Merge branch 'main' into copilot/improve-branded-variable-handling

Author: ilaflott

.github/workflows/create_test_conda_env.yml

@@ -65,8 +65,3 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           verbose: true
-
-      - name: Run pylint
-        if: ${{ always() }}
-        run: |
-          pylint --rcfile pylintrc fremorizer/

.gitignore

@@ -155,6 +155,10 @@ cython_debug/
 *.nc
 tmp/
 
+# experiment-config JSONs are generated by conftest fixtures at test time
+fremorizer/tests/test_files/CMOR_input_example.json
+fremorizer/tests/test_files/CMOR_CMIP7_input_example.json
+
 # QA results
 wcrp_compliance_reports/
 

README.md

@@ -10,7 +10,7 @@
 [![readthedocs](https://app.readthedocs.org/projects/fremorizer/badge/?version=latest&style=flat)](https://fremorizer.readthedocs.io/en/latest/)
 
 [![pylint](https://github.com/ilaflott/fremorizer/actions/workflows/pylint.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/pylint.yml)
-[![pylint](https://img.shields.io/badge/pylint-%E2%89%A59.6-brightgreen)](https://github.com/NOAA-GFDL/epmt/actions/workflows/build_and_test_epmt.yml)
+[![pylint](https://img.shields.io/badge/pylint-%E2%89%A59.7-brightgreen)](https://github.com/NOAA-GFDL/epmt/actions/workflows/build_and_test_epmt.yml)
 [![codecov](https://codecov.io/gh/ilaflott/fremorizer/branch/main/graph/badge.svg)](https://codecov.io/gh/ilaflott/fremorizer)
 
 

fremorizer/__init__.py

@@ -8,7 +8,7 @@
 
 fre_logger = logging.getLogger(__name__)
 
-FORMAT = "[%(levelname)5s:%(filename)24s:%(funcName)24s] %(message)s"
+FORMAT = '[%(levelname)5s:%(filename)24s:%(funcName)24s] %(message)s'
 logging.basicConfig( level = logging.WARNING,
                      format = FORMAT,
                      filename = None,

fremorizer/cli.py

@@ -215,7 +215,7 @@ def cmor_config_subtool(
                 lines.append(f"        - component_name: '{component_name}'")
                 lines.append(f"          variable_list: '{variable_list}'")
                 lines.append("          data_series_type: 'ts'")
-                lines.append("          chunk: *PP_CMIP_CHUNK")
+                lines.append('          chunk: *PP_CMIP_CHUNK')
 
 
     # ---- write output YAML ----

fremorizer/cmor_config.py

@@ -28,21 +28,21 @@
 # Vertical-coordinate classification (used by cmor_mixer)
 # ---------------------------------------------------------------------------
 ACCEPTED_VERT_DIMS = [
-    "z_l", "landuse",
-    "plev39", "plev30", "plev19", "plev8",
-    "height2m",
-    "level", "lev", "levhalf",
+    'z_l', 'landuse',
+    'plev39', 'plev30', 'plev19', 'plev8',
+    'height2m',
+    'level', 'lev', 'levhalf',
 ]
 
 NON_HYBRID_SIGMA_COORDS = [
-    "landuse",
-    "plev39", "plev30", "plev19", "plev8",
-    "height2m",
+    'landuse',
+    'plev39', 'plev30', 'plev19', 'plev8',
+    'height2m',
 ]
 
-ALT_HYBRID_SIGMA_COORDS = ["level", "lev", "levhalf"]
+ALT_HYBRID_SIGMA_COORDS = ['level', 'lev', 'levhalf']
 
-DEPTH_COORDS = ["z_l"]
+DEPTH_COORDS = ['z_l']
 
 
 # ---------------------------------------------------------------------------
@@ -62,10 +62,10 @@
 # equivalents.  Dimensions whose names already match (e.g. plev39, height2m)
 # need no entry; the look-up falls back to using the input name directly.
 INPUT_TO_MIP_VERT_DIM = {
-    "z_l":      "olevel",
-    "level":    "alevel",
-    "lev":      "alevel",
-    "levhalf":  "alevhalf",
+    'z_l':      'olevel',
+    'level':    'alevel',
+    'lev':      'alevel',
+    'levhalf':  'alevhalf',
 }
 
