Merge branch 'main' into translations-update

.readthedocs.yml

@@ -18,5 +18,9 @@ build:
   tools:
     python: "mambaforge-4.10"
   jobs:
+    post_create_environment:
+      - pip install --upgrade-strategy=only-if-needed -r requirements.txt
+      - pip install --upgrade-strategy=only-if-needed -r requirements-dev.txt
+      - pip install --upgrade-strategy=only-if-needed -r requirements-docs.txt
     post_install:
       - make install

.readthedocs_environment.yml

@@ -11,9 +11,5 @@ channels:
 - nodefaults
 dependencies:
 - python=3.11
-- gdal>=3.4.2,<3.6.0
+- gdal>=3.4.2
 - pip
-- pip:
-  - -r requirements.txt
-  - -r requirements-dev.txt
-  - -r requirements-docs.txt

HISTORY.rst

@@ -35,10 +35,26 @@
 
 .. :changelog:
 
-
 Unreleased Changes
 ------------------
+* Workbench
+    * Several small updates to the model input form UI to improve usability
+      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)
+    * Fixed a bug that was allowing readonly workspace directories on Windows
+      (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)
+
+3.14.2 (2024-05-29)
+-------------------
 * General
+    * Validation now covers file paths contained in CSVs. CSV validation
+      will fail if the files listed in a CSV fail to validate.
+      https://github.com/natcap/invest/issues/327
     * We have updated validation in several ways that will improve the
       developer experience of working with InVEST models, and we hope will also
       improve the user experience:
@@ -59,15 +75,52 @@ Unreleased Changes
         versions of InVEST would skip these parameters' type-specific
         validation. Now, these parameters will be validated with their
         type-specific validation checks.
-
+    * Add support for latest GDAL versions; remove test-specific constraint on
+      GDAL versions from invest requirements.
+      https://github.com/natcap/invest/issues/916
+    * Updated to Cython 3 (https://github.com/natcap/invest/issues/556)
 * Annual Water Yield
     * Added the results_suffix to a few intermediate files where it was
       missing. https://github.com/natcap/invest/issues/1517
+* Coastal Blue Carbon
+    * Updated model validation to prevent the case where a user provides only
+      one snapshot year and no analysis year
+      (`#1534 <https://github.com/natcap/invest/issues/1534>`_).
+      Also enforces that the analysis year, if provided, is greater than the
+      latest snapshot year. An analysis year equal to the latest snapshot year
+      is no longer allowed.
 * Coastal Vulnerability
     * Fixed a bug in handling ``nan`` as the nodata value of the bathymetry
       raster. ``nan`` pixels will now be propertly ignored before calculating
       mean depths along fetch rays.
       https://github.com/natcap/invest/issues/1528
+* HRA
+    * Fixed a bug where habitat and stressor vectors were not being rasterized
+      with the `ALL_TOUCHED=TRUE` setting.
+* Scenic Quality
+    * Fixed an issue with viewshed calculations where some slight numerical
+      error was introduced on M1 Macs, but not on x86-based computers. This
+      numerical error was leading to slightly different visibility results.
+      https://github.com/natcap/invest/issues/1562
+* SDR
+    * Fixed an issue encountered in the sediment deposition function where
+      rasters with more than 2^32 pixels would raise a cryptic error relating
+      to negative dimensions. https://github.com/natcap/invest/issues/1431
+    * Optimized the creation of the summary vector by minimizing the number of
+      times the target vector needs to be rasterized.
+* Seasonal Water Yield
+    * Fixed an issue with the precip directory units. Units for these input
+      rasters are now correctly stated as mm/month.
+      https://github.com/natcap/invest/issues/1571
+    * Fixed an issue where the monthly quickflow values were being summed over
+      a block area and not summed pixelwise. This caused the quickflow
+      output ``QF.tif`` to have malformed values.
+      https://github.com/natcap/invest/issues/1541
+* Wind Energy
+    * Fixed a bug where some number inputs were not being properly cast to
+      ``float`` or ``int`` types. If the inputs happened to be passed as
+      a ``str`` this caused unintended side effects such as a concatenation
+      error. (https://github.com/natcap/invest/issues/1498)
 * Urban Nature Access
     * Fixed a ``NameError`` that occurred when running the model using
       search radii defined per population group with an exponential search
@@ -91,12 +144,6 @@ Unreleased Changes
     * Fixed an issue where an LULC raster without a nodata value would
       always raise in exception during reclassification.
       https://github.com/natcap/invest/issues/1539
-* SDR
-    * Fixed an issue encountered in the sediment deposition function where
-      rasters with more than 2^32 pixels would raise a cryptic error relating
-      to negative dimensions. https://github.com/natcap/invest/issues/1431
-    * Optimized the creation of the summary vector by minimizing the number of
-      times the target vector needs to be rasterized.
 
