Merge branch 'main' into bugfix/1635-pollination-inf-values-in-outputs

HISTORY.rst

@@ -37,6 +37,25 @@
 
 Unreleased Changes
 ------------------
+* General
+    * InVEST has been updated to build against numpy 2.
+      https://github.com/natcap/invest/issues/1641
+    * Updating validation to handle a change in exceptions raised by GDAL in
+      ``pygeoprocessing.get_raster_info`` and
+      ``pygeoprocessing.get_vector_info``.
+      https://github.com/natcap/invest/issues/1645
+* Coastal Vulnerability
+    * Fixed a regression where an AOI with multiple features could raise a
+      TypeError after intersecting with the landmass polygon.
+      https://github.com/natcap/invest/issues/1657
+* Forest Carbon Edge Effects
+    * Updating vector reprojection to allow partial reprojection.  Related to
+      https://github.com/natcap/invest/issues/1645
+* Habitat Quality
+    * Access raster is now generated from the reprojected access vector
+      (https://github.com/natcap/invest/issues/1615).
+    * Rarity values are now output in CSV format (as well as in raster format)
+      (https://github.com/natcap/invest/issues/721).
 * Pollination
     * Fixed an issue with nodata handling that was causing some outputs to be
       filled either with the float32 value for positive infinity, or else with
@@ -45,27 +64,26 @@ Unreleased Changes
       updated the stated dtype of most pollination model outputs to be float32
       instead of the float64 dtype that was being assumed previously.  This
       will result in smaller output filesizes with minimal loss of precision.
+* Urban Flood Risk
+    * Fields present on the input AOI vector are now retained in the output.
+      (https://github.com/natcap/invest/issues/1600)
 * Urban Nature Access
     * The model now works as expected when the user provides an LULC raster
       that does not have a nodata value defined.
       https://github.com/natcap/invest/issues/1293
 * Workbench
     * Several small updates to the model input form UI to improve usability
-      and visual consistency (https://github.com/natcap/invest/issues/912)
+      and visual consistency (https://github.com/natcap/invest/issues/912).
     * Fixed a bug that caused the application to crash when attempting to
       open a workspace without a valid logfile
-      (https://github.com/natcap/invest/issues/1598)
+      (https://github.com/natcap/invest/issues/1598).
     * Fixed a bug that was allowing readonly workspace directories on Windows
-      (https://github.com/natcap/invest/issues/1599)
+      (https://github.com/natcap/invest/issues/1599).
     * Fixed a bug that, in certain scenarios, caused a datastack to be saved
       with relative paths when the Relative Paths checkbox was left unchecked
-      (https://github.com/natcap/invest/issues/1609)
-* Habitat Quality
-    * Access raster is now generated from the reprojected access vector.
-      (https://github.com/natcap/invest/issues/1615)
-* Urban Flood Risk
-    * Fields present on the input AOI vector are now retained in the output.
-      (https://github.com/natcap/invest/issues/1600)
+      (https://github.com/natcap/invest/issues/1609).
+    * Improved error handling when a datastack cannot be saved with relative
+      paths across drives (https://github.com/natcap/invest/issues/1608).
 
 3.14.2 (2024-05-29)
 -------------------

Makefile

@@ -10,7 +10,7 @@ GIT_TEST_DATA_REPO_REV      := 324abde73e1d770ad75921466ecafd1ec6297752
 
 GIT_UG_REPO                 := https://github.com/natcap/invest.users-guide
 GIT_UG_REPO_PATH            := doc/users-guide
-GIT_UG_REPO_REV             := 0404bc5d4d43085cdc58f50f8fc29944b10cefb1
+GIT_UG_REPO_REV             := f203ec069f9f03560c9a85b268e67ebb6b994953
 
 ENV = "./env"
 ifeq ($(OS),Windows_NT)

constraints_tests.txt

@@ -6,9 +6,6 @@
 # occur with regular use of invest. https://github.com/OSGeo/gdal/issues/8497
 GDAL!=3.6.*,!=3.7.*
 
-# https://github.com/natcap/pygeoprocessing/issues/387
-GDAL<3.8.5
-
 # Pyinstaller 6.10 breaks our windows builds.  Until we can figure out the
 # root cause, let's cap the versions to those that work.
 # https://github.com/natcap/invest/issues/1622

pyproject.toml

@@ -46,7 +46,8 @@ invest = "natcap.invest.cli:main"
 # available at runtime.
 requires = [
     'setuptools>=61', 'wheel', 'setuptools_scm>=8.0', 'cython>=3.0.0', 'babel',
-    'oldest-supported-numpy'
+    'oldest-supported-numpy; python_version<="3.8"',
+    'numpy>=2; python_version>="3.9"',  # numpy 2 only available for 3.9+
 ]
 build-backend = "setuptools.build_meta"
 

requirements.txt

@@ -13,11 +13,11 @@
 GDAL>=3.4.2
 Pyro4==4.77  # pip-only
 pandas>=1.2.1
-numpy>=1.11.0,!=1.16.0,<2.0
+numpy>=1.11.0,!=1.16.0
 Rtree>=0.8.2,!=0.9.1
 shapely>=2.0.0
 scipy>=1.9.0,!=1.12.*
-pygeoprocessing>=2.4.2  # pip-only
+pygeoprocessing>=2.4.6  # pip-only
 taskgraph>=0.11.0
 psutil>=5.6.6
 chardet>=3.0.4

