Replace whitespace in Ref and Dev version labels in benchmarking code

CHANGELOG.md

@@ -26,6 +26,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - In environment files `read_the_docs_environment.yml` and `read_the_docs_requirements.txt`
   - Update `jinja` to 3.1.4 (fixes a security issue)
 - Update `gcpy/setup.py` with the new Python package version numbers
+- Updated code in `gcpy/benchmark/modules/` to replace whitespace in Ref and Dev labels with underscores
 
 ### Fixed
 - Fixed formatting error in `.github/workflows/stale.yml` that caused the Mark Stale Issues action not to run

gcpy/benchmark/modules/benchmark_drydep.py

@@ -1,14 +1,13 @@
 """
 Specific utilities for creating plots from GEOS-Chem benchmark simulations.
 """
-import os
 import gc
 import numpy as np
 from gcpy import util
 from gcpy.plot.compare_single_level import compare_single_level
 from gcpy.benchmark.modules.benchmark_utils import \
-    get_lumped_species_definitions, make_output_dir, \
-    pdf_filename, print_sigdiffs, read_ref_and_dev
+    get_common_varnames, make_output_dir, pdf_filename, \
+    print_sigdiffs, read_ref_and_dev
 
 # Suppress numpy divide by zero warnings to prevent output spam
 np.seterr(divide="ignore", invalid="ignore")
@@ -95,6 +94,10 @@ def make_benchmark_drydep_plots(
         msg = "The spcdb_dir argument has not been specified!"
         raise ValueError(msg)
 
+    # Replace whitespace in the ref and dev labels
+    refstr = util.replace_whitespace(refstr)
+    devstr = util.replace_whitespace(devstr)
+
     # Create directory for plots (if it doesn't exist)
     dst = make_output_dir(
         dst,

gcpy/benchmark/modules/benchmark_funcs.py

@@ -16,6 +16,7 @@
 from gcpy import util
 from gcpy.regrid import create_regridders
 from gcpy.grid import get_troposphere_mask
+from gcpy.util import replace_whitespace
 from gcpy.units import convert_units
 from gcpy.constants import COL_WIDTH, MW_AIR_g, skip_these_vars, TABLE_WIDTH
 from gcpy.plot.compare_single_level import compare_single_level
@@ -155,6 +156,10 @@ def create_total_emissions_table(
         quiet=True
     )
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # ==================================================================
     # Get the list of emission variables for which we will print totals
     # ==================================================================
@@ -447,6 +452,10 @@ def create_global_mass_table(
         quiet=True
     )
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # ==================================================================
     # Open file for output
     # ==================================================================
@@ -692,6 +701,10 @@ def create_mass_accumulation_table(
         quiet=True
     )
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # ==================================================================
     # Open file for output
     # ==================================================================
@@ -1032,6 +1045,10 @@ def make_benchmark_conc_plots(
     else:
         extra_title_txt = None
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # Pick the proper function to read the data
     reader = util.dataset_reader(time_mean, verbose=verbose)
 
@@ -1710,6 +1727,10 @@ def make_benchmark_emis_plots(
     else:
         extra_title_txt = None
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # Get the function that will read the dataset
     reader = util.dataset_reader(time_mean, verbose=verbose)
 
@@ -2098,6 +2119,10 @@ def make_benchmark_emis_tables(
     if not os.path.isdir(emisdir):
         os.mkdir(emisdir)
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # ==================================================================
     # Read data from netCDF into Dataset objects
     # ==================================================================
@@ -2343,6 +2368,10 @@ def make_benchmark_jvalue_plots(
     # Create the directory for output
     util.make_directory(dst, overwrite)
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # Get the function that will read file(s) into a Dataset
     reader = util.dataset_reader(time_mean, verbose=verbose)
 
@@ -2727,6 +2756,10 @@ def make_benchmark_aod_plots(
     else:
         extra_title_txt = None
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # Get the function that will read file(s) into a dataset
     reader = util.dataset_reader(time_mean, verbose=verbose)
 