 

fremorizer/cmor_constants.py

@@ -53,17 +53,17 @@ def print_var_content(table_config_file: IO[str],
 
     table_name = None
     try:
-        table_name = proj_table_vars["Header"].get('table_id').split(' ')[1]
+        table_name = proj_table_vars['Header'].get('table_id').split(' ')[1]
     except KeyError:
-        fre_logger.warning("couldn't get header and table_name field")
+        fre_logger.warning('couldn\'t get header and table_name field')
 
     if table_name is not None:
         fre_logger.info('looking for %s data in table %s!', var_name, table_name)
     else:
         fre_logger.info('looking for %s data in table %s, but could not find its table_name!',
                         var_name, table_config_file.name)
 
-    var_content = proj_table_vars.get("variable_entry", {}).get(var_name)
+    var_content = proj_table_vars.get('variable_entry', {}).get(var_name)
     if var_content is None:
         fre_logger.debug('variable %s not found in %s, moving on!', var_name, Path(table_config_file.name).name)
         return
@@ -107,7 +107,7 @@ def cmor_find_subtool( json_var_list: Optional[str] = None,
 
     var_list = None
     if json_var_list is not None:
-        with open(json_var_list, "r", encoding="utf-8") as var_list_file:
+        with open(json_var_list, 'r', encoding='utf-8') as var_list_file:
             var_list = json.load(var_list_file)
 
     if opt_var_name is None and var_list is None:
@@ -116,14 +116,14 @@ def cmor_find_subtool( json_var_list: Optional[str] = None,
     if opt_var_name is not None:
         fre_logger.info('opt_var_name is not None: looking for only ONE variables worth of info!')
         for json_table_config in json_table_configs:
-            with open(json_table_config, "r", encoding="utf-8") as table_config_file:
+            with open(json_table_config, 'r', encoding='utf-8') as table_config_file:
                 print_var_content(table_config_file, opt_var_name)
 
     elif var_list is not None:
         fre_logger.info('opt_var_name is None, and var_list is not None, looking for many variables worth of info!')
         for var in var_list:
             for json_table_config in json_table_configs:
-                with open(json_table_config, "r", encoding="utf-8") as table_config_file:
+                with open(json_table_config, 'r', encoding='utf-8') as table_config_file:
                     print_var_content(table_config_file, str(var_list[var]))
 
 
@@ -132,7 +132,7 @@ def make_simple_varlist( dir_targ: str,
                          json_mip_table: Optional[str] = None) -> Optional[Dict[str, str]]:
     """
     Generate a JSON file containing a list of variable names from NetCDF files in a specified directory.
-    This function searches for NetCDF files in the given directory, or a subdirectory, "ts/monthly/5yr",
+    This function searches for NetCDF files in the given directory, or a subdirectory, 'ts/monthly/5yr',
     if not already included. It then extracts variable names from the filenames, and writes these variable
     names to a JSON file.
 
@@ -154,22 +154,22 @@ def make_simple_varlist( dir_targ: str,
 
     """
     # if the variable is in the filename, it's likely delimited by another period.
-    all_nc_files = glob.glob(os.path.join(dir_targ, "*.*.nc"))
+    all_nc_files = glob.glob(os.path.join(dir_targ, '*.*.nc'))
     if not all_nc_files:
-        fre_logger.error("No files found in the directory.") #uncovered
+        fre_logger.error('No files found in the directory.') #uncovered
         return None
 
     if len(all_nc_files) == 1:
-        fre_logger.warning("Warning: Only one file found matching the pattern.")
+        fre_logger.warning('Warning: Only one file found matching the pattern.')
 
-    fre_logger.info("Files found matching pattern. Number of files: %d", len(all_nc_files))
+    fre_logger.info('Files found matching pattern. Number of files: %d', len(all_nc_files))
 
     mip_vars = None
     if json_mip_table is not None:
         try:
             # read in mip vars to check against later
             fre_logger.debug('attempting to read in variable entries in specified mip table')
-            full_mip_vars_list=get_json_file_data(json_mip_table)["variable_entry"].keys()
+            full_mip_vars_list=get_json_file_data(json_mip_table)['variable_entry'].keys()
 
         except Exception as exc:
             raise Exception( 'problem opening mip table and getting variable entry data.'