Merge remote-tracking branch 'origin/main' into local_time_preproc

.circleci/config.yml

@@ -182,7 +182,7 @@ jobs:
     # Test building documentation
     docker:
       - image: condaforge/mambaforge
-    resource_class: small
+    resource_class: medium
     steps:
       - checkout
       - run:

.github/workflows/build-and-deploy-on-pypi.yml

@@ -12,12 +12,18 @@ jobs:
   build-n-publish:
     name: Build and publish ESMValCore on PyPi
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/ESMValCore/
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Set up Python 3.11
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: "3.11"
       - name: Install pep517
@@ -34,14 +40,10 @@ jobs:
           --binary
           --out-dir dist/
           .
-      #- name: Publish distribution 📦 to Test PyPI
-      #  uses: pypa/gh-action-pypi-publish@master
-      #  with:
-      #    password: ${{ secrets.test_pypi_password }}
-      #    repository_url: https://test.pypi.org/legacy/
+      # - name: Publish distribution to Test PyPI
+      #   uses: pypa/gh-action-pypi-publish@release/v1
+      #   with:
+      #     repository-url: https://test.pypi.org/legacy/
       - name: Publish distribution 📦 to PyPI
         if: startsWith(github.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}

CITATION.cff

@@ -201,11 +201,11 @@ authors:
     given-names: Joerg
 
 cff-version: 1.2.0
-date-released: 2023-11-01
+date-released: 2023-12-19
 doi: "10.5281/zenodo.3387139"
 license: "Apache-2.0"
 message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/ESMValGroup/ESMValCore/"
 title: ESMValCore
-version: "v2.10.0rc1"
+version: "v2.10.0"
 ...

doc/conf.py

@@ -60,6 +60,7 @@
     'nbsphinx',
     'sphinx.ext.autodoc',
     'sphinx.ext.doctest',
+    'sphinx.ext.extlinks',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
@@ -450,6 +451,36 @@
     'scipy': ('https://docs.scipy.org/doc/scipy/', None),
 }
 
+# -- Extlinks extension -------------------------------------------------------
+# See https://www.sphinx-doc.org/en/master/usage/extensions/extlinks.html
+
+extlinks = {
+    "discussion": (
+        "https://github.com/ESMValGroup/ESMValCore/discussions/%s",
+        "Discussion #%s",
+    ),
+    "issue": (
+        "https://github.com/ESMValGroup/ESMValCore/issues/%s",
+        "Issue #%s",
+    ),
+    "pull": (
+        "https://github.com/ESMValGroup/ESMValCore/pull/%s",
+        "Pull request #%s",
+    ),
+    "release": (
+        "https://github.com/ESMValGroup/ESMValCore/releases/tag/%s",
+        "ESMValCore %s",
+    ),
+    "team": (
+        "https://github.com/orgs/ESMValGroup/teams/%s",
+        "@ESMValGroup/%s",
+    ),
+    "user": (
+        "https://github.com/%s",
+        "@%s",
+    ),
+}
+
 # -- Custom Document processing ----------------------------------------------
 
 sys.path.append(os.path.dirname(__file__))

doc/quickstart/configure.rst

@@ -243,8 +243,7 @@ Extensive documentation on setting up Dask Clusters is available
 
   If not all preprocessor functions support lazy data, computational
   performance may be best with the default scheduler.
-  See `issue #674 <https://github.com/ESMValGroup/ESMValCore/issues/674>`_ for
-  progress on making all preprocessor functions lazy.
+  See :issue:`674` for progress on making all preprocessor functions lazy.
 
