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Recent Releases of gcpy

gcpy - GCPy 1.7.1

DOI

From CHANGELOG.md

Changed

  • Bumped pip to version 26.0 in setup.py and environment files

Fixed

  • Fixed error in get_input_res for numpy 2.x versions; we first copy the lon and lat arrays before sorting

Pull requests included

Full Changelog: https://github.com/geoschem/gcpy/compare/1.7.0...1.7.1

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca 4 months ago

gcpy - GCPy 1.7.0

DOI

From CHANGELOG.md

Added

  • Added gcpy/profile/vtune_plot_hotspots.py to plot a bargraph of hotspots from Intel VTune reports
  • Added ReadTheDocs documentation for plotting hotspots from Intel VTune reports
  • Added "Lint" GitHub Action to check other actions for security issues
  • Added gcpy_environment_py314.ym1 to specify the GCPy environment packages with Python 3.14
  • Added GitHub action build-gcpy-environment-py314.yml to test building the GCPy environment with Python 3.14
  • Added call to drop GC-Classic variables when regridding a GC-Classic restart file to cubed-sphere
  • Added Ap and Bp parameters for GCAP2 vertical grids
  • Added new constants for default lon/lat and stretched-grid settings in gcpy/constants.py
  • Added PyDoc headers in routines where they were missing
  • Added examples/grids/display_gcclassic_grid_info.py to display info about a GEOS-Chem Classic horizontal grid
  • Added functions get_molwt_from_metadata and read_species_metadata to gcpy/util.py
  • Added function get_species_database_files to gcpy/benchmark/modules/benchmark_utils.py
  • Added constant SPECIES_DATABASE to gcpy/benchmark/modules/benchmark_utils.py
  • Added manual garbage collection in create_regridders, compare_single_level, and compare_zonal_mean functions.
  • Added helpful tips to the gcpy/benchmark/benchmark.slurm.sh script
  • Added function datetime64_to_str to gcpy/date_time.py
  • Added keyword arguments ref_hdr_label and dev_hdr_label to make_benchmark_mass_tables
  • Added "HEMCO Examples" chapter to ReadTheDocs documentation

Changed

  • Modified criteria for terminating read of log files in benchmark_scrape_gcclassic_timers.py to avoid being spoofed by output that is attached by Intel VTune
  • Moved gprofng_text_to_data_units to function text_to_data_units in gcpy/plot/core.py so that it can be used by gprofng_functions and vtune_plot_hotspots
  • Updated GitHub badges in README.md and docs/source/index.rst
  • Expanded possible stretched grid attribute names to include STRETCH_FACTOR, TARGET_LAT, and TARGET_LON
  • Changed regridding for plots to always compare stretched-grid to uniform CS grid on the uniform CS grid rather than whatever grid is ref
  • Updated PDF writing algorithm in compare_single_level and compare_zonal_mean to use PdfReader and PdfWriter instead of PdfMerger
  • Bumped pypdf from version 4.2.0 to 6.6.2 in setup.py and environment files
  • Moved Ap and Bp parameters that define vertical grids from grid.py to vgrid_defs.py
  • Replaced hardwired default lon/lat and stretched-grid settings with new constants from gcpy/constants.py
  • Modified code in several modules as directed by Pylint to better conform to the Python style guide
  • Renamed grid routines to use all lower-case letters in order to conform to Python snake-case convention
  • Remamed vert_grid class in gcpy/grid.py to VertGrid to conform to PascalCase naming convention
  • Replaced hashlib.sha1 with hashlib.sha256 in routine sg_hash in gcpy/regrid.py
  • Bumped pip to version 25.2 as suggested by Dependabot
  • Required passing template output file to offline restart regridding that has grid dimensions that do not match target restart grid
  • Changed offline restart regridding to preserve source restart file precision
  • Changed mamba to conda in benchmarks/benchmark_slurm.sh
  • Separated plot and table options for clarity in benchmarks/config/*yml and benchmarks/cloud/*.yml
  • Clarified the GCPy installation process in ReadTheDocs documentation
  • Updated the instructions in the "Create a Test Plot" example in ReadTheDocs documentation
  • Updated default GCPy Python environment to use Python 3.13 (instead of 3.12)
  • Benchmark routines now look for species_database.yml in the Ref and Dev run directories
  • Replaced get_species_database_dir with get_species_database_files in gcpy/benchmark/modules/benchmark_funcs.py
  • Updated gcpy/benchmark/modules/benchmark_scrape_gchp_timers.py to look for GCHP timers in allPEs.log if not found in the log file
  • Updated routine make_benchmark_aerosol_tables to include all dust species in the aerosol burdens table
  • Optimized function get_diff_of_diffs (in gcpy/util.py) for performance
  • Optimized function add_lumped_species_to_dataset (in gcpy/benchmark/modules/benchmark_utils.py) for performance
  • Optimized the algorithm to generate varlist in make_benchmark_conc_plots. Also truncated datasets to only contain variables in varlist.
  • Updated make_benchmark_aod_plots to include column AOD plots for DSTbin1..DSTbin7 species
  • Updated benchmark/modules/aod_species.py with metadata for DSTbin1..DSTbin7 species
  • Updated make_benchmark_mass_tables and create_global_mass_table to allow Ref and Dev to have different dates if so chosen
  • Updated run_benchmark.py to generate mass tables at start and end of the simulation
  • Updated run_1yr_fullchem_benchmark.py and run_1yr_tt_benchmark.py to generate mass tables at the 1st day of each month from Jan 2019 thru Jan 2020
  • Updated run_benchmark.py to take the AREA field from the GCHP restart file at the end of the month when computing mass tables for 1hr/1mon benchmarks
  • Updated routine convert_units to reshape the area variable tomatch input data on the GCHP checkpoint grid

