Merge pull request #174 from ImperialCollegeLondon/feature/split_testing

Feature/split testing

docs/source/development/defining_new_models.md

@@ -19,10 +19,11 @@ You should first start by defining a new folder for your model (within
 mkdir virtual_rainforest/models/freshwater
 ```
 
-Within this folder a `python` script defining the model should be created.
+Within this folder a `python` script defining the model should be created. This script
+should be called "{MODEL_NAME}_model.py".
 
 ```bash
-touch virtual_rainforest/models/freshwater/model.py
+touch virtual_rainforest/models/freshwater/freshwater_model.py
 ```
 
 This script must import a number of things to be able to set up a new `Model` class

tests/data/test_data/test.toml → tests/core/data/test.toml

@@ -1,12 +1,12 @@
 [[core.data.variable]]
-file = "test_data/cellid_coords.nc"
+file = "cellid_coords.nc"
 var_name = "temp"
 [[core.data.variable]]
-file = "test_data/cellid_coords.nc"
+file = "cellid_coords.nc"
 var_name = "prec"
 [[core.data.variable]]
-file = "test_data/cellid_coords.nc"
+file = "cellid_coords.nc"
 var_name = "elev"
 [[core.data.variable]]
-file = "test_data/cellid_coords.nc"
+file = "cellid_coords.nc"
 var_name = "vapd"

tests/data/test_data/test_dupes.toml → tests/core/data/test_dupes.toml

@@ -1,12 +1,12 @@
 [[core.data.variable]]
-file = "test_data/cellid_coords.nc"
+file = "cellid_coords.nc"
 var_name = "temp"
 [[core.data.variable]]
-file = "test_data/cellid_coords.nc"
+file = "cellid_coords.nc"
 var_name = "prec"
 [[core.data.variable]]
-file = "test_data/cellid_coords.nc"
+file = "cellid_coords.nc"
 var_name = "elev"
 [[core.data.variable]]
-file = "test_data/cellid_coords.nc"
+file = "cellid_coords.nc"
 var_name = "elev"

tests/test_config.py → tests/core/test_config.py

@@ -13,10 +13,9 @@
 import pytest
 
 import virtual_rainforest.core.config as config
+from tests.conftest import log_check
 from virtual_rainforest.core.config import register_schema
 
-from .conftest import log_check
-
 
 @pytest.mark.parametrize(
     "d_a,d_b,overlap",
@@ -98,8 +97,7 @@ def test_check_outfile(caplog, mocker, out_path, expected_log_entries):
             (
                 (
                     CRITICAL,
-                    "The following (user provided) config paths do not exist:\n"
-                    "['Nonsense/file/location']",
+                    "The following (user provided) config paths do not exist:",
                 ),
             ),
         ),
@@ -111,13 +109,13 @@ def test_check_outfile(caplog, mocker, out_path, expected_log_entries):
                 (
                     CRITICAL,
                     "The following (user provided) config folders do not contain any "
-                    "toml files:\n['.']",
+                    "toml files:",
                 ),
             ),
         ),
         (
-            ["tests/fixtures/", "tests/fixtures/all_config.toml"],
-            [Path("tests/fixtures/all_config.toml")],
+            ["", "all_config.toml"],
+            ["all_config.toml"],
             config.ConfigurationError,
             (
                 (
@@ -130,17 +128,23 @@ def test_check_outfile(caplog, mocker, out_path, expected_log_entries):
     ],
 )
 def test_collect_files(
-    caplog, mocker, cfg_paths, contents, expected_exception, expected_log_entries
+    caplog,
+    mocker,
+    shared_datadir,
+    cfg_paths,
+    contents,
+    expected_exception,
+    expected_log_entries,
 ):
     """Checks errors for missing config files."""
 
-    # Configure the mock to return a specific list of files
+    # Configure the mock to return a specific list of files when globbing a directory
     mock_get = mocker.patch("virtual_rainforest.core.config.Path.glob")
-    mock_get.return_value = contents
+    mock_get.return_value = [shared_datadir / fn for fn in contents]
 
     # Check that file collection fails as expected
     with pytest.raises(expected_exception):
-        config.collect_files(cfg_paths)
+        config.collect_files([shared_datadir / fn for fn in cfg_paths])
 
     log_check(caplog, expected_log_entries)
 
@@ -252,41 +256,30 @@ def test_construct_combined_schema(caplog: pytest.LogCaptureFixture) -> None:
     "file_path,expected_log_entries",
     [
         (
-            "tests/fixtures/default_config.toml",  # File entirely of defaults
+            "default_config.toml",  # File entirely of defaults
             (
-                (
-                    INFO,
-                    "Configuration files successfully validated!",
-                ),
-                (
-                    INFO,
-                    "Saving all configuration details to complete_config.toml",
-                ),
+                (INFO, "Configuration files successfully validated!"),
+                (INFO, "Saving all configuration details to"),
             ),
         ),
         (
-            "tests/fixtures/all_config.toml",  # File with no defaults
+            "all_config.toml",  # File with no defaults
             (
-                (
-                    INFO,
-                    "Configuration files successfully validated!",
-                ),
-                (
-                    INFO,
-                    "Saving all configuration details to complete_config.toml",
-                ),
+                (INFO, "Configuration files successfully validated!"),
+                (INFO, "Saving all configuration details to"),
             ),
         ),
     ],
 )
-def test_final_validation_log(caplog, file_path, expected_log_entries):
+def test_final_validation_log(caplog, shared_datadir, file_path, expected_log_entries):
     """Checks that validation passes as expected and produces the correct output."""
 
-    config.validate_config([file_path], Path("./complete_config.toml"))
+    outfile = shared_datadir / "complete_config.toml"
