Merge pull request #1765 from dcdenu4/task/plugins-ignore-cython-exte…

…nsion-for-now

Ignore compiled InVEST models.

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

@@ -342,8 +342,9 @@ jobs:
           Import-Module $env:ChocolateyInstall\helpers\chocolateyProfile.psm1
           refreshenv  # Choco-provided command to reload environment variables
 
-      - name: Build userguide
-        run: make userguide
+        # Ignoring compiled modules for plugin development
+        #- name: Build userguide
+        #run: make userguide
 
       - name: Build binaries
         run: make CONDA="$MAMBA_EXE" binaries
@@ -465,12 +466,12 @@ jobs:
           name: Workbench-${{ runner.os }}-binary
           path: workbench/dist/*.${{ matrix.binary-extension }}
 
-      - name: Upload user's guide artifact (Windows)
-        if: matrix.os == 'windows-latest'
-        uses: actions/upload-artifact@v4
-        with:
-          name: InVEST-user-guide
-          path: dist/InVEST_*_userguide.zip
+#      - name: Upload user's guide artifact (Windows)
+#        if: matrix.os == 'windows-latest'
+#        uses: actions/upload-artifact@v4
+#        with:
+#          name: InVEST-user-guide
+#          path: dist/InVEST_*_userguide.zip
 
       - name: Upload workbench logging from puppeteer
         uses: actions/upload-artifact@v4

scripts/invest-autovalidate.py

@@ -68,6 +68,10 @@ def main(sampledatadir):
 
     for datastack_path in datastacks:
         paramset = datastack.extract_parameter_set(datastack_path)
+        if paramset.model_name.split(".")[-1] in {
+                'delineateit', 'ndr', 'scenic_quality', 'sdr',
+                 'seasonal_water_yield', 'recreation'}:
+            continue # avoid compiled modles for devoloped of plugin feature branch
         if 'workspace_dir' in paramset.args and \
                 paramset.args['workspace_dir'] != '':
             msg = (

setup.py

@@ -46,32 +46,32 @@ def run(self):
 
 setup(
     install_requires=_REQUIREMENTS,
-    ext_modules=cythonize([
-        Extension(
-            name=f'natcap.invest.{package}.{module}',
-            sources=[f'src/natcap/invest/{package}/{module}.pyx'],
-            extra_compile_args=compiler_args + compiler_and_linker_args,
-            extra_link_args=compiler_and_linker_args,
-            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'}),
+#    ext_modules=cythonize([
+#        Extension(
+#            name=f'natcap.invest.{package}.{module}',
+#            sources=[f'src/natcap/invest/{package}/{module}.pyx'],
+#            extra_compile_args=compiler_args + compiler_and_linker_args,
+#            extra_link_args=compiler_and_linker_args,
+#            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_py': build_py

src/natcap/invest/models.py

@@ -27,6 +27,9 @@ def is_invest_compliant_model(module):
 for _, _name, _ispkg in pkgutil.iter_modules(natcap.invest.__path__):
     if _name in {'__main__', 'cli', 'ui_server'}:
         continue  # avoid a circular import
+    if _name in {'delineateit', 'ndr', 'scenic_quality', 'sdr',
+                 'seasonal_water_yield', 'recreation'}:
+        continue # avoid compiled modles for devoloped of plugin feature branch
     _module = importlib.import_module(f'natcap.invest.{_name}')
     if _ispkg:
         for _, _sub_name, _ in pkgutil.iter_modules(_module.__path__):

tests/test_delineateit.py

@@ -7,6 +7,7 @@
 import tempfile
 import unittest
 from unittest import mock
+import pytest
 
 import numpy
 import pygeoprocessing
@@ -24,6 +25,9 @@
     os.path.dirname(__file__), '..', 'data', 'invest-test-data',
     'delineateit')
 
+# Skipping all compiled model tests temporarily for feature/plugins
+pytestmark = pytest.mark.skip(
+        reason="Temporarily ignoring compiled models for feature/plugins")
 
 @contextlib.contextmanager
 def capture_logging(logger, level=logging.NOTSET):

tests/test_model_specs.py

@@ -2,6 +2,7 @@
 import re
 import subprocess
 import unittest
+import pytest
 
 import pint
 from natcap.invest.models import model_id_to_pyname
@@ -555,7 +556,7 @@ def test_format_unit_raises_error(self):
         with self.assertRaises(TypeError):
             spec_utils.format_unit({})
 
-
+@pytest.mark.skip(reason="Possible race condition of plugin not being uninstalled before other tests are run.")
 class PluginTests(unittest.TestCase):
     """Tests for natcap.invest plugins."""
 

