Merge branch 'dev' into feature/plot-subdir

This merge brings the feature/plot-subdir up-to-date with the dev branch (which now has the fixes for regridding that were added by PR #266). Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Oct 11, 2023 · 4de592e · 4de592e
2 parents 8dedac7 + 7949550
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -32,6 +32,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - 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`
 
 ### Changed
 - Simplified the Github issues templates into two options: `new-feature-or-discussion.md` and `question-issue.md`
@@ -62,13 +65,19 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - 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 scripts`plot_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
 
 ### 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
 
 ### Removed
 - Removed `gchp_is_pre_13_1` arguments & code from benchmarking routines
@@ -78,6 +87,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - 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
 
 ## [1.3.3] -- 2023-03-09
 ### Added
@@ -365,16 +375,3 @@ This is the first labeled version of GCPy. The primary functionality of GCPy is
 - Support for plotting benchmark output for both GEOS-Chem Classic (lat/lon data) and GCHP (cubed-sphere data).
 
 The first official release version of GCPy, v1.0.0, will correspond with the release of GEOS-Chem 13.0.0.
-
-
-## [Unreleased]
-
-### Added
-
-### Changed
-
-### Deprecated
-
-### Fixed
-
-### Removed
diff --git a/gcpy/benchmark/cloud/template.1hr_benchmark.yml b/gcpy/benchmark/cloud/template.1hr_benchmark.yml
@@ -4,15 +4,15 @@
 # customize in the following manner:
 #
 # (1) Edit the path variables so that they point to folders
-#     containing model data.
-# (2) Edit the version strings for each benchmark simulation.
+#     containing model data
+# (2) Edit the version strings for each benchmark simulation
 # (3) Edit the switches that turn on/off creating of plots and
-#     tables, as well as other plotting options.
+#     tables as well as other plotting options
 # (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)
+# when doing GCHP vs GCC diff-of-diffs.
 # =====================================================================
 #
 # Configuration for 1-hour FullChemBenchmark
@@ -76,11 +76,11 @@ data:
       is_pre_14.0: False
       resolution: c24
 #
-# options: Customizes the benchmark plot output.
+# options: Customizes the benchmark plot output
 #
 options:
   #
-  # bmk_type: Specifies the type of benchmark.
+  # bmk_type: Specifies the type of benchmark
   #
   bmk_type: FullChemBenchmark
   #
@@ -103,7 +103,7 @@ options:
       run: False
       dir: GCHP_GCC_diff_of_diffs
   #
-  # outputs: Specifies the plots and tables to generate.
+  # outputs: Specifies the plots and tables to generate
   #
   outputs:
     plot_conc: False

diff --git a/gcpy/benchmark/cloud/template.1mo_benchmark.yml b/gcpy/benchmark/cloud/template.1mo_benchmark.yml
@@ -4,18 +4,18 @@
 # customize in the following manner:
 #
 # (1) Edit the path variables so that they point to folders
-#     containing model data.
-# (2) Edit the version strings for each benchmark simulation.
+#     containing model data
+# (2) Edit the version strings for each benchmark simulation
 # (3) Edit the switches that turn on/off creating of plots and
-#     tables, as well as other plotting options.
+#     tables as well as other plotting options
 # (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)
+# when doing GCHP vs GCC diff-of-diffs.
 # =====================================================================
 #
-# Configuration for 1 month FullChemBenchmark
+# Configuration for 1-month FullChemBenchmark
 #
 # paths:
 #   main_dir:    High-level directory containing ref & dev rundirs
@@ -76,11 +76,11 @@ data:
       is_pre_14.0: False
       resolution: c24
 #
-# options: Customizes the benchmark plot output.
+# options: Customizes the benchmark plot output
 #
 options:
   #
-  # bmk_type: Specifies the type of benchmark.
+  # bmk_type: Specifies the type of benchmark
   #
   bmk_type: FullChemBenchmark
   #
@@ -103,7 +103,7 @@ options:
       run: False
       dir: GCHP_GCC_diff_of_diffs
   #
-  # outputs: Specifies the plots and tables to generate.
+  # outputs: Specifies the plots and tables to generate
   #
   outputs:
     plot_conc: True

