Support monthly average and variable name convention for EAMxx #712

chengzhuzhang · 2023-07-27T23:45:31Z

Two use cases:
For longer than 1 year simulation:
Support both monthly average ['01', '02', ..., '12'] in viewer in addition to seasonal and annual mean.

For shorter than 1 year simulation:
Support visualization the averaged snapshot.

This PR is to support the first use case, it closes #348 and partially #652.
This PR also add support for variable names from EAMxx to support its output.

An example run with regridded EAMxx output is shown here.
The run script for this run is linked here.

chengzhuzhang · 2023-08-19T17:42:21Z

Commit #0c74dd9 to enable 12 months means as default in core sets. I considered to add logic in season selector to support monthly means other than the original 5 (ANN, and 4 seasons), but it appears to adding these 12 month to each cfg files is less intrusive.

With this PR the default option for seasons parameter is still ["ANN", "DJF", "MAM", "JJA", "SON"], if any of the 12 months i.e. "01", "06" is present in seasons, they can be calculated can presented in viewer.

chengzhuzhang · 2023-10-06T22:19:45Z

Note to myself: remember to update code here to support monthly data.

Update: handled in 9772f90

chengzhuzhang · 2024-02-06T20:42:03Z

@kaizhangpnl Just for your information, this PR to support EAMxx regridded data in E3SM Diags is ready for review. I think you or someone from you team can be great early testers. I also included the result viewer in this thread for review. We can work together to refine this feature.

On the other hand, @golaz has another PR in zppy to support processing native EAMxx output. We are planning to merge shortly. I will tag you again when the PR is ready to merge after some testing...

chengzhuzhang · 2024-02-06T20:43:50Z

@tomvothecoder Tagging you for review. Changes from this PR might need to be carried to cdat migration branch at a later time..

kaizhangpnl · 2024-02-06T21:10:18Z

@kaizhangpnl Just for your information, this PR to support EAMxx regridded data in E3SM Diags is ready for review. I think you or someone from you team can be great early testers. I also included the result viewer in this thread for review. We can work together to refine this feature.

On the other hand, @golaz has another PR in zppy to support processing native EAMxx output. We are planning to merge shortly. I will tag you again when the PR is ready to merge after some testing...

Great. I'd be happy to test it. Thanks for the useful information!

tomvothecoder · 2024-02-07T17:53:30Z

e3sm_diags/derivations/acme.py

+    "SOLIN": OrderedDict(
+        [
+            (("rsdt",), rename),
+            (("SW_flux_dn_at_model_top",), rename),  # EAMxx
        ]


Suggested change

"SOLIN": OrderedDict(

[

(("rsdt",), rename),

(("SW_flux_dn_at_model_top",), rename), # EAMxx

]

"SOLIN": {

("rsdt",): rename,

("SW_flux_dn_at_model_top",): rename, # EAMxx

}

I don't think you need need to use an OrderedDict in the nested derived variables dictionary. I just use a regular dictionary in my refactored version (derivations.py). The old Dataset class will probably be able to parse this the same way as the new Dataset class in the CDAT migration branch because order of the keys shouldn't matter (as far as I'm aware).

e3sm_diags/e3sm_diags/derivations/derivations.py

Lines 592 to 604 in 6b296b1

# ISCCP

"CLDTOT_TAU1.3_ISCCP": {

("FISCCP1_COSP",): cosp_bin_sum,

("CLISCCP",): cosp_bin_sum,

},

"CLDTOT_TAU1.3_9.4_ISCCP": {

("FISCCP1_COSP",): cosp_bin_sum,

("CLISCCP",): cosp_bin_sum,

},

"CLDTOT_TAU9.4_ISCCP": {

("FISCCP1_COSP",): cosp_bin_sum,

("CLISCCP",): cosp_bin_sum,

},

I recognize you're updating existing elements that are already OrderedDict. Up to you if you want to use a regular dict for new or existing elements that you've modified. Just a suggestion since it is easier to read and cleaner, but I'm aware this file is going to be replaced anyways.

Hi @tomvothecoder Thank you for reviewing. It's been a while since the ordered dictionary was designed. I think we made it ordered dictionary to support edge cases when some datasets include multiple variables in the key, and we wanted to loop over keys in order. I'm not sure if this is still needed given that lots of datasets are being updated over years.

