Fix invalid standard names, add standard name checking script and github action

.github/workflows/pull_request_ci.yml

@@ -2,12 +2,13 @@ name: Pull request checks
 
 on:
   pull_request:
+  workflow_dispatch:
 
 jobs:
   check-unique-standard-names:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:
@@ -21,10 +22,33 @@ jobs:
       - name: Check for duplicate standard names
         run: tools/check_xml_unique.py standard_names.xml
 
+  check-name-rules:
+    name: Check standard names against rules
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get -y install libxml2-utils
+
+
+      - name: Checks standard names against character rules
+        run: |
+          python3 tools/check_name_rules.py -s standard_names.xml
+
   check-rerendered-markdown:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:
@@ -43,3 +67,5 @@ jobs:
             checksum=$(sha256sum Metadata-standard-names.md)
             tools/write_standard_name_table.py standard_names.xml
             test "$checksum" = "$(sha256sum Metadata-standard-names.md)"
+
+

Metadata-standard-names.md

@@ -200,7 +200,7 @@ Note that appending '_on_previous_timestep' to standard_names in this section yi
     * `real(kind=kind_phys)`: units = W m-2
 * `cumulative_boundary_flux_of_total_water`: Cumulative boundary flux of total water
     * `real(kind=kind_phys)`: units = W m-2
-* `US_standard_air_pressure_at_sea_level`: US Standard Atmospheric pressure at sea level
+* `us_standard_air_pressure_at_sea_level`: US Standard Atmospheric pressure at sea level
     * `real(kind=kind_phys)`: units = Pa
 * `reference_pressure`: reference pressure used in definition of potential temperature, Exner function, etc.
     * `real(kind=kind_phys)`: units = Pa
@@ -428,9 +428,9 @@ Standard / required CCPP variables
     * `real(kind=kind_phys)`: units = frac
 * `critical_relative_humidity_at_toa`: Critical relative humidity at toa
     * `real(kind=kind_phys)`: units = frac
-* `date_and_time_at_model_initialization_in_ISO_order`: Date and time at model initialization in ISO order
+* `date_and_time_at_model_initialization_in_iso_order`: Date and time at model initialization in iso order
     * `integer(kind=)`: units = 1
-* `date_and_time_at_model_initialization_in_United_States_order`: Date and time at model initialization in United States order
+* `date_and_time_at_model_initialization_in_united_states_order`: Date and time at model initialization in united states order
     * `integer(kind=)`: units = 1
 * `decorrelation_length_used_by_overlap_method`: Decorrelation length used by overlap method
     * `real(kind=kind_phys)`: units = km
@@ -496,13 +496,13 @@ Standard / required CCPP variables
     * `logical(kind=)`: units = flag
 * `do_diagnostics`: Do diagnostics
     * `logical(kind=)`: units = flag
-* `do_XYZ_dimensioned_diagnostics`: Do XYZ dimensioned diagnostics
+* `do_xyz_dimensioned_diagnostics`: Do xyz dimensioned diagnostics
     * `logical(kind=)`: units = flag
 * `do_flip`: Do flip
     * `logical(kind=)`: units = flag
 * `control_for_flux_adjusting_surface_data_assimilation_system`: Control for flux adjusting surface data assimilation system
     * `integer(kind=)`: units = 1
-* `do_flux_form_in chikira_sugiyama_deep_convection_scheme`: Do flux form in chikira sugiyama deep convection scheme
+* `do_flux_form_in_chikira_sugiyama_deep_convection_scheme`: Do flux form in chikira sugiyama deep convection scheme
     * `logical(kind=)`: units = flag
 * `do_nrl_2015_ozone_scheme`: Do nrl 2015 ozone scheme
     * `logical(kind=)`: units = flag
@@ -560,7 +560,7 @@ Standard / required CCPP variables
     * `logical(kind=)`: units = flag
 * `control_for_land_surface_scheme_frozen_soil_permeability`: Control for land surface scheme frozen soil permeability
     * `integer(kind=)`: units = 1
-* ` do_cellular_automata_gaussian_spatial_filter`:  do cellular automata gaussian spatial filter
