Geoschem-gcpy

Changed
- Bug fix: Remove extraneous character from setup.py

Added
- New features in benchmarking scripts (lizziel, yantosca)
- Force garbage collection at end benchmarking functions (yantosca)
- Extra print statements (lizziel)
- Diff-of-diffs plots for 1-year benchmarks (lizziel)
- sparselt is now a GCPy requirement (lizziel)
- Removed obsolete environment.yml files (yantosca)
- Added requirements.yml to docs folder for Sphinx/RTD documentation (yantosca)
- New regridding script `regrid_restart_file.py` (liambindle)

Changed
- Fixed several issues in benchmarking scripts (laestrada, lizziel, yantosca)
- Fixed bug in `budget_ox.py`; The drydep loss of Ox for GCHP was 12x too high
- Add OMP_NUM_THREADS and OMP_STACKSIZE in `plot_driver.sh` (yantosca)
- Increase requested memory to 50MB in `plot_driver.sh` (yantosca)
- Benchmark scripts print a message upon completion (yantosca)
- Linted several benchmarking routines with Pylint (yantosca)
- Rewrote algorithm of add_lumped_species_to_dataset for speed (yantosca)
- Can now specify the path to species_database.yml for 1yr benchmarks (yantosca)
- 1-yr benchmarks now save output in subdirs of the same path (lizziel)
- Avoid hardwiring restart file paths in benchmark scripts (yantosca)
- Now use outputs_subdir tag from YAML file for paths to diagnostic files (yantosca)
- Now use restarts_subdir tag from YAML file for paths to restart files (yantosca)
- GCPy now uses proper year for dev in 1-yr benchmarks (laestrada)
- Fixed date string issue in benchmarking scripts (lizziel)
- Updates for new GCHP restart file format (lizziel)
- Updated environment.yml with package versions that work together (yantosca)
- Updated the AUTHORS.txt and LICENSE.txt files (yantosca)

Added
- Added Parameter for single_panel to support return of all 6 cubedsphere plots
- Added flexible time period for benchmark plotting scripts
Changed
- Modified single_panel to vmin/vmax parameters with newer versions of matplotlib (>3.5.0)
- Modified run_benchmark script to select correct species database depending on benchmark type
- Modified filename for Ox budget
- Modified readthedocs build to use mamba instead of conda to fix build failures
- Modified benchmark plotting scripts to use a single run_benchmark.py script
- Modified benchmark categories and species database yaml files
- Fixed bug in mass conservation table percent difference

- Added date_time.py module to help manage datetime utility functions
- Added GLYC, HAC, and pFe to benchmark categories
- Added gcpy/budget_ox.py to compute Ox budgets from 1-yr benchmarks
- Added capability to use GCHP 13.1.0+ or legacy file names in benchmark scripts
- Added new methods dataset_reader and get_dataset_mean to util.py

Changed
- Modified benchmarking scripts to use yaml config files.
- Modified dry-run scripts to use yaml config files.
- Updated benchmark/run_1yr_fullchem_benchmark.py to call the budget_ox.py for GCC vs GCC benchmark generation.
- NOTE: we are waiting to make sure that the GCHP benchmarks output wetdep fields before activating this feature for GCHP.
- Modified plotting methods in benchmark.py to compute the mean of datasets over the time dimension, if the "time_mean" keyword is passed.
- This feature is used to generate annual mean plots from 1-yr benchmark output.
- Modified run_1yr_tt_benchmark.py and run_1yr_fullchem_benchmark.py to generate both annual mean and seasonal plots
- Fixed formatting and import order issues in benchmark.py, util.py, budget_ox.py, and the run_*benchmark.py scripts as identified by pylint.
- Modified budget_ox.py to use Ox instead of O3 for computing budget terms

Fixed
- Automatic benchmark script copying no longer overwrites existing files
- Color scales for non-global plots are no longer calculated from full global data
- Regional datasets can now be plotted with cubed-sphere datasets in plot.compare_single_level

Added
- Added GCPy version number and automatic script copying to benchmark scripts
- Added line clarifying lack of Windows support in ReadTheDocs

Fixed
- Fixed benchmark month seconds calculation for GCHP in 1-month benchmark script
- Fixed label typo in benchmark script GCHP vs. GCC emission plots
- Fixed grid creation for non-global grids in plot.single_panel
- Fixed issue in get_grid_extents when maxlon was in Western Hemisphere