Fixed

  • Fixed grid area calculation scripts of grid_area in gcpy/gcpy/cstools.py
  • Fixed various security issues in GitHub Actions workflows
  • Fixed colorbar bounds for case of comparing cubed-sphere grids
  • Fixed the restart regridding for stretched GCHP when target lat/lon is exactly 0.0 in gcpy/regrid_restart_file.py
  • Fixed computation of the global AOD benchmark table caused by hardwired species names
  • Fixed error in create_benchmark_emissions_table where all species were assumed to be in Ref and Dev even if they were not
  • Fixed error that caused the GCHP vs GCC diff-of-diffs AnnualMean plots to be computed as a difference of means instead of a mean of differences

Removed

  • Removed PdfMerger() from compare_single_level and compare_zonal_mean, it has been removed in pypdf >= 5.0.0
  • Removed .load() statements from xarray Datasets to improve performance
  • Removed paths:spcdb_dir YAML tag in benchmark configuration files
  • Removed st_Ox from benchmark_categories.yml; this species is no longer used in TransportTracers simulations
  • Removed keyword argument label from make_benchmark_mass_tables

Pull requests included

New Contributors

Full Changelog: https://github.com/geoschem/gcpy/compare/1.6.2...1.7.0

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca 4 months ago

gcpy - GCPy 1.6.2

Release date: 12 Jun 2025
DOI

From CHANGELOG.md

Added

  • Added create_benchmark_sanity_check_table routine to gcpy/benchmark/benchmark_funcs.py to test if variables are all zero or NaN
  • Added a chapter on using code profiling tools in the ReadTheDocs documentatio
    n
  • Added code profiling scripts (in gcpy/gcpy/profile) to read and display output from gprofng and Intel VTune profilers
  • Added check_gchp_emission_diags.py example script and documentation
  • Added new benchmark functions make_benchmark_collection_2d_var_plots and make_benchmark_collection_3d_var_plots which can be used with any GEOS-Chem output collection
  • Added 1-month benchmark comparison plot options for Budget, UVFlux, and StateMet collections (2D and 3D vars separately) which are off by default
  • Added export MPLBACKEND=agg to gcpy/benchmark/modules/benchmark_slurm.sh to request a non-interactive MatPlotLib backend
  • Added method keyword argument to make_regridder_* routines in regrid.py, with default value conservative

Changed

  • Updated gcpy_environment_py313.yml to use esmf==8.8.1 and esmpy==8.8.1 to fix package inconsistency issues

Fixed

  • Fixed logic error in compare_varnames that caused 2D data variables to be flagged as 3D (esp. for GCHP vs GCC comparisons)
  • Replaced incorrect collection name AOD with Aerosols in the GCC vs. GCC 1-month AOD plots
  • Fix the logic of ravel_1D that creates orbit file for 1D GCHP diagnostic

Pull Requests Included

Full Changelog: https://github.com/geoschem/gcpy/compare/1.6.1...1.6.2

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca 12 months ago

gcpy - GCPy 1.6.1

Release Date: 24 Mar 2025
DOI

From CHANGELOG.md

Added

  • Added GCPy environment file docs/environment_files/gcpy_environment_py313.yml, which is based on Python 3.13
  • Added GitHub Actions config file.github/workflows/build-gcpy-environment-py313.yml
  • Added Install-Mamba-Conda.rst ReadTheDocs supplmental guide for Mamba/Conda installation
  • Added Anaconda, PyPI, Platforms, Downloads badges to README.md and docs/source/index.rst

