Merge PR #277 (Update model vs. obs benchmark scripts)

This merge brings PR # (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) into the GCPy development
stream.

This PR adds the following functionality:

1. Inquiry functions to return nearest model data to a (lat,lon) location
   for both GCClassic and GCHP grids

2. Updated benchmark vs. model scripts.  Also added a script to plot
   model vs. sonde data

3. Updated get_vert_grid in gcpy/util.py to accept a surface pressure,
   so that we can generate GEOS-Chem vertical level information starting
   at other pressures than the default 1013.25 hPa.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

CHANGELOG.md

@@ -15,6 +15,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - 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`
 
 ### Changed
 - Bump pip from 23.2.1 to 23.3 (dependabot suggested this)
@@ -26,6 +27,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - `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`
 
 ### Fixed
 - CS inquiry functions in `gcpy/cstools.py` now work properly for `xr.Dataset` and `xr.DataArray` objects
@@ -39,8 +45,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Removed
 - Example script `gcpy/examples/plotting/mda8_o3_timeseries.py`
 - Removed `Pylint` GitHub action
-
-### Removed
 - 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

gcpy/benchmark/benchmark_slurm.sh

@@ -34,7 +34,7 @@ config="1yr_fullchem_benchmark.yml"
 #config="1yr_tt_benchmark.yml"
 
 # Call the run_benchmark script to make the plots
-python -m gcpy.benchmark.run_benchmark "${config}" > benchmark.log 2>&1
+python -m gcpy.benchmark.run_benchmark "${config}" > "${config/.yml/.log}: 2>&1
 
 # Turn off python environment
 mamba deactivate

gcpy/benchmark/config/1yr_fullchem_benchmark.yml

@@ -24,14 +24,24 @@
 #   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.
-#   obs_data_dir: Path to observational data (for models vs obs plots)
+#   obs_data:     Paths to observations (for models vs. obs plots)
 #
 paths:
   main_dir: /path/to/benchmark/main/dir
   results_dir: /path/to/BenchmarkResults
   weights_dir: /n/holyscratch01/external_repos/GEOS-CHEM/gcgrid/data/ExtData/GCHP/RegriddingWeights
   spcdb_dir: default
-  obs_data_dir: /path/to/observational/data
+  #
+  # Observational data dirs are on Harvard Cannon, edit if necessary
+  #
+  obs_data:
+    ebas_o3:
+      data_dir: /n/jacob_lab/Lab/obs_data_for_bmk/ebas_sfc_o3_2019
+      data_label: "O3 (EBAS, 2019)"
+    sondes:
+      data_dir: /n/jacob_lab/Lab/obs_data_for_bmk/sondes_2010-2019
+      data_file: allozonesondes_2010-2019.csv
+      site_file: allozonesondes_site_elev.csv
 #
 # data: Contains configurations for ref and dev runs
 #   version:         Version string (must not contain spaces)