Merge branch 'main' into impact_diagnostics

lauracasp · lauracasp · commit 5d2f160b8848 · 2026-05-07T13:50:54.000+02:00
diff --git a/.github/workflows/create-condalock-file.yml b/.github/workflows/create-condalock-file.yml
@@ -24,7 +24,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           auto-update-conda: true
           activate-environment: esmvaltool-fromlock
diff --git a/.github/workflows/install-from-conda.yml b/.github/workflows/install-from-conda.yml
@@ -24,7 +24,7 @@ jobs:
         python-version: ["3.12", "3.13"]
     name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           python-version: ${{ matrix.python-version }}
           miniforge-version: "latest"
@@ -63,7 +63,7 @@ jobs:
 #    name: OSX Python ${{ matrix.python-version }}
 #    steps:
 #      - uses: actions/checkout@v2
-#      - uses: conda-incubator/setup-miniconda@v3
+#      - uses: conda-incubator/setup-miniconda@v4
 #        with:
 #          python-version: ${{ matrix.python-version }}
 #          miniconda-version: "latest"
diff --git a/.github/workflows/install-from-condalock-file.yml b/.github/workflows/install-from-condalock-file.yml
@@ -38,7 +38,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: esmvaltool-fromlock
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/install-from-source.yml b/.github/workflows/install-from-source.yml
@@ -27,7 +27,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: esmvaltool
           environment-file: environment.yml
@@ -66,7 +66,7 @@ jobs:
 #    name: OSX Python ${{ matrix.python-version }}
 #    steps:
 #      - uses: actions/checkout@v2
-#      - uses: conda-incubator/setup-miniconda@v3
+#      - uses: conda-incubator/setup-miniconda@v4
 #        with:
 #          activate-environment: esmvaltool
 #          environment-file: environment.yml
diff --git a/.github/workflows/pypi-build-and-deploy.yml b/.github/workflows/pypi-build-and-deploy.yml
@@ -58,4 +58,4 @@ jobs:
           name: python-package-distributions
           path: dist/
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.13.0
+        uses: pypa/gh-action-pypi-publish@v1.14.0
diff --git a/.github/workflows/run-tests-monitor.yml b/.github/workflows/run-tests-monitor.yml
@@ -30,7 +30,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: esmvaltool
           environment-file: environment.yml
@@ -73,7 +73,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           architecture: ${{ matrix.architecture }}
           activate-environment: esmvaltool
diff --git a/.github/workflows/test-development.yml b/.github/workflows/test-development.yml
@@ -33,7 +33,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: esmvaltool
           environment-file: environment.yml
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -27,7 +27,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: esmvaltool
           environment-file: environment.yml
@@ -74,7 +74,7 @@ jobs:
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           architecture: ${{ matrix.architecture }}
           activate-environment: esmvaltool
diff --git a/conda-linux-64.lock b/conda-linux-64.lock
diff --git a/doc/sphinx/source/faq.rst b/doc/sphinx/source/faq.rst
@@ -22,8 +22,7 @@ encountered this language before. The key information about this format is:
 - yaml is case sensitive;
 
 More information can be found in the `yaml tutorial
-<https://learnxinyminutes.com/docs/yaml/>`_ and `yaml quick reference card
-<https://yaml.org/refcard.html>`_. ESMValTool uses the `yamllint
+<https://learnxinyminutes.com/docs/yaml/>`_. ESMValTool uses the `yamllint
 <https://www.yamllint.com>`_ linter tool to check recipe syntax.
 
