Releases: geoschem/gcpy
Releases · geoschem/gcpy
GCPy 1.5.0
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
ingcpy/benchmark/config/*.yml
files - Badge for
build-gcpy-environment
GitHub Action inREADME.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
anddocs/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
ingcpy/benchmark/modules/benchmark_utils.py
- Function
copy_file_to_dir
ingcpy/util.py
. This is a wrapper forshutil.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 togcpy/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
ingcpy/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
, andget_log_filepaths
ingcpy/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
ingcpy/benchmark/modules/benchmark_utils.py
- Function
replace_whitespace
ingcpy/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 nowops_budget_table
ingcpy/benchmark/config/1yr_tt_benchmark.yml
- Now require
matplotlib=3.8.0
indocs/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
togcpy_environment.yml
environment.yml
links todocs/environment_files/gcpy_environment.yml
requirements.txt
links todocs/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 fromgrid.py
to return data nearest to a (lat,lon) location - Moved routine
get_geoschem_level_metadata
togcpy/benchmark/modules/benchmark_utils.py
- Refactored
get_vert_grid.py
(ingcpy/grid.py
) to accept thep_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 filebenchmark_models_vs_obs.py
now reads the observational data paths and metadata from1yr_fullchem_benchmark.yml
- Moved benchmark code from
gcpy/
togcpy/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 forxr.Dataset
andxr.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 withDELP_DRY
instead ofDELPDRY
- 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
togcpy/examples/diagnostics/compare_diags.yml
- Added missing
plot_drydep
option togcpy/gcpy/benchmark/config/1yr_ch4_benchmark.yml
- Add
docs/requirements.txt
symbolic link todocs/environment_files/read_the_docs_requirements.txt
for RTD builds gcpy/file_regrid.py
now tests iflon_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
inbenchmark_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 togcpy/file_regrid.py
Pull Requests Included
Full Changelog: 1.4.0...1.4.1
GCPy 1.4.0
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
andSUPPORT.md
, replacingdocs/source/Contributing.rst
anddocs/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 ingcpy/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 toreshape_MAPL_CS
function ingcpy/util.py
- Added FURA to
emission_species.yml
andbenchmark_categories.yml
- Added new routine
format_number_for_table
ingcpy/util.py
- Added module
gcpy/cstools.py
with utility functions for cubed-sphere grids - Added new routine
verify_variable_type
function ingcpy/util.py
- Added new routine
format_number_for_table
inutil.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 ofgcpy/gcpy
gcpy/benchmark/modules/*.py
scripts are now chmod 644- Added
ENCODING = "UTF-8"
togcpy/constants.py
- Added statement
from dask.array import Array as DaskArray
ingcpy 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
andget_lev_coord
togcpy/grid.py
- Add
tk
package todocs/environment_files/environment.yml
Changed
- Simplified the Github issues templates into two options:
new-feature-or-discussion.md
andquestion-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 tobenchmark/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
tobenchmark_funcs.py
to remove a name collision - Folder
gcpy/benchmark
is nowgcpy/gcpy/benchmark
- Folder
benchmark/modules
is nowgcpy/gcpy/benchmark/modules
- Folder
gcpy/examples
is nowgcpy/gcpy/examples
- Pass
sys.argv
to themain()
routine ofrun_benchmark.py
,compare_diags.py
- Updated
docs/environment_files/environment.yml
for MambaForge (also addedgridspec
) - Now use
pypdf
instead ofPyPDF2
inplot.py
andutil.py
- Added coding suggestions made by
pylint
where possible - Abstracted and never-nested code from
six_plot
into functions (inplot.py
) - Added
main()
routine togcpy/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 typedask.array.Array
inplot.py
routinessix_plot
andsingle_panel
- Now add
if
statements to turn ofParallel()
commands whenn_jobs==1
. - Do not hardwire fontsize in
gcpy/plot.py
; get defaults fromgcpy_plot_style
gcpy/plot.py
has been split up into smaller modules in thegcpy/plot
folder- Updated and cleaned up code in
gcpy/regrid.py
- Example scripts
plot_single_level
andplot_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/orilev:positive
properly inregrid_restart_file.py
andfile_regrid.py
- Prevent overwriting of
lev
coord infile_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
withREADME.md
- Removed
gcpy_test_dir
option fromexamples/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
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
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.
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: 1.3.0...1.3.1
GCPy 1.3.0
What's New
- New features in benchmarking scripts (@lizziel, @yantosca)
- 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 #159
- Add fix for GEOS-Chem Classic restart file path by @msulprizio in #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 #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: 1.2.0...1.3.0
GCPy: 1.2.0
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.
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