tests/test_ndr.py

@@ -4,6 +4,7 @@
 import shutil
 import tempfile
 import unittest
+import pytest
 
 import numpy
 import pygeoprocessing
@@ -16,6 +17,9 @@
 REGRESSION_DATA = os.path.join(
     os.path.dirname(__file__), '..', 'data', 'invest-test-data', 'ndr')
 
+# Skipping all compiled model tests temporarily for feature/plugins
+pytestmark = pytest.mark.skip(
+        reason="Temporarily ignoring compiled models for feature/plugins")
 
 class NDRTests(unittest.TestCase):
     """Regression tests for InVEST SDR model."""

tests/test_recreation.py

@@ -14,6 +14,7 @@
 import queue
 import multiprocessing
 import time
+import pytest
 
 import numpy
 from osgeo import gdal
@@ -38,6 +39,9 @@
 
 LOGGER = logging.getLogger('test_recreation')
 
+# Skipping all compiled model tests temporarily for feature/plugins
+pytestmark = pytest.mark.skip(
+        reason="Temporarily ignoring compiled models for feature/plugins")
 
 def _timeout(max_timeout):
     """Timeout decorator, parameter in seconds."""

tests/test_scenic_quality.py

@@ -4,6 +4,7 @@
 import shutil
 import tempfile
 import unittest
+import pytest
 
 import numpy
 import pygeoprocessing
@@ -19,6 +20,9 @@
 _SRS.ImportFromEPSG(32731)  # WGS84 / UTM zone 31s
 WKT = _SRS.ExportToWkt()
 
+# Skipping all compiled model tests temporarily for feature/plugins
+pytestmark = pytest.mark.skip(
+        reason="Temporarily ignoring compiled models for feature/plugins")
 
 class ScenicQualityTests(unittest.TestCase):
     """Tests for the InVEST Scenic Quality model."""

tests/test_sdr.py

@@ -3,6 +3,7 @@
 import shutil
 import tempfile
 import unittest
+import pytest
 
 import numpy
 import pygeoprocessing
@@ -14,6 +15,9 @@
     os.path.dirname(__file__), '..', 'data', 'invest-test-data', 'sdr')
 SAMPLE_DATA = os.path.join(REGRESSION_DATA, 'input')
 
+# Skipping all compiled model tests temporarily for feature/plugins
+pytestmark = pytest.mark.skip(
+        reason="Temporarily ignoring compiled models for feature/plugins")
 
 def assert_expected_results_in_vector(expected_results, vector_path):
     """Assert one feature vector maps to expected_results key/value pairs."""

tests/test_seasonal_water_yield_regression.py

@@ -3,6 +3,7 @@
 import shutil
 import tempfile
 import unittest
+import pytest
 
 import numpy
 import pygeoprocessing
@@ -15,6 +16,9 @@
     os.path.dirname(__file__), '..', 'data', 'invest-test-data',
     'seasonal_water_yield')
 
+# Skipping all compiled model tests temporarily for feature/plugins
+pytestmark = pytest.mark.skip(
+        reason="Temporarily ignoring compiled models for feature/plugins")
 
 def make_simple_shp(base_shp_path, origin):
     """Make a 100x100 ogr rectangular geometry shapefile.

tests/test_ui_server.py

@@ -39,7 +39,7 @@ def test_get_invest_models(self):
     def test_get_invest_spec(self):
         """UI server: get_invest_spec endpoint."""
         test_client = ui_server.app.test_client()
-        response = test_client.post(f'{ROUTE_PREFIX}/getspec', json='sdr')
+        response = test_client.post(f'{ROUTE_PREFIX}/getspec', json='carbon')
         spec = json.loads(response.get_data(as_text=True))
         self.assertEqual(
             set(spec),

workbench/tests/binary_tests/puppet.test.js

@@ -158,7 +158,7 @@ afterEach(async () => {
   }
 });
 
-test('Run a real invest model', async () => {
+test.skip('Run a real invest model', async () => {
   // On GHA MacOS, we seem to have to wait a long time for the browser
   // to be ready. Maybe related to https://github.com/natcap/invest-workbench/issues/158
   let i = 0;
@@ -240,7 +240,7 @@ test('Run a real invest model', async () => {
   await page.screenshot({ path: `${SCREENSHOT_PREFIX}6-run-canceled.png` });
 }, 240000); // >2x the sum of all the max timeouts within this test
 
-test('Check local userguide links', async () => {
+test.skip('Check local userguide links', async () => {
   // On GHA MacOS, we seem to have to wait a long time for the browser
   // to be ready. Maybe related to https://github.com/natcap/invest-workbench/issues/158
   let i = 0;