GCPy 1.3.3 release

Important features include - Updates and fixes for benchmark scripts - Improved documentation for installing Conda and GCPy - Improved documentation for GCHP regridding - General code cleanup Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Mar 9, 2023 · 84d11cb · 84d11cb
2 parents f8da728 + f620801
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,15 +4,34 @@ All notable changes to GCPy will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## [1.3.3] -- 2023-03-09
+### Added
+- Updated installation documentation, we now recommend users to create
+  a conda environment using the `environment.yml` file
+- Benchmark summary table output (intended for 1hr & 1mo benchmarks)
+- Species/emissions/inventories that differ between Dev & Ref versions are now printed at the top of the benchmark emissions, inventory, and global mass tables.  if there are too many species with diffs, an alternate message is printed.
+- New functions in `benchmark.py` and `util.py` to facilitate printing of the species/emissions/inventories that differ between Dev & Ref versions.
+- Added new RTD documentation for installing Conda 4.12.0 with Miniconda
+- Added GCHP regridding environnment file `docs/environment_files/gchp_regridding.yml`
+
+### Changed
+- Applied cleanup susggestions from pylint to `benchmark.py`, `util.py`, `plot.py`, `oh_metrics.py`, `ste_flux.py`
+- Replaced format with f-strings in `benchmark.py`, `util.py`, `plot.py`, `oh_metrics.py`, `ste_flux.py`
+- Abstract some common in `benchmark.py` into functions
+- Replaced direct calls to `yaml.load` with `util.read_config.file`
+- Restore tag information to benchmark `refstr` and `devstr` labels
+- Add a newline to diff-of-diffs refstr and devstr if the string is too long.
+- Updated GCHP regridding documentation
+- Restored `ipython` and `jupyter ` to environment file `environment.yml`
 
 ## [1.3.2] -- 2022-10-25
 
-### Changed
-- Bug fix: Fixed malformed version declaration for cartopy (use `==`
+### Fixes
+- Fixed malformed version declaration for cartopy (use `==`
   instead of `=`) in setup.py.  This was preventing upload to
   conda-forge.
-
+- Vertically flip GCHP emissions when computing transport tracers budget
+
 ## [1.3.1] -- 2022-10-25
 
