Merge branch 'main' into python3.14

Author: valeriupredoi

.circleci/config.yml

@@ -200,10 +200,11 @@ jobs:
             # https://docs.esmvaltool.org/en/latest/quickstart/installation.html#install-from-source
             . /opt/conda/etc/profile.d/conda.sh
             mkdir /logs
-            # Temporarily install intake-esgf here until it is an ESMValCore dependency in v2.14.
-            echo "  - intake-esgf" >> environment.yml
             conda env create -n esmvaltool -f environment.yml --verbose
             conda activate esmvaltool
+            # Temporarily install intake-esgf here until there is a new release
+            # that includes https://github.com/esgf2-us/intake-esgf/pull/160.
+            pip install git+https://github.com/esgf2-us/intake-esgf@main
             mamba list >> /logs/conda.txt
             pip install --no-deps --editable .[develop]
             git clone https://github.com/ESMValGroup/ESMValCore $HOME/ESMValCore
@@ -215,7 +216,13 @@ jobs:
           command: |
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
-            esmvaltool config copy data-esmvalcore-esgf.yml
+            esmvaltool config copy data-intake-esgf.yml
+            python -c '
+            import intake_esgf
+            intake_esgf.conf["solr_indices"]["esgf.ceda.ac.uk"] = True
+            intake_esgf.conf["solr_indices"]["esgf-data.dkrz.de"] = True
+            intake_esgf.conf.save()
+            '
             for recipe in esmvaltool/recipes/testing/recipe_*.yml; do
               esmvaltool run --max-parallel-tasks=2 "$recipe"
             done

conda-linux-64.lock

@@ -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

esmvaltool/cmorizers/data/cmor_config/WOA.yml

@@ -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:

esmvaltool/cmorizers/data/downloaders/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

esmvaltool/cmorizers/data/formatters/datasets/woa.py

@@ -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

esmvaltool/recipes/examples/recipe_check_obs.yml

@@ -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}
+}

esmvaltool/references/woa2023.bibtex

@@ -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: