Update mass conservation tables to include Ref & Dev in the same file

CHANGELOG.md

@@ -19,6 +19,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added fixed level budget diagnostic to budget operations table
 - Function `rename_speciesconc_to_speciesconcvv` in `gcpy/benchmark/modules/benchmark_utils.py`
 - Function `copy_file_to_dir` in `gcpy/util.py`.  This is a wrapper for `shutil.copyfile`.
+- Script `gcpy/benchmark/modules/benchmark_mass_cons_table.py`, with code to create mass conservation tables
+- Expanded statistics output in benchmark mass conservation tables
+- Function `get_datetimes_from_filenames` in `gcpy/benchmark/modules/benchmark_utils.py`
+- Function `replace_whitespace` in `gcpy/util.py`
 
 ### Changed
 - Bump pip from 23.2.1 to 23.3 (dependabot suggested this)
@@ -58,6 +62,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Environment file `docs/environment_files/environment.yml`
 - Environment file `docs/environment_files/requirements.txt`
 - Removed `awscli` from the GCPy environment; version 2 is no longer available on conda-forge or PyPi
+- Routine `make_benchmark_mass_conservation_table` in `benchmark_funcs.py`; this is now obsolete
 
 ## [1.4.2] - 2024-01-26
 ### Added

gcpy/benchmark/modules/benchmark_funcs.py

@@ -4915,172 +4915,6 @@ def make_benchmark_operations_budget(
     gc.collect()
 
 
-def make_benchmark_mass_conservation_table(
-        datafiles,
-        runstr,
-        dst="./benchmark",
-        overwrite=False,
-        areapath=None,
-        spcdb_dir=os.path.dirname(__file__)
-):
-    """
-    Creates a text file containing global mass of the PassiveTracer
-    from Transport Tracer simulations across a series of restart files.
-
-    Args:
-        datafiles: list of str
-            Path names of restart files.
-        runstr: str
-            Name to put in the filename and header of the output file
-
-    Keyword Args (optional):
-        dst: str
-            A string denoting the destination folder where the file
-            containing emissions totals will be written.
-            Default value: "./benchmark"
-        overwrite: bool
-            Set this flag to True to overwrite files in the
-            destination folder (specified by the dst argument).
-            Default value: False
-        areapath: str
-            Path to a restart file containing surface area data.
-            Default value: None
-        spcdb_dir: str
-            Path to the species_database.yml
-            Default value: points to gcpy/gcpy folder
-    """
-
-    # ==================================================================
-    # Initialize
-    # ==================================================================
-
-    # Create the destination folder
-    util.make_directory(dst, overwrite)
-
-    # Load a YAML file containing species properties (such as
-    # molecular weights), which we will need for unit conversions.
-    properties = util.read_config_file(
-        os.path.join(
-            spcdb_dir,
-            "species_database.yml"
-        ),
-        quiet=True
-    )
-
-    # Get the species name
-    spc_name = 'PassiveTracer'
-
-    # Get a list of properties for the given species
-    species_properties = properties.get(spc_name)
-
-    # Specify target units
-    target_units = "Tg"
-
-    dates = []
-    masses = []
-
-    # ==================================================================
-    # Make sure that surface area data is found
-    # ==================================================================
-    with warnings.catch_warnings():
-        warnings.filterwarnings("ignore", category=xr.SerializationWarning)
-
-
-    # ==================================================================
-    # Calculate global mass for the tracer at all restart dates
-    # ==================================================================
-    for f in datafiles:
-        ds = xr.open_dataset(f, drop_variables=skip_these_vars)
-
-        # Save date in desired format
-        #datestr = str(pd.to_datetime(ds.time.values[0]))
-        #dates.append(datestr[:4] + '-' + datestr[5:7] + '-' + datestr[8:10])
-
-        # Find the area variable in Dev
-        if areapath is None:
-            area = util.get_area_from_dataset(ds)
-        else:
-            area = util.get_area_from_dataset(
-                xr.open_dataset(
-                    areapath,
-                    drop_variables=skip_these_vars
-                )
-            )
-
-        # Assume typical restart file name format, but avoid using dates
-        # from within files which may be incorrect for the initial restart
-        datestr = f.split('/')[-1].split('.')[2][:9]
-        dates.append(datestr[:4] + '-' + datestr[4:6] + '-' + datestr[6:8])
-
-        # Select for GCC or GCHP
-        delta_p = ds['Met_DELPDRY'] if 'Met_DELPDRY' in list(ds.data_vars) else ds['DELP_DRY']
-
-        # ==============================================================
-        # Convert units of Ref and save to a DataArray
-        # (or skip if Ref contains NaNs everywhere)
-        # ==============================================================
-        # Select for GCC or GCHP
-        if 'SpeciesRst_PassiveTracer' in list(ds.data_vars):
-            attrs = ds['SpeciesRst_PassiveTracer'].attrs
-            da = ds['SpeciesRst_PassiveTracer'].astype(np.float64)
-            da.attrs = attrs
-        else:
-            attrs = ds['SPC_PassiveTracer'].attrs
-            da = ds['SPC_PassiveTracer'].astype(np.float64)
-            da.attrs = attrs
-        da = convert_units(
-            da,
-            spc_name,
-            species_properties,
-            target_units,
-            area_m2=area,
-            delta_p=delta_p
-        )
-
-        # Save total global mass
-        masses.append(np.sum(da.values))
-
-        # Clean up
-        del ds
-        del da
-        gc.collect()
-
-    # Calclate max and min mass, absolute diff, percent diff
-    max_mass = np.max(masses)
-    min_mass = np.min(masses)
-    # Convert absdiff to grams
-    absdiff = (max_mass-min_mass) * 10**12
-    pctdiff = (max_mass-min_mass)/min_mass * 100
-
-    # ==================================================================
-    # Print masses to file
-    # ==================================================================
-    # Create file
-    outfilename = os.path.join(dst, f"Passive_mass.{runstr}.txt")
-
-    with open(outfilename, 'w') as f:
-        titlestr = '  Global Mass of Passive Tracer in ' + runstr + '  '
-        #headers
-        print('%' * (len(titlestr)+4), file=f)
-        print(titlestr, file=f)
-        print('%' * (len(titlestr)+4), file=f)
-        print('', file=f)
-        print(' Date' + ' ' * 8 + 'Mass [Tg]', file=f)
-        print(' ' + '-' * 10 + '  ' + '-' * 16, file=f)
-        #masses
-        for i in range(len(masses)):
-            print(f" {dates[i]}  {masses[i] : 11.13f}", file=f)
-        print(' ', file=f)
-        print(' Summary', file=f)
-        print(' ' + '-' * 30, file=f)
-        print(f" Max mass =  {max_mass : 2.13f} Tg", file=f)
-        print(f" Min mass =  {min_mass : 2.13f} Tg", file=f)
-        print(f" Abs diff =  {absdiff : >16.3f} g", file=f)
-        print(f" Pct diff =  {pctdiff : >16.10f} %", file=f)
-
-    gc.collect()
-
-
 def get_species_database_dir(config):
     """
     Returns the directory in which the species_database.yml file is