Merge branch 'main' into target-grid-cordex-domain

ghossh · ghossh · commit d5db3523281f · 2026-06-12T14:52:07.000+02:00
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -2,7 +2,7 @@
 version: 2.1
 
 orbs:
-  codecov: codecov/codecov@5.3.0
+  codecov: codecov/codecov@6.0.0
   pixi: prefix-dev/pixi@0.1.0
 
 jobs:
diff --git a/.github/ISSUE_TEMPLATE/data_issue_report.md b/.github/ISSUE_TEMPLATE/data_issue_report.md
@@ -3,39 +3,33 @@ name: Dataset issue report
 about: Create a report about a problematic dataset
 title: 'Dataset problem: '
 labels: ''
-assignees: valeriupredoi, zklaus
+assignees: valeriupredoi
 
 ---
 
 **Describe the dataset issue**
 A clear and concise description of what the problem with the data is is. Here are some guidelines that you can use
-right out the box by filling in the blanks (note that, if needed we will assist you with writing a fix; also note that
-if the problem is with a CMIP6 dataset, we will alert the ESGF and/or the model developers for them to fix the problem
-in the long run; fixes for CMIP5 by the model developers are no longer possible):
+right out the box by filling in the blanks. If needed we will assist you with writing a fix.
+Please check the [ESGF errata service](https://errata.ipsl.fr/static/index.html) to
+see if the problem has already been reported and report it there if it is not.
+Please link to the errata issue in your report here.
 
 - Data file has been changed by you in any way (if you answer yes the issue will be void and closed, we are not
 supporting custom-made datasets that present problems, it is your resposability to fix those problems):
-- Project (CMIP5/CMIP6/OBS/obs4MIPs/etc):
+- Project (CMIP7/CMIP6/obs4MIPs/CORDEX/OBS/etc.):
 - Full dataset description (fill out as many as you know, please):
   - dataset:
+  - ensemble:
   - experiment:
   - mip:
   - grid:
-  - type:
-  - version:
-  - tier:
   - variable used:
-  - data version:
+  - version:
 - Problems encountered (please describe what the actual problems are: e.g. wrong standard name, issue with dimensions):
 - Pointer to existing copy of data on ESGF node (it would be very useful if you could provide a physical
 fullpath to the file(s) that are causing the problem, e.g. on CEDA Jasmin or DKRZ):
 - Other notes and mentions:
 
-**Assign the right people**
-If you are already a member of the ESMValTool GitHub project, please assign Valeriu Predoi (valeriupredoi) and
-Klaus Zimmermann (zklaus) to the issue. They will then check the issue raised and propagate it further to the
-data model developers.
-
 **Please attach**
   - The recipe that you are trying to run, you can find a copy in the `run` directory in the output directory
   - The `main_log_debug.txt` file, this can also be found in the `run` directory in the output directory
diff --git a/.github/workflows/build-and-deploy-on-pypi.yml b/.github/workflows/build-and-deploy-on-pypi.yml
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           fetch-depth: 0
           persist-credentials: false
diff --git a/.github/workflows/citation_file_validator.yml b/.github/workflows/citation_file_validator.yml
@@ -19,7 +19,7 @@ jobs:
     if: github.repository == 'ESMValGroup/ESMValCore' # avoid GAs in forks
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           persist-credentials: false
       - name: Check whether the citation metadata from CITATION.cff is valid
diff --git a/.github/workflows/run-tests-monitor.yml b/.github/workflows/run-tests-monitor.yml
@@ -31,7 +31,7 @@ jobs:
           - test-py314
     name: ${{ matrix.os }} ${{ matrix.environment }}
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           fetch-depth: 0
           persist-credentials: false
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -32,7 +32,7 @@ jobs:
           - test-r
     name: ${{ matrix.os }} ${{ matrix.environment }}
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           fetch-depth: 0
           persist-credentials: false
diff --git a/.github/workflows/update-lockfiles.yml b/.github/workflows/update-lockfiles.yml
@@ -14,7 +14,7 @@ jobs:
   pixi-update:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           fetch-depth: 0
           persist-credentials: false
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -26,7 +26,7 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.15.15"
+    rev: "v0.15.16"
     hooks:
       - id: ruff-check
         args: [--fix]
diff --git a/.zenodo.json b/.zenodo.json
@@ -224,6 +224,11 @@
       "affiliation": "SMHI, Sweden",
       "name": "Lenhardt, Julien",
       "orcid": "https://orcid.org/0000-0002-9949-3989"
+    },
+    {
+      "affiliation": "Climate Resource, Australia",
+      "name": "Lewis, Jared",
+      "orcid": "https://orcid.org/0000-0002-8155-8924"
     }
   ],
   "description": "ESMValCore: A community tool for pre-processing data from Earth system models in CMIP and running analysis scripts.",
diff --git a/CITATION.cff b/CITATION.cff
@@ -228,6 +228,11 @@ authors:
     family-names: Lenhardt
     given-names: Julien
     orcid: "https://orcid.org/0000-0002-9949-3989"
+  -
+    affiliation: "Climate Resource, Australia"
+    family-names: Lewis
+    given-names: Jared
+    orcid: "https://orcid.org/0000-0002-8155-8924"
 