 3.14.1 (2023-12-18)
 -------------------

Makefile

@@ -2,15 +2,15 @@
 DATA_DIR := data
 GIT_SAMPLE_DATA_REPO        := https://bitbucket.org/natcap/invest-sample-data.git
 GIT_SAMPLE_DATA_REPO_PATH   := $(DATA_DIR)/invest-sample-data
-GIT_SAMPLE_DATA_REPO_REV    := 2e7cd618c661ec3f3b2a3bddfd2ce7d4704abc05
+GIT_SAMPLE_DATA_REPO_REV    := ab8c74a62a93fd0019de2bca064abc0a5a07afab
 
 GIT_TEST_DATA_REPO          := https://bitbucket.org/natcap/invest-test-data.git
 GIT_TEST_DATA_REPO_PATH     := $(DATA_DIR)/invest-test-data
-GIT_TEST_DATA_REPO_REV      := da013683e80ea094fbb2309197e2488c02794da8
+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             := fa6b181d49136089dce56d4ff8f3dcaf12eb4ced
+GIT_UG_REPO_REV             := 0404bc5d4d43085cdc58f50f8fc29944b10cefb1
 
 ENV = "./env"
 ifeq ($(OS),Windows_NT)
@@ -251,6 +251,7 @@ $(INVEST_BINARIES_DIR): | $(DIST_DIR) $(BUILD_DIR)
 	-$(RMDIR) $(INVEST_BINARIES_DIR)
 	$(PYTHON) -m PyInstaller --workpath $(BUILD_DIR)/pyi-build --clean --distpath $(DIST_DIR) exe/invest.spec
 	$(CONDA) list > $(INVEST_BINARIES_DIR)/package_versions.txt
+	$(PYTHON) -m pip list >> $(INVEST_BINARIES_DIR)/package_versions.txt
 	$(INVEST_BINARIES_DIR)/invest list
 
 # Documentation.

constraints_tests.txt

@@ -0,0 +1,15 @@
+# This file contains package constraints needed to run the invest test suite.
+# It follows the pip constraints file format:
+# https://pip.pypa.io/en/stable/user_guide/#constraints-files
+
+# A gdal bug caused our test suite to fail, but this issue is unlikely to
+# 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
+#pyinstaller<6.10

docker/Dockerfile

@@ -13,11 +13,15 @@ RUN cd / && \
 
 # Create the container for distribution that has runtime dependencies.
 FROM mambaorg/micromamba:1.5.0-bookworm-slim
+# Python version should match the version used in stage 1.
+# If we update the stage 1 debian version, also update this python version
+ARG PYTHON_VERSION="3.11"
 COPY --from=build /invest/dist/*.whl /tmp/
 
 # The environment.yml file will be built during github actions.
 COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
-RUN micromamba install -y -n base -c conda-forge -f /tmp/environment.yml && \
+RUN micromamba install -y -n base -c conda-forge python==${PYTHON_VERSION} && \
+        micromamba install -y -n base -c conda-forge -f /tmp/environment.yml && \
         micromamba clean --all --yes && \
         /opt/conda/bin/python -m pip install /tmp/*.whl && \
         /opt/conda/bin/python -m pip cache purge && \

exe/hooks/rthook.py

@@ -1,9 +1,6 @@
-import sys
 import os
-import multiprocessing
 import platform
-
-multiprocessing.freeze_support()
+import sys
 
 os.environ['PROJ_LIB'] = os.path.join(sys._MEIPASS, 'proj')
 

