gcpy/benchmark/benchmark_slurm.sh
- "${config/.yml/.log}: -> "${config/.yml/.log}"

Signed-off-by: Bob Yantosca <[email protected]>

gcpy/aod_species.yml
gcpy/benchmark_categories.yml
gcpy/benchmark_funcs.py
gcpy/budget_ox.py
gcpy/budget_tt.py
gcpy/emission_inventories.yml
gcpy/emission_species.yml
gcpy/lumped_species.yml
gcpy/oh_metrics.[py
gcpy/species_database.yml
gcpy/ste_flux.py
- Moved from gcpy -> gcpy/benchmark/modules

gcpy/benchmark/run_benchmark.py
gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py
gcpy/benchmark/modules/run_1yr_tt_benchmark.py
- Updated import statements accordingly
- Import benchmark routines by name

gcpy/mean_oh_from_logs.py
- Removed, this is obsolete

gcpy/__init__.py
- Removed references to benchmark_funcs, budget_ox, budget_tt,
  mean_oh_from_logs, oh_metrics, and ste_flux
CHANGELOG.md
- Updated accordingly

The following benchmark-related functions were moved from
gcpy/util.py to gcpy/benchmark/modules/benchmark_utils.py:
- get_species_categories
- archive_species_categories
- get_lumped_species_definitions
- archive_lumped_species_definitions
- add_lumped_species_to_dataset

Also:

gcpy/benchmark/modules/benchmark_util.py
- Now import xarray
- Add constants for YAML files that are now contained in the
  gcpy/benchmark/modules folder.  These should not change very much,
  except when  benchmark categories or lumped species change.
- Updated Pydoc headers

gcpy/benchmark/modules/benchmark_funcs.py
- Now import several constants and functions from benchmark_utils.py
- Removed local constants for YAML files
- Updated function calls accordingly to be consistent with the new
  functions in benchmark_utils.py

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

gcpy/benchmark/modules/benchmark_utils.py
- Now use "ofile" instead of "lumped_spc" in print statements
  in these functions:
  - archive_lumped_species_definitions
  - archive_species_categoriews

Signed-off-by: Bob Yantosca <[email protected]>

gcpy/util.py
- Removed "import shutil" statement

gcpy/benchmark/modules/benchmark_utils.py
- Added "import shutil" statement.  This is necessary to use the
  shutil.copyfile command

Signed-off-by: Bob Yantosca <[email protected]>

…file

docs/requirements.txt
- Symbolic link to docs/environment_files/read_the_docs_requirements.txt.
  The online RTD builds looks for a requirements.txt file.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

gcpy/benchmark/modules/benchmark_utils.py
- Added function "rename_speciesconc_to_speciesconcvv", to centralize
  the renaming of variables starting with "SpeciesConc_" to
  "SpeciesConcVV_". This is necessary for backwards compatibility
  with GEOS-Chem versions prior to 14.1.0.

gcpy/benchmark/modules/benchmark_funcs.py
gcpy/benchmark/modules/benchmark_models_vs_obs.py
gcpy/benchmark/modules/benchmark_models_vs_sondes.py
gcpy/benchmark/modules/budget_tt.py
- Now import and call "rename_speciesconc_to_speciesconcvv" from
  benchmark_utils.py

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

gcpy/benchmark/modules/budget_tt.py
- Add quiet=True to read_config_file to suppress printout of the
  species_database.yml path
- Add the version number (globvars.devstr) to the file path, so we can
  save Ref & Dev radionuclide budget tables

gcpy/benchmark/modules/ste_flux.py
- Add the version number (globvars.devstr) to the file path, so we
  can save Ref & Dev STE flux tables

gcpy/benchmark/modules/benchmark_funcs.py
- Updated Pydoc headers
- Add the version number to the output file name in routine
  make_benchmark_mass_conservation_table

gcpy/benchmark/modules/run_1yr_tt_benchmark.py
- Updated function calls to transport_tracers_budgets,
  make_benchmark_ste_tables, and make_benchmark_massconv_tables so that
  we can now print Ref & Dev tables for GCC vs GCC, GCHP vs GCC, and
  GCHP vs GCHP comparisons.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

gcpy/util.py
- Add new function, copy_file_to_dir, which is a wrapper for the
  shutil.copyfile function.  This abstracts the use of shutil.copyfile
  to a single location.

gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py
gcpy/benchmark/modules/run_1yr_tt_benchmark.py
gcpy/benchmark/run_benchmark.py
- Updated Pydoc header documentation w/ more up-to-date usage information
- Import copy_file_to_dir from gcpy/util.py
- No longer import shutil.copyfile
- Call copy_file_to_dir to copy __file__ (i.e. the name of the scripb
  being run) to the benchmark results directories
- Call copy_file_to_dir to copy the YAML configuration file
  to the benchmark results directories

Also in gcpy/benchmark/run_benchmark.py:
- In main: Add the configuration file name (the 1st argument)
  to the config dict (as config["configuration_file_name"]) so that
  we can use it to copy the config file to benchmark results directories.
  to the benchmark run folders

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

gcpy/benchmark/modules/benchmark_utils.py
- Now call util.copy_file_to_dir instead of shutil.copyfile
  in the following functions:
  - archive_lumped_species_definitions
  - archive_species_categories

Signed-off-by: Bob Yantosca <[email protected]>

gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py
- Fixed incorrect comment in Pydoc header

gcpy/benchmark/modules/run_1yr_tt_benchmark.py
- Bug fix: gchp_vs_gchp_refrstdir should use ["data"]["ref"] instead
  of ["data"]["dev"] search keys
- Removed commented-out code that defines bmk_mons_gchp_{ref,dev}
  and bmk_sec_per_month_{ref,dev} variables, these aren't used.