+* `do_cellular_automata_gaussian_spatial_filter`: Do cellular automata gaussian spatial filter
     * `logical(kind=)`: units = flag
 * `do_gcycle_surface_option`: Do gcycle surface option
     * `logical(kind=)`: units = flag
@@ -584,7 +584,7 @@ Standard / required CCPP variables
     * `logical(kind=)`: units = flag
 * `do_global_cellular_automata_closure`: Do global cellular automata closure
     * `logical(kind=)`: units = flag
-* ` do_global_cellular_automata_deep_convective_entrainment`:  do global cellular automata deep convective entrainment
+* `do_global_cellular_automata_deep_convective_entrainment`: Do global cellular automata deep convective entrainment
     * `logical(kind=)`: units = flag
 * `do_global_cellular_automata_trigger`: Do global cellular automata trigger
     * `logical(kind=)`: units = flag
@@ -826,11 +826,11 @@ Standard / required CCPP variables
     * `logical(kind=)`: units = flag
 * `do_longwave_scattering_in_cloud_optics`: Do longwave scattering in cloud optics
     * `logical(kind=)`: units = flag
-* `do_tracer_XYZ_dimensioned_diagnostics`: Do tracer XYZ dimensioned diagnostics
+* `do_tracer_xyz_dimensioned_diagnostics`: Do tracer xyz dimensioned diagnostics
     * `logical(kind=)`: units = flag
 * `control_for_variable_bulk_richardson_number`: Control for variable bulk richardson number
     * `real(kind=kind_phys)`: units = 1
-* `date_and_time_of_forecast_in_United_States_order`: Date and time of forecast in United States order
+* `date_and_time_of_forecast_in_united_states_order`: Date and time of forecast in united states order
     * `integer(kind=)`: units = 1
 * `forecast_utc_hour`: Forecast utc hour
     * `real(kind=kind_phys)`: units = h
@@ -1048,11 +1048,11 @@ Standard / required CCPP variables
     * `character(kind=len=64)`: units = none
 * `filename_of_internal_namelist`: Filename of internal namelist
     * `character(kind=len=256)`: units = none
-* `number_of_XY_dimensioned_auxiliary_arrays`: Number of XY dimensioned auxiliary arrays
+* `number_of_xy_dimensioned_auxiliary_arrays`: Number of xy dimensioned auxiliary arrays
     * `integer(kind=)`: units = count
 * `number_of_pdf_based_variables_in_xyz_dimensioned_restart_array`: Number of pdf based variables in xyz dimensioned restart array
     * `integer(kind=)`: units = count
-* `number_of_XYZ_dimensioned_auxiliary_arrays`: Number of XYZ dimensioned auxiliary arrays
+* `number_of_xyz_dimensioned_auxiliary_arrays`: Number of xyz dimensioned auxiliary arrays
     * `integer(kind=)`: units = count
 * `number_of_radiatively_active_gases`: Number of radiatively active gases
     * `integer(kind=)`: units = count
@@ -1192,7 +1192,7 @@ Standard / required CCPP variables
     * `real(kind=kind_phys)`: units = 1
 * `thickness_of_soil_layers_for_land_surface_model`: Thickness of soil layers for land surface model
     * `real(kind=kind_phys)`: units = m
-* ` cellular_automata_vertical_velocity_perturbation_threshold_for_deep_convection`:  cellular automata vertical velocity perturbation threshold for deep convection
+* `cellular_automata_vertical_velocity_perturbation_threshold_for_deep_convection`: Cellular automata vertical velocity perturbation threshold for deep convection
     * `real(kind=kind_phys)`: units = m s-1
 * `period_of_maximum_diagnostics_reset`: Period of maximum diagnostics reset
     * `real(kind=kind_phys)`: units = s
@@ -1236,6 +1236,8 @@ Standard / required CCPP variables
     * `integer(kind=)`: units = mm
 * `index_of_water_vegetation_category`: Index of water vegetation category
     * `integer(kind=)`: units = index
+* `filename_of_micm_configuration`: Filename of micm configuration
+    * `character(kind=len=*)`: units = none
 ## GFS_typedefs_GFS_interstitial_type
 * `cloud_ice_mixing_ratio_wrt_moist_air_interstitial`: Cloud ice mixing ratio wrt moist air interstitial
     * `real(kind=kind_phys)`: units = kg kg-1