 **Example configurations**
 

environment.yml

@@ -20,7 +20,7 @@ dependencies:
   - geopy
   - humanfriendly
   - importlib_metadata  # required for Python < 3.10
-  - iris >=3.6.0
+  - iris >=3.6.1
   - iris-esmf-regrid >=0.7.0
   - isodate
   - jinja2
@@ -37,7 +37,7 @@ dependencies:
   - psutil
   - py-cordex
   - pybtex
-  - python >=3.9
+  - python >=3.9,<3.12
   - python-stratify >=0.3
   - pyyaml
   - requests

esmvalcore/cmor/_fixes/cmip6/mpi_esm1_2_hr.py

@@ -47,6 +47,10 @@ def fix_metadata(self, cubes):
         return cubes
 
 
+class Tasmax(Tas):
+    """Fixes for tasmax."""
+
+
 class Ta(Fix):
     """Fixes for ta."""
 
@@ -100,3 +104,11 @@ def fix_metadata(self, cubes):
             add_scalar_height_coord(cube, height=10.0)
 
         return cubes
+
+
+class Uas(SfcWind):
+    """Fixes for uas."""
+
+
+class Vas(SfcWind):
+    """Fixes for vas."""

esmvalcore/cmor/_fixes/cmip6/mpi_esm1_2_xr.py

@@ -9,6 +9,14 @@ class Tas(BaseTas):
     """Fixes for tas."""
 
 
+class Tasmax(BaseTas):
+    """Fixes for tasmax."""
+
+
+class Tasmin(BaseTas):
+    """Fixes for tasmin."""
+
+
 class Ta(BaseFix):
     """Fixes for ta."""
 
@@ -27,3 +35,11 @@ class Ua(BaseFix):
 
 class SfcWind(BaseSfcWind):
     """Fixes for sfcWind."""
+
+
+class Uas(BaseSfcWind):
+    """Fixes for uas."""
+
+
+class Vas(BaseSfcWind):
+    """Fixes for vas."""

setup.py

@@ -58,7 +58,7 @@
         'scipy>=1.6',
         # See the following issue for info on the iris pin below:
         # https://github.com/ESMValGroup/ESMValTool/issues/3239#issuecomment-1613298587
-        'scitools-iris>=3.4.0',
+        'scitools-iris>=3.6.1',
         'shapely>=2.0.0',
         'stratify>=0.3',
         'yamale',

tests/integration/cmor/_fixes/cmip6/test_mpi_esm1_2_hr.py

@@ -1,9 +1,19 @@
 """Test fixes for MPI-ESM1-2-HR."""
 import iris
-
-from esmvalcore.cmor._fixes.cmip6.mpi_esm1_2_hr import AllVars, Cl, Cli, Clw
+import pytest
+from cf_units import Unit
+
+from esmvalcore.cmor._fixes.cmip6.mpi_esm1_2_hr import (
+    AllVars,
+    Cl,
+    Cli,
+    Clw,
+    SfcWind,
+    Tas,
+)
 from esmvalcore.cmor._fixes.common import ClFixHybridPressureCoord
 from esmvalcore.cmor._fixes.fix import Fix
+from esmvalcore.cmor.table import get_var_info
 
 
 def test_get_allvars_fix():
@@ -42,6 +52,58 @@ def test_allvars_r2i1p1f1():
     assert fixed_cubes[1].coord('latitude').points[0] == -86.49036676628
 
