update cmorizer

Author: bettina-gier

esmvaltool/cmorizers/data/cmor_config/CarboScope.yml

@@ -1,15 +1,15 @@
 ---
 # Filename (will be extended by variable name)
-filename: 'nbetEXToc_v2024E.flux.nc'
+filename: 'nbetEXToc_v2025.flux.nc'
 
 attributes:
   dataset_id: CarboScope
-  version: 'v2024E'
+  version: 'v2025'
   tier: 2
-  modeling_realm: reanaly
+  type: reanaly
   project_id: OBS6
-  source: 'https://www.bgc-jena.mpg.de/CarboScope/?file=nbetEXToc_v2024E.flux.nc'
-  reference: 'carboscope2024'
+  source: 'https://www.bgc-jena.mpg.de/CarboScope/?file=nbetEXToc_v2025.flux.nc'
+  reference: 'carboscope2025'
   comment: ''
 
 # Variables to cmorize

esmvaltool/cmorizers/data/datasets.yml

@@ -124,7 +124,7 @@ datasets:
   CarboScope:
     tier: 2
     source: https://www.bgc-jena.mpg.de/CarboScope/?ID=s
-    last_access: 2024-09-09
+    last_access: 2026-07-16
     info: |
       Data is freely available.
       For previous versions, click on archive of outdated results.

esmvaltool/cmorizers/data/downloaders/datasets/carboscope.py

@@ -8,14 +8,19 @@
 
 
 def download_dataset(
-    config, dataset, dataset_info, start_date, end_date, overwrite
+    original_data_dir,
+    dataset,
+    dataset_info,
+    start_date,
+    end_date,
+    overwrite,
 ):
     """Download dataset.
 
     Parameters
     ----------
-    config : dict
-        ESMValTool's user configuration
+    original_data_dir : Path
+        Directory where original data will be stored.
     dataset : str
         Name of the dataset
     dataset_info : dict
@@ -28,14 +33,14 @@ def download_dataset(
         Overwrite already downloaded files
     """
     downloader = WGetDownloader(
-        config=config,
+        original_data_dir=original_data_dir,
         dataset=dataset,
         dataset_info=dataset_info,
         overwrite=overwrite,
     )
 
     downloader.download_file(
         "https://www.bgc-jena.mpg.de/CarboScope/s/INVERSION/OUTPUT/"
-        "nbetEXToc_v2024E/nbetEXToc_v2024E.flux.nc",
+        "nbetEXToc_v2025/nbetEXToc_v2025.flux.nc",
         [],
     )

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

@@ -6,16 +6,16 @@
 Source
     v2020:
         https://www.bgc-jena.mpg.de/CarboScope/?ID=sEXTocNEET_v2020
-    v2024:
-        https://www.bgc-jena.mpg.de/CarboScope/?file=nbetEXToc_v2024E.flux.nc
+    v2025:
+        https://www.bgc-jena.mpg.de/CarboScope/?file=nbetEXToc_v2025.flux.nc
 
 Last access
-    20240909
+    20260716
 
 Download and processing instructions
     Download the file corresponding to the version you require:
     v2020: 'sEXTocNEET_v2020_daily.nc.gz'.
-    v2024: nbetEXToc_v2024E.flux.nc
+    v2025: nbetEXToc_v2025.flux.nc
 
 """
 
@@ -28,10 +28,9 @@
 
 import dask.array as da
 import iris
-from iris import NameConstraint
 from cf_units import Unit
-
 from esmvalcore.preprocessor import monthly_statistics
+from iris import NameConstraint
 
 from esmvaltool.cmorizers.data import utilities as utils
 
@@ -47,29 +46,31 @@ def _clean(filepath):
 
 def _calculate_flux(cube, filename, area_type):
     """Calculate flux (dividing by land/sea area) and mask land/sea."""
-    if area_type == 'land':
+    if area_type == "land":
         area_idx = 0
-    elif area_type == 'ocean':
+    elif area_type == "ocean":
         area_idx = 1
     else:
         raise ValueError(
-            f"Expected 'land' or 'ocean' for 'area_type', got '{area_type}'")
+            f"Expected 'land' or 'ocean' for 'area_type', got '{area_type}'"
+        )
 
     # Get land/sea area fraction
     with warnings.catch_warnings():
         warnings.filterwarnings(
-            'ignore',
+            "ignore",
             message="Ignoring netCDF variable '.*?' invalid units '.*?'",
             category=UserWarning,
-            module='iris',
+            module="iris",
+        )
+        area_cube = iris.load_cube(
+            str(filename), NameConstraint(var_name="area")
         )
-        area_cube = iris.load_cube(str(filename),
-                                   NameConstraint(var_name='area'))
     area = area_cube[area_idx].core_data()
     area = da.broadcast_to(area, cube.shape)
 
     # Mask
-    mask = (area == 0.0)
+    mask = area == 0.0
     area = da.ma.masked_array(area, mask=mask)
     cube.data = da.ma.masked_array(cube.core_data(), mask=mask)
 