 ### Changed

diff --git a/benchmark/1mo_benchmark.yml b/benchmark/1mo_benchmark.yml
@@ -108,6 +108,7 @@ options:
     ops_budget_table: False
     OH_metrics: True
     ste_table: True # GCC only
+    summary_table: True
     plot_options: # Plot concentrations and emissions by category?
       by_spc_cat: True
       by_hco_cat: True
diff --git a/benchmark/1yr_ch4_benchmark.yml b/benchmark/1yr_ch4_benchmark.yml
@@ -0,0 +1,115 @@
+&---
+# =====================================================================
+# Benchmark configuration file (**EDIT AS NEEDED**)
+# customize in the following manner:
+# (1) Edit the path variables so that they point to folders w/ model data
+# (2) Edit the version strings for each benchmark simulation
+# (3) Edit the switches that turn on/off creating of plots and tables
+# (4) If necessary, edit labels for the dev and ref versions
+# Note: When doing GCHP vs GCC comparisions gchp_dev will be compared
+# to gcc_dev (not gcc_ref!). This ensures consistency in version names
+# when doing GCHP vs GCC diff-of-diffs (mps, 6/27/19)
+# =====================================================================
+#
+# Configuration for 1yr CH4Benchmark
+#
+# paths:
+#   main_dir:    High-level directory containing ref & dev rundirs
+#   results_dir: Directory where plots/tables will be created
+#   weights_dir: Path to regridding weights
+#   spcdb_dir:   Folder in which the species_database.yml file is
+#                located.  If set to "default", then will look for
+#                species_database.yml in one of the Dev rundirs.
+#
+paths:
+  main_dir: /n/holyscratch01/external_repos/GEOS-CHEM/gcgrid/geos-chem/validation/gcpy_test_data/1yr_fullchem
+  results_dir: /path/to/BenchmarkResults
+  weights_dir: /n/holyscratch01/external_repos/GEOS-CHEM/gcgrid/data/ExtData/GCHP/RegriddingWeights
+  spcdb_dir: default
+#
+# data: Contains configurations for ref and dev runs
+#   version:         Version string (must not contain spaces)
+#   dir:             Path to run directory
+#   outputs_subdir:  Subdirectory w/ GEOS-Chem diagnostic files
+#   restarts_subdir: Subdirectory w/ GEOS-Chem restarts
+#   bmk_start:       Simulation start date (YYYY-MM-DDThh:mm:ss)
+#   bmk_end:         Simulation end date (YYYY-MM-DDThh:mm:ss)
+#   resolution:      GCHP resolution string
+#
+data:
+  ref:
+    gcc:
+      version: GCC_ref
+      dir: GCC_ref
+      outputs_subdir: OutputDir
+      restarts_subdir: Restarts
+      bmk_start: "2019-01-01T00:00:00"
+      bmk_end: "2020-01-01T00:00:00"
+    gchp:
+      version: GCHP_ref
+      dir: GCHP_ref
+      outputs_subdir: OutputDir
+      restarts_subdir: Restarts
+      bmk_start: "2019-01-01T00:00:00"
+      bmk_end: "2020-01-01T00:00:00"
+      is_pre_13.1: False               # for gcpy_test_data, edit if needed
+      is_pre_14.0: False               # for gcpy_test_data, edit if needed
+      resolution: c24                  # for gcpy_test_data, edit if needed
+  dev:
+    gcc:
+      version: GCC_dev
+      dir: GCC_dev
+      outputs_subdir: OutputDir
+      restarts_subdir: Restarts
+      bmk_start: "2019-01-01T00:00:00"
+      bmk_end: "2020-01-01T00:00:00"
+    gchp:
+      version: GCHP_dev
+      dir: GCHP_dev
+      outputs_subdir: OutputDir
+      restarts_subdir: Restarts
+      bmk_start: "2019-01-01T00:00:00"
+      bmk_end: "2020-01-01T00:00:00"
+      is_pre_13.1: False              # for gcpy_test_data, edit if needed
+      is_pre_14.0: False              # for gcpy_test_data, edit if needed
+      resolution: c24                 # for gcpy_test_data, edit if needed   
+#
+# options: Specify the types of comparisons to perform
+# 
+options:
+  bmk_type: CH4Benchmark
+  gcpy_test: False # Specify if this is a gcpy test validation run
+  comparisons:
+    gcc_vs_gcc: 
+      run: True # True to run this comparison
+      dir: GCC_version_comparison
+      tables_subdir: Tables
+    gchp_vs_gcc: 
+      run: False
+      dir: GCHP_GCC_comparison 
+      tables_subdir: Tables
+    gchp_vs_gchp: 
+      run: False
+      dir: GCHP_version_comparison
+      tables_subdir: Tables
+    gchp_vs_gcc_diff_of_diffs:
+      run: False
+      dir: GCHP_GCC_diff_of_diffs
+#
+# outputs: Types of output to generate (plots/tables)
+#
+  outputs:
+    plot_conc: True
+    plot_emis: True
+    emis_table: True
+    plot_jvalues: False
+    plot_aod: False
+    mass_table: True
+    ops_budget_table: False
+    aer_budget_table: False
+    Ox_budget_table: False
+    ste_table: False
+    OH_metrics: True
+    plot_options:
+      by_spc_cat: True
+      by_hco_cat: True
diff --git a/benchmark/modules/run_1yr_fullchem_benchmark.py b/benchmark/modules/run_1yr_fullchem_benchmark.py
@@ -242,17 +242,9 @@ def run_benchmark(config, bmk_year_ref, bmk_year_dev):
     gchp_vs_gcc_devstr = config["data"]["dev"]["gchp"]["version"]
     gchp_vs_gchp_refstr = config["data"]["ref"]["gchp"]["version"]
     gchp_vs_gchp_devstr = config["data"]["dev"]["gchp"]["version"]
-    diff_of_diffs_refstr = (
-        config["data"]["dev"]["gcc"]["version"]
-        + " - "
-        + config["data"]["ref"]["gcc"]["version"]
-    )
-    diff_of_diffs_devstr = (
-        config["data"]["dev"]["gchp"]["version"]
-        + " - "
-        + config["data"]["ref"]["gchp"]["version"]
-    )
-
+    diff_of_diffs_refstr = bmk.diff_of_diffs_toprow_title(config, "gcc")
+    diff_of_diffs_devstr = bmk.diff_of_diffs_toprow_title(config, "gchp")
+
     ########################################################################
     ###    THE REST OF THESE SETTINGS SHOULD NOT NEED TO BE CHANGED      ###
     ########################################################################
@@ -477,6 +469,7 @@ def run_benchmark(config, bmk_year_ref, bmk_year_dev):
                     "plot_options"]["by_spc_cat"],
                 plot_by_hco_cat=config["options"]["outputs"][
                     "plot_options"]["by_hco_cat"],
+                benchmark_type=bmk_type,
                 overwrite=True,
                 spcdb_dir=spcdb_dir,
             )
@@ -501,6 +494,7 @@ def run_benchmark(config, bmk_year_ref, bmk_year_dev):
                         "plot_options"]["by_spc_cat"],
                     plot_by_hco_cat=config["options"]["outputs"][
                         "plot_options"]["by_hco_cat"],
+                    benchmark_type=bmk_type,
                     overwrite=True,
                     spcdb_dir=spcdb_dir,
                 )
@@ -530,6 +524,7 @@ def run_benchmark(config, bmk_year_ref, bmk_year_dev):
                 dev,
                 gcc_vs_gcc_devstr,
                 dst=gcc_vs_gcc_resultsdir,
+                benchmark_type=bmk_type,
                 ref_interval=sec_per_month_ref,
                 dev_interval=sec_per_month_dev,
                 overwrite=True,