 cff-version: 1.2.0
 date-released: 2026-03-10
diff --git a/doc/recipe/overview.rst b/doc/recipe/overview.rst
@@ -109,6 +109,7 @@ For example, a datasets section could be:
       - {dataset: CanESM2, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
       - {dataset: UKESM1-0-LL, project: CMIP6, exp: historical, ensemble: r1i1p1f2, start_year: 2001, end_year: 2004, grid: gn}
       - {dataset: ACCESS-CM2, project: CMIP6, exp: historical, ensemble: r1i1p1f2, timerange: 'P5Y/*', grid: gn}
+      - {dataset: CCLM4-8-17, project: CORDEX, domain: EUR-11, driver: CNRM-CERFACS-CNRM-CM5, exp: historical, ensemble: r1i1p1, institute: CLMcom, rcm_version: v1, timerange: '2001/2004'}
       - {dataset: EC-EARTH3, alias: custom_alias, project: CMIP6, exp: historical, ensemble: r1i1p1f1, start_year: 2001, end_year: 2004, grid: gn}
       - {dataset: CMCC-CM2-SR5, project: CMIP6, exp: historical, ensemble: r1i1p1f1, timerange: '2001/P10Y', grid: gn}
       - {dataset: HadGEM3-GC31-MM, project: CMIP6, exp: dcppA-hindcast, ensemble: r1i1p1f1, sub_experiment: s2000, grid: gn, start_year: 2000, end_year, 2002}
@@ -378,6 +379,89 @@ When using the ``timerange`` tag to specify the start and end points, possible v
 Note that this section is not required, as datasets can also be provided in the
 Diagnostics_ section.
 
+CORDEX datasets
+---------------
+
+The horizontal coordinates of CORDEX data are often not accurate. Therefore,
+the tool provides the option to specify that the standard CORDEX grid for the
+domain should be used instead of the grid defined in the files. This can be
+enabled by adding ``use_standard_grid: true`` and disabled by adding
+``use_standard_grid: false`` to the dataset definition of the CORDEX data.
+
+For example:
+
+.. code-block:: yaml
+
+  datasets:
+    - dataset: CCLM4-8-17
+      rcm_version: v1
+      driver: CNRM-CERFACS-CNRM-CM5
+      institute: CLMcom
+      project: CORDEX
+      domain: EUR-11
+      exp: historical
+      ensemble: r1i1p1
+      use_standard_grid: true
+
+will use the standard CORDEX grid for the EUR-11 domain, as defined by the
+`py-cordex <https://py-cordex.readthedocs.io>`_ package for datasets on a
+rotated pole grid. For datasets on a Lambert conformal grid, ESMValCore provides
+an algorithm to calculate the standard grid, but this only works if the
+`grid mapping <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.13/cf-conventions.html#grid-mappings-and-projections>`_
+is correct.
+
+This feature is disabled by default, but enabled by default for models with
+known issues through the default
+`CORDEX extra facets file <https://github.com/ESMValGroup/ESMValCore/blob/main/esmvalcore/config/configurations/defaults/extra_facets_cordex.yml>`__.
+
+.. warning::
+
+  If ``use_standard_grid: true`` is used, the tool will overwrite the existing grid
+  information. It is recommended to visualize the resulting data and compare it
+  to easily recognizable features (e.g. coastlines) to make sure the grid is
+  correct before using it in an aggregated manner.
+
+  Example Python script to visualize the grid of a CORDEX dataset and compare it
+  to coastlines:
+
+  .. code-block:: python
+
+      from esmvalcore.dataset import Dataset
+      import iris.quickplot
+      import matplotlib.pyplot as plt
+
+      ds = Dataset(
+          short_name="sftlf",
+          mip="fx",
+          project="CORDEX",
+          domain="EUR-11",
+          dataset="ALADIN63",
+          driver="CNRM-CERFACS-CNRM-CM5",
+          institute="CNRM",
+          exp="historical",
+          ensemble="r1i1p1",
+          rcm_version="v2",
+          use_standard_grid=True,
+      )
+      cube = ds.load()
+
+      plt.figure()
+      iris.quickplot.pcolormesh(
+          cube,
+          coords=["projection_x_coordinate", "projection_y_coordinate"],
+      )
+      plt.gca().coastlines()
+
+      plt.figure()
+      iris.quickplot.pcolormesh(
+          cube,
+          coords=["longitude", "latitude"],
+      )
+      plt.gca().coastlines()
+
+      plt.show()
+
+
 .. _`yaml`: https://yaml.org/refcard.html
 