 
diff --git a/environment.yml b/environment.yml
@@ -10,7 +10,6 @@ channels:
 
 dependencies:
   - aiohttp
-  - arviz
   - cartopy
   - cdo >=2.3.0
   - cdsapi
diff --git a/environment_osx.yml b/environment_osx.yml
@@ -10,7 +10,6 @@ channels:
 
 dependencies:
   - aiohttp
-  - arviz
   - cartopy
   - cdo >=2.3.0
   - cdsapi
diff --git a/esmvaltool/cmorizers/data/cmor_config/WOA.yml b/esmvaltool/cmorizers/data/cmor_config/WOA.yml
@@ -13,29 +13,29 @@ attributes:
   # source: 'https://www.ncei.noaa.gov/data/oceans/woa/WOA13/DATAv2/'
   # reference: 'woa2013v2'
 
-  # WOA18
+  # WOA23
   project_id: OBS6
-  short_name: woa18
-  version: '2018'
-  source: 'https://www.ncei.noaa.gov/data/oceans/woa/WOA18/DATA/'
-  reference: 'woa2018'
+  short_name: woa23
+  version: '2023'
+  source: 'https://www.ncei.noaa.gov/data/oceans/woa/WOA23/DATA/'
+  reference: 'woa2023'
 
   comment: ''
 
 # Variables to cmorize (here use only filename prefix)
-# Temperature and salinity from 1981-2010 climatology (81B0)
+# decav seven decadal means 1955 - 2022 # WOA23 update
 variables:
   thetao:
     mip: Omon
     raw_var: t_an
     name: temperature
-    file: decav81B0_t
+    file: decav_t
     srf_var: tos
   so:
     mip: Omon
     raw_var: s_an
     name: salinity
-    file: decav81B0_s
+    file: decav_s
     srf_var: sos
   o2:
     mip: Oyr
@@ -61,4 +61,4 @@ variables:
 # Custom dictionary for this cmorizer
 custom:
   reference_year: 2000
-  resolution: '1.00'
+  resolution: '1.00' # 0.25 or 1.00 available for temperature and salinity
diff --git a/esmvaltool/cmorizers/data/downloaders/datasets/woa.py b/esmvaltool/cmorizers/data/downloaders/datasets/woa.py
@@ -43,17 +43,17 @@ def download_dataset(
 
     def download(file):
         downloader.download_file(
-            "https://www.ncei.noaa.gov/data/oceans/woa/WOA18/DATA/" + file,
+            "https://www.ncei.noaa.gov/data/oceans/woa/WOA23/DATA/" + file,
             wget_options=[],
         )
 
     data_paths = [
-        "nitrate/netcdf/all/1.00/woa18_all_n00_01.nc",
-        "oxygen/netcdf/all/1.00/woa18_all_o00_01.nc",
-        "phosphate/netcdf/all/1.00/woa18_all_p00_01.nc",
-        "salinity/netcdf/decav81B0/1.00/woa18_decav81B0_s00_01.nc",
-        "silicate/netcdf/all/1.00/woa18_all_i00_01.nc",
-        "temperature/netcdf/decav81B0/1.00/woa18_decav81B0_t00_01.nc",
+        "nitrate/netcdf/all/1.00/woa23_all_n00_01.nc",
+        "oxygen/netcdf/all/1.00/woa23_all_o00_01.nc",
+        "phosphate/netcdf/all/1.00/woa23_all_p00_01.nc",
+        "salinity/netcdf/decav/1.00/woa23_decav_s00_01.nc",
+        "silicate/netcdf/all/1.00/woa23_all_i00_01.nc",
+        "temperature/netcdf/decav/1.00/woa23_decav_t00_01.nc",
     ]
 
     for source_file in data_paths:
diff --git a/esmvaltool/cmorizers/data/formatters/datasets/esacci_cloud.py b/esmvaltool/cmorizers/data/formatters/datasets/esacci_cloud.py
@@ -196,8 +196,6 @@ def _concatenate_and_save_monthly_cubes(
 
     if attach == "-AMPM":
         cube = monthly_statistics(cube)
-        cube.remove_coord("month_number")
-        cube.remove_coord("year")
 
     # Regrid the cube to the target grid (e.g., 0.5x0.5)
     cube = regrid(cube, target_grid="0.5x0.5", scheme="area_weighted")
diff --git a/esmvaltool/cmorizers/data/formatters/datasets/woa.py b/esmvaltool/cmorizers/data/formatters/datasets/woa.py
@@ -4,6 +4,7 @@
    Tier 2: other freely-available dataset.
 