@@ -79,7 +80,7 @@ def _calculate_flux(cube, filename, area_type):
 
     # Adapt metadata
     cube.units /= area_cube.units
-    cube.attributes['positive'] = 'down'
+    cube.attributes["positive"] = "down"
 
     return cube
 
@@ -89,78 +90,85 @@ def _load_cube(filename, raw_name):
     logger.info("Loading '%s' from file %s", raw_name, filename)
     with warnings.catch_warnings():
         warnings.filterwarnings(
-            'ignore',
+            "ignore",
             message="Ignoring netCDF variable '.*?' invalid units '.*?'",
             category=UserWarning,
-            module='iris',
+            module="iris",
         )
-        cube = iris.load_cube(str(filename),
-                              NameConstraint(var_name=raw_name))
+        cube = iris.load_cube(str(filename), NameConstraint(var_name=raw_name))
     return cube
 
 
 def _time_operations(cube):
     """Temporal operations on cube."""
-    valid_start_year = cube.attributes['yrfi_valid']
-    valid_end_year = cube.attributes['yrfe_valid']
-    logger.info("Extracting valid years: %d-%d", valid_start_year,
-                valid_end_year)
-    cube = cube.extract(iris.Constraint(
-        time=lambda cell: valid_start_year <= cell.point.year <= valid_end_year
-    ))
+    valid_start_year = cube.attributes["yrfi_valid"]
+    valid_end_year = cube.attributes["yrfe_valid"]
+    logger.info(
+        "Extracting valid years: %d-%d", valid_start_year, valid_end_year
+    )
+    cube = cube.extract(
+        iris.Constraint(
+            time=lambda cell: valid_start_year
+            <= cell.point.year
+            <= valid_end_year
+        )
+    )
     logger.info("Calculating monthly means")
     cube = monthly_statistics(cube)
     return cube
 
 
 def _fix_metadata(cube, short_name, var, cfg):
     """Fix metadata of cube."""
-    cmor_info = cfg['cmor_table'].get_variable(var['mip'], short_name)
+    cmor_info = cfg["cmor_table"].get_variable(var["mip"], short_name)
 
     # Fix cell measures
-    if 'fx' not in var['mip']:
-        cell_measure = cube.cell_measure('area per grid cell')
+    if "fx" not in var["mip"]:
+        cell_measure = cube.cell_measure("area per grid cell")
         cell_measure.attributes = {}
-        cell_measure.standard_name = 'cell_area'
-        if short_name == 'nbp':
-            cell_measure.var_name = 'areacella'
-            cell_measure.long_name = ('Grid-Cell Area for Atmospheric Grid '
-                                      'Variables')
-        elif short_name == 'fgco2':
-            cell_measure.var_name = 'areacello'
-            cell_measure.long_name = 'Grid-Cell Area for Ocean Variables'
+        cell_measure.standard_name = "cell_area"
+        if short_name == "nbp":
+            cell_measure.var_name = "areacella"
+            cell_measure.long_name = (
+                "Grid-Cell Area for Atmospheric Grid Variables"
+            )
+        elif short_name == "fgco2":
+            cell_measure.var_name = "areacello"
+            cell_measure.long_name = "Grid-Cell Area for Ocean Variables"
 
     # Fix cell methods
-    if short_name == 'nbp':
-        cube.add_cell_method(iris.coords.CellMethod('mean where land',
-                                                    coords='area'))
-    elif short_name == 'fgco2':
-        cube.add_cell_method(iris.coords.CellMethod('mean where sea',
-                                                    coords='area'))
-    elif short_name in ('areacella', 'areacello'):
-        cube.add_cell_method(iris.coords.CellMethod('sum', coords='area'))
-    elif short_name in ('sftlf', 'sftof'):
-        cube.add_cell_method(iris.coords.CellMethod('mean', coords='area'))
+    if short_name == "nbp":
+        cube.add_cell_method(
+            iris.coords.CellMethod("mean where land", coords="area")
+        )
+    elif short_name == "fgco2":
+        cube.add_cell_method(
+            iris.coords.CellMethod("mean where sea", coords="area")
+        )
+    elif short_name in ("areacella", "areacello"):
+        cube.add_cell_method(iris.coords.CellMethod("sum", coords="area"))
+    elif short_name in ("sftlf", "sftof"):
+        cube.add_cell_method(iris.coords.CellMethod("mean", coords="area"))
 
