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GCPy Changelog

All notable changes to GCPy will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased] - TBD

Fixed

  • Fixed formatting error in .github/workflows/stale.yml that caused the Mark Stale Issues action not to run

[1.5.0] - 2024-05-29

Added

  • Script gcpy/benchmark/modules/benchmark_utils.py, with common benchmark utility functions
  • Script gcpy/benchmark/modules/benchmark_drydep.py, with code to create drydep velocity plots
  • YAML tag plot_drydep in gcpy/benchmark/config/*.yml files
  • Badge for build-gcpy-environment GitHub Action in README.md
  • Badges in docs/source/index.rst
  • GitHub action to push GCPy releases to PyPi
  • Script ./release/changeVersionNumbers.sh, used to update version numbers in various files before release
  • Mamba/Conda enviroment file docs/environment_files/read_the_docs_environment.yml, for building ReadTheDocs documentation
  • Environment files docs/environment_files/gcpy_requirements.txt and docs/environment_files/read_the_docs_requirements.txt
  • New benchmark script gcpy/benchmark/modules/benchmark_models_vs_sondes.py
  • Added fixed level budget diagnostic to budget operations table
  • Function rename_speciesconc_to_speciesconcvv in gcpy/benchmark/modules/benchmark_utils.py
  • Function copy_file_to_dir in gcpy/util.py. This is a wrapper for shutil.copyfile.
  • GitHub Action config file .github/workflows/stale.yml, which replaces StaleBot
  • Added gcpy/community/format_hemco_data.py from @hannahnesser
  • Added gcpy/examples/hemco/format_hemco_demo.py from @hannahnesser
  • Added HCl to gcpy/benchmark/modules/emission_species.yml and GTChlorine to gcpy/benchmark/modules/emission_inventories.yml for GEOS-Chem 14.4.0
  • Example script gcpy/examples/working_with_files/make_mask_file.py
  • Convenience function replace_whitespace in gcpy/util.py
  • Benchmark script gcpy/benchmark/modules/benchmark_scrape_gcclassic_timers.py
  • Benchmark script gcpy/benchmark/modules/benchmark_scrape_gchp_timers.py
  • 1-year benchmark scripts now produce GCC vs GCC and GCHP vs GCHP timing tables
  • Functions gcc_vs_gcc_dirs, gchp_vs_gcc_dirs, gchp_vs_gchp_dirs, and get_log_filepaths in gcpy/benchmark/modules/benchmark_utils.py
  • Script gcpy/benchmark/modules/benchmark_mass_cons_table.py, with code to create mass conservation tables
  • Expanded statistics output in benchmark mass conservation tables
  • Function get_datetimes_from_filenames in gcpy/benchmark/modules/benchmark_utils.py
  • Function replace_whitespace in gcpy/util.py

Changed

  • Bump pip from 23.2.1 to 23.3 (dependabot suggested this)
  • Bump pypdf from 3.16.1 to 3.17.0 (dependabot suggested this)
  • YAML tag operations_budget is now ops_budget_table in gcpy/benchmark/config/1yr_tt_benchmark.yml
  • Now require matplotlib=3.8.0 in docs/environment_files/environment.yml (with other pegged versions)
  • Now run the stale GitHub action at 00:00 UTC on the 1st of each month
  • Renamed docs/environment_files/environment.yml to gcpy_environment.yml
  • environment.yml links to docs/environment_files/gcpy_environment.yml
  • requirements.txt links to docs/environment_files/requirements.txt
  • Python packages for RTD documenation builds from docs/environment_files/environment.yml
  • Script benchmark_model_vs_obs.py now uses grid inquiry functions from grid.py to return data nearest to a (lat,lon) location
  • Moved routine get_geoschem_level_metadata to gcpy/benchmark/modules/benchmark_utils.py
  • Refactored get_vert_grid.py (in gcpy/grid.py) to accept the p_sfc argument; Also never-nested the if-block logic.
  • benchmark_slurm.sh script now saves output to a log file with the same base name as the YAML config file
  • benchmark_models_vs_obs.py now reads the observational data paths and metadata from 1yr_fullchem_benchmark.yml
  • Moved benchmark code from gcpy/ to gcpy/benchmark/modules/
  • Benchmark functions now call rename_speciesconc_to_speciesconcvv
  • Create radionuclide, STE flux, and mass conservation tables for Ref and Dev versions in TransportTracers benchmarks
  • Use new function copy_file_to_dir to copy the benchmark script and configuration file to the benchmark results folders
  • Updated GitHub stalebot config file stale.yml with new issue/PR labels that should not go stale
  • Updated benchmark driver scripts and config files to print GCClassic & GCHP timing information
  • Updated documentation for GCPy 1.5.0 release
  • Converted Github issue templates to issue forms using YAML definition files

