GCPy 1.4.0

Release date 2023-11-20

From CHANGELOG.md

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 scriptsplot_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

Pull Requests Included

• Add C2H2 and C2H4 to emissions_species.yml by @msulprizio in #208
• Simplify Github issue and pull request templates by @msulprizio in #209
• Update run_benchmark.py to allow for other benchmark types by @msulprizio in #212
• Allow for other benchmark types for GCHP plotting as well by @msulprizio in #213
• Bump requests from 2.26.0 to 2.31.0 by @dependabot in #221
• Optional mass accumulation table in 1-month benchmark by @lizziel in #216
• Feature/benchmark cloud plotting templates by @laestrada in #223
• Bug fixes in transport tracer benchmark code by @lizziel in #224
• Remove references to gcpy_test and gchp_is_pre_13_1 from benchmarking routines and config files by @yantosca in #222
• Remove gcpy_test YAML key from benchmark config files by @yantosca in #226
• Shorten the filename of the benchmark operations budget table by @yantosca in #227
• Update species database and benchmark categories for TransportTracer changes in GEOS-Chem 14.2.0 by @msulprizio in #225
• Add capability to plot GEOS-Chem Classic and/or GCHP data vs. O3 model observations by @yantosca in #234
• Add lumped furans to emission_species.yml and benchmark_categories.yml by @msulprizio in #235
• Arrange models vs. observations plots from north to south by site latitude by @yantosca in #236
• Fix formatting of mass & emission tables; add mass table option to 1-year TransportTracers benchmarks by @yantosca in #238
• GCGridObj tools for cubed-sphere grids by @lizziel in #239
• Fix issue where wrong GCHP grid boxes were being looked up in models vs. obs plots by @yantosca in #240
• Now use a consistent width for columns in emissions tables and mass table output by @yantosca in #248
• Update gcpy_env environment to install with MambaForge and to use latest package versions; Update scripts accordingly by @yantosca in #251
• Fixed broken regridding code in file_regrid.py; Updated GCPy regridding documentation by @yantosca in #253
• Peg xarray to version 2023.2.0 in the environment.yml file by @yantosca in #255
• Rename PassiveTracers to TransportTracers in run_1yr_tt_benchmark.py by @msulprizio in #256
• Update plot.py for more recent xarray; also allow dask arrays to be passed to single_panel, six_plot routines by @yantosca in #257
• Now allow specification of the number of cores for benchmark plotting jobs by @yantosca in #246
• Rearrange folders according to Python packaging best practices by @yantosca in #250
• Prevent subplots from overlapping in 6-panel plots; Prevent colorbar labels from overlapping by @yantosca in #260
• Make benchmark configuration files consistent by @msulprizio in #264
• Fixed online regridding code (file_regrid.py) for restart-to-restart file regridding only by @yantosca in #266
• Add GitHub actions: CodeQL, Pylint, Stale by @yantosca in #268
• Fix several issues in file regridding; Also prevent double-flipping of vertical indices by @yantosca in #270
• Abstract routines out of gcpy/plot.py into smaller modules within the gcpy/plot folder by @yantosca in #263
• Fix bug preventing comparison plots of ref and dev with different units by @lizziel in #271
• Now let user specify X11 backend with "export MPLBACKEND="tkagg" (or "MacOSX") by @yantosca in #275

Full Changelog: 1.3.3...1.4.0