Processing/processing tools basal contacts test

.github/workflows/tester.yml

@@ -2,16 +2,12 @@ name: "🎳 Tester"
 
 on:
   push:
-    branches:
-      - main
     paths:
       - '**.py'
       - .github/workflows/tester.yml
       - requirements/testing.txt
 
   pull_request:
-    branches:
-      - main
     paths:
       - '**.py'
       - .github/workflows/tester.yml
@@ -45,55 +41,62 @@ jobs:
       - name: Run Unit tests
         run: pytest -p no:qgis tests/unit/
 
-  # test-qgis:
-  #   runs-on: ubuntu-latest
-
-  #   container:
-  #     image: qgis/qgis:3.4
-  #     env:
-  #       CI: true
-  #       DISPLAY: ":1"
-  #       MUTE_LOGS: true
-  #       NO_MODALS: 1
-  #       PYTHONPATH: "/usr/share/qgis/python/plugins:/usr/share/qgis/python:."
-  #       QT_QPA_PLATFORM: "offscreen"
-  #       WITH_PYTHON_PEP: false
-  #     # be careful, things have changed since QGIS 3.40. So if you are using this setup 
-  #     #  with a QGIS version older than 3.40, you may need to change the way you set up the container
-  #     volumes:
-  #       # Mount the X11 socket to allow GUI applications to run
-  #       - /tmp/.X11-unix:/tmp/.X11-unix
-  #       # Mount the workspace directory to the container
-  #       - ${{ github.workspace }}:/home/root/
-
-  #   steps:
-  #     - name: Get source code
-  #       uses: actions/checkout@v4
-
-  #     - name: Print QGIS version
-  #       run: qgis --version
-
-  #     # Uncomment if you need to run a script to set up the plugin in QGIS docker image < 3.40
-  #     # - name: Setup plugin
-  #     #   run: qgis_setup.sh ${{ env.PROJECT_FOLDER }}
-
-  #     - name: Install Python requirements
-  #       run: |
-  #         apt update && apt install -y python3-pip python3-venv pipx
-  #         # Create a virtual environment
-  #         cd /home/root/
-  #         pipx run qgis-venv-creator --venv-name ".venv"
-  #         # Activate the virtual environment
-  #         . .venv/bin/activate
-  #         # Install the requirements
-  #         python3 -m pip install -U -r requirements/testing.txt
-
-  #     - name: Run Unit tests
-  #       run: |
-  #         cd /home/root/
-  #         # Activate the virtual environment
-  #         . .venv/bin/activate
-  #         # Run the tests
-  #         # xvfb-run is used to run the tests in a virtual framebuffer
-  #         # This is necessary because QGIS requires a display to run
-  #         xvfb-run python3 -m pytest tests/qgis --junitxml=junit/test-results-qgis.xml --cov-report=xml:coverage-reports/coverage-qgis.xml
+  test-qgis:
+    runs-on: ubuntu-latest
+
+    container:
+      image: qgis/qgis:latest
+      env:
+        CI: true
+        DISPLAY: ":1"
+        MUTE_LOGS: true
+        NO_MODALS: 1
+        PYTHONPATH: "/usr/share/qgis/python/plugins:/usr/share/qgis/python:."
+        QT_QPA_PLATFORM: "offscreen"
+        WITH_PYTHON_PEP: false
+      # be careful, things have changed since QGIS 3.40. So if you are using this setup 
+      #  with a QGIS version older than 3.40, you may need to change the way you set up the container
+      volumes:
+        # Mount the X11 socket to allow GUI applications to run
+        - /tmp/.X11-unix:/tmp/.X11-unix
+        # Mount the workspace directory to the container
+        - ${{ github.workspace }}:/home/root/
+
+    steps:
+      - name: Get source code
+        uses: actions/checkout@v4
+
+      - name: Print QGIS version
+        run: qgis --version
+
+      # Uncomment if you need to run a script to set up the plugin in QGIS docker image < 3.40
+      # - name: Setup plugin
+      #   run: qgis_setup.sh ${{ env.PROJECT_FOLDER }}
+
+      - name: Install Python requirements
+        run: |
+          apt update && apt install -y python3-pip python3-venv pipx
+          # Create a virtual environment
+          cd /home/root/
+          pipx run qgis-venv-creator --venv-name ".venv"
+          # Activate the virtual environment
+          . .venv/bin/activate
+          # Install the requirements
+          python3 -m pip install -U -r requirements/testing.txt
+          python3 -m pip install git+https://github.com/Loop3D/map2loop.git@noelle/contact_extractor
+
+      - name: verify input data
+        run: |
+          cd /home/root/
+          . .venv/bin/activate
+          ls -la tests/qgis/input/ || echo "Input directory not found"
+
+      - name: Run Unit tests
+        run: |
+          cd /home/root/
+          # Activate the virtual environment
+          . .venv/bin/activate
+          # Run the tests
+          # xvfb-run is used to run the tests in a virtual framebuffer
+          # This is necessary because QGIS requires a display to run
+          xvfb-run python3 -m pytest tests/qgis --junitxml=junit/test-results-qgis.xml --cov-report=xml:coverage-reports/coverage-qgis.xml