@@ -3009,11 +3042,19 @@ def make_benchmark_mass_tables(
             which do not contain the Area variable.
             Default value: ''
     """
+    # ==================================================================
+    # Initialization
+    # ==================================================================
+
     # Make sure the species database folder is passed
     if spcdb_dir is None:
         msg = "The 'spcdb_dir' argument has not been specified!"
         raise ValueError(msg)
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # ==================================================================
     # Define destination directory
     # ==================================================================
@@ -3275,11 +3316,19 @@ def make_benchmark_mass_accumulation_tables(
             Directory of species_datbase.yml file
             Default value: None
     """
+    # ==================================================================
+    # Initialization
+    # ==================================================================
+
     # Make sure the species database folder is passed
     if spcdb_dir is None:
         msg = "The 'spcdb_dir' argument has not been specified!"
         raise ValueError(msg)
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # ==================================================================
     # Define destination directory
     # ==================================================================
@@ -3543,10 +3592,16 @@ def make_benchmark_oh_metrics(
     """
 
     # ==================================================================
-    # Define destination directory
+    # Initialization
     # ==================================================================
+
+    # Define destination directory
     util.make_directory(dst, overwrite)
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # ==================================================================
     # Read data from netCDF into Dataset objects
     # ==================================================================
@@ -3833,6 +3888,10 @@ def make_benchmark_wetdep_plots(
         if not os.path.isdir(targetdst):
             os.mkdir(targetdst)
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # Get the function that will read file(s) into a dataset
     reader = util.dataset_reader(time_mean, verbose=verbose)
 
@@ -4388,6 +4447,9 @@ def make_benchmark_operations_budget(
             Directory containing the species_database.yml file.
             Default value: None
     """
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
 
     # ------------------------------------------
     # Column sections
@@ -5083,6 +5145,10 @@ def create_benchmark_summary_table(
     # Open file for output
     # ==================================================================
 
+    # Replace whitespace in the ref and dev labels
+    refstr = replace_whitespace(refstr)
+    devstr = replace_whitespace(devstr)
+
     # Create the directory for output
     util.make_directory(dst, overwrite)
 

gcpy/benchmark/modules/benchmark_gcclassic_stats.py

@@ -9,7 +9,7 @@
 """
 import sys
 import requests
-from gcpy.util import verify_variable_type
+from gcpy.util import replace_whitespace, verify_variable_type
 
 # ----------------------------------------------------------------------
 # Global variables
@@ -113,7 +113,7 @@ def scrape_stats(text):
             stats["CH3CCl3"] = line.split(":")[1].strip()
         if line_count == 18 and "Dev" in line:
             stats["Mean OH"] = line.split(":")[1].strip()
-            
+
         # Skip commands
         if "++ sed" in line:
             line_count += 1
@@ -168,6 +168,10 @@ def main(ref_label, dev_label):
     verify_variable_type(ref_label, str)
     verify_variable_type(dev_label, str)
 
+    # Replace whitespace in the ref and dev labels
+    ref_label = replace_whitespace(ref_label)
+    dev_label = replace_whitespace(dev_label)
+
     # Scrape the log file text into a variable
     bmk_id = f"gcc-4x5-1Mon-{dev_label}"
     text = get_text_from_web(LOG_TEMPLATE.replace("ID", bmk_id))

gcpy/benchmark/modules/benchmark_mass_cons_table.py

@@ -9,8 +9,8 @@
 from gcpy.constants import skip_these_vars
 from gcpy.units import convert_units
 from gcpy.util import \
-    replace_whitespace, dataset_reader, get_area_from_dataset, \
-    make_directory, read_config_file, verify_variable_type
+    dataset_reader, get_area_from_dataset, make_directory, \
+    read_config_file, replace_whitespace, verify_variable_type
 from gcpy.benchmark.modules.benchmark_utils import \
     get_datetimes_from_filenames
 
@@ -317,6 +317,10 @@ def make_benchmark_mass_conservation_table(
     # Create the destination folder
     make_directory(dst, overwrite)
 
