Overhaul of Python architecture (#731)

Fixes #512
Groundwork for #630 & #252

The code has become much simpler in some places (e.g. write_toml).

```python
from ribasim import Model

m = Model(filepath="generated_testmodels/basic/ribasim.toml")
m.database.node.df # Node table
m.basin.static.df # BasinStatc table
m.write("test")
```

### Some notes:
- The config.py file cannot be autogenerated anymore. The schemas still
can, but I disabled it for now to be sure (some imports error).

### Changes:
I created new (parent) classes:
- BaseModel, from Pydantic, with our own config
- FileModel, like hydrolib-core (but now Pydantic v2), which can take a
single filepath for initilization. Models who inherit require defining
_load and _save, dealing with that filepath.
- NodeModel, a class for nodes (where `add` will be).
- TableModel, a class to read/write individual tables from/to
gpkg/arrow.
- SpatialTableModel, inherits TableModel, but reads/writes spatial
stuff.

I changed:
- the Model class to be a carbon copy of Config (which has been
deleted), so it mirrors the toml.
- in turn this created a `database` NodeModel class (reflecting the
field in the toml), with only Node and Edge underneath.
- the NodeModel classes Basin from their node_type version to the one in
Config, and set the type of the underlying table with a TypeVar like so:
```python
class Terminal(NodeModel):
    static: TableModel[TerminalStaticSchema]
```

### Yet to do:
- [x] Update tests
- [x] Fix sort! rules
- [x] Delete node_types folder
- [x] Link schemas to their Pydantic class
(TableModel[TerminalStaticSchema] => TerminalStatic)

---------

Co-authored-by: Martijn Visser <[email protected]>
Co-authored-by: Hofer-Julian <[email protected]>
Co-authored-by: Hofer-Julian <[email protected]>

docs/contribute/addnode.qmd

@@ -115,6 +115,7 @@ from typing import Optional
 import pandera as pa
 from pandera.engines.pandas_engine import PydanticModel
 from pandera.typing import DataFrame
+from pydantic import ConfigDict
 
 from ribasim import models
 from ribasim.input_base import TableModel
@@ -145,8 +146,7 @@ class NewNodeType(TableModel):
     static: Optional[DataFrame[StaticSchema]] = None
     # possible other schemas
 
-    class Config:
-        validate_assignment = True
+    model_config = ConfigDict(validate_assignment=True)
 
     def sort(self):
         self.static.sort_values("node_id", ignore_index=True, inplace=True)