Fixed

  • CS inquiry functions in gcpy/cstools.py now work properly for xr.Dataset and xr.DataArray objects
  • Prevent an import error by using seaborn-v0_8-darkgrid ingcpy/benchmark/modules/benchmark_models_vs_obs.py
  • gcpy/file_regrid.py now creates GCHP files with DELP_DRY instead of DELPDRY
  • Fixed bugs in GCHP vs GCHP sections of 1-yr benchmark run scripts to allow comparison of GCHP runs with different grid resolutions
  • Fixed silent bug in transport tracer benchmark GCC vs GCHP mass tables preventi ng them from being generated
  • Import error in gcpy/examples/diagnostics/compare_diags.py
  • Added missing n_cores to gcpy/examples/diagnostics/compare_diags.yml
  • Added missing plot_drydep option to gcpy/gcpy/benchmark/config/1yr_ch4_benchmark.yml
  • Add docs/requirements.txt symbolic link to docs/environment_files/read_the_docs_requirements.txt for RTD builds
  • gcpy/file_regrid.py now tests if lon_bnds, lat_bnds are in the dataset before trying to drop them

Removed

  • Example script gcpy/examples/plotting/mda8_o3_timeseries.py
  • Removed Pylint GitHub action
  • Environment file docs/environment_files/environment.yml
  • Environment file docs/environment_files/requirements.txt
  • Removed awscli from the GCPy environment; version 2 is no longer available on conda-forge or PyPi
  • GitHub config files .github/stale.yml and .github/no-response.yml
  • Routine make_benchmark_mass_conservation_table in benchmark_funcs.py; this is now obsolete

[1.4.2] - 2024-01-26

Added

  • Example script create_test_plot.py, which can be used to check that GCPy has been installed properly
  • GitHub action build-gcpy-environment which tests installation of the mamba environment specified in in docs/environment_files/environment.yml
  • YAML filedocs/environment_files/testing.yml for building an environment without pegged package versions (for testing)
  • GitHub action build-test-environment to test the environment specified in testing.yml

Changed

  • build-gcpy-environment GitHub action now runs with several Python versions

Fixed

  • Prevent overwriting of the results variable when parallel plotting is deactivated (n_cores: 1)

[1.4.1] - 2023-12-08

Fixed

  • Now use the proper default value for the --weightsdir argument to gcpy/file_regrid.py

[1.4.0] - 2023-11-20

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

[1.3.3] -- 2023-03-09

Added

  • Updated installation documentation, we now recommend users to create a conda environment using the environment.yml file
  • Benchmark summary table output (intended for 1hr & 1mo benchmarks)
  • Species/emissions/inventories that differ between Dev & Ref versions are now printed at the top of the benchmark emissions, inventory, and global mass tables. if there are too many species with diffs, an alternate message is printed.
  • New functions in benchmark.py and util.py to facilitate printing of the species/emissions/inventories that differ between Dev & Ref versions.
  • Added new RTD documentation for installing Conda 4.12.0 with Miniconda
  • Added GCHP regridding environnment file docs/environment_files/gchp_regridding.yml
  • Added new benchmark type CH4Benchmark

Changed

  • Applied cleanup susggestions from pylint to benchmark.py, util.py, plot.py, oh_metrics.py, ste_flux.py
  • Replaced format with f-strings in benchmark.py, util.py, plot.py, oh_metrics.py, ste_flux.py
  • Abstract some common in benchmark.py into functions
  • Replaced direct calls to yaml.load with util.read_config.file
  • Restore tag information to benchmark refstr and devstr labels
  • Add a newline to diff-of-diffs refstr and devstr if the string is too long.
  • Updated GCHP regridding documentation
  • Restored ipython and jupyter to environment file environment.yml

[1.3.2] -- 2022-10-25

Fixes

  • Fixed malformed version declaration for cartopy (use == instead of =) in setup.py. This was preventing upload to conda-forge.
  • Vertically flip GCHP emissions when computing transport tracers budget

[1.3.1] -- 2022-10-25

Changed

  • Bug fix: Remove extraneous character from setup.py

[1.3.0] -- 2022-10-25

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)

[1.2.0] - 2021-09-22

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

[1.1.0] - 2021-09-22

  • 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

[1.0.3] - 2021-03-26

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

[1.0.2] - 2021-03-18

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

[1.0.1] - 2021-02-09

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

[1.0.0] - 2021-01-05

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()

[0.3.1] - 2020-08-21

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.