Changed

  • Updated paths to regridding weights in benchmark/config/*.yml and examples/diagnostics/compare_diags.yml files
  • Renamed docs/environment_files/gcpy_environment.yml to gcpy_environment_py312.yml
  • Updated symbolic link environment.yml to point to docs/source/gcpy_environment_py312.yml
  • Renamed GitHub Actions config file .github/workflows/build-gcpy-environment.yml to build-gcpy-environment-py312.yml
  • Updated package version information in ReadTheDocs documentation
  • Bumped dask from version 2024.5.2 to 2025.3.0 to fix a security issue (raised by @dependabot)
  • Bumped jinja2 from version 3.1.5 to 3.1.6 to fix a security issue (raised by @dependabot)
  • Edited installation instructions via Mamba/Conda to more accurately reflect the needed commands
  • Updated the ReadTheDocs "Releasing new versions" guide with info on conda-forge

Removed

  • Removed PyPi configuration file docs/environment_files/gcpy_requirements.txt and symbolic link ./requirements.txt
  • Removed Python 3.8 from the python-version list in .github/workflows/*.yml files
  • Remove Mamba/Conda installation instructions from Getting-Started-from-GCPy.rst
  • Removed "Latest pre-release" bade from README.md and docs/source/index.rst

Pull requests included

Full Changelog: https://github.com/geoschem/gcpy/compare/1.6.0...1.6.1

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca about 1 year ago

gcpy - GCPy 1.6.0

Release date: 29 Jan 2025
DOI

From CHANGELOG.md

Added

  • Added example script gcpy/examples/hemco/make_hemco_sa_spec.py (creates the HEMCO standalone configuration file HEMCO_sa_Spec.rc)
  • Added module benchmark_gcclassic_stats.py for scraping statistics from GEOS-Chem Classic cloud benchmarks
  • Added dry deposition velocity comparison plots in 1-month cloud benchmarks
  • Added gcpy/benchmark/modules/benchmark_species_changes.py to compute the table of species changes between versions
  • Added gcpy/kpp/ folder containing scripts to plot output from the KPP-Standalone box model

Changed

  • Changed format of % diff column from 12.3e to 12.3f in benchmark timing tables
  • Updated gcpy/benchmark/modules/emission_species.yml file with emission species for GEOS-Chem 14.5.0
  • Updated gcpy/benchmark/modules/benchmark_categories.yml with the latest categories for GEOS-Chem 14.5.0
  • Updated gcpy/benchmark/modules/lumped_species.yml with speciations for GEOS-Chem 14.5.0
  • Add DryDep to list of collections included in benchmark summary table
  • Updated checkout GitHub action to v4
  • Updated CodeQL GitHub action to v3
  • Updated publish-python GitHub action to v5
  • In environment files gcpy_environment.yml and gcpy_requirements.txt:
    • Update python to 3.12.0
    • Update xesmf to 0.8.5
    • Update esmf and esmpy to 8.6.1
  • In environment files read_the_docs_environment.yml and read_the_docs_requirements.txt
    • Update jinja to 3.1.5 (fixes a security issue)
  • Update gcpy/setup.py with the new Python package version numbers
  • Updated code in gcpy/benchmark/modules/ to replace whitespace in Ref and Dev labels with underscores

Fixed

  • Fixed formatting error in .github/workflows/stale.yml that caused the Mark Stale Issues action not to run
  • Now flag differences greater than +/- 10% in benchmark timing table outputs
  • Fixed error in computation of dynamic ratio plot min & max values in plot/six_plot.py
  • Fixed erroneous species classification in gcpy/benchmark/modules/benchmark_categories.yml
  • Fixed type errors in calc_rectilinear_lon_edge and calc_rectangular_lat_edge by casting the length of the output array from float to int

Removed

  • Removed gcpy/benchmark/modules/species_database.yml file and corresponding code pointing to this

Pull requests included

Full Changelog: https://github.com/geoschem/gcpy/compare/1.5.0...1.6.0

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca over 1 year ago

gcpy - GCPy 1.5.0

Release Date: 29 May 2024
DOI

Known issues

The pip install geoschem-gcpy command (as described on ReadTheDocs) is broken due to the xesmf 0.5.1 package having been de-listed from the Python Package Index (PyPi). For the time being, users should follow the manual installation instructions. See issue #326 for more information.