m2l/processing/algorithms/extract_basal_contacts.py

@@ -78,6 +78,17 @@ def initAlgorithm(self, config: Optional[dict[str, Any]] = None) -> None:
             )
         )
 
+        self.addParameter(
+            QgsProcessingParameterField(
+                'FORMATION_FIELD',
+                'Formation Field',
+                parentLayerParameterName=self.INPUT_GEOLOGY,
+                type=QgsProcessingParameterField.String,
+                defaultValue='formation',
+                optional=True
+            )
+        )
+
         self.addParameter(
             QgsProcessingParameterFeatureSource(
                 self.INPUT_FAULTS,
@@ -127,7 +138,14 @@ def processAlgorithm(
         geology = self.parameterAsVectorLayer(parameters, self.INPUT_GEOLOGY, context)
         faults = self.parameterAsVectorLayer(parameters, self.INPUT_FAULTS, context)
         strati_column = self.parameterAsMatrix(parameters, self.INPUT_STRATI_COLUMN, context)
-        ignore_units = self.parameterAsMatrix(parameters, self.INPUT_IGNORE_UNITS, context) 
+        ignore_units = self.parameterAsMatrix(parameters, self.INPUT_IGNORE_UNITS, context)
+
+        if not strati_column or all(isinstance(unit, str) and not unit.strip() for unit in strati_column):
+            raise QgsProcessingException("no stratigraphic column found")
+
+        if not ignore_units or all(isinstance(unit, str) and not unit.strip() for unit in ignore_units):
+            feedback.pushInfo("no units to ignore specified")
+
         # if strati_column and strati_column.strip():
         #     strati_column = [unit.strip() for unit in strati_column.split(',')]
         # Save stratigraphic column settings
@@ -138,10 +156,15 @@ def processAlgorithm(
         ignore_settings.setValue("m2l/ignore_units", ignore_units)
 
         unit_name_field = self.parameterAsString(parameters, 'UNIT_NAME_FIELD', context)
+        formation_field = self.parameterAsString(parameters, 'FORMATION_FIELD', context)
 
         geology = qgsLayerToGeoDataFrame(geology)
-        mask = ~geology['Formation'].astype(str).str.strip().isin(ignore_units)
-        geology = geology[mask].reset_index(drop=True)
+        if formation_field and formation_field in geology.columns:
+            mask = ~geology[formation_field].astype(str).str.strip().isin(ignore_units)
+            geology = geology[mask].reset_index(drop=True)
+            feedback.pushInfo(f"filtered by formation field: {formation_field}")
+        else:
+            feedback.pushInfo(f"no formation field found: {formation_field}")
 
         faults = qgsLayerToGeoDataFrame(faults) if faults else None
         if unit_name_field != 'UNITNAME' and unit_name_field in geology.columns:
@@ -154,7 +177,7 @@ def processAlgorithm(
         feedback.pushInfo("Exporting Basal Contacts Layer...")
         basal_contacts = GeoDataFrameToQgsLayer(
             self, 
-            contact_extractor.basal_contacts,
+            basal_contacts,
             parameters=parameters,
             context=context,
             output_key=self.OUTPUT,

m2l/processing/algorithms/sorter.py

@@ -92,7 +92,7 @@ def initAlgorithm(self, config: Optional[dict[str, Any]] = None) -> None:
         self.addParameter(
             QgsProcessingParameterFeatureSink(
                 self.OUTPUT,
-                self.tr("Stratigraphic column"),
+                "Stratigraphic column",
             )
         )
 
