Release date 2023-11-20
[](https://doi.org/10.5281/zenodo.10161227)
CHANGELOG
Added
- Added C2H2 and C2H4 to `emission_species.yml`
- Updated `species_database.yml` for consistency with GEOS-Chem 14.2.0
- Added `.github/ISSUE_TEMPLATE/config.yml` file w/ Github issue options
- Added `CONTRIBUTING.md` and `SUPPORT.md`, replacing `docs/source/Contributing.rst` and `docs/source/Report_Request.rst`
- Added option to pass the benchmark type to plotting routines
- Updated `AUTHORS.txt` as of Apr 2023 (concurrent w/ GEOS-Chem 14.2.0)
- Added ReadTheDocs badge in `README.md`
- Added `.readthedocs.yaml` to configure ReadTheDocs builds
- Added cloud benchmarking YAML configuration files to `benchmark/cloud` folder
- Added `README.md` files in `gcpy/benchmark` directory structure
- Added `benchmark/modules/benchmark_models_vs_obs.py` script
- Added `benchmark/modules/GC_72_vertical_levels.csv` file
- Added `multi_index_lat` keyword to `reshape_MAPL_CS` function in `gcpy/util.py`
- Added FURA to `emission_species.yml` and `benchmark_categories.yml`
- Added new routine `format_number_for_table` in `gcpy/util.py`
- Added module `gcpy/cstools.py` with utility functions for cubed-sphere grids
- Added new routine `verify_variable_type` function in `gcpy/util.py`
- Added new routine `format_number_for_table` in `util.py`
- Added BrSALA and BrSALC to `emission_species.yml`
- Added `options:n_cores` to all benchmark YAML config files
- Added `__init__.py` files in subfolders of `gcpy/gcpy`
- `gcpy/benchmark/modules/*.py` scripts are now chmod 644
- Added `ENCODING = "UTF-8"` to `gcpy/constants.py`
- Added statement `from dask.array import Array as DaskArray` in `gcpy plot.py`
- Added SLURM run script `gcpy/benchmark/benchmark_slurm.sh`
- Added `gcpy/plot/gcpy_plot_style` style sheet for title and label default settings
- Added `gcpy/gcpy_plot_style` style sheet for title and label default settings
- Added new cubed-sphere grid inquiry functions to `gcpy/cstools.py`
- Added functions `get_ilev_coord` and `get_lev_coord` to `gcpy/grid.py`
- Add `tk` package to `docs/environment_files/environment.yml`
Changed
- Simplified the Github issues templates into two options: `new-feature-or-discussion.md` and `question-issue.md`
- The GitHub PR template is now named `./github/PULL_REQUEST_TEMPLATE.md`
- Updated badge links in `README.md`
- Construct ops budget table filename without using the `label` argument
- Updated species_database.yml for consistency with GEOS-Chem 14.2.0
- Renamed TransportTracers species in `benchmark_categories.yml`, `run_1yr_tt_benchmark.py`, and in documentation
- YAML files in `benchmark/` have been moved to `benchmark/config`
- Models vs. O3 obs plots are now arranged by site latitude from north to south
- Routine `print_totals` now prints small and/or large numbers in scientific notation
- Truncate names in benchmark & emissions tables to improve readability
- Add TransportTracers species names to `gcpy/emissions_*.yml` files
- Now pass `n_job=config["options"]["n_cores"]` to benchmark plotting routines
- Script `benchmark.py` to `benchmark_funcs.py` to remove a name collision
- Folder `gcpy/benchmark` is now `gcpy/gcpy/benchmark`
- Folder `benchmark/modules` is now `gcpy/gcpy/benchmark/modules`
- Folder `gcpy/examples` is now `gcpy/gcpy/examples`
- Pass `sys.argv` to the `main()` routine of `run_benchmark.py`,` compare_diags.py`
- Updated `docs/environment_files/environment.yml` for MambaForge (also added `gridspec`)
- Now use `pypdf` instead of `PyPDF2` in `plot.py` and `util.py`
- Added coding suggestions made by `pylint` where possible
- Abstracted and never-nested code from `six_plot` into functions (in `plot.py`)
- Added `main()` routine to `gcpy/file_regrid.py`; Also added updates suggested by Pylint
- Fixed broken regridding code in `gcpy/file_regrid.py`; also refactored for clarity
- Rewrote `Regridding.rst` page; Confirmed that regridding examples work properly
- Now allow `plot_val` to be of type `dask.array.Array` in `plot.py` routines `six_plot` and `single_panel`
- Now add `if` statements to turn of `Parallel()` commands when `n_jobs==1`.
- Do not hardwire fontsize in `gcpy/plot.py`; get defaults from `gcpy_plot_style`
- `gcpy/plot.py` has been split up into smaller modules in the `gcpy/plot` folder
- Updated and cleaned up code in `gcpy/regrid.py`
- Example scripts`plot_single_level` and `plot_comparisons` can now accept command-line arguments
- Example scripts `plot_single_level.py`, `plot_comparisons.py`, `compare_diags.py` now handle GCHP restart files properly
- Now specify the X11 backend with by setting the `MPLBACKEND` environment variable
Fixed
- Generalized test for GCHP or GCClassic restart file in `regrid_restart_file.py`
- Fixed bug in transport tracer benchmark mass conservation table file write
- Routine `create_display_name` now splits on only the first `_` in species & diag names
- Prevent plot panels from overlapping in six-panel plots
- Prevent colorbar tick labels from overlapping in dynamic-range ratio plots
- Updated `seaborn` plot style names to conform to the latest matplotlib
- Set `lev:positive` and/or `ilev:positive` properly in `regrid_restart_file.py` and `file_regrid.py`
- Prevent overwriting of `lev` coord in `file_regrid.py` at netCDF write time
- Fixed bug in option to allow different units when making comparison plots
Removed
- Removed `gchp_is_pre_13_1` arguments & code from benchmarking routines
- Removed `is_pre_13_1` tags from `*_benchmark.yml` config files
- Removed `benchmark_emission_totals.ipynb`, this is obsolete
- Replaced `gcpy/benchmark/README` with `README.md`
- Removed `gcpy_test_dir` option from `examples/diagnostics/compare_diags.*`
- Removed `docs/environment_files/gchp_regridding.yml` environment file
- Removed `gcpy/gcpy/benchmark/plot_driver.sh`
- Made benchmark configuration files consistent
**Full Changelog**: https://github.com/geoschem/gcpy/compare/1.3.3...1.4.0