Maybe e3sm_diags development started around Python 3.5/3.6? I learned that the regular dict will maintain order with Python >=3.6, so we probably don't need to use OrderedDict anymore.

Starting with CPython 3.6, dictionaries return items in the order you inserted them.
Source - https://stackoverflow.com/a/47849121

Since Python 3.7, all dictionaries are guaranteed to be ordered. The Python contributors determined that switching to making dict ordered would not have a negative performance impact. I don't know how the performance of OrderedDict compares to dict in Python >= 3.7, but I imagine they would be comparable since they are both ordered.

Note that there are still differences between the behaviour of OrderedDict and dict. See also: Will OrderedDict become redundant in Python 3.7?
Source - https://stackoverflow.com/a/53535866

Yeah, i think the development started around 3.5 and 3.6. In this case we should go with regular dictionary. Good call for the cdat migration!

No problem!

tomvothecoder · 2024-02-07T17:54:35Z

e3sm_diags/derivations/acme.py

+    "FLUT": OrderedDict(
+        [
+            (("rlut",), rename),
+            (("LW_flux_up_at_model_top",), rename),  # EAMxx
+        ]
+    ),


Same comment about not needing to use an OrderedDict.

tomvothecoder · 2024-02-07T17:54:41Z

e3sm_diags/derivations/acme.py

+    "FLUTC": OrderedDict(
+        [
+            (("rlutcs",), rename),
+            (("LW_clrsky_flux_up_at_model_top",), rename),  # EAMxx
+        ]
+    ),


Same comment about not needing to use an OrderedDict.

tomvothecoder · 2024-02-07T17:55:30Z

e3sm_diags/derivations/acme.py

+    "SOLIN": OrderedDict(
+        [
+            (("rsdt",), rename),
+            (("SW_flux_dn_at_model_top",), rename),  # EAMxx
        ]


I recognize you're updating existing elements that are already OrderedDict. Up to you if you want to use a regular dict for new or existing elements that you've modified. Just a suggestion since it is easier to read and cleaner, but I'm aware this file is going to be replaced anyways.

tomvothecoder · 2024-02-07T17:55:46Z

e3sm_diags/derivations/acme.py

+    "SHFLX": OrderedDict(
+        [
+            (("hfss",), rename),
+            (("surf_sens_flux",), rename),  # EAMxx
        ]


Same comment about not needing to use an OrderedDict.

tomvothecoder · 2024-02-07T17:55:51Z

e3sm_diags/derivations/acme.py

+    "TS": OrderedDict(
+        [
+            (("ts",), rename),
+            (("surf_radiative_T",), rename),  # EAMxx
+        ]
+    ),


Same comment about not needing to use an OrderedDict.

tomvothecoder · 2024-02-07T17:55:57Z

e3sm_diags/derivations/acme.py

+    "TAUX": OrderedDict(
+        [
+            (("tauu",), lambda tauu: -tauu),
+            (("surf_mom_flux_U",), lambda tauu: -tauu),  # EAMxx
+        ]
+    ),
+    "TAUY": OrderedDict(
+        [
+            (("tauv",), lambda tauv: -tauv),
+            (("surf_mom_flux_V",), lambda tauv: -tauv),  # EAMxx
+        ]
+    ),


Same comment about not needing to use an OrderedDict.

examples/run_v2_9_0_all_sets_E3SM_machines.py

kaizhangpnl · 2024-02-07T06:49:13Z

e3sm_diags/derivations/acme.py

@@ -705,6 +725,10 @@ def cosp_histogram_standardize(cld: "FileVariable"):
                lambda fsntoa, fsntoac: swcf(fsntoa, fsntoac),
            ),
            (("rsut", "rsutcs"), lambda rsutcs, rsut: swcf(rsut, rsutcs)),
+            (
+                ("SW_flux_up_at_model_top", "SW_clrsky_flux_up_at_model_top"),
+                lambda rsutcs, rsut: swcf(rsut, rsutcs),


I'm a beginner in using Python. Does the order of variable names and fields matter here (should "SW_flux_up_at_model_top" match rsut)?

Is it equivalent to the following?

