Geopackage support (#357)

Update modelchecker to work with schema 220

.github/workflows/test.yml

@@ -17,16 +17,19 @@ jobs:
         include:
           # 2019
           - python: 3.8
-            pins: "sqlalchemy==1.4.0 alembic==1.8.* geoalchemy2==0.9.* rasterio==1.3.0"
+            pins: "sqlalchemy==1.4.44 alembic==1.8.* geoalchemy2==0.14.* rasterio==1.3.0"
           # 2021
           - python: 3.9
-            pins: "sqlalchemy==1.4.30 alembic==1.8.* geoalchemy2==0.10.* rasterio==1.3.3"
+            pins: "sqlalchemy==1.4.44 alembic==1.8.* geoalchemy2==0.14.* rasterio==1.3.3"
           # 2022
           - python: "3.10"
-            pins: "sqlalchemy==1.4.44 alembic==1.8.* geoalchemy2==0.12.* rasterio==1.3.5.post1"
-          # current
+            pins: "sqlalchemy==1.4.44 alembic==1.8.* geoalchemy2==0.14.* rasterio==1.3.5.post1"
+          # 2023
           - python: "3.11"
-            pins: ""
+            pins: "sqlalchemy==2.0.24 alembic==1.13.1 geoalchemy2==0.14.3 rasterio==1.3.9"
+          # current
+          - python: "3.12"
+            #pins: "sqlalchemy==2.0.* alembic==1.13.* geoalchemy2==0.14.* rasterio==1.3.9.*"
 
     steps:
       - uses: actions/checkout@v3

CHANGES.rst

@@ -4,8 +4,8 @@ Changelog of threedi-modelchecker
 
 2.6.3 (unreleased)
 ------------------
-
-- Nothing changed yet.
+- Support geopackage
+- Support changes in threedi-schema (0.220) needed for geopackage support
 
 
 2.6.2 (2024-02-29)

pyproject.toml

@@ -19,7 +19,7 @@ dependencies = [
     "Click",
     "GeoAlchemy2>=0.9,!=0.11.*",
     "SQLAlchemy>=1.4",
-    "threedi-schema==0.219.*",
+    "threedi-schema==0.220.*"
 ]
 
 [project.optional-dependencies]

requirements.txt

@@ -1,5 +1,5 @@
 Click
-GeoAlchemy2>=0.9,!=0.11.*
-SQLAlchemy>=1.2
+GeoAlchemy2>=0.14
+SQLAlchemy>=1.4.44
 Click==7.0
-alembic>=0.9
+alembic>=1.8

threedi_modelchecker/checks/base.py

@@ -221,7 +221,9 @@ def __init__(self, *args, **kwargs):
         self.expected_types = _sqlalchemy_to_sqlite_types(self.column.type)
 
     def get_invalid(self, session):
-        if "sqlite" not in session.bind.dialect.dialect_description:
+        if ("sqlite" not in session.bind.dialect.dialect_description) and (
+            "geopackage" not in session.bind.dialect.dialect_description
+        ):
             return []
         q_invalid = self.to_check(session)
         invalid_type_query = q_invalid.filter(
@@ -311,7 +313,7 @@ def description(self):
 def _get_geometry_type(column, dialect):
     if column.type.geometry_type == "GEOMETRY":
         return  # should skip the check
-    if dialect == "sqlite":
+    if dialect in ["sqlite", "geopackage"]:
         return column.type.geometry_type
     elif dialect == "postgresql":
         geom_type = column.type.geometry_type.capitalize()

threedi_modelchecker/config.py

@@ -877,16 +877,6 @@ def is_none_or_empty(col):
     LinestringLocationCheck(error_code=205, column=table.the_geom, max_distance=1)
     for table in [models.Channel, models.Culvert]
 ]
-CHECKS += [
-    QueryCheck(
-        error_code=206,
-        column=models.ConnectionNode.the_geom_linestring,
-        invalid=Query(models.ConnectionNode).filter(
-            models.ConnectionNode.the_geom_linestring != None
-        ),
-        message=f"{models.ConnectionNode.the_geom_linestring} must be NULL",
-    )
-]
 CHECKS += [
     SpatialIndexCheck(
         error_code=207, column=models.ConnectionNode.the_geom, level=CheckLevel.WARNING

threedi_modelchecker/tests/conftest.py

@@ -20,8 +20,8 @@ def threedi_db(tmpdir_factory):
     https://factoryboy.readthedocs.io/en/latest/orms.html#managing-sessions
     """
     tmp_path = tmpdir_factory.mktemp("spatialite4")
-    tmp_sqlite = tmp_path / "empty_v4.sqlite"
-    shutil.copyfile(data_dir / "empty_v4.sqlite", tmp_sqlite)
+    tmp_sqlite = tmp_path / "empty.gpkg"
+    shutil.copyfile(data_dir / "empty.gpkg", tmp_sqlite)
     db = ThreediDatabase(tmp_sqlite)
     schema = ModelSchema(db)
     schema.upgrade(backup=False, upgrade_spatialite_version=False)
@@ -52,7 +52,7 @@ def session(threedi_db):
 
 @pytest.fixture
 def empty_sqlite_v4(tmp_path):
-    """An function-scoped empty spatialite v4 in the latest migration state"""
-    tmp_sqlite = tmp_path / "empty_v4.sqlite"
-    shutil.copyfile(data_dir / "empty_v4.sqlite", tmp_sqlite)
+    """An function-scoped empty geopackage v4 in the latest migration state"""
+    tmp_sqlite = tmp_path / "empty.gpkg"
+    shutil.copyfile(data_dir / "empty.gpkg", tmp_sqlite)
     return ThreediDatabase(tmp_sqlite)

threedi_modelchecker/tests/test_checks_factories.py

@@ -36,7 +36,7 @@ def test_gen_not_null_checks():
 def test_gen_geometry_check():
     geometry_checks = generate_geometry_checks(models.ConnectionNode.__table__)
 
-    assert len(geometry_checks) == 2
+    assert len(geometry_checks) == 1
     geometry_check_columns = [check.column for check in geometry_checks]
     assert models.ConnectionNode.the_geom in geometry_check_columns