exe/invest.spec

@@ -30,6 +30,9 @@ kwargs = {
         'pkg_resources.py2_warn',
         'cmath',
         'charset_normalizer',
+        'scipy.special._cdflib',
+        'scipy.special._special_ufuncs',
+        'scipy._lib.array_api_compat.numpy.fft',
     ],
     'datas': [proj_datas],
     'cipher': block_cipher,

pyproject.toml

@@ -2,7 +2,7 @@
 name = "natcap.invest"
 description = "InVEST Ecosystem Service models"
 readme = "README_PYTHON.rst"
-requires-python = ">=3.8,<3.12"
+requires-python = ">=3.8"
 license = {file = "LICENSE.txt"}
 maintainers = [
     {name = "Natural Capital Project Software Team"}
@@ -21,6 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Programming Language :: Cython",
     "License :: OSI Approved :: BSD License",
     "Topic :: Scientific/Engineering :: GIS"
@@ -44,7 +45,7 @@ invest = "natcap.invest.cli:main"
 # that we can provide a much easier build experience so long as GDAL is
 # available at runtime.
 requires = [
-    'setuptools>=61', 'wheel', 'setuptools_scm>=8.0', 'cython', 'babel',
+    'setuptools>=61', 'wheel', 'setuptools_scm>=8.0', 'cython>=3.0.0', 'babel',
     'oldest-supported-numpy'
 ]
 build-backend = "setuptools.build_meta"
@@ -78,4 +79,11 @@ where = ["src"]
 
 [tool.pytest.ini_options]
 # raise warnings to errors, except for deprecation warnings
-filterwarnings = ["error", "default::DeprecationWarning"]
+filterwarnings = [
+    "error",
+    "default::DeprecationWarning",
+    "default::FutureWarning",
+    # don't error on a specific runtime warning coming from a shapely
+    # issue on M1: https://github.com/natcap/invest/issues/1562
+    "default:invalid value encountered in intersection:RuntimeWarning",
+]

requirements-dev.txt

@@ -9,15 +9,18 @@
 # Any lines with "# pip-only" at the end will be processed by
 # scripts/convert-requirements-to-conda-yml.py as though it can only be found
 # on pip.
+# Sometimes conda-forge does not install the latest available version,
+# pip-only can be a workaround for that.
 
-Cython<3.0.0
 virtualenv>=12.0.1
 pytest
 pytest-subtests
 wheel>=0.27.0
 pypiwin32; sys_platform == 'win32'  # pip-only
-setuptools>=8.0,<60.7.0 # https://github.com/pyinstaller/pyinstaller/issues/6564
-PyInstaller>=4.10
+
+# 60.7.0 exception because of https://github.com/pyinstaller/pyinstaller/issues/6564
+setuptools>=8.0,!=60.7.0
+PyInstaller>=4.10  # pip-only
 setuptools_scm>=6.4.0
 requests
 coverage

requirements.txt

@@ -10,10 +10,10 @@
 # scripts/convert-requirements-to-conda-yml.py as though it can only be found
 # on pip.
 
-GDAL>=3.4.2,<3.6.0
+GDAL>=3.4.2
 Pyro4==4.77  # pip-only
 pandas>=1.2.1
-numpy>=1.11.0,!=1.16.0
+numpy>=1.11.0,!=1.16.0,<2.0
 Rtree>=0.8.2,!=0.9.1
 shapely>=2.0.0
 scipy>=1.9.0,!=1.12.*

setup.py

@@ -2,8 +2,8 @@
 import platform
 import subprocess
 
-import Cython.Build
 import numpy
+from Cython.Build import cythonize
 from setuptools import setup
 from setuptools.command.build_py import build_py as _build_py
 from setuptools.extension import Extension
@@ -46,25 +46,34 @@ def run(self):
 