@@ -177,7 +177,7 @@ def build_input_frames(layer: QgsVectorLayer, feedback) -> tuple:
     (units_df, relationships_df, contacts_df, map_data)
     """
     import pandas as pd
-    from m2l.map2loop.mapdata import MapData  # adjust import path if needed
+    from map2loop.map2loop.mapdata import MapData  # adjust import path if needed
 
     # Example: convert the geology layer to a very small units_df
     units_records = []

tests/qgis/input/faults_clip.cpg

@@ -0,0 +1 @@
+ISO-8859-1

tests/qgis/input/faults_clip.prj

@@ -0,0 +1 @@
+PROJCS["GDA94_MGA_zone_50",GEOGCS["GCS_GDA94",DATUM["D_Geocentric_Datum_of_Australia_1994",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",10000000.0],PARAMETER["Central_Meridian",117.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]

tests/qgis/input/folds_clip.cpg

@@ -0,0 +1 @@
+ISO-8859-1

tests/qgis/input/folds_clip.prj

@@ -0,0 +1 @@
+PROJCS["GDA94_MGA_zone_50",GEOGCS["GCS_GDA94",DATUM["D_Geocentric_Datum_of_Australia_1994",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",10000000.0],PARAMETER["Central_Meridian",117.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]

tests/qgis/input/geol_clip_no_gaps.cpg

@@ -0,0 +1 @@
+ISO-8859-1

tests/qgis/input/geol_clip_no_gaps.prj

@@ -0,0 +1 @@
+PROJCS["GDA94_MGA_zone_50",GEOGCS["GCS_GDA94",DATUM["D_Geocentric_Datum_of_Australia_1994",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",10000000.0],PARAMETER["Central_Meridian",117.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]

tests/qgis/input/structure_clip.cpg

@@ -0,0 +1 @@
+ISO-8859-1

tests/qgis/input/structure_clip.prj

@@ -0,0 +1 @@
+PROJCS["GDA94_MGA_zone_50",GEOGCS["GCS_GDA94",DATUM["D_Geocentric_Datum_of_Australia_1994",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",10000000.0],PARAMETER["Central_Meridian",117.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]

