climate-ref-ilamb 0.6.5__tar.gz → 0.6.6__tar.gz

{climate_ref_ilamb-0.6.5 → climate_ref_ilamb-0.6.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: climate-ref-ilamb
-Version: 0.6.5
+Version: 0.6.6
 Summary: ILAMB diagnostic provider for the Rapid Evaluation Framework
 Author-email: Nathan Collier <nathaniel.collier@gmail.com>, Jared Lewis <jared.lewis@climate-resource.com>
 License-Expression: Apache-2.0
@@ -19,7 +19,7 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.11
 Requires-Dist: climate-ref-core
-Requires-Dist: ilamb3>=2025.5.20
+Requires-Dist: ilamb3>=2025.9.9
 Requires-Dist: scipy<1.16
 Description-Content-Type: text/markdown
 

{climate_ref_ilamb-0.6.5 → climate_ref_ilamb-0.6.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "climate-ref-ilamb"
-version = "0.6.5"
+version = "0.6.6"
 description = "ILAMB diagnostic provider for the Rapid Evaluation Framework"
 readme = "README.md"
 authors = [
@@ -24,8 +24,8 @@ classifiers = [
 ]
 dependencies = [
   "climate-ref-core",
-  "ilamb3>=2025.5.20",
-  "scipy<1.16",  # https://github.com/statsmodels/statsmodels/issues/9584
+  "ilamb3>=2025.9.9",
+  "scipy<1.16",       # https://github.com/statsmodels/statsmodels/issues/9584
 ]
 [project.entry-points."climate-ref.providers"]
 ilamb = "climate_ref_ilamb:provider"

{climate_ref_ilamb-0.6.5 → climate_ref_ilamb-0.6.6}/src/climate_ref_ilamb/configure/ilamb.yaml

@@ -25,7 +25,7 @@ mrsos-WangMao:
     mrsol: ilamb/mrsol/WangMao/mrsol_olc.nc
   alternate_vars:
   - mrsos
-  transform:
+  transforms:
   - select_depth:
       value: 0
   - soil_moisture_to_vol_fraction

{climate_ref_ilamb-0.6.5 → climate_ref_ilamb-0.6.6}/src/climate_ref_ilamb/configure/iomb.yaml

@@ -5,7 +5,7 @@ thetao-WOA2023-surface:
     # TODO: Update to use the obs4REF equiv
     thetao: ilamb/WOA/thetao_mon_WOA_A5B4_gn_200501-201412.nc
   variable_cmap: Reds
-  transform:
+  transforms:
   - select_depth:
       value: 0
   alternate_vars:
@@ -15,7 +15,7 @@ so-WOA2023-surface:
   sources:
     # TODO: Update to use the obs4REF equiv
     so: ilamb/WOA/so_mon_WOA_A5B4_gn_200501-201412.nc
-  transform:
+  transforms:
   - select_depth:
       value: 0
   variable_cmap: YlGn
@@ -27,7 +27,7 @@ amoc-RAPID:
   - timeseries
   related_vars:
   - msftmz
-  transform:
+  transforms:
   - msftmz_to_rapid
   sources:
     # TODO: Update to use the obs4REF equiv
@@ -39,7 +39,7 @@ ohc-NOAA:
   related_vars:
   - thetao
   - volcello
-  transform:
+  transforms:
   - select_depth:
       min: 0
       max: 2000

{climate_ref_ilamb-0.6.5 → climate_ref_ilamb-0.6.6}/src/climate_ref_ilamb/standard.py

@@ -1,14 +1,14 @@
 from pathlib import Path
 from typing import Any
 
-import ilamb3  # type: ignore
-import ilamb3.regions as ilr  # type: ignore
-import matplotlib.pyplot as plt
+import ilamb3
+import ilamb3.regions as ilr
 import pandas as pd
 import pooch
+import xarray as xr
 from ilamb3 import run
 
-from climate_ref_core.constraints import AddSupplementaryDataset
+from climate_ref_core.constraints import AddSupplementaryDataset, RequireFacets
 from climate_ref_core.dataset_registry import dataset_registry_manager
 from climate_ref_core.datasets import FacetFilter, SourceDatasetType
 from climate_ref_core.diagnostics import (
@@ -17,8 +17,9 @@ from climate_ref_core.diagnostics import (
     ExecutionDefinition,
     ExecutionResult,
 )
+from climate_ref_core.metric_values.typing import SeriesMetricValue
 from climate_ref_core.pycmec.metric import CMECMetric
-from climate_ref_core.pycmec.output import CMECOutput
+from climate_ref_core.pycmec.output import CMECOutput, OutputCV
 from climate_ref_ilamb.datasets import (
     registry_to_collection,
 )
@@ -101,16 +102,7 @@ def _build_cmec_bundle(df: pd.DataFrame) -> dict[str, Any]:
     # reference_df = df[df["source"] == "Reference"]
     model_df = df[df["source"] != "Reference"]
 