scripts/invest-autovalidate.py

@@ -1,14 +1,14 @@
 #!python
 
-import os
-import tempfile
-import logging
 import argparse
-import unittest
 import glob
 import importlib
-import shutil
+import logging
+import os
 import pprint
+import shutil
+import tempfile
+import unittest
 
 from natcap.invest import datastack
 
@@ -81,7 +81,7 @@ def main(sampledatadir):
 
         model_warnings = []  # define here in case of uncaught exception.
         try:
-            LOGGER.info('validating %s ', datastack_path)
+            LOGGER.info('validating %s ', os.path.abspath(datastack_path))
             model_warnings = getattr(
                 model_module, 'validate')(paramset.args)
         except AttributeError as err:

src/natcap/invest/coastal_vulnerability.py

@@ -21,6 +21,7 @@
 from osgeo import gdal
 from osgeo import ogr
 from osgeo import osr
+from shapely.geometry import LineString, MultiLineString
 from shapely.geometry.base import BaseMultipartGeometry
 from shapely.strtree import STRtree
 
@@ -1104,7 +1105,6 @@ def prepare_landmass_line_index_and_interpolate_shore_points(
     # Get shapely geometries from landmass
     landmass_polygon_shapely_list = _ogr_to_geometry_list(landmass_vector_path)
     landmass_shapely = shapely.ops.unary_union(landmass_polygon_shapely_list)
-
     landmass_polygon_shapely_list = None
 
     # store polygon geom for point-in-poly check later in ray-casting
@@ -1170,19 +1170,13 @@ def prepare_landmass_line_index_and_interpolate_shore_points(
             if aoi_shapely_prepped.intersects(landmass_line):
                 intersected_shapely_geom = aoi_shapely.intersection(
                     landmass_line)
-                if intersected_shapely_geom.geom_type == 'LineString':
-                    lines_in_aoi_list.append(intersected_shapely_geom)
-                elif intersected_shapely_geom.geom_type == 'MultiLineString':
-                    shapely_geom_explode = [
-                        shapely.geometry.LineString(x)
-                        for x in intersected_shapely_geom]
-
-                    lines_in_aoi_list.extend(shapely_geom_explode)
-                else:
-                    # intersection could generate a point geom
-                    # or if somehow the intersection is empty,
-                    # type will be GeometryCollection.
-                    continue
+                # intersection could generate a point geom,
+                # or if somehow the intersection is empty,
+                # type will be GeometryCollection.
+                if isinstance(intersected_shapely_geom,
+                              (LineString, MultiLineString)):
+                    lines_in_aoi_list.extend(
+                        _list_geometry(intersected_shapely_geom))
 
         # if none of the lines were disjoint before this linemerge,
         # unioned_line will now be a LineString.

src/natcap/invest/datastack.py

@@ -535,6 +535,9 @@ def build_parameter_set(args, model_name, paramset_path, relative=False):
 
     Returns:
         ``None``
+
+    Raises:
+        ValueError if creating a relative path fails.
     """
     def _recurse(args_param):
         if isinstance(args_param, dict):
@@ -552,8 +555,16 @@ def _recurse(args_param):
                     if (normalized_path == '.' or
                             os.path.dirname(paramset_path) == normalized_path):
                         return '.'
-                    temp_rel_path = os.path.relpath(
-                        normalized_path, os.path.dirname(paramset_path))
+                    try:
+                        temp_rel_path = os.path.relpath(
+                            normalized_path, os.path.dirname(paramset_path))
+                    except ValueError:
+                        # On Windows, ValueError is raised when ``path`` and
+                        # ``start`` are on different drives
+                        raise ValueError(
+                            """Error: Cannot save datastack with relative
+                            paths across drives. Choose a different save
+                            location, or use absolute paths.""")
                     # Always save unix paths.
                     linux_style_path = temp_rel_path.replace('\\', '/')
                 else:

src/natcap/invest/forest_carbon_edge_effect.py

@@ -583,13 +583,14 @@ def _aggregate_carbon_map(
     for poly_feat in target_aggregate_layer:
         poly_fid = poly_feat.GetFID()
         poly_feat.SetField(
-            'c_sum', serviceshed_stats[poly_fid]['sum'])
+            'c_sum', float(serviceshed_stats[poly_fid]['sum']))
         # calculates mean pixel value per ha in for each feature in AOI
         poly_geom = poly_feat.GetGeometryRef()
         poly_area_ha = poly_geom.GetArea() / 1e4  # converts m^2 to hectare
         poly_geom = None
         poly_feat.SetField(
-            'c_ha_mean', serviceshed_stats[poly_fid]['sum']/poly_area_ha)
+            'c_ha_mean',
+            float(serviceshed_stats[poly_fid]['sum'] / poly_area_ha))
 
         target_aggregate_layer.SetFeature(poly_feat)
     target_aggregate_layer.CommitTransaction()
@@ -765,9 +766,11 @@ def _build_spatial_index(
         local_model_dir, 'local_carbon_shape.shp')
     lulc_projection_wkt = pygeoprocessing.get_raster_info(
         base_raster_path)['projection_wkt']
-    pygeoprocessing.reproject_vector(
-        tropical_forest_edge_carbon_model_vector_path, lulc_projection_wkt,
-        carbon_model_reproject_path)
+
+    with utils._set_gdal_configuration('OGR_ENABLE_PARTIAL_REPROJECTION', 'TRUE'):
+        pygeoprocessing.reproject_vector(
+            tropical_forest_edge_carbon_model_vector_path, lulc_projection_wkt,
+            carbon_model_reproject_path)
 
     model_vector = gdal.OpenEx(carbon_model_reproject_path)
     model_layer = model_vector.GetLayer()