docs/python/examples.ipynb

@@ -319,7 +319,7 @@
     ")\n",
     "node_xy = gpd.points_from_xy(x=xy[:, 0], y=xy[:, 1])\n",
     "\n",
-    "node_id, node_type = ribasim.Node.get_node_ids_and_types(\n",
+    "node_id, node_type = ribasim.Node.node_ids_and_types(\n",
     "    basin,\n",
     "    manning_resistance,\n",
     "    rating_curve,\n",
@@ -333,7 +333,7 @@
     "\n",
     "# Make sure the feature id starts at 1: explicitly give an index.\n",
     "node = ribasim.Node(\n",
-    "    static=gpd.GeoDataFrame(\n",
+    "    df=gpd.GeoDataFrame(\n",
     "        data={\"type\": node_type},\n",
     "        index=pd.Index(node_id, name=\"fid\"),\n",
     "        geometry=node_xy,\n",
@@ -363,7 +363,7 @@
     ")\n",
     "lines = ribasim.utils.geometry_from_connectivity(node, from_id, to_id)\n",
     "edge = ribasim.Edge(\n",
-    "    static=gpd.GeoDataFrame(\n",
+    "    df=gpd.GeoDataFrame(\n",
     "        data={\n",
     "            \"from_node_id\": from_id,\n",
     "            \"to_node_id\": to_id,\n",
@@ -390,8 +390,10 @@
    "outputs": [],
    "source": [
     "model = ribasim.Model(\n",
-    "    node=node,\n",
-    "    edge=edge,\n",
+    "    database=ribasim.Database(\n",
+    "        node=node,\n",
+    "        edge=edge,\n",
+    "    ),\n",
     "    basin=basin,\n",
     "    level_boundary=level_boundary,\n",
     "    flow_boundary=flow_boundary,\n",
@@ -520,7 +522,7 @@
     "    .to_xarray()\n",
     ")\n",
     "\n",
-    "basin_ids = model.basin.static[\"node_id\"].to_numpy()\n",
+    "basin_ids = model.basin.static.df[\"node_id\"].to_numpy()\n",
     "basin_nodes = xr.DataArray(\n",
     "    np.ones(len(basin_ids)), coords={\"node_id\": basin_ids}, dims=[\"node_id\"]\n",
     ")\n",
@@ -548,8 +550,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.basin.time = forcing\n",
-    "model.basin.state = state"
+    "model.basin.time.df = forcing\n",
+    "model.basin.state.df = state"
    ]
   },
   {
@@ -675,7 +677,7 @@
     "\n",
     "# Make sure the feature id starts at 1: explicitly give an index.\n",
     "node = ribasim.Node(\n",
-    "    static=gpd.GeoDataFrame(\n",
+    "    df=gpd.GeoDataFrame(\n",
     "        data={\"type\": node_type},\n",
     "        index=pd.Index(np.arange(len(xy)) + 1, name=\"fid\"),\n",
     "        geometry=node_xy,\n",
@@ -705,7 +707,7 @@
     "\n",
     "lines = ribasim.utils.geometry_from_connectivity(node, from_id, to_id)\n",
     "edge = ribasim.Edge(\n",
-    "    static=gpd.GeoDataFrame(\n",
+    "    df=gpd.GeoDataFrame(\n",
     "        data={\"from_node_id\": from_id, \"to_node_id\": to_id, \"edge_type\": edge_type},\n",
     "        geometry=lines,\n",
     "        crs=\"EPSG:28992\",\n",
@@ -903,8 +905,10 @@
    "outputs": [],
    "source": [
     "model = ribasim.Model(\n",
-    "    node=node,\n",
-    "    edge=edge,\n",
+    "    database=ribasim.Database(\n",
+    "        node=node,\n",
+    "        edge=edge,\n",
+    "    ),\n",
     "    basin=basin,\n",
     "    pump=pump,\n",
     "    level_boundary=level_boundary,\n",
@@ -994,7 +998,7 @@
     "\n",
     "ax = df_basin_wide[\"level\"].plot()\n",
     "\n",
-    "greater_than = model.discrete_control.condition.greater_than\n",
+    "greater_than = model.discrete_control.condition.df.greater_than\n",
     "\n",
     "ax.hlines(\n",
     "    greater_than,\n",
@@ -1103,7 +1107,7 @@
     "\n",
     "# Make sure the feature id starts at 1: explicitly give an index.\n",
     "node = ribasim.Node(\n",
-    "    static=gpd.GeoDataFrame(\n",
+    "    df=gpd.GeoDataFrame(\n",
     "        data={\"type\": node_type},\n",
     "        index=pd.Index(np.arange(len(xy)) + 1, name=\"fid\"),\n",
     "        geometry=node_xy,\n",
@@ -1130,7 +1134,7 @@
     "\n",
     "lines = ribasim.utils.geometry_from_connectivity(node, from_id, to_id)\n",
     "edge = ribasim.Edge(\n",
-    "    static=gpd.GeoDataFrame(\n",
+    "    df=gpd.GeoDataFrame(\n",
     "        data={\n",
     "            \"from_node_id\": from_id,\n",
     "            \"to_node_id\": to_id,\n",
@@ -1325,8 +1329,10 @@
    "outputs": [],
    "source": [
     "model = ribasim.Model(\n",
-    "    node=node,\n",
-    "    edge=edge,\n",
+    "    database=ribasim.Database(\n",
+    "        node=node,\n",
+    "        edge=edge,\n",
+    "    ),\n",
     "    basin=basin,\n",
     "    flow_boundary=flow_boundary,\n",
     "    level_boundary=level_boundary,\n",
@@ -1415,8 +1421,8 @@
     "ax.set_ylabel(\"level [m]\")\n",
     "\n",
     "# Plot target level\n",
-    "target_levels = model.pid_control.time.target.to_numpy()[::2]\n",
-    "times = date2num(model.pid_control.time.time)[::2]\n",
+    "target_levels = model.pid_control.time.df.target.to_numpy()[::2]\n",
+    "times = date2num(model.pid_control.time.df.time)[::2]\n",
     "ax.plot(times, target_levels, color=\"k\", ls=\":\", label=\"target level\")\n",
     "pass"
    ]
@@ -1445,7 +1451,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,