This merge brings PR #388 (Update "benchmark_scrape_gchp_timers.py"
to look for timing information in "allPEs.log" if not found in the
GCHP log file, by @yantosca) into the GCPy 1.7.0 development stream.

PR #388 updates the "benchmark_scrape_gchp_timers.py" script to check
if the GCHP timers output is present in the log file.  If not, it will
read it from the allPEs.log file in the run directory.  This is needed
because GCHP simulations with MAPL v2.59+ now send timers output to
the allPEs.log file.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_utils.py
- Import verify_variable_type from gcpy.util
- Added function get_species_database_files, which reads the config
  object and returns paths to the species_database.yml files
  in Ref and Dev rundirs

gcpy/util.py
- Added function read_species_metadata, which returns the species
  metadata for the union of species in multiple species_database.yml
  files.
- Added code updates suggested by Pylint
- Updated comments

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/cloud/*.yml
gcpy/benchmark/config/*.yml
- Removed "paths:spcdb_dir" YAML tag
- Added "ref:gcc:species_metadata", "ref:gchp:species_metadata",
  "dev"gcc:species_metadata", and "dev:gchp:species_metadata" YAML
  tags to specify separate species_database.yml files for Ref and
  Dev rundirs

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/plot/compare_single_level.py
gcpy/plot/compare_zonal_mean.py
- Import "read_species_metadata" from gcpy.util
- Add "spcdb_files=None" as a keyword argument
- Throw an error if spcdb_files is None while convert_to_ugm3=True


Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/oh_metrics.py
- Import constants from gcpy_constants by name
- Import functions from gcpy.util by name
- Updated PyDoc headers
- Removed special handling for xr.open_mfdataset
- Renamed "ds" to "data"
- Implement suggestions from Pylint:
  - Snake case naming for variables

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/budget_ox.py
gcpy/benchmark/modules/budget_tt.py
- Import constants from gcpy.constants by name
- Pass spcdb_file as an argument; remove spcdb_dir
- Updated PyDoc headers
- Implemented suggestions from Pylint:
  - Snake case/lower case for variables
  - Do not use a list as a default value for keyword arguments
  - Specify an encoding in open() statements
  - Use f-strings instead of ".format" in print statements

gcpy/benchmark/ste_flux.py
- Removed "import os"
- Import constants from gcpy.constatns by name
- Removed special handling for xr.open_mfdataset
- Implemented suggestions from Pylint:
  - Snake case/lower case for variables
  - Do not use a list as a default value for keyword arguments
  - Specify an encoding in open() statements

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_funcs.py
- Pass spcdb_files as a positional argument
- Removed spcdb_dir keyword argument
- Import functions by name from gcpy.util
- Updated PyDoc headers
- Verify argument types with verify_variable_type()
- Use "read_species_metadata" function to read the species database
  files from Ref & Dev and return the union of species
- Cosmetic changes (indentation, line breaks, comments)
- Pass spcdb_files as a keyword argument to compute_single_level
- Pass spcdb_files as a keyword argument to compute_zonal_mean
- Implemented suggestions from Pylint:
  - Use snake case/lower case for variables
  - Specify encoding when opening text files for output

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_drydep.py
- Add spcdb_files as a positional argument
- Remove spcdb_dir keyword argument
- Updated PyDoc headers
- Pass spcdb_files as a keyword argument to make_benchmark_drydep_plots

gcpy/benchmark/modules/benchmark_mass_cons_table.py
- Use "read_species_metadata" to read species database files from Ref
  & Dev, and return the union of all species
- Pass spcdb_files as an argument

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_scrape_gchp_timers.py
- Added "check=False" as an argument to subprocess.run,
  as suggested by Pylint.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_species_changes.py
- Pass spcdb_files as a keyword argument
- Use "read_species_metadata" to read the species_database.yml files
  for Ref & Dev, and return the union of all species
- Updated PyDoc headers

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py
gcpy/modules/run_1yr_tt_benchmark.py
gcpy/benchmark/run_benchmark.py
- Remove "import get_species_database_dir" from benchmark_funcs.py
- Added "import get_species_database_files" from benchmark_utils.py
- Call get_species_database_files at the beginning of GCC vs GCC,
  GCHP vs GCC, GCHP vs GCHP and Diff of Diffs to get species_database.yml
  files from Ref & Dev folders.  Store in spcdb_files.
- Pass spcdb_files as an argument to benchmarking routines
- Remove spcdb_dir keyword argument from calls to benchmarking routines
- Implement fixes and suggestions from Pylint

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_funcs.py
- In make_benchmark_conc_plots and make_benchmark_emis_plots,
  test if ref and dev are of types (str, list)

gcpy/benchmark/modules/benchmark_utils.py
- Added missing print statement for the path to the species_database.yml
  in the Ref run directory

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/run_1yr_tt_benchmark.py
- Bug fix: Make sure "spcdb_files" is the 5th argument (following
  dev_label) in the call to make_benchmark_mass_conservation_table
  for GCC vs GCC.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_categories.yml
- Removed the st_Ox species, this is no longer included in
  TransportTracers simulations

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/config/1yr_fullchem_benchmark.yml
- Restored the following YAML tags, which were inadvertently
  omitted from a previous commit
  - "plot_models_vs_obs: True
  - "aer_budget_table: True"
  - "Ox_budget_table: True"

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/cstools.py
- Changed x_lat = i_lat + i_vert in (0, 3)
  to      x_lat = i_lat + (i_vert in (0, 3))
  in order to enforce proper evaluation order.

This fixes an error that was introduced in commit 2b0c6ad, when we
added some improvements suggested by Pylint.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_funcs.py
- Now include old and new dust species names in species_list
- Update logic so that all dust species are included in the
  aerosol burdens table
- Skip dust species (DST* or DSTbin*) that are not found in the data
  files
- Renamed spc2name to full_names, and use the species database to
  get the long name for each species
- Updated the logic so that DST1 is not hardwired as a species name
  in the AOD table section
- Added internal routine print_aods to print the global AOD table
  separately from routine print_aerosol_metrics

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/util.py
- Bug fix: Function get_molwt_from_metadata now returns the
  Ref species metadata first, followed by Dev.  The order had been
  reversed inadvertently.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/plot/compare_single_level.py
gcpy/plot/compare_zonal_mean.py
- Edited the program logic when converting units to ug/m3 so that:
  - If both Ref and Dev metadata do not contain a molecular weight,
    print a warning message and skip to the next species.
  - If the Ref metadata contains a molecular weight but Dev does not,
    do the unit conversion for Ref, but set Dev to np.nan.   Also
    print a warning message.
  - If the Dev metadata contains a molecular weight but Ref does not,
    do the unit conversion for Dev but set Ref to np.nan.  Also
    print a warning message.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

…s code

gcpy/benchmark/modules/benchmark_funcs.py
- Call "compare_varnames" and construct the "cvars", "refonly", and
  "devonly" variables before adding missing variables (as NaN fields)
  to refdata and devdata.  This fixes a problem where all of the variables
  are considered common to both Ref & Dev even when they are not.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/budget_ox.py
- Renamed "spcdb_file" -> "spcdb_files" and updated comments
- In routine "self.get_conv_factors", skip the spcdb (species
  metdata) from Ref and take the spcdb from Dev

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>