 Source
+   WOA23: https://www.ncei.noaa.gov/data/oceans/woa/WOA23/DATA
    WOA18: https://www.ncei.noaa.gov/data/oceans/woa/WOA18/DATA
    WOA13: https://www.ncei.noaa.gov/data/oceans/woa/WOA13/DATAv2
 
@@ -24,6 +25,7 @@
 
 
 Modification history
+   20230213-chun_felicity: WOA23 update
    20210311-lovato_tomas: handle WOA18/WOA13, raw data download, use OBS6
    20200911-bock_lisa: extend to WOA18
    20190328-lovato_tomas: cmorizer revision
@@ -53,7 +55,7 @@ def _fix_data(cube, var, version):
     """Specific data fixes for different variables."""
     logger.info("Fixing data ...")
 
-    if version == "2018":
+    if version in ["2018", "2023"]:
         with constant_metadata(cube):
             if var in ["o2", "po4", "si", "no3"]:
                 cube /= 1000.0  # Convert from umol/kg to mol/m^3
diff --git a/esmvaltool/diag_scripts/fire/diagnostic_run_confire.py b/esmvaltool/diag_scripts/fire/diagnostic_run_confire.py
@@ -22,7 +22,6 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-import arviz as az
 import cartopy.crs as ccrs
 import cf_units
 import iris
@@ -32,6 +31,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+import xarray as xr
 from matplotlib.colors import ListedColormap
 
 from esmvaltool.diag_scripts.shared import ProvenanceLogger
@@ -357,11 +357,11 @@ def _select_post_param_name(name: str) -> np.array:
         return np.reshape(out, new_shape)
 
     try:
-        trace = az.from_netcdf(trace, engine="netcdf4")
+        trace = xr.open_datatree(trace, engine="netcdf4")
     except (ValueError, OSError) as expt:
         logger.debug("_select_post_param error %s", expt)
-    params = trace.to_dict()["posterior"]
-    params_names = params.keys()
+    params = trace["posterior"]
+    params_names = list(trace["posterior"].data_vars)
     params = [_select_post_param_name(var) for var in params_names]
     return params, list(params_names)
 