 
+@pytest.fixture
+def sfcwind_cubes():
+    correct_lat_coord = iris.coords.DimCoord([0.0],
+                                             var_name='lat',
+                                             standard_name='latitude')
+    wrong_lat_coord = iris.coords.DimCoord([0.0],
+                                           var_name='latitudeCoord',
+                                           standard_name='latitude')
+    correct_lon_coord = iris.coords.DimCoord([0.0],
+                                             var_name='lon',
+                                             standard_name='longitude')
+    wrong_lon_coord = iris.coords.DimCoord([0.0],
+                                           var_name='longitudeCoord',
+                                           standard_name='longitude')
+    correct_cube = iris.cube.Cube([[10.0]], var_name='sfcWind',
+                                  dim_coords_and_dims=[(correct_lat_coord, 0),
+                                                       (correct_lon_coord, 1)]
+                                  )
+    wrong_cube = iris.cube.Cube([[10.0]],
+                                var_name='ta',
+                                dim_coords_and_dims=[(wrong_lat_coord, 0),
+                                                     (wrong_lon_coord, 1)])
+    scalar_cube = iris.cube.Cube(0.0, var_name='ps')
+    return iris.cube.CubeList([correct_cube, wrong_cube, scalar_cube])
+
+
+@pytest.fixture
+def tas_cubes():
+    correct_lat_coord = iris.coords.DimCoord([0.0],
+                                             var_name='lat',
+                                             standard_name='latitude')
+    wrong_lat_coord = iris.coords.DimCoord([0.0],
+                                           var_name='latitudeCoord',
+                                           standard_name='latitude')
+    correct_lon_coord = iris.coords.DimCoord([0.0],
+                                             var_name='lon',
+                                             standard_name='longitude')
+    wrong_lon_coord = iris.coords.DimCoord([0.0],
+                                           var_name='longitudeCoord',
+                                           standard_name='longitude')
+    correct_cube = iris.cube.Cube([[10.0]],
+                                  var_name='tas',
+                                  dim_coords_and_dims=[(correct_lat_coord, 0),
+                                                       (correct_lon_coord, 1)])
+    wrong_cube = iris.cube.Cube([[10.0]],
+                                var_name='ta',
+                                dim_coords_and_dims=[(wrong_lat_coord, 0),
+                                                     (wrong_lon_coord, 1)])
+    scalar_cube = iris.cube.Cube(0.0, var_name='ps')
+    return iris.cube.CubeList([correct_cube, wrong_cube, scalar_cube])
+
+
 def test_get_cl_fix():
     """Test getting of fix."""
     fixes = Fix.get_fixes('CMIP6', 'MPI-ESM1-2-HR', 'Amon', 'cl')
@@ -73,3 +135,51 @@ def test_get_clw_fix():
 def test_clw_fix():
     """Test fix for ``clw``."""
     assert Clw is ClFixHybridPressureCoord
+
+
+def test_get_sfcwind_fix():
+    fixes = Fix.get_fixes('CMIP6', 'MPI_ESM1_2_HR', 'day', 'sfcWind')
+    assert SfcWind(None) in fixes
+
+
+def test_sfcwind_fix_metadata(sfcwind_cubes):
+    for cube in sfcwind_cubes:
+        with pytest.raises(iris.exceptions.CoordinateNotFoundError):
+            cube.coord('height')
+    height_coord = iris.coords.AuxCoord(10.0,
+                                        var_name='height',
+                                        standard_name='height',
+                                        long_name='height',
+                                        units=Unit('m'),
+                                        attributes={'positive': 'up'})
+    vardef = get_var_info('CMIP6', 'day', 'sfcWind')
+    fix = SfcWind(vardef)
+
+    out_cubes = fix.fix_metadata(sfcwind_cubes)
+    assert out_cubes[0].var_name == 'sfcWind'
+    coord = out_cubes[0].coord('height')
+    assert coord == height_coord
+
+
+def test_get_tas_fix():
+    fixes = Fix.get_fixes('CMIP6', 'MPI_ESM1_2_HR', 'day', 'tas')
+    assert Tas(None) in fixes
+
+
+def test_tas_fix_metadata(tas_cubes):
+    for cube in tas_cubes:
+        with pytest.raises(iris.exceptions.CoordinateNotFoundError):
+            cube.coord('height')
+    height_coord = iris.coords.AuxCoord(2.0,
+                                        var_name='height',
+                                        standard_name='height',
+                                        long_name='height',
+                                        units=Unit('m'),
+                                        attributes={'positive': 'up'})
+    vardef = get_var_info('CMIP6', 'day', 'tas')
+    fix = Tas(vardef)
+
+    out_cubes = fix.fix_metadata(tas_cubes)
+    assert out_cubes[0].var_name == 'tas'
+    coord = out_cubes[0].coord('height')
+    assert coord == height_coord