CHANGELOG

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

New Contributors

Full Changelog: https://github.com/geoschem/gcpy/compare/1.4.2...1.5.0

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca about 2 years ago

gcpy - GCPy 1.4.2

Release date 26 Jan 2024

CHANGELOG

Full Changelog: https://github.com/geoschem/gcpy/compare/1.4.1...1.4.2

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca over 2 years ago

gcpy - GCPy 1.4.1

Release date 08 Dec 2023

CHANGELOG

Fixed

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

Full Changelog: https://github.com/geoschem/gcpy/compare/1.4.0...1.4.1

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca over 2 years ago

gcpy - GCPy 1.4.0

Release date 2023-11-20
DOI

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 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

Full Changelog: https://github.com/geoschem/gcpy/compare/1.3.3...1.4.0

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca over 2 years ago

gcpy - GCPy 1.3.3

Release date: 09 Mar 2023
DOI

CHANGELOG

Added

  • Add capability to generate CH4 benchmark output by @msulprizio in #186
  • Added documentation for installing Conda 4.12.0 with Miniconda by @yantosca
  • Add stretching parameters to GCHP regridding example by @kilicomu in #206

Changed

  • Update SpeciesConc variable name to SpeciesConcVV for consistency with GEOS-Chem 14.1.0 updates by @msulprizio in #187
  • Update benchmark table output to better show which diagnostics have Ref = Dev by @yantosca in #200
  • Updated GCHP regridding documentation by @kilicomu in #205
  • Additional cleanup of gcpy routines by @yantosca in #204

Fixed

  • Fix bug in GCHP transport tracer budget table by @lizziel in #192
  • Fixed GCHP regridding issues by @kilicomu in #190

Full Changelog: https://github.com/geoschem/gcpy/compare/1.3.2...1.3.3

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca about 3 years ago

gcpy - GCPy 1.3.2

Release date: 26 Oct 2022

Changed

  • Bug fix: Fixed malformed version declaration for cartopy (use == instead of =) in setup.py. This was preventing upload to conda-forge.

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca over 3 years ago

gcpy - GCPy 1.3.1

Release date 26 Oct 2022

What Changed:

  • Bug fix in setup.py, removed extraneous character
  • Updated version numbers in various files

Full Changelog: https://github.com/geoschem/gcpy/compare/1.3.0...1.3.1

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca over 3 years ago

gcpy - GCPy 1.3.0

Release date: 25 Oct 2022
DOI

What's New

  • 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)
  • Added regrid_restart_file.py by @LiamBindle in https://github.com/geoschem/gcpy/pull/159
  • Add fix for GEOS-Chem Classic restart file path by @msulprizio in https://github.com/geoschem/gcpy/pull/160

What's Changed

  • Fixed several issues in benchmarking scripts (@laestrada, @lizziel, @yantosca), also see PR #164
    • Updates for new GCHP restart file format by @lizziel in https://github.com/geoschem/gcpy/pull/151
    • 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)

Full Changelog: https://github.com/geoschem/gcpy/compare/1.2.0...1.3.0

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca over 3 years ago

gcpy - GCPy: 1.2.0

Release date 02 May 2022
DOI

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

For installation instructions, please see our GCPy manual at https://gcpy.readthedocs.io.

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by laestrada about 4 years ago

gcpy - GCPy: 1.1.0

Added

  • 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

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by laestrada over 4 years ago

gcpy - GCPy 1.0.3

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

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns about 5 years ago

gcpy - GCPy 1.0.2

DOI License: MIT

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

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns about 5 years ago

gcpy - GCPy 1.0.1

DOI License: MIT

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

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns over 5 years ago

gcpy - GCPy 1.0.0

Release date: 05 Jan 2021
DOI License: MIT

This if the first official version of GCPy.

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()

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns over 5 years ago

gcpy - 1.0.0-beta.0

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns over 5 years ago

gcpy - GCPY 0.3.1

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.

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns almost 6 years ago

gcpy - GCPy 0.3.0

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 functi

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns almost 6 years ago

gcpy - GCPy 0.2.1

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

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns about 6 years ago

gcpy - GCPy 0.2.0

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.

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns about 6 years ago

gcpy - GCPy 0.1.1

  • 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.

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by yantosca about 6 years ago

gcpy - GCPy 0.1.0

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

  1. Functions for comparing GEOS-Chem benchmark output for multiple versions of GEOS-Chem, including 2D plots and mass and budget table creation.
  2. 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.

Atmosphere - Atmospheric Chemistry and Aerosol - Jupyter Notebook
Published by WilliamDowns over 6 years ago