Merge branch 'dev' into docs/dev

Ths branch brings the docs/dev branch up to date with PR #321.

Signed-off-by: Bob Yantosca <[email protected]>

.github/workflows/stale.yml

@@ -1,17 +1,17 @@
-# This workflow warns and then closes issues and PRs that have had no activity for a specified amount of time.
+# This workflow warns and then closes issues that have had no activity for a specified amount of time.
 #
 # You can adjust the behavior by modifying this file.
 # For more information, see:
 # https://github.com/actions/stale
-name: Mark stale issues and pull requests
+name: Mark stale issues
 
 on:
   schedule:
-    # Job will run at midnight on the 1st of each month (POSIX time syntax)
-    - cron: '0 0 1 * *'
+  - cron: '0 0 * * *' # Run every night at midnight
 
 jobs:
   stale:
+
     runs-on: ubuntu-latest
     permissions:
       issues: write
@@ -21,12 +21,18 @@ jobs:
     - uses: actions/stale@v5
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
-        # Stale issue settings
-        days-before-issue-stale: 30
-        days-before-issue-close: 30
         stale-issue-label: 'stale'
-        stale-issue-message: 'This issue is stale because it has been open for 30 days with no activity.'
-        close-issue-message: "This issue was closed because it has been inactive for 30 days since being marked as stale."
-        # Never mark PRs as stale
+        exempt-issue-labels:
+          - 'category: Discussion'
+          - 'category: Feature Request'
+          - 'deferred'
+          - 'help needed: Open Research Problem'
+          - 'help needed: Request Input from Community'
+          - 'never stale'
+          - 'TODO: Documentation'
+        days-before-issue-stale: 30
+        days-before-issue-close: 7
+        stale-issue-message: 'This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the issue from closing this issue.'
+        close-issue-message: 'Closing due to inactivity'
         days-before-pr-stale: -1
         days-before-pr-close: -1

CHANGELOG.md

@@ -19,6 +19,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added fixed level budget diagnostic to budget operations table
 - Function `rename_speciesconc_to_speciesconcvv` in `gcpy/benchmark/modules/benchmark_utils.py`
 - Function `copy_file_to_dir` in `gcpy/util.py`.  This is a wrapper for `shutil.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 to `gcpy/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` in `gcpy/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`, and `get_log_filepaths` in `gcpy/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` in `gcpy/benchmark/modules/benchmark_utils.py`
+- Function `replace_whitespace` in `gcpy/util.py`
 
 ### Changed
 - Bump pip from 23.2.1 to 23.3 (dependabot suggested this)
@@ -39,7 +53,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - 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 
+
 ### Fixed
 - CS inquiry functions in `gcpy/cstools.py` now work properly for `xr.Dataset` and `xr.DataArray` objects
 - Prevent an import error by using `seaborn-v0_8-darkgrid` in`gcpy/benchmark/modules/benchmark_models_vs_obs.py`
@@ -51,13 +67,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added missing `n_cores` to `gcpy/examples/diagnostics/compare_diags.yml`
 - Added missing `plot_drydep` option to `gcpy/gcpy/benchmark/config/1yr_ch4_benchmark.yml`
 - Add `docs/requirements.txt` symbolic link to `docs/environment_files/read_the_docs_requirements.txt` for RTD builds 
+- `gcpy/file_regrid.py` now tests if `lon_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` in `benchmark_funcs.py`; this is now obsolete
 
 ## [1.4.2] - 2024-01-26
 ### Added

gcpy/__init__.py

@@ -3,6 +3,7 @@
 """
 
 from .benchmark import *
+from .community import *
 from .examples import *
 
 from .append_grid_corners import *

gcpy/benchmark/cloud/template.1hr_benchmark.yml

@@ -47,13 +47,17 @@ data:
       dir: ref-gcc/run-directory
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: runlog.txt
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-07-01T01:00:00"
     gchp:
       version: ${GEOSCHEM_BENCHMARK_REF_PRIMARY_KEY}
       dir: ref-gchp/run-directory
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: runlog.txt
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-07-01T01:00:00"
       is_pre_14.0: False
@@ -64,13 +68,17 @@ data:
       dir: dev-gcc/run-directory
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: runlog.txt
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-07-01T01:00:00"
     gchp:
       version: ${GEOSCHEM_BENCHMARK_DEV_PRIMARY_KEY}
       dir: dev-gchp/run-directory
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: runlog.txt
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-07-01T01:00:00"
       is_pre_14.0: False
@@ -117,6 +125,7 @@ options:
     ops_budget_table: False
     OH_metrics: True
     ste_table: True # GCC only
+    timing_table: True
     summary_table: True
     plot_options:
       by_spc_cat: True

