Merge pull request #592 from jGaboardi/sql_geomet_issue

MAINT: dealing with `sqlalchemy` & `geomet`

ci/310-oldest.yaml

@@ -27,6 +27,7 @@ dependencies:
   - numba=0.55
   - pyarrow>=7.0
   - scikit-learn=1.1
+  - sqlalchemy=2.0
   - zstd
   - pip
   - pip:

ci/310.yaml

@@ -27,4 +27,5 @@ dependencies:
   - numba
   - pyarrow
   - scikit-learn
+  - sqlalchemy
   - zstd

ci/311.yaml

@@ -20,11 +20,12 @@ dependencies:
   - pytest-cov
   - pytest-mpl
   - pytest-xdist
-  # optional
+    # optional
   - geodatasets
   - joblib
   - networkx
   - numba
   - pyarrow
   - scikit-learn
+  - sqlalchemy
   - zstd

ci/312-dev.yaml

@@ -25,6 +25,7 @@ dependencies:
   - packaging
   - pyarrow
   - pyproj
+  - sqlalchemy
   - zstd
   - pip
   - pip:

ci/312.yaml

@@ -27,6 +27,7 @@ dependencies:
   # - numba # follow up when numba is ready for 3.12
   - pyarrow
   - scikit-learn
+  - sqlalchemy
   - zstd
   # for docs build action (this env only)
   - mkdocs-jupyter

libpysal/io/iohandlers/__init__.py

@@ -22,4 +22,4 @@
 try:
     from . import db
 except:
-    warnings.warn("SQLAlchemy and Geomet not installed, database I/O disabled")
+    warnings.warn("SQLAlchemy not installed, database I/O disabled")

libpysal/io/iohandlers/db.py

@@ -1,17 +1,8 @@
 from .. import fileio
+from shapely import wkb
 
 errmsg = ""
 
-try:
-    try:
-        from geomet import wkb
-    except ImportError:
-        from shapely import wkb
-except ImportError:
-    wkb = None
-    errmsg += "No WKB parser found. Please install one of the following packages "
-    errmsg += "to enable this functionality: [geomet, shapely].\n"
-
 try:
     from sqlalchemy.ext.automap import automap_base
     from sqlalchemy import create_engine
@@ -20,13 +11,14 @@
     nosql_mode = False
 except ImportError:
     nosql_mode = True
-    errmsg += "No module named sqlalchemy. Please install"
-    errmsg += " sqlalchemy to enable this functionality."
+    errmsg += (
+        "No module named sqlalchemy. Please install"
+        " sqlalchemy to enable this functionality."
+    )
 
 
 class SQLConnection(fileio.FileIO):
-    """Reads an SQL mappable.
-    """
+    """Reads an SQL mappable."""
 
     FORMATS = ["sqlite", "db"]
     MODES = ["r"]
@@ -41,7 +33,7 @@ def __init__(self, *args, **kwargs):
         self.dbname = args[0]
         self.Base = automap_base()
         self._engine = create_engine(self.dbname)
-        self.Base.prepare(self._engine, reflect=True)
+        self.Base.prepare(autoload_with=self._engine)
         self.metadata = self.Base.metadata
 
     def read(self, *args, **kwargs):
@@ -58,11 +50,9 @@ def close(self):
         fileio.FileIO.close(self)
 
     def _get_gjson(self, tablename: str, geom_column="GEOMETRY"):
-
         gjson = {"type": "FeatureCollection", "features": []}
 
         for row in self.session.query(self.metadata.tables[tablename]):
-
             feat = {"type": "Feature", "geometry": {}, "properties": {}}
             feat["GEOMETRY"] = wkb.loads(getattr(row, geom_column))
 
@@ -76,7 +66,6 @@ def _get_gjson(self, tablename: str, geom_column="GEOMETRY"):
 
     @property
     def tables(self) -> list:
-
         if not hasattr(self, "_tables"):
             self._tables = list(self.metadata.tables.keys())
 