     # Fix coordinates
-    if 'fx' not in var['mip']:
-        cube.remove_coord('month_number')
-        cube.remove_coord('year')
-        cube.coord('time').var_name = 'time'
-        cube.coord('time').long_name = 'time'
-        cube.coord('time').points = da.around(
-            cube.coord('time').core_points(), 3)
-        cube.coord('time').bounds = da.around(
-            cube.coord('time').core_bounds(), 3)
+    if "fx" not in var["mip"]:
+        cube.coord("time").var_name = "time"
+        cube.coord("time").long_name = "time"
+        cube.coord("time").points = da.around(
+            cube.coord("time").core_points(), 3
+        )
+        cube.coord("time").bounds = da.around(
+            cube.coord("time").core_bounds(), 3
+        )
     utils.fix_coords(cube)
-    if 'depth0m' in cmor_info.dimensions:
+    if "depth0m" in cmor_info.dimensions:
         depth_coord = iris.coords.AuxCoord(
             0.0,
-            var_name='depth',
-            standard_name='depth',
-            long_name='depth',
-            units=Unit('m'),
-            attributes={'positive': 'down'},
+            var_name="depth",
+            standard_name="depth",
+            long_name="depth",
+            units=Unit("m"),
+            attributes={"positive": "down"},
         )
         cube.add_aux_coord(depth_coord, ())
 
@@ -169,82 +177,80 @@ def _fix_metadata(cube, short_name, var, cfg):
     utils.fix_var_metadata(cube, cmor_info)
 
     # Fix global attributes
-    attrs = cfg['attributes']
-    attrs['mip'] = var['mip']
+    attrs = cfg["attributes"]
+    attrs["mip"] = var["mip"]
     utils.set_global_atts(cube, attrs)
 
     return (cube, attrs)
 
 
 def _extract_variable(short_name, var, cfg, filename, out_dir):
     """Extract variable."""
-    raw_name = var.get('raw_name', short_name)
+    raw_name = var.get("raw_name", short_name)
     cube = _load_cube(filename, raw_name)
 
     # Fix metadata of raw input
     cube.cell_methods = ()
-    if 'raw_units' in var:
-        cube.units = var['raw_units']
-        cube.attributes.pop('invalid_units', None)
+    if "raw_units" in var:
+        cube.units = var["raw_units"]
+        cube.attributes.pop("invalid_units", None)
 
     # Temporal operations
-    if 'fx' not in var['mip']:
+    if "fx" not in var["mip"]:
         cube = _time_operations(cube)
 
     # Variable-specific calculations
-    if short_name == 'nbp':
-        cube = _calculate_flux(cube, filename, 'land')
-    elif short_name == 'fgco2':
-        cube = _calculate_flux(cube, filename, 'ocean')
-    elif short_name in ('areacella', 'areacello'):
+    if short_name == "nbp":
+        cube = _calculate_flux(cube, filename, "land")
+    elif short_name == "fgco2":
+        cube = _calculate_flux(cube, filename, "ocean")
+    elif short_name in ("areacella", "areacello"):
         cube = cube[2]
-        cube.remove_coord('rt')
-    elif short_name in ('sftlf', 'sftof'):
+        cube.remove_coord("rt")
+    elif short_name in ("sftlf", "sftof"):
         total_area = cube[2]
-        area_idx = 0 if short_name == 'sftlf' else 1
+        area_idx = 0 if short_name == "sftlf" else 1
         cube = cube[area_idx]
         cube.data = cube.core_data() / total_area.core_data()
-        cube.units = '1'
-        cube.remove_coord('rt')
+        cube.units = "1"
+        cube.remove_coord("rt")
 
     # Fix metadata
     (cube, attrs) = _fix_metadata(cube, short_name, var, cfg)
 
     # Save variable
-    utils.save_variable(cube,
-                        short_name,
-                        out_dir,
-                        attrs,
-                        unlimited_dimensions=['time'])
+    utils.save_variable(
+        cube, short_name, out_dir, attrs, unlimited_dimensions=["time"]
+    )
 
 
 def _unzip(zip_path, out_dir):
     """Unzip `*.gz` file."""
     logger.info("Found input file '%s'", zip_path)
-    unzip_path = Path(out_dir) / zip_path.with_suffix('').name
+    unzip_path = Path(out_dir) / zip_path.with_suffix("").name
     logger.info("Unzipping file")
-    with gzip.open(zip_path, 'rb') as zip_file:
-        with open(unzip_path, 'wb') as unzip_file:
+    with gzip.open(zip_path, "rb") as zip_file:
+        with open(unzip_path, "wb") as unzip_file:
             shutil.copyfileobj(zip_file, unzip_file)
     logger.info("Succefully extracted file to %s", unzip_path)
     return unzip_path
 
 
 def cmorization(in_dir, out_dir, cfg, cfg_user, start_date, end_date):
     """Cmorization func call."""
-    in_path = Path(in_dir) / cfg['filename']
+    in_path = Path(in_dir) / cfg["filename"]
 
     # Unzip file if necessary
-    if '.gz' in cfg['filename']:
+    if ".gz" in cfg["filename"]:
         data_path = _unzip(in_path, out_dir)
     else:
         data_path = in_path
 
     # Run the cmorization
-    for (short_name, var) in cfg['variables'].items():
+    for short_name, var in cfg["variables"].items():
         logger.info("CMORizing variable '%s'", short_name)
         _extract_variable(short_name, var, cfg, data_path, out_dir)
 
     # Remove unzipped file if necessary
-    if '.gz' in cfg['filename']:
+    if ".gz" in cfg["filename"]:
         _clean(data_path)