GCPy 1.7.1

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

• Bump pip from 25.2 to 25.3 by @dependabot[bot] in #407
• Bump pip from 25.2 to 26.0 by @dependabot[bot] in #408

Full Changelog: 1.7.0...1.7.1

GCPy 1.7.0

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

• Add script to plot hotspots from Intel VTune reports by @yantosca in #364
• Update the "end of search" criteria in benchmark_scrape_classic_timers.py to avoid being spoofed by output from Intel VTune by @yantosca in #365
• Fix grid area calculation by @1Dandan in #367
• Add "Lint" GitHub actions and fixed security issues in other actions by @yantosca in #370
• Bug fixes for stretched grid comparison plots by @lizziel in #371
• Rewrite algorithm to save PDF output to avoid using PdfMerger; Use PdfReader and PdfWriter instead by @yantosca in #373
• Bump pypdf from 4.2.0 to 6.0.0 by @dependabot[bot] in #375
• Bug fixes for stretched grid restart file generation and benchmarking by @lizziel in #377
• Update pypdf to 6.0.0 by @yantosca in #376
• Add vertical grid information for the GCAP2 102-level, 74-level, and 40-level grids by @yantosca in #378
• Bump pip from 24.0 to 25.2 by @dependabot[bot] in #380
• Fixes for offline regridding and stretched grid plotting by @lizziel in #381
• Use conda in benchmark_slurm.sh; Separate plot & table options in benchmark template files by @yantosca in #382
• Bump pypdf from 4.2.0 to 6.1.3 by @dependabot[bot] in #383
• Add constants for stretched-grid and lat-lon parameters; Modify code according to suggestions from Pylint by @yantosca in #374
• Add example script to display lons & lats for GEOS-Chem Classic horizontal grids by @yantosca in #379
• Update GCPy conda env to use Python 3.13 instead of 3.12 by @yantosca in #387
• Update "benchmark_scrape_gchp_timers.py" to look for timing information in "allPEs.log" if not found in the GCHP log file by @yantosca in #388
• Bump pypdf from 6.4.0 to 6.6.0 by @dependabot[bot] in #391
• Remove xr.Dataset.load() commands to improve performance by @yantosca in #395
• Allow args to create_regridders to be xr.Dataset or xr.DataArray by @yantosca in #396
• Modify benchmark scripts to look for species_database.yml files in Ref and Dev rundirs by @yantosca in #389
• Fix errors in annual mean GCHP vs GC-Classic "diff-of-diffs" plots by @yantosca in #397
• Bump pypdf from 4.2.0 to 6.6.2 by @dependabot[bot] in #399
• Optimize get_diff_of_diffs and add_lumped_species_to_dataset by @yantosca in #402
• Generate AOD plots for DSTbin1..7 species by @yantosca in #398
• Generate...

GCPy 1.6.2

Release date: 12 Jun 2025

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

• Add benchmark diagnostic sanity check table by @yantosca in #356
• Now use esmf/esmpy 8.8.1 in the GCPy environment based on Python 3.13 by @yantosca in #358
• Add profiling routines to display output from GNU gprofng and Intel Vtune profilers by @yantosca in #359
• Add example script to check GCHP emission diagnostics entries in HISTORY.rc and HEMCO_Diagn.rc by @yantosca in #357
• Expand 1-month benchmark plot options by @lizziel in #350
• Fix logic for orbit direction time offset by @yuanjianz in #360
• Add "method" keyword argument to make_regridder_* routines in gcpy/regrid.py by @yantosca in #362
• Bump requests from 2.32.3 to 2.32.4 by @dependabot in #363

Full Changelog: 1.6.1...1.6.2

GCPy 1.6.1

Release Date: 24 Mar 2025

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

• Update default paths to regridding weights in YAML files by @yantosca in #351
• Add support for Python 3.13 -- update environment files and GitHub Actions by @yantosca in #353
• Update to dask 2025.3.0 and jinja2 3.1.6 to fix security issues identified by dependabot by @yantosca in #354

Full Changelog: 1.6.0...1.6.1

GCPy 1.6.0

Release date: 29 Jan 2025

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

• Now use comma-separated list for exempt-issue-labels YAML tag in stale.yml by @yantosca in #327
• Now flag GEOS-Chem Classic/GCHP timers that differ by more than 10% in the benchmark timing tables by @yantosca in #332
• Add make_hemco_sa_spec.py example script by @yantosca in #334
• Update benchmark YAML files with new species for GEOS-Chem 14.5.0 by @yantosca in #331
• Add script for scraping stats from GCClassic cloud benchmarks by @yantosca in #335
• Add the DryDep collection to the benchmark summary table, and DryDepVel plots to 1-mon cloud benchmarks by @yantosca in #336
• Update package versions used in the GCPy environment; Also update GitHub actions to avoid deprecation warnings by @yantosca in #329
• Remove the default gcpy/benchmark/modules/species_database.yml file by @yantosca in #339
• Fix missing headers in aerosol table by @yuanjianz in #341
• Replace whitespace in Ref and Dev version labels in benchmarking code by @yantosca in #340
• Hotfix: Restore stale workflow functionality by @msulprizio in #342
• Use ALK6 species name for >= C6 alkanes instead of ALK7 by @msulprizio in #343
• Add benchmark script to create species changes tables for GEOS-Chem wiki by @yantosca in #337
• Fix computation of dynamic ratio colorbar min/max values in six_plot.py by @yantosca in #344
• Fix incorrect species classification in benchmark_categories.yml by @yantosca in #345
• Fix type errors in calc_rectilinear_lon_edge and calc_rectilinear_lat_edge in grid.py by @yantosca in #347
• Bump jinja2 to 3.1.5 as suggested by Dependabot by @yantosca in #348
• Add scripts to plot vertical profiles from the KPP-Standalone box model by @yantosca in #346

Full Changelog: 1.5.0...1.6.0

GCPy 1.5.0

Release Date: 29 May 2024

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.

From CHANGELOG.md

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

Pull Requests Included

• Bump pypdf from 3.16.1 to 3.17.0 by @dependabot in #293
• Add option to create drydep velocity plots from benchmark output by @yantosca in #280
• Add a GitHub action to auto-push GCPy releases directly to PyPi by @yantosca in #294
• file_regrid.py now uses DELP_DRY for delta-dry pressure variable name when creating GCHP files by @yantosca in #297
• Fix bugs in 1-yr benchmarks for different GCHP grid resolutions by @lizziel in #298
• Fix bugs in GCC vs GCHP transport tracer benchmark mass tables by @lizziel in #300
• Implement several minor bug fixes (matplotlib 3.8+, GitHub actions, remove obsolete features) by @yantosca in #283
• Split python packages needed for RTD documentation builds out of the GCPy conda environment and into a separate environment; remove awscli by @yantosca in #295
• Bug fix for operations budget name in transport tracer benchmark run script by @lizziel in #301
• Add inquiry functions to return nearest model data to a (lat,lon) location; Update benchmark model vs. obs scripts; Add models vs sondes output by @yantosca in #277
• Add fixed level diagnostic to operations budget table by @lizziel in #304
• Added missing options to 1yr_ch4_benchmark.yml config file by @msulprizio in #307
• Move remaining benchmark-related code out of gcpy and into gcpy/benchmark/modules folder (plus other improvements) by @yantosca in #305
• Replace stalebot with "stale" GitHub action by @yantosca in #315
• Fix issues in cubed-sphere regridding by @yuanjianz in #311
• Add example script to create mask files by @yantosca in #317
• Add HCl to emissions_species.yml for GEOS-Chem 14.4.0 by @msulprizio in #320
• Add benchmark scripts to scrape timing information from log files by @yantosca in #319
• Update mass conservation tables to include Ref & Dev in the same file by @yantosca in #309
• Bump requests from 2.31.0 to 2.32.0 by @dependabot in #321
• Update Github issue templates to use issue forms by @msulprizio in #323
• Bump requests from 2.31.0 to 2.32.2 in /docs/environment_files by @dependabot in #324

New Contributors

• @yuanjianz made their first contribution in #311

Full Changelog: 1.4.2...1.5.0

GCPy 1.4.2

Release date 26 Jan 2024

Pull Requests Included

• Add GitHub action to build GCPy environment and test installation by @yantosca in #286
• Fix dictionary key error when benchmark plots are generated sequentially by @yantosca in #287
• Use pegged version numbers for the GCPy environment; Also add testing environment without pegged versions; Updated GitHub actions by @yantosca in #289

Full Changelog: 1.4.1...1.4.2

GCPy 1.4.1

Release date 08 Dec 2023

From CHANGELOG.md

Fixed

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

Pull Requests Included

• Bug fix: Use proper default value for weightsdir in file_regrid.py by @yantosca in #279

Full Changelog: 1.4.0...1.4.1

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 https://github.com/geosche...

GCPy 1.3.3

Release date: 09 Mar 2023

Pull Requests Included

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: 1.3.2...1.3.3