Merge branch 'main' of https://github.com/natcap/invest into task/152…

…3-try-gh-actions-artifact-attestations

.github/workflows/build-and-test.yml

@@ -21,7 +21,7 @@ env:
   # nomkl: make sure numpy w/out mkl
   # setuptools_scm: needed for versioning to work
   CONDA_DEFAULT_DEPENDENCIES: python-build nomkl setuptools_scm
-  LATEST_SUPPORTED_PYTHON_VERSION: "3.11"
+  LATEST_SUPPORTED_PYTHON_VERSION: "3.12"
 
 permissions:
   attestations: write
@@ -76,7 +76,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
         os: [windows-latest, macos-latest]
     steps:
       - uses: actions/checkout@v3
@@ -168,7 +168,7 @@ jobs:
     needs: check-syntax-errors
     strategy:
       matrix:
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
         os: [windows-latest, macos-latest]
     steps:
       - uses: actions/checkout@v3
@@ -190,7 +190,7 @@ jobs:
       - name: Install from source distribution
         run : |
           # Install natcap.invest from the sdist in dist/
-          pip install $(find dist -name "natcap.invest*")
+          pip install $(find dist -name "natcap[._-]invest*")
 
           # Model tests should cover model functionality, we just want
           # to be sure that we can import `natcap.invest` here.
@@ -286,7 +286,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: workbench/node_modules
-          key: ${{ runner.os }}-${{ hashFiles('workbench/yarn.lock') }}
+          key: ${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('workbench/yarn.lock') }}
 
       - name: Install workbench dependencies
         if: steps.nodemodules-cache.outputs.cache-hit != 'true'
@@ -327,7 +327,11 @@ jobs:
         uses: ./.github/actions/setup_env
         with:
           python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }}
-          requirements-files: requirements.txt requirements-dev.txt requirements-docs.txt
+          requirements-files: |
+            requirements.txt
+            requirements-dev.txt
+            requirements-docs.txt
+            constraints_tests.txt
           requirements: ${{ env.CONDA_DEFAULT_DEPENDENCIES }} pandoc
 
       - name: Make install
@@ -361,7 +365,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: workbench/node_modules
-          key: ${{ runner.os }}-${{ hashFiles('workbench/yarn.lock') }}
+          key: ${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('workbench/yarn.lock') }}
 
       - name: Install Workbench Dependencies
         if: steps.nodemodules-cache.outputs.cache-hit != 'true'

HISTORY.rst

@@ -68,6 +68,13 @@ Unreleased Changes
 * 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
@@ -76,6 +83,11 @@ Unreleased Changes
 * 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

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    := 8f78a4873f1fa4253d3ab9a01d6e23f11499b975
 
 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      := 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)

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 && \

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"
@@ -78,4 +79,11 @@ where = ["src"]
 
 [tool.pytest.ini_options]
 # raise warnings to errors, except for deprecation warnings
-filterwarnings = ["error", "default::DeprecationWarning", "default::FutureWarning"]
+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

@@ -16,7 +16,9 @@ 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
+
+# 60.7.0 exception because of https://github.com/pyinstaller/pyinstaller/issues/6564
+setuptools>=8.0,!=60.7.0
 PyInstaller>=4.10
 setuptools_scm>=6.4.0
 requests

src/natcap/invest/coastal_blue_carbon/coastal_blue_carbon.py

@@ -114,8 +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})")
+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}.")
@@ -2174,9 +2176,14 @@ def validate(args, limit_to=None):
             **MODEL_SPEC['args']['landcover_snapshot_csv']
         )['raster_path'].to_dict()
 
+        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(

src/natcap/invest/scenic_quality/viewshed.pyx

@@ -815,8 +815,23 @@ def viewshed(dem_raster_path_band,
             if target_distance > max_visible_radius:
                 break
 
-            z = (((previous_height-r_v)/slope_distance) *
-                 target_distance + r_v)
+            # This is a weird platform-specific workaround addressing
+            # https://github.com/natcap/invest/issues/1562
+            # On M1 macs, the all-in-one-line addition of _product and r_v
+            # would create small but noticeable numerical error.  Breaking the
+            # calculation onto two lines eliminates the numerical error.  This
+            # behavior is reproducible in C, outside of Cython on an M1 mac.
+            # So, this calculation would introduce error:
+            #   z = (((previous_height-r_v)/slope_distance) * target_distance) + r_v
+            # while the formlation below does not.
+            # For the script used for testing, see
+            #  https://gist.github.com/phargogh/c4264b37e7f0beed31661eacce53d14a
+            #
+            # Some of this may be related to the fact that x86 chips have
+            # extended precision for FPU-based calculations while M1 ARM chips
+            # do not.  Still, that doesn't explain why the error is introduced.
+            _product = (((previous_height-r_v)/slope_distance) * target_distance)
+            z = _product + r_v
 