+    # Replace whitespace in the ref and dev labels
+    ref_label = replace_whitespace(ref_label)
+    dev_label = replace_whitespace(dev_label)
+
     # Get a list of properties for the given species
     metadata = get_passive_tracer_metadata(spcdb_dir)
 

gcpy/benchmark/modules/benchmark_models_vs_obs.py

@@ -21,7 +21,8 @@
 import numpy as np
 import xarray as xr
 from gcpy.constants import skip_these_vars
-from gcpy.util import verify_variable_type, dataset_reader, make_directory
+from gcpy.util import \
+    dataset_reader, make_directory, replace_whitespace, verify_variable_type
 from gcpy.cstools import extract_grid
 from gcpy.grid import get_nearest_model_data
 from gcpy.benchmark.modules.benchmark_utils import \
@@ -51,6 +52,11 @@ def read_nas(
     if verbose:
         print(f"read_nas: Reading {input_file}")
 
+    # Initialize
+    lon = 0.0
+    lat = 0.0
+    alt = 0.0
+
     with open(input_file, encoding='UTF-8') as the_file:
         header = np.array(
             [next(the_file) for x in range(155) ]
@@ -113,11 +119,11 @@ def read_nas(
         index=obs_dataframe.index
     )
     obs_site_coords = { site:
-          {
-              'lon': lon,
-              'lat': lat,
-              'alt': alt
-          }
+        {
+            'lon': lon,
+            'lat': lat,
+            'alt': alt
+        }
     }
 
     return obs_dataframe, obs_site_coords
@@ -194,13 +200,12 @@ def read_model_data(
     Returns
     dataarray : xr.DataArray : GEOS-Chem data read from disk
     """
-
     # Read the Ref and Dev model data
     reader = dataset_reader(
         multi_files=True,
         verbose=verbose,
     )
-    
+
     # Read data and rename SpeciesConc_ to SpeciesConcVV_, if necessary
     # (needed for backwards compatibility with older versions.)
     dataset = reader(filepaths,drop_variables=skip_these_vars).load()
@@ -755,6 +760,10 @@ def make_benchmark_models_vs_obs_plots(
     verify_variable_type(dev_filepaths, (str, list))
     verify_variable_type(dev_label, str)
 
+    # Replace whitespace in the ref and dev labels
+    ref_label = replace_whitespace(ref_label)
+    dev_label = replace_whitespace(dev_label)
+
     # Create the destination folder
     make_directory(
         dst,

gcpy/benchmark/modules/benchmark_models_vs_sondes.py

@@ -11,7 +11,7 @@
 import matplotlib.pyplot as plt
 from gcpy.cstools import extract_grid
 from gcpy.grid import get_nearest_model_data, get_vert_grid
-from gcpy.util import make_directory, verify_variable_type
+from gcpy.util import make_directory, replace_whitespace, verify_variable_type
 from gcpy.benchmark.modules.benchmark_utils import \
     read_ref_and_dev, rename_speciesconc_to_speciesconcvv
 
@@ -522,6 +522,10 @@ def make_benchmark_models_vs_sondes_plots(
     verify_variable_type(dev_filepaths, (str, list))
     verify_variable_type(dev_label, str)
 
+    # Replace whitespace in the ref and dev labels
+    ref_label = replace_whitespace(ref_label)
+    dev_label = replace_whitespace(dev_label)
+
     # Create the destination folder
     make_directory(
         dst,

gcpy/benchmark/modules/benchmark_scrape_gcclassic_timers.py

@@ -261,6 +261,10 @@ def make_benchmark_gcclassic_timing_table(
     # Create the destination folder
     make_directory(dst, overwrite)
 
+    # Replace whitespace in the ref and dev labels
+    ref_label = replace_whitespace(ref_label)
+    dev_label = replace_whitespace(dev_label)
+
     # Strip timing info from JSON/text file(s) and sum the them.
     ref_timers = sum_timers(read_gcclassic(ref_files))
     dev_timers = sum_timers(read_gcclassic(dev_files))

gcpy/benchmark/modules/benchmark_scrape_gchp_timers.py

@@ -331,6 +331,10 @@ def make_benchmark_gchp_timing_table(
     # Create the destination folder
     make_directory(dst, overwrite)
 
+    # Replace whitespace in the ref and dev labels
+    ref_label = replace_whitespace(ref_label)
+    dev_label = replace_whitespace(dev_label)
+
     # Strip timing info from JSON/text file(s) and sum the them.
     ref_timers = sum_timers(read_timing_data(ref_files))
     dev_timers = sum_timers(read_timing_data(dev_files))