+    config.validate_config([shared_datadir / file_path], outfile)
 
     # Remove generated output file
     # As a bonus tests that output file was generated correctly + to the right location
-    Path("./complete_config.toml").unlink()
+    outfile.unlink()
 
     # Then check that the correct (critical error) log messages are emitted
     log_check(caplog, expected_log_entries)

tests/test_data.py → tests/core/test_data.py

@@ -7,10 +7,9 @@
 import pytest
 from xarray import DataArray, Dataset
 
+from tests.conftest import log_check
 from virtual_rainforest.core.config import ConfigurationError
 
-from .conftest import log_check
-
 
 @pytest.mark.parametrize(
     argnames=["use_grid", "exp_err", "expected_log"],
@@ -251,7 +250,7 @@ def test_Data_contains(fixture_data, var_name, expected):
 def test_Data_load_to_dataarray_naming(caplog, shared_datadir, name, exp_log):
     """Test the coding of the name handling and replacement."""
 
-    # Setup a Data instance to match the example files generated in test_data/
+    # Setup a Data instance to match the example files generated in tests/core/data
 
     from virtual_rainforest.core.data import Data
     from virtual_rainforest.core.grid import Grid
@@ -272,7 +271,7 @@ def test_Data_load_to_dataarray_naming(caplog, shared_datadir, name, exp_log):
     caplog.clear()
 
     # Load the data from file
-    datafile = shared_datadir / "test_data/cellid_coords.nc"
+    datafile = shared_datadir / "cellid_coords.nc"
 
     data[name] = load_to_dataarray(file=datafile, var_name=name)
 
@@ -323,7 +322,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["__any__"],
-            "test_data/cellid_dims.nc",
+            "cellid_dims.nc",
             does_not_raise(),
             None,
             (
@@ -335,7 +334,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["__any__"],
-            "test_data/cellid_dim_too_few.nc",
+            "cellid_dim_too_few.nc",
             pytest.raises(ValueError),
             "Grid defines 100 cells, data provides 60",
             (
@@ -348,7 +347,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["__any__"],
-            "test_data/cellid_dim_too_many.nc",
+            "cellid_dim_too_many.nc",
             pytest.raises(ValueError),
             "Grid defines 100 cells, data provides 200",
             (
@@ -361,7 +360,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["__any__"],
-            "test_data/cellid_coords.nc",
+            "cellid_coords.nc",
             does_not_raise(),
             None,
             (
@@ -373,7 +372,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["__any__"],
-            "test_data/cellid_coords_too_few.nc",
+            "cellid_coords_too_few.nc",
             pytest.raises(ValueError),
             "The data cell ids do not provide a one-to-one map onto grid " "cell ids.",
             (
@@ -390,7 +389,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["__any__"],
-            "test_data/cellid_coords_bad_cellid.nc",
+            "cellid_coords_bad_cellid.nc",
             pytest.raises(ValueError),
             "The data cell ids do not provide a one-to-one map onto grid " "cell ids.",
             (
@@ -407,7 +406,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["square"],
-            "test_data/xy_dim.nc",
+            "xy_dim.nc",
             does_not_raise(),
             None,
             (
@@ -419,7 +418,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["square"],
-            "test_data/xy_dim_small.nc",
+            "xy_dim_small.nc",
             pytest.raises(ValueError),
             "Data XY dimensions do not match square grid",
             (
@@ -432,7 +431,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["square"],
-            "test_data/xy_coords.nc",
+            "xy_coords.nc",
             does_not_raise(),
             None,
             (
@@ -444,7 +443,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["square"],
-            "test_data/xy_coords_small.nc",
+            "xy_coords_small.nc",
             pytest.raises(ValueError),
             "Mapped points do not cover all cells.",
             (
@@ -457,7 +456,7 @@ def fixture_load_data_grids(request):
         ),
         pytest.param(
             ["square"],
-            "test_data/xy_coords_shifted.nc",
+            "xy_coords_shifted.nc",
             pytest.raises(ValueError),
             "Mapped points fall outside grid.",
             (
@@ -493,7 +492,7 @@ def test_Data_load_to_dataarray_data_handling(
     data name and name replacement functionality
     """
 
-    # Setup a Data instance to match the example files generated in test_data/
+    # Setup a Data instance to match the example files generated in tests/core/data
 
     from virtual_rainforest.core.data import Data
     from virtual_rainforest.core.readers import load_to_dataarray
@@ -527,7 +526,7 @@ def test_Data_load_to_dataarray_data_handling(
     argnames=["file", "exp_error", "exp_msg", "exp_log"],
     argvalues=[
         pytest.param(
-            "test_data/test.toml",
+            "test.toml",
             does_not_raise(),
             None,
             (
@@ -544,7 +543,7 @@ def test_Data_load_to_dataarray_data_handling(
             id="valid config",
         ),
         pytest.param(
-            "test_data/test_dupes.toml",
+            "test_dupes.toml",
             pytest.raises(ConfigurationError),
             "Data configuration did not load cleanly",
             (
@@ -578,7 +577,7 @@ def test_Data_load_from_config(
            config loader part of the mechanism
     """
 
-    # Setup a Data instance to match the example files generated in test_data/
+    # Setup a Data instance to match the example files generated in tests/core/data
 
     from virtual_rainforest.core.config import load_in_config_files
     from virtual_rainforest.core.data import Data