Move configuration use in main over to new configuration

docs/source/_toc.yaml

@@ -93,6 +93,8 @@ subtrees:
                 title: The base_model submodule
               - file: api/core/config.md
                 title: The config submodule
+              - file: api/core/config_builder.md
+                title: The config_builder submodule
               - file: api/core/configuration.md
                 title: The configuration submodule
               - file: api/core/constants.md

docs/source/api/core/config_builder.md

@@ -0,0 +1,33 @@
+---
+jupytext:
+  cell_metadata_filter: -all
+  formats: md:myst
+  main_language: python
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.18.1
+kernelspec:
+  display_name: Python 3 (ipykernel)
+  language: python
+  name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
+---
+
+# API documentation for the {mod}`~virtual_ecosystem.core.config_builder` module
+
+```{eval-rst}
+.. automodule:: virtual_ecosystem.core.config_builder
+    :autosummary:
+    :members:
+```

docs/source/using_the_ve/data/data.md

@@ -11,16 +11,6 @@ kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
   name: python3
-language_info:
-  codemirror_mode:
-    name: ipython
-    version: 3
-  file_extension: .py
-  mimetype: text/x-python
-  name: python
-  nbconvert_exporter: python
-  pygments_lexer: ipython3
-  version: 3.10.14
 ---
 
 # Adding and using data with the Virtual Ecosystem
@@ -83,8 +73,12 @@ from pathlib import Path
 import numpy as np
 from xarray import DataArray
 
+
+from virtual_ecosystem.core.config_builder import (
+    ConfigurationLoader,
+    generate_configuration,
+)
 from virtual_ecosystem.core.grid import Grid
-from virtual_ecosystem.core.config import Config
 from virtual_ecosystem.core.data import Data
 from virtual_ecosystem.core.axes import *
 from virtual_ecosystem.core.readers import load_to_dataarray
@@ -234,13 +228,14 @@ file_path = "../../data/xy_dim.nc"
 var_name = "temp"
 """
 
-config = Config(cfg_strings=data_toml)
+config_data = ConfigurationLoader(cfg_strings=data_toml)
+config = generate_configuration(config_data.data)
 ```
 
 The `Config` object can then be passed to the `load_data_config` method:
 
 ```{code-cell} ipython3
-data.load_data_config(config)
+data.load_data_config(config.core)
 ```
 