standard_names.xml

@@ -310,7 +310,7 @@
     <standard_name name="cumulative_boundary_flux_of_total_water">
       <type kind="kind_phys" units="W m-2">real</type>
     </standard_name>
-    <standard_name name="US_standard_air_pressure_at_sea_level"
+    <standard_name name="us_standard_air_pressure_at_sea_level"
                    long_name="US Standard Atmospheric pressure at sea level">
       <type kind="kind_phys" units="Pa">real</type>
     </standard_name>
@@ -712,10 +712,10 @@
       <standard_name name="critical_relative_humidity_at_toa">
          <type kind="kind_phys" units="frac">real</type>
       </standard_name>
-      <standard_name name="date_and_time_at_model_initialization_in_ISO_order">
+      <standard_name name="date_and_time_at_model_initialization_in_iso_order">
          <type kind="" units="1">integer</type>
       </standard_name>
-      <standard_name name="date_and_time_at_model_initialization_in_United_States_order">
+      <standard_name name="date_and_time_at_model_initialization_in_united_states_order">
          <type kind="" units="1">integer</type>
       </standard_name>
       <standard_name name="decorrelation_length_used_by_overlap_method">
@@ -814,7 +814,7 @@
       <standard_name name="do_diagnostics">
          <type kind="" units="flag">logical</type>
       </standard_name>
-      <standard_name name="do_XYZ_dimensioned_diagnostics">
+      <standard_name name="do_xyz_dimensioned_diagnostics">
          <type kind="" units="flag">logical</type>
       </standard_name>
       <standard_name name="do_flip">
@@ -823,7 +823,7 @@
       <standard_name name="control_for_flux_adjusting_surface_data_assimilation_system">
          <type kind="" units="1">integer</type>
       </standard_name>
-      <standard_name name="do_flux_form_in chikira_sugiyama_deep_convection_scheme">
+      <standard_name name="do_flux_form_in_chikira_sugiyama_deep_convection_scheme">
          <type kind="" units="flag">logical</type>
       </standard_name>
       <standard_name name="do_nrl_2015_ozone_scheme">
@@ -910,7 +910,7 @@
       <standard_name name="control_for_land_surface_scheme_frozen_soil_permeability">
          <type kind="" units="1">integer</type>
       </standard_name>
-      <standard_name name=" do_cellular_automata_gaussian_spatial_filter">
+      <standard_name name="do_cellular_automata_gaussian_spatial_filter">
          <type kind="" units="flag">logical</type>
       </standard_name>
       <standard_name name="do_gcycle_surface_option">
@@ -946,7 +946,7 @@
       <standard_name name="do_global_cellular_automata_closure">
          <type kind="" units="flag">logical</type>
       </standard_name>
-      <standard_name name=" do_global_cellular_automata_deep_convective_entrainment">
+      <standard_name name="do_global_cellular_automata_deep_convective_entrainment">
          <type kind="" units="flag">logical</type>
       </standard_name>
       <standard_name name="do_global_cellular_automata_trigger">
@@ -1309,13 +1309,13 @@
       <standard_name name="do_longwave_scattering_in_cloud_optics">
          <type kind="" units="flag">logical</type>
       </standard_name>
-      <standard_name name="do_tracer_XYZ_dimensioned_diagnostics">
+      <standard_name name="do_tracer_xyz_dimensioned_diagnostics">
          <type kind="" units="flag">logical</type>
       </standard_name>
       <standard_name name="control_for_variable_bulk_richardson_number">
          <type kind="kind_phys" units="1">real</type>
       </standard_name>
-      <standard_name name="date_and_time_of_forecast_in_United_States_order">
+      <standard_name name="date_and_time_of_forecast_in_united_states_order">
          <type kind="" units="1">integer</type>
       </standard_name>
       <standard_name name="forecast_utc_hour">
@@ -1642,13 +1642,13 @@
       <standard_name name="filename_of_internal_namelist">
          <type kind="len=256" units="none">character</type>
       </standard_name>
-      <standard_name name="number_of_XY_dimensioned_auxiliary_arrays">
+      <standard_name name="number_of_xy_dimensioned_auxiliary_arrays">
          <type kind="" units="count">integer</type>
       </standard_name>
       <standard_name name="number_of_pdf_based_variables_in_xyz_dimensioned_restart_array">
          <type kind="" units="count">integer</type>
       </standard_name>
-      <standard_name name="number_of_XYZ_dimensioned_auxiliary_arrays">
+      <standard_name name="number_of_xyz_dimensioned_auxiliary_arrays">
          <type kind="" units="count">integer</type>
       </standard_name>
       <standard_name name="number_of_radiatively_active_gases">
@@ -1858,7 +1858,7 @@
       <standard_name name="thickness_of_soil_layers_for_land_surface_model">
          <type kind="kind_phys" units="m">real</type>
       </standard_name>
-      <standard_name name=" cellular_automata_vertical_velocity_perturbation_threshold_for_deep_convection">
+      <standard_name name="cellular_automata_vertical_velocity_perturbation_threshold_for_deep_convection">
          <type kind="kind_phys" units="m s-1">real</type>
       </standard_name>
       <standard_name name="period_of_maximum_diagnostics_reset">