-    # Source is formatted as "ACCESS-ESM1-5-r1i1p1f1-gn"
-    # This assumes that the member_id and grid_label are always the last two parts of the source string
-    # and don't contain '-'
-    extracted_source = model_df.source.str.extract(r"([\w-]+)-([\w\d]+)-([\w\d]+)")
-    model_df.loc[:, "source_id"] = extracted_source[0]
-    model_df.loc[:, "member_id"] = extracted_source[1]
-    model_df.loc[:, "grid_label"] = extracted_source[2]
-
-    # Strip out units from the name
-    # These are available in the attributes
+    # Strip out units from the name (available in the attributes)
     extracted_source = model_df.name.str.extract(r"(.*)\s\[.*\]")
     model_df.loc[:, "name"] = extracted_source[0]
 
@@ -149,20 +141,11 @@ def _build_cmec_bundle(df: pd.DataFrame) -> dict[str, Any]:
     return bundle
 
 
-def _form_bundles(df: pd.DataFrame) -> tuple[CMECMetric, CMECOutput]:
-    """
-    Create the output bundles (really a lift to make Ruff happy with the size of run()).
-    """
-    metric_bundle = _build_cmec_bundle(df)
-    output_bundle = CMECOutput.create_template()
-    return CMECMetric.model_validate(metric_bundle), CMECOutput.model_validate(output_bundle)
-
-
 def _set_ilamb3_options(registry: pooch.Pooch, registry_file: str) -> None:
     """
     Set options for ILAMB based on which registry file is being used.
     """
-    ilamb3.conf.reset()
+    ilamb3.conf.reset()  # type: ignore
     ilamb_regions = ilr.Regions()
     if registry_file == "ilamb":
         ilamb_regions.add_netcdf(registry.fetch("ilamb/regions/GlobalLand.nc"))
@@ -213,29 +196,52 @@ class ILAMBStandard(Diagnostic):
                         facets={
                             "variable_id": (
                                 self.variable_id,
-                                *ilamb_kwargs.get("relationships", {}).keys(),
                                 *ilamb_kwargs.get("alternate_vars", []),
                                 *ilamb_kwargs.get("related_vars", []),
+                                *ilamb_kwargs.get("relationships", {}).keys(),
                             )
                         }
                     ),
                     FacetFilter(facets={"frequency": ("mon",)}),
                     FacetFilter(facets={"experiment_id": ("historical", "land-hist")}),
-                    # Exclude unneeded snc tables
                     FacetFilter(facets={"table_id": ("ImonAnt", "ImonGre")}, keep=False),
                 ),
                 constraints=(
-                    AddSupplementaryDataset.from_defaults("areacella", SourceDatasetType.CMIP6),
-                    AddSupplementaryDataset.from_defaults("sftlf", SourceDatasetType.CMIP6),
-                )
-                if registry_file == "ilamb"
-                else (
-                    AddSupplementaryDataset.from_defaults("areacello", SourceDatasetType.CMIP6),
-                    AddSupplementaryDataset.from_defaults("sftof", SourceDatasetType.CMIP6),
+                    RequireFacets(
+                        "variable_id",
+                        (
+                            self.variable_id,
+                            *ilamb_kwargs.get("alternate_vars", []),
+                            *ilamb_kwargs.get("related_vars", []),
+                        ),
+                        operator="any",
+                    ),
+                    *(
+                        [
+                            RequireFacets(
+                                "variable_id",
+                                required_facets=tuple(ilamb_kwargs.get("relationships", {}).keys()),
+                            )
+                        ]
+                        if "relationships" in ilamb_kwargs
+                        else []
+                    ),
+                    *(
+                        (
+                            AddSupplementaryDataset.from_defaults("areacella", SourceDatasetType.CMIP6),
+                            AddSupplementaryDataset.from_defaults("sftlf", SourceDatasetType.CMIP6),
+                        )
+                        if registry_file == "ilamb"
+                        else (
+                            AddSupplementaryDataset.from_defaults("areacello", SourceDatasetType.CMIP6),