 ```{code-cell} ipython3
@@ -266,3 +261,7 @@ data.save_to_netcdf(
     variables_to_save=variables_to_save
 )
 ```
+
+```{code-cell} ipython3
+
+```

docs/source/using_the_ve/virtual_ecosystem_in_static_mode.md

@@ -11,9 +11,6 @@ kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
   name: python3
-mystnb:
-  execution_timeout: 60
-  execution_mode: 'off'
 ---
 
 # Running the Virtual Ecosystem in Static Mode

tests/core/test_base_model.py

@@ -4,7 +4,7 @@
 """
 
 from contextlib import nullcontext as does_not_raise
-from logging import CRITICAL, DEBUG, ERROR
+from logging import CRITICAL, ERROR
 from typing import Any
 
 import pytest
@@ -320,133 +320,6 @@ class InitVarModel(
     assert str(err.value).startswith("Can't instantiate abstract class InitVarModel ")
 
 
-@pytest.mark.skip(
-    "This functionality is going to be handed off to the variables system "
-    "so skipping for now but this will probably be deleted"
-)
-@pytest.mark.parametrize(
-    argnames="req_init_vars, raises, exp_err_msg, exp_log",
-    argvalues=[
-        pytest.param(
-            [("temperature", ("spatial",))],
-            does_not_raise(),
-            None,
-            ((DEBUG, "init_var model: required var 'temperature' checked"),),
-            id="single var with axes ok",
-        ),
-        pytest.param(
-            [("precipitation", tuple())],
-            does_not_raise(),
-            None,
-            ((DEBUG, "init_var model: required var 'precipitation' checked"),),
-            id="single var without axes ok",
-        ),
-        pytest.param(
-            [("temperature", ("spatial",)), ("precipitation", tuple())],
-            does_not_raise(),
-            None,
-            (
-                (DEBUG, "init_var model: required var 'temperature' checked"),
-                (DEBUG, "init_var model: required var 'precipitation' checked"),
-            ),
-            id="multivar ok",
-        ),
-        pytest.param(
-            [("precipitation", ("spatial",))],
-            pytest.raises(ValueError),
-            "init_var model: error checking vars_required_for_init, see log.",
-            (
-                (
-                    ERROR,
-                    "init_var model: required var 'precipitation' not on required "
-                    "axes: spatial",
-                ),
-                (
-                    ERROR,
-                    "init_var model: error checking vars_required_for_init, see log.",
-                ),
-            ),
-            id="missing axis",
-        ),
-    ],
-)
-def test_check_vars_required_for_init(
-    caplog,
-    fixture_data_instance_for_model_validation,
-    fixture_core_components,
-    req_init_vars,
-    raises,
-    exp_err_msg,
-    exp_log,
-):
-    """Tests the validation of the vars_required_for_init property on init."""
-
-    # This gets registered for each parameterisation but I can't figure out how to
-    # create the instance via a module-scope fixture and the alternative is just
-    # defining it at the top, which isn't encapsulated in a test.
-
-    from virtual_ecosystem.core.base_model import BaseModel
-    from virtual_ecosystem.core.config import Config
-    from virtual_ecosystem.core.configuration import CompiledConfiguration
-    from virtual_ecosystem.core.core_components import CoreComponents
-    from virtual_ecosystem.core.data import Data
-
-    class TestCaseModel(
-        BaseModel,
-        model_name="init_var",
-        model_update_bounds=("1 second", "1 year"),
-        vars_required_for_init=(),
-        vars_updated=[],
-    ):
-        def spinup(self) -> None:
-            pass
-
-        def update(self, time_index: int, **kwargs: Any) -> None:
-            pass
-
-        def cleanup(self) -> None:
-            pass
-
-        @classmethod
-        def from_config(
-            cls,
-            data: Data,
-            configuration: CompiledConfiguration,
-            core_components: CoreComponents,
-            config: Config,
-        ) -> Any:
-            return super().from_config(
-                data=data,
-                configuration=configuration,
-                core_components=core_components,
-                config=config,
-            )
-
-    # Registration of TestClassModel emits logging messages - discard.
-    caplog.clear()
-
-    # Override the vars_required_for_init for different test cases against the
-    # data_instance
-    TestCaseModel.vars_required_for_init = req_init_vars
-
-    # Create an instance to check the handling
-    with raises as err:
-        inst = TestCaseModel(
-            data=fixture_data_instance_for_model_validation,
-            core_components=fixture_core_components,
-        )
-
-    if err:
-        # Check any error message
-        assert str(err.value) == exp_err_msg
-    else:
-        # Check the special methods
-        assert repr(inst).startswith("TestCaseModel(")
-        assert str(inst) == "A init_var model instance"
-
-    log_check(caplog, exp_log)
-
-
 @pytest.mark.parametrize(
     argnames=["config_string", "raises", "expected_log"],
     argvalues=[
@@ -510,7 +383,6 @@ def test_check_update_speed(
     """Tests check on update speed."""
 
     from virtual_ecosystem.core.base_model import BaseModel
-    from virtual_ecosystem.core.config import Config
     from virtual_ecosystem.core.config_builder import (
         ConfigurationLoader,
         generate_configuration,
@@ -547,13 +419,11 @@ def from_config(
             data: Data,
             configuration: CompiledConfiguration,
             core_components: CoreComponents,
-            config: Config,
         ) -> Any:
             return super().from_config(
                 data=data,
                 configuration=configuration,
                 core_components=core_components,
-                config=config,
             )
 
     # Process the configuration
@@ -645,7 +515,6 @@ def test_bypass_setup_due_to_static_configuration(
 ):
     """Test the _bypass_setup_due_to_static_configuration method."""
     from virtual_ecosystem.core.base_model import BaseModel
-    from virtual_ecosystem.core.config import Config
     from virtual_ecosystem.core.configuration import CompiledConfiguration
     from virtual_ecosystem.core.core_components import (
         CoreComponents,
@@ -680,13 +549,11 @@ def from_config(
             data: Data,
             configuration: CompiledConfiguration,
             core_components: CoreComponents,
-            config: Config,
         ) -> BaseModel:
             return super().from_config(
                 data=data,
                 configuration=configuration,
                 core_components=core_components,
-                config=config,
             )
 
     for var in data_vars.keys():
@@ -784,7 +651,6 @@ def test_run_update_due_to_static_configuration(
     """Test the _run_update_due_to_static_configuration method."""
 
     from virtual_ecosystem.core.base_model import BaseModel
-    from virtual_ecosystem.core.config import Config
     from virtual_ecosystem.core.configuration import CompiledConfiguration
     from virtual_ecosystem.core.core_components import CoreComponents
     from virtual_ecosystem.core.data import Data
@@ -817,13 +683,11 @@ def from_config(
             data: Data,
             configuration: CompiledConfiguration,
             core_components: CoreComponents,
-            config: Config,
         ) -> BaseModel:
             return super().from_config(
                 data=data,
                 configuration=configuration,
                 core_components=core_components,
-                config=config,
             )
 
     for var in data_vars.keys():
@@ -890,7 +754,6 @@ def test_bypass_setup_but_run_update_fails(
 ):
     """Test the _bypass_setup_due_to_static_configuration method."""
     from virtual_ecosystem.core.base_model import BaseModel
-    from virtual_ecosystem.core.config import Config
     from virtual_ecosystem.core.configuration import CompiledConfiguration
     from virtual_ecosystem.core.core_components import (
         CoreComponents,
@@ -925,13 +788,11 @@ def from_config(
             data: Data,
             configuration: CompiledConfiguration,
             core_components: CoreComponents,
-            config: Config,
         ) -> BaseModel:
             return super().from_config(
                 data=data,
                 configuration=configuration,
                 core_components=core_components,
-                config=config,
             )
 
     for var in data_vars.keys():

tests/core/test_config.py

@@ -16,6 +16,12 @@
 from virtual_ecosystem.core.exceptions import ConfigurationError
 
 
+@pytest.fixture(autouse=True)
+def skip_these_tests():
+    """Do not run tests in this module."""
+    pytest.skip("These tests rely on the old configuration system and will be deleted.")
+
+
 @pytest.mark.parametrize(
     "dest,source,exp_result, exp_conflicts",
     [

tests/core/test_constants_loader.py

@@ -9,6 +9,12 @@
 from virtual_ecosystem.core.exceptions import ConfigurationError
 
 
+@pytest.fixture(autouse=True)
+def skip_these_tests():
+    """Do not run tests in this module."""
+    pytest.skip("These tests rely on the old configuration system and will be deleted.")
+
+
 @pytest.mark.parametrize(
     "cfg_strings,model_name,class_name,raises,exp_val,exp_log",
     [