[0.3.0] - 2020-07-30

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.

[0.2.1] - 2020-05-07

Fixed

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

[0.2.0] - 2020-05-06

Added

  • Added strat/trop exchange fluxes to 1-year benchmark output (gcpy/ste_flux.py)
  • Added operations budgets to 1-year benchmark output (gcpy/budget_ops.py)
  • Added seasonal mass table output for 1-year FullChemBenchmark.
  • Added mean OH from log files for 1-year FullChemBenchmark (GEOS-Chem Classic only).
  • Added function gcplot in core.py for creating individual (rather than six-panel) plots of GEOS-Chem data.
  • 47-level model output can now be plotted in addition to the standard 72-level output.
  • Added Loader=yaml.FullLoader to the yaml.load command to avoid generating excess warnings.
  • Add benchmark plotting option to write concentration and emissions plots to one file
  • Add gcpy testing mode for all GEOS-Chem benchmark run scripts using test data on gcgrid.
  • Add function to flip and rename GCHP restart files to match GCC names and level convention.
  • Add capability to generate GCHP vs GCC and GCHP vs GCHP mass tables.
  • Add handling in convert_units for datasets without a time dimension.
  • Add initial and final mass to GHCP radionuclide budget tables.

Changed

  • Significant difference files are now written out to the Plots/Sig_Diffs folder for the 1-year benchmarks.
  • Updated file names for Pb/Be budget tables in gcpy/budgets_tt.py.
  • Created separate driver routines for 1-year FullChem and TransportTracers benchmarks
  • Useless warnings when creating benchmark output should now be suppressed
  • Can now create benchmark plots in a single file instead of by category.
  • Can now plot non-global output files from GEOS-Chem Classic.
  • Can now limit plot extents using lat/lon parameters for GEOS-Chem Classic and GCHP.
  • L2L regridder filenames now include the grid extent when the regridder does not span the whole globe.
  • Input GEOS-Chem Classic data can now be any lat/lon resolution rather than only 4x5, 2x2.5, or 1x1.25.
  • Replaced fractional difference plots ((Dev-Ref)/Ref) with ratio plots (Dev/Ref).
  • Moved diff-of-diffs functionality from standalone code in the benchmark scripts to benchmark.py.
  • The bottom row of diff-of-diffs plotting now shows (Dev2/Dev1)-(Ref2/Ref1) values.
  • Paths in example scripts now point to /n/holyscratch01/external_repos/GEOS-CHEM instead of /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM.
  • Cleaned up run_1mo_benchmark.py driver scripts
  • Operations budgets are now printed as Ref, Dev, Dev-Ref, %diff
  • Updated examples/compare_diags.py to point to test benchmark data
  • Updated benchmark_categories.yml, species_database.yml, lumped_species.yml, and emission_inventories.yml for recent changes in GEOS-Chem 12.8.0
  • Update benchmark run scripts to use version strings rather than subtitle strings in tables filenames.

Fixed

  • Latitude ticks again appear in benchmark zonal mean plots.
  • Colorbar tick formatting now never uses offset format, which made colorbar ticks difficult to interpret for small value ranges.
  • The list of non-plotted emissions species now populates properly.
  • Fixed sig diffs file creation for AOD and JValues.
  • Missing values in mass tables are now NaN
  • Fix area normalization issues in benchmark plotting functions when using GCHP data.

Removed

  • Removed runnable docstring content.

[0.1.1] - 2020-02-28

Added

  • This CHANGELOG file to track notable changes in GCPy.

Changed

  • Pb210, Be7, and Be10 species are now added to species_database.yml.
  • gcpy/budget_aer.py and gcpy/budget_tt.py now get molecular weights from species_database.yml.
  • Updated the value of MW_AIR in constants.py to add more precision.
  • gcpy/benchmark.py now writes OH metrics output to the Plots/Tables folder.
  • Updated CHANGELOG.md for 0.1.1.
  • Updated download_data.py to properly obtain 2 x 2.5 and nested data sets.

[0.1.0] - 2020-02-26

Summary

This is the first labeled version of GCPy. The primary functionality of GCPy is plotting and tabling diagnostics from GEOS-Chem. Main features include:

  • Functions for comparing GEOS-Chem benchmark output for multiple versions of GEOS-Chem, including 2D plots and mass and budget table creation.
  • Support for plotting benchmark output for both GEOS-Chem Classic (lat/lon data) and GCHP (cubed-sphere data).

The first official release version of GCPy, v1.0.0, will correspond with the release of GEOS-Chem 13.0.0.