             # add on refractivity/curvature-of-earth calculations.
             adjustment = 0.0  # increase in required height due to curvature

tests/test_coastal_blue_carbon.py

@@ -1034,3 +1034,28 @@ def test_track_later_disturbance(self):
                 expected_year_of_disturbance)
         finally:
             raster = None
+
+    def test_validate_required_analysis_year(self):
+        """CBC: analysis year validation (regression test for #1534)."""
+        from natcap.invest.coastal_blue_carbon import coastal_blue_carbon
+
+        args = TestCBC2._create_model_args(self.workspace_dir)
+        args['workspace_dir'] = self.workspace_dir
+        args['analysis_year'] = None
+        # truncate the CSV so that it has only one snapshot year
+        with open(args['landcover_snapshot_csv'], 'r') as file:
+            lines = file.readlines()
+        with open(args['landcover_snapshot_csv'], 'w') as file:
+            file.writelines(lines[:2])
+        validation_warnings = coastal_blue_carbon.validate(args)
+        self.assertEqual(
+            validation_warnings,
+            [(['analysis_year'], coastal_blue_carbon.MISSING_ANALYSIS_YEAR_MSG)])
+
+        args['analysis_year'] = 2000  # set analysis year equal to snapshot year
+        validation_warnings = coastal_blue_carbon.validate(args)
+        self.assertEqual(
+            validation_warnings,
+            [(['analysis_year'],
+                coastal_blue_carbon.INVALID_ANALYSIS_YEAR_MSG.format(
+                    analysis_year=2000, latest_year=2000))])

tests/test_ndr.py

@@ -380,7 +380,7 @@ def test_masking_invalid_geometry(self):
         # bowtie geometry is invalid; verify we can still create a mask.
         coordinates = []
         for pixel_x_offset, pixel_y_offset in [
-                (0, 0), (0, 1), (1, 0), (1, 1), (0, 0)]:
+                (0, 0), (0, 1), (1, 0.25), (1, 0.75), (0, 0)]:
             coordinates.append((
                 default_origin[0] + default_pixel_size[0] * pixel_x_offset,
                 default_origin[1] + default_pixel_size[1] * pixel_y_offset

tests/test_utils.py

@@ -1199,7 +1199,7 @@ def test_os_path_normalization_linux(self):
         relative_to = os.path.join(self.workspace_dir, 'test.csv')
         expected_path = os.path.join(self.workspace_dir, "foo/bar.shp")
         path = utils.expand_path(rel_path, relative_to)
-        self.assertEquals(path, expected_path)
+        self.assertEqual(path, expected_path)
 
     @unittest.skipIf(platform.system() != 'Windows',
                      "Function behavior differs across systems.")
@@ -1213,7 +1213,7 @@ def test_os_path_normalization_windows(self):
         relative_to = os.path.join(self.workspace_dir, 'test.csv')
         expected_path = os.path.join(self.workspace_dir, "foo\\bar.shp")
         path = utils.expand_path(rel_path, relative_to)
-        self.assertEquals(path, expected_path)
+        self.assertEqual(path, expected_path)
 
     def test_falsey(self):
         """Utils: test return None when falsey."""

workbench/tests/binary_tests/puppet.test.js

@@ -38,7 +38,7 @@ const TMP_AOI_PATH = path.join(TMP_DIR, 'aoi.geojson');
 
 if (process.platform === 'darwin') {
   // https://github.com/electron-userland/electron-builder/issues/2724#issuecomment-375850150
-  [BINARY_PATH] = glob.sync('./dist/mac/*.app/Contents/MacOS/InVEST*');
+  [BINARY_PATH] = glob.sync('./dist/mac*/*.app/Contents/MacOS/InVEST*');
   SCREENSHOT_PREFIX = path.join(
     os.homedir(), 'Library/Logs', pkg.name, 'invest-workbench-'
   );