@@ -458,9 +458,11 @@ def _read_variable_from_netcdf(
             callback=_sort_time,
         )
     else:
+        # Fallback for CMIP7 data for tasmax
+        var = "tas" if "tasmax/tas_tmaxavg" in filename[0] else filename[1]
         dataset = iris.load_raw(
             Path(directory) / filename[0],
-            filename[1],
+            var,
             callback=_sort_time,
         )
     dataset = dataset[0]
diff --git a/esmvaltool/diag_scripts/fire/fire_diagnostic.py b/esmvaltool/diag_scripts/fire/fire_diagnostic.py
@@ -341,7 +341,15 @@ def main(cfg: dict) -> None:
         vars_file = {}
         for i, attributes in enumerate(group):
             logger.info("Variable %s", attributes["short_name"])
-            vars_file[attributes["short_name"]] = attributes
+            # Fallback for CMIP7 data for tasmax
+            short_name_key = (
+                "tasmax"
+                if attributes.get("branding_suffix")
+                and attributes["short_name"] == "tas"
+                and "tmax" in attributes["branding_suffix"]
+                else attributes["short_name"]
+            )
+            vars_file[short_name_key] = attributes
             # Save model information for output plot name
             if i == 0:
                 plot_file_info = "_".join(
diff --git a/esmvaltool/recipes/examples/recipe_check_obs.yml b/esmvaltool/recipes/examples/recipe_check_obs.yml
@@ -1179,7 +1179,7 @@ diagnostics:
         mip: Oyr
     additional_datasets:
       - {dataset: WOA, project: OBS6, tier: 2,
-         type: clim, version: 2018, start_year: 2000, end_year: 2000}
+         type: clim, version: 2023, start_year: 2000, end_year: 2000}
       - {dataset: WOA, project: OBS, tier: 2,
          type: clim, version: 2013v2, start_year: 2000, end_year: 2000}
     scripts: null
diff --git a/esmvaltool/references/woa2023.bibtex b/esmvaltool/references/woa2023.bibtex
@@ -0,0 +1,8 @@
+@misc{https://doi.org/10.25921/va26-hv25,
+  doi = {10.25921/VA26-HV25},
+  url = {https://www.ncei.noaa.gov/archive/accession/NCEI-WOA23},
+  author = {Reagan,  James R. and Boyer,  Tim P. and García,  Hernán E. and Locarnini,  Ricardo A. and Baranova,  Olga K. and Bouchard,  Courtney and Cross,  Scott L. and Mishonov,  Alexey V. and Paver,  Christopher R. and Seidov,  Dan and Wang,  Zhankun and Dukhovskoy,  Dmitry},
+  title = {World Ocean Atlas 2023},
+  publisher = {NOAA National Centers for Environmental Information},
+  year = {2023}
+}
diff --git a/esmvaltool/utils/recipe_test_workflow/opt/rose-suite-jasmin.conf b/esmvaltool/utils/recipe_test_workflow/opt/rose-suite-jasmin.conf
@@ -2,9 +2,9 @@
 DRS_CMIP5="BADC"
 DRS_CMIP6="BADC"
 ENV_NAME="latest"
-KGO_ROOT_PATH="/gws/nopw/j04/esmeval/KGO"
+KGO_ROOT_PATH="/gws/ssde/j25a/esmeval/KGO"
 ROOTPATH_CMIP5="/badc/cmip5/data/cmip5/output1"
 ROOTPATH_CMIP6="/badc/cmip6/data/CMIP6"
-ROOTPATH_OBS="/gws/nopw/j04/esmeval/obsdata-v2"
-ROOTPATH_OBS4MIPS="/gws/nopw/j04/esmeval/obsdata-v2"
+ROOTPATH_OBS="/gws/ssde/j25a/esmeval/obsdata-v2"
+ROOTPATH_OBS4MIPS="/gws/ssde/j25a/esmeval/obsdata-v2"
 SITE="jasmin"
diff --git a/pyproject.toml b/pyproject.toml
@@ -31,7 +31,6 @@ dynamic = [
 ]
 dependencies = [
     "aiohttp",
-    "arviz",
     "cartopy",
     "cdo",
     "cdsapi",
diff --git a/tests/integration/test_cmorizer.py b/tests/integration/test_cmorizer.py
@@ -87,12 +87,12 @@ def put_dummy_data(data_path: Path) -> None:
     """Create a small dummy netCDF file to be cmorized."""
     data_info = [
         # dir_name, file_name_prefix, var_name
-        ("temperature", "woa18_decav81B0_t", "t_an"),
-        ("salinity", "woa18_decav81B0_s", "s_an"),
-        ("oxygen", "woa18_all_o", "o_an"),
-        ("nitrate", "woa18_all_n", "n_an"),
-        ("phosphate", "woa18_all_p", "p_an"),
-        ("silicate", "woa18_all_i", "i_an"),
+        ("temperature", "woa23_decav_t", "t_an"),
+        ("salinity", "woa23_decav_s", "s_an"),
+        ("oxygen", "woa23_all_o", "o_an"),
+        ("nitrate", "woa23_all_n", "n_an"),
+        ("phosphate", "woa23_all_p", "p_an"),
+        ("silicate", "woa23_all_i", "i_an"),
     ]
 
     for dir_name, file_name_prefix, var_name in data_info:
