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