+                            AddSupplementaryDataset.from_defaults("sftof", SourceDatasetType.CMIP6),
+                        )
+                    ),
                 ),
-                group_by=("experiment_id",),
+                group_by=("experiment_id", "source_id", "member_id", "grid_label"),
             ),
         )
+
         self.facets = (
             "experiment_id",
             "source_id",
@@ -257,12 +263,11 @@ class ILAMBStandard(Diagnostic):
         """
         Run the ILAMB standard analysis.
         """
-        plt.rcParams.update({"figure.max_open_warning": 0})
         _set_ilamb3_options(self.registry, self.registry_file)
         ref_datasets = self.ilamb_data.datasets.set_index(self.ilamb_data.slug_column)
-        run.run_simple(
-            ref_datasets,
+        run.run_single_block(
             self.slug,
+            ref_datasets,
             definition.datasets[SourceDatasetType.CMIP6].datasets,
             definition.output_directory,
             **self.ilamb_kwargs,
@@ -281,15 +286,91 @@ class ILAMBStandard(Diagnostic):
         -------
             An execution result object
         """
-        selectors = definition.datasets[SourceDatasetType.CMIP6].selector_dict()
         _set_ilamb3_options(self.registry, self.registry_file)
-
+        # In ILAMB, scalars are saved in CSV files in the output directory. To
+        # be compatible with the REF system we will need to add the metadata
+        # that is associated with the execution group, called the selector.
         df = _load_csv_and_merge(definition.output_directory)
-        # Add the selectors to the dataframe
+        selectors = definition.datasets[SourceDatasetType.CMIP6].selector_dict()
         for key, value in selectors.items():
             df[key] = value
-        metric_bundle, output_bundle = _form_bundles(df)
+        metric_bundle = CMECMetric.model_validate(_build_cmec_bundle(df))
+
+        # Add each png file plot to the output
+        output_bundle = CMECOutput.create_template()
+        for plotfile in definition.output_directory.glob("*.png"):
+            output_bundle[OutputCV.PLOTS.value][f"{plotfile}"] = {
+                OutputCV.FILENAME.value: f"{plotfile}",
+                OutputCV.LONG_NAME.value: _caption_from_filename(plotfile),
+                OutputCV.DESCRIPTION.value: "",
+            }
+
+        # Add the html page to the output
+        index_html = str(definition.to_output_path("index.html"))
+        output_bundle[OutputCV.HTML.value][index_html] = {
+            OutputCV.FILENAME.value: index_html,
+            OutputCV.LONG_NAME.value: "Results page",
+            OutputCV.DESCRIPTION.value: "Page displaying scalars and plots from the ILAMB execution.",
+        }
+        output_bundle[OutputCV.INDEX.value] = index_html
+
+        # Add series to the output based on the time traces we find in the
+        # output files
+        series = []
+        for ncfile in definition.output_directory.glob("*.nc"):
+            ds = xr.open_dataset(ncfile)
+            for name, da in ds.items():
+                # Only create series for 1d DataArray's with these dimensions
+                if not (da.ndim == 1 and set(da.dims).intersection(["time", "month"])):
+                    continue
+                # Convert dimension values
+                attrs = {}
+                str_name = str(name)
+                index_name = str(da.dims[0])
+                index = ds[index_name].values.tolist()
+                if hasattr(index[0], "isoformat"):
+                    index = [v.isoformat() for v in index]
+                if hasattr(index[0], "calendar"):
+                    attrs["calendar"] = index[0].calendar
+                # Parse out some CVs
+                dimensions = {"metric": str_name, "source_id": ncfile.stem}
+                if "_" in str_name:
+                    dimensions["region"] = str_name.split("_")[1]
+                series.append(
+                    SeriesMetricValue(
+                        dimensions=dimensions,
+                        values=da.values.tolist(),
+                        index=index,
+                        index_name=index_name,
+                        attributes=attrs,
+                    )
+                )
 