@@ -85,12 +74,12 @@ def tables(self) -> list:
     @property
     def session(self):
         """Create an ``sqlalchemy.orm.Session`` instance.
-        
+
         Returns
         -------
         self._session : sqlalchemy.orm.Session
             An ``sqlalchemy.orm.Session`` instance.
-            
+
         """
 
         # What happens if the session is externally closed?  Check for None?

libpysal/io/iohandlers/tests/test_db.py

@@ -4,50 +4,38 @@
 import unittest as ut
 from .... import examples as pysal_examples
 
+import platform
+import shapely
+
 try:
     import sqlalchemy
 
     missing_sql = False
 except ImportError:
     missing_sql = True
 
-try:
-    import geomet
-
-    missing_geomet = False
-except ImportError:
-    missing_geomet = True
-
-
-def to_wkb_point(c):
-    """Super quick hack that does not actually belong in here."""
 
-    point = {"type": "Point", "coordinates": [c[0], c[1]]}
+windows = platform.system() == "Windows"
 
-    return geomet.wkb.dumps(point)
 
-
-@ut.skipIf(
-    missing_sql or missing_geomet,
-    "Missing dependencies: Geomet ({}) & SQLAlchemy ({}).".format(
-        missing_geomet, missing_sql
-    ),
-)
+@ut.skipIf(windows, "Skipping Windows due to `PermissionError`.")
+@ut.skipIf(missing_sql, f"Missing dependency: SQLAlchemy ({missing_sql}).")
 class Test_sqlite_reader(ut.TestCase):
     def setUp(self):
         path = pysal_examples.get_path("new_haven_merged.dbf")
         if path is None:
             pysal_examples.load_example("newHaven")
             path = pysal_examples.get_path("new_haven_merged.dbf")
         df = pdio.read_files(path)
-        df["GEOMETRY"] = df["geometry"].apply(to_wkb_point)
+        df["GEOMETRY"] = shapely.to_wkb(shapely.points(df["geometry"].values.tolist()))
         # This is a hack to not have to worry about a custom point type in the DB
         del df["geometry"]
-        engine = sqlalchemy.create_engine("sqlite:///test.db")
-        conn = engine.connect()
+        self.dbf = "iohandlers_test_db.db"
+        engine = sqlalchemy.create_engine(f"sqlite:///{self.dbf}")
+        self.conn = engine.connect()
         df.to_sql(
             "newhaven",
-            conn,
+            self.conn,
             index=True,
             dtype={
                 "date": sqlalchemy.types.UnicodeText,  # Should convert the df date into a true date object, just a hack again
@@ -60,14 +48,15 @@ def setUp(self):
         )  # This is converted to TEXT as lowest type common sqlite
 
     def test_deserialize(self):
-        db = psopen("sqlite:///test.db")
+        db = psopen(f"sqlite:///{self.dbf}")
         self.assertEqual(db.tables, ["newhaven"])
 
         gj = db._get_gjson("newhaven")
         self.assertEqual(gj["type"], "FeatureCollection")
 
-    def tearDown(self):
-        os.remove("test.db")
+        self.conn.close()
+
+        os.remove(self.dbf)
 
 
 if __name__ == "__main__":

libpysal/weights/tests/test_user.py

@@ -17,6 +17,7 @@ def test_build_lattice_shapefile(self):
         user.build_lattice_shapefile(20, 20, of)
         w = Rook.from_shapefile(of)
         self.assertEqual(w.n, 400)
+        os.remove("lattice.dbf")
         os.remove("lattice.shp")
         os.remove("lattice.shx")
 

pyproject.toml

@@ -48,6 +48,7 @@ plus = [
     "numba>=0.55",
     "pyarrow>=7.0",
     "scikit-learn>=1.1",
+    "sqlalchemy>=2.0",
     "zstd",
 ]
 dev = [