gcpy/benchmark/cloud/template.1mo_benchmark.yml

@@ -47,13 +47,17 @@ data:
       dir: ref-gcc/run-directory
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: runlog.txt
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
     gchp:
       version: ${GEOSCHEM_BENCHMARK_REF_PRIMARY_KEY}
       dir: ref-gchp/run-directory
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: runlog.txt
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
       is_pre_14.0: False
@@ -64,13 +68,17 @@ data:
       dir: dev-gcc/run-directory
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: runlog.txt
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
     gchp:
       version: ${GEOSCHEM_BENCHMARK_DEV_PRIMARY_KEY}
       dir: dev-gchp/run-directory
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: runlog.txt
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
       is_pre_14.0: False
@@ -117,6 +125,7 @@ options:
     ops_budget_table: False
     OH_metrics: True
     ste_table: True # GCC only
+    timing_table: True
     summary_table: True
     plot_options:
       by_spc_cat: True

gcpy/benchmark/config/1mo_benchmark.yml

@@ -47,13 +47,17 @@ data:
       dir: GCC_ref
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: "GC.log"
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
     gchp:
       version: GCHP_ref
       dir: GCHP_ref
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: "gchp.%Y%m%d_0000z.log"      
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
       is_pre_14.0: False
@@ -64,13 +68,17 @@ data:
       dir: GCC_dev
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: .
+      logs_template: "GC.log"      
       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
+      logs_subdir: Logs
+      logs_template: "gchp.%Y%m%d_0000z.log"
       bmk_start: "2019-07-01T00:00:00"
       bmk_end: "2019-08-01T00:00:00"
       is_pre_14.0: False
@@ -117,6 +125,7 @@ options:
     ops_budget_table: False
     OH_metrics: True
     ste_table: True # GCC only
+    timing_table: True
     summary_table: True
     plot_options:
       by_spc_cat: True

gcpy/benchmark/config/1yr_fullchem_benchmark.yml

@@ -59,13 +59,17 @@ data:
       dir: GCC_ref
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: Logs
+      logs_template: "log.%Y%m%d"
       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
+      logs_subdir: Logs
+      logs_template: "gchp.%Y%m%d_0000z.log"
       bmk_start: "2019-01-01T00:00:00"
       bmk_end: "2020-01-01T00:00:00"
       is_pre_14.0: False
@@ -76,13 +80,17 @@ data:
       dir: GCC_dev
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: Logs
+      logs_template: "log.%Y%m%d"
       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
+      logs_subdir: Logs
+      logs_template: "gchp.%Y%m%d_0000z.log"
       bmk_start: "2019-01-01T00:00:00"
       bmk_end: "2020-01-01T00:00:00"
       is_pre_14.0: False
@@ -130,6 +138,7 @@ options:
     Ox_budget_table: True
     ste_table: True # GCC only
     OH_metrics: True
+    timing_table: True
     plot_models_vs_obs: True
     plot_options:
       by_spc_cat: True

gcpy/benchmark/config/1yr_tt_benchmark.yml

@@ -48,13 +48,17 @@ data:
       dir: GCC_ref
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: Logs
+      logs_template: "log.%Y%m%d"
       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
+      logs_subdir: Logs
+      logs_template: "gchp.%Y%m%d_0000z.log"
       bmk_start: "2019-01-01T00:00:00"
       bmk_end: "2020-01-01T00:00:00"
       is_pre_14.0: False
@@ -65,13 +69,17 @@ data:
       dir: GCC_dev
       outputs_subdir: OutputDir
       restarts_subdir: Restarts
+      logs_subdir: Logs
+      logs_template: "log.%Y%m%d"
       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
+      logs_subdir: Logs
+      logs_template: "gchp.%Y%m%d_0000z.log"
       bmk_start: "2019-01-01T00:00:00"
       bmk_end: "2020-01-01T00:00:00"
       is_pre_14.0: False
@@ -115,6 +123,7 @@ options:
     mass_table: True
     ste_table: True
     cons_table: True
+    timing_table: False
   #
   # n_cores: Specify the number of cores to use.
   # -1: Use $OMP_NUM_THREADS         cores