead of
osr.CoordinateTransformation() as the GDAL 3 call.
* Fixed a bug in convolve_2d that would not ``ignore_nodata`` if the signal
raster's nodata value was undefined. Changed the name of this flag to
``ignore_nodata_and_edges`` to reflect its expected functionality.
* Warped signed byte rasters are now also signed byte rasters.
* Adding a GitHub Actions-based build job for building wheels and a source
distribution for a given commit of pygeoprocessing.
* Updated ``setup.py`` to point the URL project link to the project's new
home on GitHub.
* Updated ``MANIFEST.in`` to only include files that should be there in the
pygeoprocessing source distribution. This fixes an issue where files
matching a variety of extensions anywhere in the pygeoprocessing directory
might be included with the source distribution.
* Added ``set_tol_to_zero`` to ``convolve_2d`` to allow for in-function masking
of near-zero results to be set to 0.0.
* Fixed malformed logging outputs which could be seen during long running
``rasterize`` calls.
* Renamed all parameters involving Spatial Projections to the form
``[var_id]_projection_wkt``, this involves optional arguments in
``reproject_vector``, ``warp_raster``, ``transform_bounding_box``,
and ``align_and_resize_raster_stack`` as well as the return value from
``get_raster_info`` and ``get_vector_info``.
* Fixed an issue in ``zonal_statistics`` that would crash if an aggregate
vector had a feature with no geometry defined. Now the function ignores
such features and prints a warning to the log.
* Fixed a malformed ``ValueError`` message when a corrupt raster was
encountered in ``raster_calculator``.
* Fixes an unnecessary calculation that pre-fills slope raster GeoTIFFs with
nodata values.
* Added a check to ``convolve_2d`` to verify that raster path/band tuples were
passed where expected and raise a useful Exception if not.
* Removed most of the `pygeoprocessing.testing` module and added the following
convenience functions to ``pygeoprocessing``, which should not be used
for production code but are useful for testing and scripting:

* ``raster_to_numpy_array`` - read a single band of a raster into a ``numpy``
array, runs the risk of memory error if the raster is too large.
* ``numpy_array_to_raster`` - writes a ``numpy`` array to a raster on disk.
* ``shapely_geometry_to_vector`` - creates a vector from a list of
``Shapely`` geometry.

* Fixed an issue in ``flow_dir_mfd`` that would cause invalid flow directions
on DEMs that had very small numerical delta heights.
* Fixes an issue in ``convolve_2d`` that would occasionally cause undefined
numerical noise in regions where the signal was nodata but ``mask_nodata``
was set to ``False``.

------------------
* Removed the ``multiprocessing`` dependency to avoid an occasional deadlock
that occurred on Mac OS X during ``align_and_resize_raster_stack``.
That function now operates serially, but multithreading can be used by
passing ``gdal_warp_options``.