 setup(
     install_requires=_REQUIREMENTS,
-    ext_modules=[
+    ext_modules=cythonize([
         Extension(
             name=f'natcap.invest.{package}.{module}',
             sources=[f'src/natcap/invest/{package}/{module}.pyx'],
-            include_dirs=[numpy.get_include()],
-            extra_compile_args=compiler_and_linker_args,
+            extra_compile_args=compiler_args + compiler_and_linker_args,
             extra_link_args=compiler_and_linker_args,
-            language='c++'
-        ) for package, module in [
-            ('delineateit', 'delineateit_core'),
-            ('recreation', 'out_of_core_quadtree'),
-            ('scenic_quality', 'viewshed'),
-            ('ndr', 'ndr_core'),
-            ('sdr', 'sdr_core'),
-            ('seasonal_water_yield', 'seasonal_water_yield_core')
+            language='c++',
+            define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")]
+        ) for package, module, compiler_args in [
+            ('delineateit', 'delineateit_core', []),
+            ('recreation', 'out_of_core_quadtree', []),
+            # clang-14 defaults to -ffp-contract=on, which causes the
+            # arithmetic of A*B+C to be implemented using a contraction, which
+            # causes an unexpected change in the precision in some viewshed
+            # tests on ARM64 (mac M1).  See these issues for more details:
+            #  * https://github.com/llvm/llvm-project/issues/91824
+            #  * https://github.com/natcap/invest/issues/1562
+            #  * https://github.com/natcap/invest/pull/1564/files
+            # Using this flag on gcc and on all versions of clang should work
+            # as expected, with consistent results.
+            ('scenic_quality', 'viewshed', ['-ffp-contract=off']),
+            ('ndr', 'ndr_core', []),
+            ('sdr', 'sdr_core', []),
+            ('seasonal_water_yield', 'seasonal_water_yield_core', [])
         ]
-    ],
+    ], compiler_directives={'language_level': '3'}),
+    include_dirs=[numpy.get_include()],
     cmdclass={
-        'build_ext': Cython.Build.build_ext,
         'build_py': build_py
     }
 )

src/natcap/invest/__main__.py

@@ -1,5 +1,11 @@
+import multiprocessing
 import sys
 
+# We want to guarantee that this is called BEFORE any other processes start,
+# which could happen at import time.
+if __name__ == '__main__':
+    multiprocessing.freeze_support()
+
 from . import cli
 
 if __name__ == '__main__':

src/natcap/invest/coastal_blue_carbon/coastal_blue_carbon.py

@@ -114,10 +114,10 @@
 LOGGER = logging.getLogger(__name__)
 
 INVALID_ANALYSIS_YEAR_MSG = gettext(
-    "Analysis year {analysis_year} must be >= the latest snapshot year "
+    "Analysis year ({analysis_year}) must be greater than the latest snapshot year "
     "({latest_year})")
-INVALID_SNAPSHOT_RASTER_MSG = gettext(
-    "Raster for snapshot {snapshot_year} could not be validated.")
+MISSING_ANALYSIS_YEAR_MSG = gettext(
+    "Analysis year is required if only one snapshot year is provided.")
 INVALID_TRANSITION_VALUES_MSG = gettext(
     "The transition table expects values of {model_transitions} but found "
     "values of {transition_values}.")
@@ -2166,7 +2166,6 @@ def validate(args, limit_to=None):
     """
     validation_warnings = validation.validate(
         args, MODEL_SPEC['args'])
-
     sufficient_keys = validation.get_sufficient_keys(args)
     invalid_keys = validation.get_invalid_keys(validation_warnings)
 
@@ -2177,19 +2176,14 @@ def validate(args, limit_to=None):
             **MODEL_SPEC['args']['landcover_snapshot_csv']
         )['raster_path'].to_dict()
 
-        for snapshot_year, snapshot_raster_path in snapshots.items():
-            raster_error_message = validation.check_raster(
-                snapshot_raster_path)
-            if raster_error_message:
-                validation_warnings.append((
-                    ['landcover_snapshot_csv'],
-                    INVALID_SNAPSHOT_RASTER_MSG.format(
-                        snapshot_year=snapshot_year
-                    ) + ' ' + raster_error_message))
+        snapshot_years = set(snapshots.keys())
+        if len(snapshot_years) == 1 and "analysis_year" not in sufficient_keys:
+            validation_warnings.append(
+                (['analysis_year'], MISSING_ANALYSIS_YEAR_MSG))
 
         if ("analysis_year" not in invalid_keys
                 and "analysis_year" in sufficient_keys):
-            if max(set(snapshots.keys())) > int(args['analysis_year']):
+            if max(snapshot_years) >= int(args['analysis_year']):
                 validation_warnings.append((
                     ['analysis_year'],
                     INVALID_ANALYSIS_YEAR_MSG.format(