require Python 3.10 and associated ruff updates (#39)

This is a bit of a mixed bag of changes similar to which we merged in
https://github.com/Deltares/Ribasim last weeks.

First of all we now require at least Python 3.10. Before this was 3.9.
The differences are not too big, but I don't think we need to spend out
time supporting old Python versions at this moment, 3.10 is sufficiently
old.

Since we now tell ruff to target Python 3.10, and ask it to give syntax
upgrade suggestions, we fix those. Most of this is nicer typing
annotations, using e.g. `dict` instead of `from typing import Dict`. The
ruff updates also includes some configuration to make it work well with
notebooks.

Lastly I removed the typos check. I don't think it is suitable for this
repository as there are many Dutch terms used in the code and docs.

.gitignore

@@ -1,9 +1,6 @@
 # pixi environments
 .pixi
 
-# visual studio code
-.vscode/settings.json
-
 .ipynb_checkpoints
 # Byte-compiled / optimized / DLL files
 __pycache__/

.pre-commit-config.yaml

@@ -25,7 +25,3 @@ repos:
     rev: 0.6.1
     hooks:
       - id: nbstripout
-  - repo: https://github.com/crate-ci/typos
-    rev: v1.16.21
-    hooks:
-      - id: typos

.vscode/extensions.json

@@ -3,6 +3,7 @@
         "ms-python.python",
         "ms-python.mypy-type-checker",
         "charliermarsh.ruff",
-        "njpwerner.autodocstring"
+        "njpwerner.autodocstring",
+        "quarto.quarto"
     ]
 }

.vscode/settings_template.json → .vscode/settings.json

@@ -1,5 +1,9 @@
 {
     "notebook.formatOnSave.enabled": true,
+    "notebook.codeActionsOnSave": {
+        "source.fixAll.ruff": true,
+        "source.organizeImports.ruff": true
+    },
     "[python]": {
         "editor.defaultFormatter": "charliermarsh.ruff",
         "editor.formatOnSave": true,

environment.yml

@@ -15,15 +15,14 @@ dependencies:
   - pandas
   - pandas-stubs
   - pip
-  - pip:
-    - quartodoc
   - pre-commit
   - pyarrow
   - pydantic=1
   - pyogrio
   - pytest
   - pytest-cov
   - python>=3.9
+  - quartodoc
   - rasterstats
   - ruff
   - shapely>=2.0

ruff.toml

@@ -1,6 +1,9 @@
-select = ["D", "E", "F", "NPY", "PD", "C4", "I"]
+# See https://docs.astral.sh/ruff/rules/
+select = ["D", "E", "F", "NPY", "PD", "C4", "I", "UP"]
 ignore = ["D1", "D202", "D205", "D400", "D404", "E501", "PD002", "PD901"]
 fixable = ["I"]
+extend-include = ["*.ipynb"]
+target-version = "py310"
 
 [pydocstyle]
 convention = "numpy"

src/hydamo/hydamo/datamodel.py

@@ -5,7 +5,7 @@
 import re
 import warnings
 from pathlib import Path
-from typing import Any, Dict, List, Literal, Optional
+from typing import Any, Literal
 
 import fiona
 import geopandas as gpd
@@ -40,26 +40,26 @@
     "number": "float",
 }
 
-default_properties: Dict[str, Any] = {
+default_properties: dict[str, Any] = {
     "id": None,
     "dtype": "str",
     "required": False,
     "unique": False,
 }
 
 
-def map_definition(definition: Dict[str, Any]) -> List[Dict[str, Any]]:
+def map_definition(definition: dict[str, Any]) -> list[dict[str, Any]]:
     """
 
 
     Parameters
     ----------
-    definition : Dict
+    definition : dict[str, Any]
         HyDAMO definition as specified in the HyDAMO JSON specification.
 
     Returns
     -------
-    List
+    list[dict[str, Any]]
         Validation schema for the HyDAMO class.
 
     """
@@ -70,7 +70,7 @@ def map_definition(definition: Dict[str, Any]) -> List[Dict[str, Any]]:
     for k, v in definition.items():
         # convert geometry if shape
         if k == "shape":
-            properties: Dict[str, Any] = {"id": "geometry"}
+            properties: dict[str, Any] = {"id": "geometry"}
             dtype = v["type"]
             if not isinstance(dtype, list):
                 dtype = [dtype]
@@ -116,21 +116,20 @@ class ExtendedGeoDataFrame(gpd.GeoDataFrame):  # type: ignore
 
     def __init__(
         self,
-        validation_schema: List[Dict[str, Any]],
-        geotype: Optional[
-            List[
-                Literal[
-                    "LineString",
-                    "MultiLineString",
-                    "Point",
-                    "PointZ",
-                    "Polygon",
-                    "MultiPolygon",
-                ]
+        validation_schema: list[dict[str, Any]],
+        geotype: list[
+            Literal[
+                "LineString",
+                "MultiLineString",
+                "Point",
+                "PointZ",
+                "Polygon",
+                "MultiPolygon",
             ]
-        ],
+        ]
+        | None,
         layer_name: str = "",
-        required_columns: List[str] = [],
+        required_columns: list[str] = [],
         logger=logging,
         *args,
         **kwargs,
@@ -144,7 +143,7 @@ def __init__(
         # else:
         kwargs["columns"] = required_columns
 
-        super(ExtendedGeoDataFrame, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
 
         self.validation_schema = validation_schema
         self.required_columns = required_columns
@@ -301,7 +300,7 @@ def __init__(
         self,
         version: str = "2.2",
         schemas_path: Path = SCHEMAS_DIR,
-        ignored_layers: List[str] = [
+        ignored_layers: list[str] = [
             "afvoeraanvoergebied",
             "imwa_geoobject",
             "leggerwatersysteem",
@@ -311,7 +310,7 @@ def __init__(
     ):
         self.version = version
         self.schema_json = schemas_path.joinpath(f"HyDAMO_{version}.json")
-        self.layers: List[str] = []
+        self.layers: list[str] = []
         self.ignored_layers = ignored_layers
 
         self.init_datamodel()
@@ -322,7 +321,7 @@ def data_layers(self):
 
     def init_datamodel(self) -> None:
         """Initialize DataModel from self.schemas_path."""
-        self.validation_schemas: Dict[str, Any] = {}
+        self.validation_schemas: dict[str, Any] = {}
 
         # read schema as dict
         with open(self.schema_json) as src:

src/hydamo/pyproject.toml

@@ -11,7 +11,7 @@ authors = [
 ]
 license = { text = "MIT" }
 
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "geopandas",
 ]

src/ribasim_nl/pyproject.toml

@@ -12,7 +12,7 @@ authors = [
 ]
 license = { text = "MIT" }
 
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "geopandas",
 ]