tools/check_name_rules.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+
+"""
+Check standard names database file for violations of standard name character rules
+"""
+
+import argparse
+import sys
+import os.path
+import re
+
+################################################
+#Add CCPP framework (lib) modules to python path
+################################################
+
+_CURR_DIR = os.path.dirname(os.path.abspath(__file__))
+sys.path.append(os.path.join(_CURR_DIR, "lib"))
+
+#######################################
+#Import needed framework python modules
+#######################################
+
+from xml_tools import find_schema_file, find_schema_version, validate_xml_file, read_xml_file
+
+def main():
+    """Parse the standard names database file and output a dictionary
+    where the keys are any standard names in violation of character rules,
+    and the values are lists of the specific rules violated
+    """
+    #Parse arguments
+    parser = argparse.ArgumentParser(description=__doc__)
+
+    parser.add_argument("-s","--standard_name_file",
+                        metavar='<standard names filename>',required=True,
+                        type=str, help="XML file with standard name library")
+    args = parser.parse_args()
+
+    stdname_file = os.path.abspath(args.standard_name_file)
+    tree, root = read_xml_file(stdname_file)
+
+    # Validate the XML file
+    version = find_schema_version(root)
+    schema_name = os.path.basename(stdname_file)[0:-4]
+    schema_root = os.path.dirname(stdname_file)
+    schema_path = os.path.join(schema_root,schema_name)
+    schema_file = find_schema_file(schema_path, version)
+    if schema_file:
+        try:
+            validate_xml_file(stdname_file, schema_name, version, None,
+                            schema_path=schema_root, error_on_noxmllint=True)
+        except ValueError:
+            raise ValueError(f"Invalid standard names file, {stdname_file}")
+    else:
+        raise ValueError(f'Cannot find schema file, {schema_name}, for {version=}')
+
+    #Parse list of standard names and see if any names violate one or more rules
+    violators = {}
+    legal_first_char = re.compile('[a-z]')
+    valid_chars = re.compile('[a-z0-9_]')
+    for name in root.findall('./section/standard_name'):
+        sname = name.attrib['name']
+        violations = []
+        if legal_first_char.sub('', sname[0]):
+            violations.append('First character is not a lowercase letter')
+        testchars = valid_chars.sub('', sname)
+        if testchars:
+            violations.append(f'Invalid characters are present: "{testchars}"')
+
+        # If any violations were detected, add an entry to "violators" dictionary
+        if violations:
+            violators[sname] = violations
+
+    if violators:
+        raise Exception(f"Violating standard names found:\n{violators}")
+    else:
+        print(f'Success! All standard names in {args.standard_name_file} follow the rules.')
+
+if __name__ == "__main__":
+    main()

tools/check_xml_unique.py

@@ -59,11 +59,9 @@ def main_func():
             validate_xml_file(stdname_file, schema_name, version, None,
                             schema_path=schema_root, error_on_noxmllint=True)
         except ValueError:
-            raise ValueError("Invalid standard names file, {}".format(stdname_file))
+            raise ValueError(f"Invalid standard names file, {stdname_file}")
     else:
-        raise ValueError(
-            'Cannot find schema file, {}, for version {}'.format(schema_name, version)
-        )
+        raise ValueError(f'Cannot find schema file, {schema_name}, for {version=}')
 
     #get list of all standard names
     all_std_names = []
@@ -87,8 +85,8 @@ def main_func():
             print('The following duplicate standard names were found:')
             for dup in dup_std_names:
                 rm_elements = root.findall('./section/standard_name[@name="%s"]'%dup)[1:]
-                print("{0}, ({1} duplicate(s))".format(dup, len(rm_elements)))
-            print('Removing duplicates and overwriting {}'.format(stdname_file))
+                print(f"{dup}, ({len(rm_elements)} duplicate(s))")
+            print(f'Removing duplicates and overwriting {stdname_file}')
             for dup in dup_std_names:
                 first_use = True #Logical that indicates the first use of the duplicated name
                 rm_parents = root.findall('./section/standard_name[@name="%s"]..'%dup)
@@ -110,7 +108,7 @@ def main_func():
             print('The following duplicate standard names were found:')
             for dup in dup_std_names:
                 rm_elements = root.findall('./section/standard_name[@name="%s"]'%dup)[1:]
-                print("{0}, ({1} duplicate(s))".format(dup, len(rm_elements)))
+                print(f"{dup}, ({len(rm_elements)} duplicate(s))")
             sys.exit(1)
         else:
             print('No duplicate standard names were found.')

tools/lib/xml_tools.py

@@ -11,10 +11,10 @@
 import subprocess
 import sys
 import logging
-from distutils.spawn import find_executable
+from shutil import which
 import xml.etree.ElementTree as ET
 try:
-    _XMLLINT = find_executable('xmllint')
+    _XMLLINT = which('xmllint')
 except ImportError:
     _XMLLINT = None
 # end try