("SW_flux_up_at_model_top", "SW_clrsky_flux_up_at_model_top"),
lambda rsut, rsutcs: swcf(rsut, rsutcs),

The final "SWCF" plot looks correct, so I guess it's not an issue.

https://portal.nersc.gov/cfs/e3sm/kzhang/e3sm_diag/lat_lon_eamxx_09/lat_lon/CERES-EBAF-TOA-v4.1/ceres_ebaf_toa_v4.1-SWCF-09-global.png

Hi @kaizhangpnl thanks for looking into it! I was also supersized that the final plot looks reasonable, still investigating...

Going through the code for derived variable and documentation for lamda expression. It does seem like the order of the parameters after lambda does not matter.

In the derived variable dictionary, it seems like we can further simplify without using lamda expression, we can just to use the regular functions for most if not all cases. Tagging @tomvothecoder for confirmation..

Going through the code for derived variable and documentation for lamda expression. It does seem like the order of the parameters after lambda does not matter.

In the derived variable dictionary, it seems like we can further simplify without using lamda expression, we can just to use the regular functions for most if not all cases. Tagging @tomvothecoder for confirmation..

That's correct, the lambda isn't needed because the required args will be passed directly to the function when it is called. The lambda is doing the same thing here.

Thank you @tomvothecoder !

kaizhangpnl

Tested it on Perlmutter and reproduced the plots.

chengzhuzhang · 2024-02-07T21:20:48Z

Tested it on Perlmutter and reproduced the plots.

Awesome! Thank you, Kai!

* support monthly average in viewer * add 12 monthly mean to core sets as options * Initial modifications for EAMxx variable names * add monthly mean option for aerosol budget tables * update SCREAM variable convention * more update for supporting monthly data --------- Co-authored-by: Chris Golaz <golaz1@llnl.gov>

* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

Refer to the PR for more information because the changelog is massive. Update build workflow to run on `cdat-migration-fy24` branch CDAT Migration Phase 2: Add CDAT regression test notebook template and fix GH Actions build (#743) - Add Makefile for quick access to multiple Python-based commands such as linting, testing, cleaning up cache and build files - Fix some lingering unit tests failure - Update `xcdat=0.6.0rc1` to `xcdat >=0.6.0` in `ci.yml`, `dev.yml` and `dev-nompi.yml` - Add `xskillscore` to `ci.yml` - Fix `pre-commit` issues CDAT Migration Phase 2: Regression testing for `lat_lon`, `lat_lon_land`, and `lat_lon_river` (#744) - Add Makefile that simplifies common development commands (building and installing, testing, etc.) - Write unit tests to cover all new code for utility functions - `dataset_xr.py`, `metrics.py`, `climo_xr.py`, `io.py`, `regrid.py` - Metrics comparison for `cdat-migration-fy24` `lat_lon` and `main` branch of `lat_lon` -- `NET_FLUX_SRF` and `RESTOM` have the highest spatial average diffs - Test run with 3D variables (`_run_3d_diags()`) - Fix Python 3.9 bug with using pipe command to represent Union -- doesn't work with `from __future__ import annotations` still - Fix subsetting syntax bug using ilev - Fix regridding bug where a single plev is passed and xCDAT does not allow generating bounds for coordinates of len <= 1 -- add conditional that just ignores adding new bounds for regridded output datasets, fix related tests - Fix accidentally calling save plots and metrics twice in `_get_metrics_by_region()` - Fix failing integration tests pass in CI/CD - Refactor `test_diags.py` -- replace unittest with pytest - Refactor `test_all_sets.py` -- replace unittest with pytest - Test climatology datasets -- tested with 3d variables using `test_all_sets.py` CDAT Migration Phase 2: Refactor utilities and CoreParameter methods for reusability across diagnostic sets (#746) - Move driver type annotations to `type_annotations.py` - Move `lat_lon_driver._save_data_metrics_and_plots()` to `io.py` - Update `_save_data_metrics_and_plots` args to accept `plot_func` callable - Update `metrics.spatial_avg` to return an optionally `xr.DataArray` with `as_list=False` - Move `parameter` arg to the top in `lat_lon_plot.plot` - Move `_set_param_output_attrs` and `_set_name_yr_attrs` from `lat_lon_driver` to `CoreParameter` class Regression testing for lat_lon variables `NET_FLUX_SRF` and `RESTOM` (#754) Update regression test notebook to show validation of all vars Add `subset_and_align_datasets()` to regrid.py (#776) Add template run scripts CDAT Migration Phase: Refactor `cosp_histogram` set (#748) - Refactor `cosp_histogram_driver.py` and `cosp_histogram_plot.py` - `formulas_cosp.py` (new file) - Includes refactored, Xarray-based `cosp_histogram_standard()` and `cosp_bin_sum()` functions - I wrote a lot of new code in `formulas_cosp.py` to clean up `derivations.py` and the old equivalent functions in `utils.py` - `derivations.py` - Cleaned up portions of `DERIVED_VARIABLES` dictionary - Removed unnecessary `OrderedDict` usage for `cosp_histogram` related variables (we should do this for the rest of the variables in in #716) - Remove unnecessary `convert_units()` function calls - Move cloud levels passed to derived variable formulas to `formulas_cosp.CLOUD_BIN_SUM_MAP` - `utils.py` - Delete deprecated, CDAT-based `cosp_histogram` functions - `dataset_xr.py` - Add `dataset_xr.Dataset._open_climo_dataset()` method with a catch for dataset quality issues where "time" is a scalar variable that does not match the "time" dimension array length, drops this variable and replaces it with the correct coordinate - Update `_get_dataset_with_derivation_func()` to handle derivation functions that require the `xr.Dataset` and `target_var_key` args (e.g., `cosp_histogram_standardize()` and `cosp_bin_sum()`) - `io.py` - Update `_write_vars_to_netcdf()` to write test, ref, and diff variables to individual netCDF (required for easy comparison to CDAT-based code that does the same thing) - Add `cdat_migration_regression_test_netcdf.ipynb` validation notebook template for comparing `.nc` files CDAT Migration Phase 2: Refactor `zonal_mean_2d()` and `zonal_mean_2d_stratosphere()` sets (#774) Refactor 654 zonal mean xy (#752) Co-authored-by: Tom Vo <tomvothecoder@gmail.com> CDAT Migration - Update run script output directory to NERSC public webserver (#793) [PR]: CDAT Migration: Refactor `aerosol_aeronet` set (#788) CDAT Migration: Test `lat_lon` set with run script and debug any issues (#794) CDAT Migration: Refactor `polar` set (#749) Co-authored-by: Tom Vo <tomvothecoder@gmail.com> Align order of calls to `_set_param_output_attrs` CDAT Migration: Refactor `meridional_mean_2d` set (#795) CDAT Migration: Refactor `aerosol_budget` (#800) Add `acme.py` changes from PR #712 (#814) * Add `acme.py` changes from PR #712 * Replace unnecessary lambda call Refactor area_mean_time_series and add ccb slice flag feature (#750) Co-authored-by: Tom Vo <tomvothecoder@gmail.com> [Refactor]: Validate fix in PR #750 for #759 (#815) CDAT Migration Phase 2: Refactor `diurnal_cycle` set (#819) CDAT Migration: Refactor annual_cycle_zonal_mean set (#798) * Refactor `annual_cycle_zonal_mean` set * Address PR review comments * Add lat lon regression testing * Add debugging scripts * Update `_open_climo_dataset()` to decode times as workaround to misaligned time coords - Update `annual_cycle_zonal_mean_plot.py` to convert time coordinates to month integers * Fix unit tests * Remove old plotter * Add script to debug decode_times=True and ncclimo file * Update plotter time values to month integers * Fix slow `.load()` and multiprocessing issue - Due to incorrectly updating `keep_bnds` logic - Add `_encode_time_coords()` to workaround cftime issue `ValueError: "months since" units only allowed for "360_day" calendar` * Update `_encode_time_coords()` docstring * Add AODVIS debug script * update AODVIS obs datasets; regression test results --------- Co-authored-by: Tom Vo <tomvothecoder@gmail.com> CDAT Migration Phase 2: Refactor `qbo` set (#826) CDAT Migration Phase 2: Refactor tc_analysis set (#829) * start tc_analysis_refactor * update driver * update plotting * Clean up plotter - Remove unused variables - Make `plot_info` a constant called `PLOT_INFO`, which is now a dict of dicts - Reorder functions for top-down readability * Remove unused notebook --------- Co-authored-by: tomvothecoder <tomvothecoder@gmail.com> CDAT Migration Phase 2: Refactor `enso_diags` set (#832) CDAT Migration Phase 2: Refactor `streamflow` set (#837) [Bug]: CDAT Migration Phase 2: enso_diags plot fixes (#841) [Refactor]: CDAT Migration Phase 3: testing and documentation update (#846) CDAT Migration Phase 3 - Port QBO Wavelet feature to Xarray/xCDAT codebase (#860) CDAT Migration Phase 2: Refactor arm_diags set (#842) Add performance benchmark material (#864) Add function to add CF axis attr to Z axis if missing for downstream xCDAT operations (#865) CDAT Migration Phase 3: Add Convective Precipitation Fraction in lat-lon (#875) CDAT Migration Phase 3: Fix LHFLX name and add catch for non-existent or empty TE stitch file (#876) Add support for time series datasets via glob and fix `enso_diags` set (#866) Add fix for checking `is_time_series()` property based on `data_type` attr (#881) CDAT migration: Fix African easterly wave density plots in TC analysis and convert H20LNZ units to ppm/volume (#882) CDAT Migration: Update `mp_partition_driver.py` to use Dataset from `dataset_xr.py` (#883) CDAT Migration - Port JJB tropical subseasonal diags to Xarray/xCDAT (#887) CDAT Migration: Prepare branch for merge to `main` (#885) [Refactor]: CDAT Migration - Update dependencies and remove Dataset._add_cf_attrs_to_z_axes() (#891) CDAT Migration Phase 2: Refactor core utilities and `lat_lon` set (#677) Refer to the PR for more information because the changelog is massive. Update build workflow to run on `cdat-migration-fy24` branch CDAT Migration Phase 2: Add CDAT regression test notebook template and fix GH Actions build (#743) - Add Makefile for quick access to multiple Python-based commands such as linting, testing, cleaning up cache and build files - Fix some lingering unit tests failure - Update `xcdat=0.6.0rc1` to `xcdat >=0.6.0` in `ci.yml`, `dev.yml` and `dev-nompi.yml` - Add `xskillscore` to `ci.yml` - Fix `pre-commit` issues CDAT Migration Phase 2: Regression testing for `lat_lon`, `lat_lon_land`, and `lat_lon_river` (#744) - Add Makefile that simplifies common development commands (building and installing, testing, etc.) - Write unit tests to cover all new code for utility functions - `dataset_xr.py`, `metrics.py`, `climo_xr.py`, `io.py`, `regrid.py` - Metrics comparison for `cdat-migration-fy24` `lat_lon` and `main` branch of `lat_lon` -- `NET_FLUX_SRF` and `RESTOM` have the highest spatial average diffs - Test run with 3D variables (`_run_3d_diags()`) - Fix Python 3.9 bug with using pipe command to represent Union -- doesn't work with `from __future__ import annotations` still - Fix subsetting syntax bug using ilev - Fix regridding bug where a single plev is passed and xCDAT does not allow generating bounds for coordinates of len <= 1 -- add conditional that just ignores adding new bounds for regridded output datasets, fix related tests - Fix accidentally calling save plots and metrics twice in `_get_metrics_by_region()` - Fix failing integration tests pass in CI/CD - Refactor `test_diags.py` -- replace unittest with pytest - Refactor `test_all_sets.py` -- replace unittest with pytest - Test climatology datasets -- tested with 3d variables using `test_all_sets.py` CDAT Migration Phase 2: Refactor utilities and CoreParameter methods for reusability across diagnostic sets (#746) - Move driver type annotations to `type_annotations.py` - Move `lat_lon_driver._save_data_metrics_and_plots()` to `io.py` - Update `_save_data_metrics_and_plots` args to accept `plot_func` callable - Update `metrics.spatial_avg` to return an optionally `xr.DataArray` with `as_list=False` - Move `parameter` arg to the top in `lat_lon_plot.plot` - Move `_set_param_output_attrs` and `_set_name_yr_attrs` from `lat_lon_driver` to `CoreParameter` class CDAT Migration Phase 2: Refactor `zonal_mean_2d()` and `zonal_mean_2d_stratosphere()` sets (#774) CDAT Migration Phase 2: Refactor `qbo` set (#826)

