Geoschem-gcpy

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

Added
- Added MSA to Sulfur benchmark category
- Added weightsdir parameter to single_panel()
- Added temporary file creation to file_regrid() to decrease memory consumption during cubed-sphere regridding

Changed
- Removed carbon-based units from benchmark emissions tables
- Environment files now request xESMF through conda-forge rather than pip

Fixed
- Fixed Cubed-Sphere to Lat/Lon regridding for 1-level files.
- Fixed single panel zonal mean axis selection

Added
- Added complete documentation to a new ReadTheDocs site
- Added conda-forge installation support
- Added file regridder for regridding NetCDF restart and output between GEOS-Chem's horizontal grid types
- Plotting now supports automatic regridding between lat/lon, cubed-sphere, and stretched-grid formats
- Added additional 1-year benchmark plotting capabilities for GCHP
- Added oh_metrics.py, which generates output using the new Metrics collection in GEOS-Chem 13.0.0
- Extra keyword arguments not defined in plotting functions are now passed to matplotlib.pyplot
- Added a command line tool for appending grid-box corners to cubed-sphere datasets
- Added support for arbitrary vertical grids in zonal mean plotting
- Added regridding functions for arbitrary vertical grids

Changed
- Some constants in constants.py have been tweaked to match GEOS-Chem definitions
- docs/environment.yml, setup.py, and requirements.txt now reflect up-to-date GCPy library requirements
- Most docstrings now use the same format
- Various code formatting changes have been made to align with PEP8 guidelines

Deprecated
- mean_oh_from_logs.py is replaced in functionality by oh_metrics.py for GEOS-Chem versions >=13.0.0

Fixed
- Installation through pip (from the repositoryand conda now works correctly

Removed
- Removed several functions and files that are no longer used, including budget_aer.py and create_budget_table()

Added
- Added instructions on setting PYTHONPATH to include GCPy directory when installing manually
- Added cross-dateline regional plotting capability for both lat/lon and cubed-sphere plots
- Added function to get lev dimension index that matches a requested pressure value
- Added basic up-to-date map plotting examples
- Added pip and tabulate dependencies in gcpy environment yaml file
- Added RRTMG netcdf diagnostics names for converting from bpch to nc
- Added unit string conversion for RRTMG binary diagnostics to compare easily with netcdf

Changed
- Temporary PDFs are now generated in the system's temp directory rather than within the working directory
- environment.yml now includes version numbers to ensure compatability

Fixed
- Fixed single panel zonal mean plotting for GCHP
- Fixed existing non-deleted examples code
- Fixed imports for out-of-scope variables

Removed
- Removed several code examples that were out-of-date.

Added

- Add new function to compute budgets and create budget table that incorporates new optional features.
- Require python package tabulate for generating budget tables.
- Added parallel support for mass and budget table creation in 1-year benchmarks.
- Added capability of completely disabling parallel plotting when calling make_benchmark_*_plots functions.
- Added capability of converting concentrations to ug/m3 for benchmark plotting.
- Added new function to make benchmark wet deposition plots, previously done from function to make concentration plots.

Changed
- Reorganized functions of GCPy into a more logical and streamlined file structure.
- Updated species_database.yml and benchmark_categories.yml for GEOS-Chem 12.9.2.
- Replaced "Plots" with "Results" in benchmark directory structure. This value is customizable in the benchmark scripts.
- Updated example scripts to use reorganized GCPy functions.
- Updated all benchmark run scripts for consistency, readability, reduced lines of code, and compatibility with reorganized and new GCPy functions

Fixed
- Fixed documentation and rearranged argument order for diff-of-diffs plot strings.
- Fixed accidental regridding to lat/lon in comparison plots where two cubed-sphere datasets share the same resoltuion.
Removed
- Removed budget_ops.py in deference to new make_benchmark_operations_budget function.

Fixed
- Fixed bugs calculating lumped species with some or all missing constituents.
- Added documentation for newer keyword arguments in benchmark.py