 .. _Preprocessors:
diff --git a/esmvalcore/_main.py b/esmvalcore/_main.py
@@ -607,7 +607,7 @@ def version(self):
         for project, version in self._extra_packages.items():
             print(f"{project}: {version}")  # noqa: T201
 
-    def run(self, recipe, **kwargs):
+    def run(self, recipe, session_name=None, **kwargs):
         """Execute an ESMValTool recipe.
 
         `esmvaltool run` executes the given recipe. To see a list of available
@@ -617,6 +617,15 @@ def run(self, recipe, **kwargs):
         A list of possible flags is given here:
         https://docs.esmvaltool.org/projects/ESMValCore/en/latest/quickstart/configure.html#configuration-options
 
+        Parameters
+        ----------
+        recipe:
+            Path to the recipe to run.
+        session_name:
+            Name of the session output subdirectory (relative to the configured ``output_dir``).
+            When given, this value is used instead of the default ``<recipe.stem>_<timestamp>``.
+
+            If the given name already exists, a suffix is added to the session name to avoid overwriting existing data.
         """
         from .config import CFG
         from .exceptions import InvalidConfigParameter
@@ -651,6 +660,8 @@ def run(self, recipe, **kwargs):
 
         CFG["resume_from"] = parse_resume(CFG["resume_from"], recipe)
         session = CFG.start_session(recipe.stem)
+        if session_name is not None:
+            session.session_name = str(session_name)
 
         self._run(recipe, session, cli_config_dir)
 
diff --git a/esmvalcore/_recipe/to_datasets.py b/esmvalcore/_recipe/to_datasets.py
@@ -252,7 +252,10 @@ def _append_missing_supplementaries(
 
             supplementary_facets: Facets = {
                 facet: "*"
-                for facet in FACETS.get(project, ["mip"])
+                for facet in (
+                    *tuple(FACETS.get(project, [])),
+                    "mip",
+                )
                 if facet not in _CMOR_KEYS + tuple(INHERITED_FACETS)
             }
             for key in ("frequency", "version"):
diff --git a/esmvalcore/cmor/_fixes/cordex/cnrm_cerfacs_cnrm_cm5/aladin53.py b/esmvalcore/cmor/_fixes/cordex/cnrm_cerfacs_cnrm_cm5/aladin53.py
@@ -0,0 +1,32 @@
+"""Fixes for rcm ALADIN53 driven by CNRM-CERFACS-CNRM-CM5."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from esmvalcore.cmor.fix import Fix
+
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
+    from iris.cube import Cube
+
+
+class Sftlf(Fix):
+    """Fixes for sftlf."""
+
+    def fix_metadata(self, cubes: Sequence[Cube]) -> Sequence[Cube]:
+        for cube in cubes:
+            cube.units = "1"
+            cube.convert_units(self.vardef.units)
+        return cubes
+
+
+class Ts(Fix):
+    """Fixes for ts."""
+
+    def fix_metadata(self, cubes: Sequence[Cube]) -> Sequence[Cube]:
+        for cube in cubes:
+            cube.units = "deg_C"
+            cube.convert_units(self.vardef.units)
+        return cubes
diff --git a/esmvalcore/cmor/_fixes/cordex/cordex_fixes.py b/esmvalcore/cmor/_fixes/cordex/cordex_fixes.py
diff --git a/esmvalcore/cmor/_fixes/fix.py b/esmvalcore/cmor/_fixes/fix.py
diff --git a/esmvalcore/config/configurations/defaults/extra_facets_cordex.yml b/esmvalcore/config/configurations/defaults/extra_facets_cordex.yml
diff --git a/esmvalcore/io/esgf/facets.py b/esmvalcore/io/esgf/facets.py
diff --git a/tests/integration/cmor/_fixes/cordex/test_cnrm_cerfacs_cnrm_cm5.py b/tests/integration/cmor/_fixes/cordex/test_cnrm_cerfacs_cnrm_cm5.py
diff --git a/tests/integration/cmor/_fixes/cordex/test_cordex_fixes.py b/tests/integration/cmor/_fixes/cordex/test_cordex_fixes.py
diff --git a/tests/unit/main/test_esmvaltool.py b/tests/unit/main/test_esmvaltool.py