chengzhuzhang added 2 commits July 27, 2023 16:42

support monthly average in viewer

1f7471e

add 12 monthly mean to core sets as options

0c74dd9

golaz and others added 3 commits August 23, 2023 11:38

Initial modifications for EAMxx variable names

d6c1b8a

add monthly mean option for aerosol budget tables

a39da3c

merge eamxx support from Chris

760e94c

chengzhuzhang added 2 commits February 6, 2024 11:57

update SCREAM variable convention

102f88d

more update for supporting monthly data

9772f90

chengzhuzhang changed the title ~~Support monthly average in viewer~~ Support monthly average and variable name convention for EAMxx Feb 6, 2024

Merge branch 'main' into suport_sub_seasonal_average

443b582

chengzhuzhang marked this pull request as ready for review February 6, 2024 20:24

chengzhuzhang requested review from tomvothecoder and kaizhangpnl February 6, 2024 20:25

tomvothecoder reviewed Feb 7, 2024

View reviewed changes

tomvothecoder approved these changes Feb 7, 2024

View reviewed changes

kaizhangpnl reviewed Feb 7, 2024

View reviewed changes

kaizhangpnl approved these changes Feb 7, 2024

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chengzhuzhang merged commit 3061cec into main Feb 8, 2024
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tomvothecoder mentioned this pull request May 13, 2024

[Feature]: Add derived variable changes from PR #712 into cdat-migration-fy24 branch #813

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Add acme.py changes from PR #712

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Add acme.py changes from PR #712 #814

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tomvothecoder added a commit that referenced this pull request May 13, 2024

Add acme.py changes from PR #712 (#814)

a31b83e

* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

tomvothecoder added a commit that referenced this pull request Jul 15, 2024

Add acme.py changes from PR #712 (#814)

5d1234d

* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

chengzhuzhang mentioned this pull request Jul 29, 2024

[Feature]: Support full set of variables from EAMxx including both 2D and 3D variables #831

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tomvothecoder added a commit that referenced this pull request Aug 21, 2024

Add acme.py changes from PR #712 (#814)

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* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

tomvothecoder added a commit that referenced this pull request Oct 1, 2024

Add acme.py changes from PR #712 (#814)

468fa4a

* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

tomvothecoder mentioned this pull request Oct 21, 2024

[Refactor]: CDAT Migration Phase 3 - Port changes from main to cdat-migration-fy24 #871

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Add acme.py changes from PR #712 (#814)

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* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

tomvothecoder mentioned this pull request Oct 28, 2024

Add support for multiple time series datasets via glob and fix enso_diags set #866

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tomvothecoder added a commit that referenced this pull request Oct 29, 2024

Add acme.py changes from PR #712 (#814)

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* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

tomvothecoder added a commit that referenced this pull request Oct 29, 2024

Add acme.py changes from PR #712 (#814)

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* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

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Add acme.py changes from PR #712 (#814)

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* Add `acme.py` changes from PR #712 * Replace unnecessary lambda call

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Support monthly average and variable name convention for EAMxx #712

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chengzhuzhang commented Feb 7, 2024

	# ISCCP
	"CLDTOT_TAU1.3_ISCCP": {
	("FISCCP1_COSP",): cosp_bin_sum,
	("CLISCCP",): cosp_bin_sum,
	},
	"CLDTOT_TAU1.3_9.4_ISCCP": {
	("FISCCP1_COSP",): cosp_bin_sum,
	("CLISCCP",): cosp_bin_sum,
	},
	"CLDTOT_TAU9.4_ISCCP": {
	("FISCCP1_COSP",): cosp_bin_sum,
	("CLISCCP",): cosp_bin_sum,
	},

Support monthly average and variable name convention for EAMxx #712

Support monthly average and variable name convention for EAMxx #712

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chengzhuzhang commented Feb 7, 2024

chengzhuzhang commented Jul 27, 2023 •

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chengzhuzhang commented Aug 19, 2023 •

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chengzhuzhang commented Oct 6, 2023 •

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