tests/qgis/test_basal_contacts.py

@@ -0,0 +1,116 @@
+import unittest
+from pathlib import Path
+from qgis.core import QgsVectorLayer, QgsProcessingContext, QgsProcessingFeedback, QgsMessageLog, Qgis, QgsApplication
+from qgis.testing import start_app
+from m2l.processing.algorithms.extract_basal_contacts import BasalContactsAlgorithm
+from m2l.processing.provider import Map2LoopProvider
+
+class TestBasalContacts(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        cls.qgs = start_app()
+
+        cls.provider = Map2LoopProvider()
+        QgsApplication.processingRegistry().addProvider(cls.provider)
+
+    def setUp(self):
+        self.test_dir = Path(__file__).parent
+        self.input_dir = self.test_dir / "input"
+
+        self.geology_file = self.input_dir / "geol_clip_no_gaps.shp"
+        self.faults_file = self.input_dir / "faults_clip.shp"
+
+        self.assertTrue(self.geology_file.exists(), f"geology not found: {self.geology_file}")
+
+        if not self.faults_file.exists():
+            QgsMessageLog.logMessage(f"faults not found: {self.faults_file}, will run test without faults", "TestBasalContacts", Qgis.Warning)
+
+    def test_basal_contacts_extraction(self):
+
+        geology_layer = QgsVectorLayer(str(self.geology_file), "geology", "ogr")
+
+        self.assertTrue(geology_layer.isValid(), "geology layer should be valid")
+        self.assertGreater(geology_layer.featureCount(), 0, "geology layer should have features")
+
+        faults_layer = None
+        if self.faults_file.exists():
+            faults_layer = QgsVectorLayer(str(self.faults_file), "faults", "ogr")
+            self.assertTrue(faults_layer.isValid(), "faults layer should be valid")
+            self.assertGreater(faults_layer.featureCount(), 0, "faults layer should have features")
+            QgsMessageLog.logMessage(f"faults layer: {faults_layer.featureCount()} features", "TestBasalContacts", Qgis.Critical)
+
+        QgsMessageLog.logMessage(f"geology layer: {geology_layer.featureCount()} features", "TestBasalContacts", Qgis.Critical)
+
+        strati_column = [
+            "Turee Creek Group",
+            "Boolgeeda Iron Formation",
+            "Woongarra Rhyolite",
+            "Weeli Wolli Formation",
+            "Brockman Iron Formation",
+            "Mount McRae Shale and Mount Sylvia Formation",
+            "Wittenoom Formation",
+            "Marra Mamba Iron Formation",
+            "Jeerinah Formation",
+            "Bunjinah Formation",
+            "Pyradie Formation",
+            "Fortescue Group",
+            "Hardey Formation",
+            "Boongal Formation",
+            "Mount Roe Basalt",
+            "Rocklea Inlier greenstones",
+            "Rocklea Inlier metagranitic unit"
+        ]
+
+        algorithm = BasalContactsAlgorithm()
+        algorithm.initAlgorithm()
+
+        parameters = {
+            'GEOLOGY': geology_layer,
+            'UNIT_NAME_FIELD': 'unitname',
+            'FORMATION_FIELD': 'formation',
+            'FAULTS': faults_layer,
+            'STRATIGRAPHIC_COLUMN': strati_column,
+            'IGNORE_UNITS': [],
+            'BASAL_CONTACTS': 'memory:basal_contacts'
+        }
+
+        context = QgsProcessingContext()
+        feedback = QgsProcessingFeedback()
+
+        try:
+            QgsMessageLog.logMessage("Starting basal contacts algorithm...", "TestBasalContacts", Qgis.Critical)
+
+            result = algorithm.processAlgorithm(parameters, context, feedback)
+
+            QgsMessageLog.logMessage(f"Result: {result}", "TestBasalContacts", Qgis.Critical)
+
+            self.assertIsNotNone(result, "result should not be None")
+            self.assertIn('BASAL_CONTACTS', result, "Result should contain BASAL_CONTACTS key")
+
+            basal_contacts_layer = context.takeResultLayer(result['BASAL_CONTACTS'])
+            self.assertIsNotNone(basal_contacts_layer, "basal contacts layer should not be None")
+            self.assertTrue(basal_contacts_layer.isValid(), "basal contacts layer should be valid")
+            self.assertGreater(basal_contacts_layer.featureCount(), 0, "basal contacts layer should have features")
+
+            QgsMessageLog.logMessage(f"Generated {basal_contacts_layer.featureCount()} basal contacts", 
+                                     "TestBasalContacts", Qgis.Critical)
+
+            QgsMessageLog.logMessage("Basal contacts test completed successfully!", "TestBasalContacts", Qgis.Critical)
+
+        except Exception as e:
+            QgsMessageLog.logMessage(f"Basal contacts test error: {str(e)}", "TestBasalContacts", Qgis.Critical)
+            QgsMessageLog.logMessage(f"Error type: {type(e).__name__}", "TestBasalContacts", Qgis.Critical)
+            import traceback
+            QgsMessageLog.logMessage(f"Full traceback:\n{traceback.format_exc()}", "TestBasalContacts", Qgis.Critical)
+            raise
+
+        finally:
+            QgsMessageLog.logMessage("=" * 50, "TestBasalContacts", Qgis.Critical)
+
+    @classmethod
+    def tearDownClass(cls):
+        QgsApplication.processingRegistry().removeProvider(cls.provider)
+
+if __name__ == '__main__':
+    unittest.main()