         return ExecutionResult.build_from_output_bundle(
-            definition, cmec_output_bundle=output_bundle, cmec_metric_bundle=metric_bundle
+            definition, cmec_output_bundle=output_bundle, cmec_metric_bundle=metric_bundle, series=series
         )
+
+
+def _caption_from_filename(filename: Path) -> str:
+    source, region, plot = filename.stem.split("_")
+    plot_texts = {
+        "bias": "bias",
+        "biasscore": "bias score",
+        "cycle": "annual cycle",
+        "cyclescore": "annual cycle score",
+        "mean": "period mean",
+        "rmse": "RMSE",
+        "rmsescore": "RMSE score",
+        "shift": "shift in maximum month",
+        "tmax": "maxmimum month",
+        "trace": "regional mean",
+        "taylor": "Taylor diagram",
+    }
+    if plot not in plot_texts:
+        return ""
+    caption = f"The {plot_texts.get(plot)}"
+    if source != "None":
+        caption += f" of {'the reference data' if source == 'Reference' else source}"
+    if region.lower() != "none":
+        caption += f" over the {ilr.Regions().get_name(region)} region."
+    return caption

{climate_ref_ilamb-0.6.5 → climate_ref_ilamb-0.6.6}/tests/integration/test_diagnostics.py

@@ -3,17 +3,20 @@ from climate_ref_ilamb import provider as ilamb_provider
 
 from climate_ref_core.diagnostics import Diagnostic
 
-skipped_diagnostics = [
+xfail_diagnostics = [
     "ohc-noaa",  # Missing sample data
 ]
+skipped_diagnostics = []
+
 
 diagnostics = [
     pytest.param(
         diagnostic,
         id=diagnostic.slug,
-        marks=[pytest.mark.xfail(reason="Expected failure")]
-        if diagnostic.slug in skipped_diagnostics
-        else [],
+        marks=[
+            *([pytest.mark.xfail(reason="Expected failure")] if diagnostic.slug in xfail_diagnostics else []),
+            *([pytest.mark.skip(reason="Problem test")] if diagnostic.slug in skipped_diagnostics else []),
+        ],
     )
     for diagnostic in ilamb_provider.diagnostics()
 ]

{climate_ref_ilamb-0.6.5 → climate_ref_ilamb-0.6.6}/tests/unit/test_standard_metrics.py

@@ -13,18 +13,27 @@ def test_standard_site(cmip6_data_catalog, definition_factory):
     diagnostic = ILAMBStandard(
         registry_file="ilamb-test", metric_name="test-site-tas", sources={"tas": "ilamb/test/Site/tas.nc"}
     )
-    ds = (
-        cmip6_data_catalog[
-            (cmip6_data_catalog["experiment_id"] == "historical")
-            & (cmip6_data_catalog["variable_id"] == "tas")
-        ]
-        .groupby("instance_id")
-        .first()
+    _, ds = next(
+        iter(
+            cmip6_data_catalog[
+                (cmip6_data_catalog["experiment_id"] == "historical")
+                & (cmip6_data_catalog["variable_id"] == "tas")
+            ].groupby("instance_id")
+        )
     )
-
     definition = definition_factory(
         diagnostic=diagnostic,
-        cmip6=DatasetCollection(ds, "instance_id", selector=(("experiment_id", "historical"),)),
+        cmip6=DatasetCollection(
+            ds,
+            "instance_id",
+            selector=(
+                ("experiment_id", "historical"),
+                ("variable_id", "tas"),
+                ("source_id", "CanESM5"),
+                ("member_id", "r1i1p1f1"),
+                ("grid_label", "gn"),
+            ),
+        ),
     )
     definition.output_directory.mkdir(parents=True, exist_ok=True)
 
@@ -54,15 +63,28 @@ def test_standard_grid(cmip6_data_catalog, definition_factory):
         sources={"gpp": "ilamb/test/Grid/gpp.nc"},
         relationships={"pr": "ilamb/test/Grid/pr.nc"},
     )
-    grp = cmip6_data_catalog[
-        (cmip6_data_catalog["experiment_id"] == "historical")
-        & ((cmip6_data_catalog["variable_id"] == "gpp") | (cmip6_data_catalog["variable_id"] == "pr"))
-    ].groupby(["source_id", "member_id", "grid_label"])
-    _, ds = next(iter(grp))
+    _, ds = next(
+        iter(
+            cmip6_data_catalog[
+                (cmip6_data_catalog["experiment_id"] == "historical")
+                & ((cmip6_data_catalog["variable_id"] == "gpp") | (cmip6_data_catalog["variable_id"] == "pr"))
+            ].groupby(["source_id", "member_id", "grid_label"])
+        )
+    )
 
     definition = definition_factory(
         diagnostic=diagnostic,
-        cmip6=DatasetCollection(ds, "instance_id", selector=(("experiment_id", "historical"),)),
+        cmip6=DatasetCollection(
+            ds,
+            "instance_id",
+            selector=(
+                ("experiment_id", "historical"),
+                ("variable_id", "tas"),
+                ("source_id", "CanESM5"),
+                ("member_id", "r1i1p1f1"),
+                ("grid_label", "gn"),
+            ),
+        ),
     )
     definition.output_directory.mkdir(parents=True, exist_ok=True)
 
@@ -129,17 +151,18 @@ def test_expected_executions():
         ),
     }
     executions = list(solve_executions(data_catalog, diagnostic, provider=ilamb_provider))
-    assert len(executions) == 1
-
-    # ts
-    assert executions[0].datasets[SourceDatasetType.CMIP6].selector == (("experiment_id", "historical"),)
+    assert len(executions) == 2
+    assert executions[0].datasets[SourceDatasetType.CMIP6].selector == (
+        ("experiment_id", "historical"),
+        ("grid_label", "gn"),
+        ("member_id", "r1i1p1f1"),
+        ("source_id", "ACCESS-ESM1-5"),
+    )
     assert executions[0].datasets[SourceDatasetType.CMIP6].datasets["variable_id"].tolist() == [
-        "cSoil",
         "cSoil",
         "areacella",
     ]
     assert executions[0].datasets[SourceDatasetType.CMIP6].datasets["member_id"].tolist() == [
         "r1i1p1f1",
-        "r2i1p1f1",
         "r1i1p1f1",
     ]