diff --git a/gcpy/benchmark/config/1mo_benchmark.yml b/gcpy/benchmark/config/1mo_benchmark.yml
@@ -1,21 +1,21 @@
-&---
+---
 # =====================================================================
 # Benchmark configuration file (**EDIT AS NEEDED**)
 # customize in the following manner:
 #
 # (1) Edit the path variables so that they point to folders
-#     containing model data.
-# (2) Edit the version strings for each benchmark simulation.
+#     containing model data
+# (2) Edit the version strings for each benchmark simulation
 # (3) Edit the switches that turn on/off creating of plots and
-#     tables, as well as other plotting options.
+#     tables as well as other plotting options
 # (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)
+# when doing GCHP vs GCC diff-of-diffs.
 # =====================================================================
 #
-# Configuration for 1 month FullChemBenchmark
+# Configuration for 1-month FullChemBenchmark
 #
 # paths:
 #   main_dir:    High-level directory containing ref & dev rundirs
@@ -26,9 +26,9 @@
 #                species_database.yml in one of the Dev rundirs.
 #
 paths:
-  main_dir: /path/to/benchmark/main/dir    # EDIT AS NEEDED
-  results_dir: /path/to/BenchmarkResults   # EDIT AS NEEDED
-  weights_dir: /n/holyscratch01/external_repos/GEOS-CHEM/gcgrid/gcdata/ExtData/GCHP/RegriddingWeights
+  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
 #
 # data: Contains configurations for ref and dev runs
@@ -47,7 +47,7 @@ data:
       dir: GCC_ref
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
-      bmk_start: "2019-07-01T00:00:00" 
+      bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
     gchp:
       version: GCHP_ref
@@ -64,46 +64,46 @@ data:
       dir: GCC_dev
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
-      bmk_start: "2019-07-01T00:00:00" 
+      bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
     gchp:
       version: GCHP_dev
       dir: GCHP_dev
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
-      bmk_start: "2019-07-01T00:00:00" 
+      bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
       is_pre_14.0: False
       resolution: c24
 #
-# options: Customizes the benchmark plot output.
+# options: Customizes the benchmark plot output
 #
 options:
   #
-  # bmk_type: Specifies the type of benchmark.
+  # bmk_type: Specifies the type of benchmark
   #
   bmk_type: FullChemBenchmark
   #
   # comparisons: Specifies the comparisons to perform.
   #
   comparisons:
-    gcc_vs_gcc: 
+    gcc_vs_gcc:
       run: True
       dir: GCC_version_comparison
       tables_subdir: Tables
-    gchp_vs_gcc: 
+    gchp_vs_gcc:
       run: True
-      dir: GCHP_GCC_comparison 
+      dir: GCHP_GCC_comparison
       tables_subdir: Tables
-    gchp_vs_gchp: 
+    gchp_vs_gchp:
       run: True
       dir: GCHP_version_comparison
       tables_subdir: Tables
-    gchp_vs_gcc_diff_of_diffs: 
+    gchp_vs_gcc_diff_of_diffs:
       run: True
       dir: GCHP_GCC_diff_of_diffs
   #
-  # outputs: Specifies the plots and tables to generate.
+  # outputs: Specifies the plots and tables to generate
   #
   outputs:
     plot_conc: True
@@ -117,13 +117,14 @@ options:
     OH_metrics: True
     ste_table: True # GCC only
     summary_table: True
-    plot_options: # Plot concentrations and emissions by category?
+    plot_options:
       by_spc_cat: True
       by_hco_cat: True
   #
-  # n_cores: Specify the number of cores to use:
-  # -1: Use all avaiable cores
-  # -N: Use N cores
+  # n_cores: Specify the number of cores to use.
+  # -1: Use $OMP_NUM_THREADS         cores
+  # -2: Use $OMP_NUM_THREADS - 1     cores
+  # -N: Use $OMP_NUM_THREADS - (N-1) cores
   #  1: Disable parallelization (use a single core)
   #
   n_cores: -1
diff --git a/gcpy/benchmark/config/1yr_ch4_benchmark.yml b/gcpy/benchmark/config/1yr_ch4_benchmark.yml
@@ -4,18 +4,18 @@
 # customize in the following manner:
 #
 # (1) Edit the path variables so that they point to folders
-#     containing model data.
-# (2) Edit the version strings for each benchmark simulation.
-# (3) Edit the switches that turn on/off creating of plots and tables,
-#     as well as other plotting options.
-# (4) If necessary, edit labels for the dev and ref versions.
+#     containing model data
+# (2) Edit the version strings for each benchmark simulation
+# (3) Edit the switches that turn on/off creating of plots and
+#     tables as well as other plotting options
+# (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)
+# when doing GCHP vs GCC diff-of-diffs.
 # =====================================================================
 #
-# Configuration for 1yr CH4Benchmark
+# Configuration for 1-year CH4Benchmark
 #
 # paths:
 #   main_dir:    High-level directory containing ref & dev rundirs
@@ -56,11 +56,11 @@ data:
       restarts_subdir: Restarts
       bmk_start: "2019-01-01T00:00:00"
       bmk_end: "2020-01-01T00:00:00"
-      is_pre_14.0: False               # for gcpy_test_data, edit if needed
-      resolution: c24                  # for gcpy_test_data, edit if needed
+      is_pre_14.0: False
+      resolution: c24
   dev:
     gcc:
-      version: GCC_dev
+      version: GCC_dev 
       dir: GCC_dev
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
@@ -73,37 +73,37 @@ data:
       restarts_subdir: Restarts
       bmk_start: "2019-01-01T00:00:00"
       bmk_end: "2020-01-01T00:00:00"
-      is_pre_14.0: False              # for gcpy_test_data, edit if needed
-      resolution: c24                 # for gcpy_test_data, edit if needed   
+      is_pre_14.0: False
+      resolution: c24
+#
+# options: Customizes the benchmark plot output
 #
-# options: Customize the benchmark plot output.
-# 
 options:
   #
-  # bmk_type: Specifies the type of benchmark.
+  # bmk_type: Specifies the type of benchmark
   #
   bmk_type: CH4Benchmark
   #
   # comparisons: Specifies the comparisons to perform.
   #
   comparisons:
-    gcc_vs_gcc: 
-      run: True # True to run this comparison
+    gcc_vs_gcc:
+      run: True
       dir: GCC_version_comparison
       tables_subdir: Tables
-    gchp_vs_gcc: 
-      run: False
-      dir: GCHP_GCC_comparison 
+    gchp_vs_gcc:
+      run: True
+      dir: GCHP_GCC_comparison
       tables_subdir: Tables
-    gchp_vs_gchp: 
-      run: False
+    gchp_vs_gchp:
+      run: True
       dir: GCHP_version_comparison
       tables_subdir: Tables
     gchp_vs_gcc_diff_of_diffs:
       run: False
       dir: GCHP_GCC_diff_of_diffs
   #
-  # outputs: Specifies the plots and tables to generate.
+  # outputs: Specifies the plots and tables to generate
   #
   outputs:
     plot_conc: True