Add support for multiple time series datasets via glob and fix enso_diags set
#866
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tomvothecoder
changed the title
enso_diags and tc_analysis
tomvothecoder
changed the title
enso_diags and tc_analysisenso_diags, streamflow, tc_analysis
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@forsyth2 For the failing Can you fix this file? |
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@tomvothecoder thank you for helping identify this problem. In this version of v3 Low Resolution datasets (documented here), much lower TC activity is found. It is likely that no TC is detected during the testing period (1987-1988). Therefore no file called "cyclones_stitch_v3.LR.historical_0051_1987_1988.dat" was generated from an upstream process. So the testing result that skipped tc_analysis figure is expected in case of v3.. |
Thank you for clarifying. It sounds like @forsyth2 should exclude |
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@forsyth2 The run script in zppy specifies input dir paths that contain sub-directories. e3sm_diags cannot determine which Instead, the Why?I tried implementing functionality to parse the input data path for For example:
Fix -> set Input Path to Fixes for
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tomvothecoder
commented
Oct 10, 2024
tomvothecoder
commented
Oct 10, 2024
|
@tomvothecoder Thank you for looking into all this.
I also added a failure if the stitch file is empty (included in E3SM-Project/zppy#628) to catch this in the future. But yes, for now, we'll just have to exclude tc_analysis from v3 testing.
I'm going to have to dive deeper into this. In theory, |
This was referenced Oct 12, 2024
Got it. I will do final testing then merge this PR soon for you to try in |
tomvothecoder
commented
Oct 17, 2024
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Hey @chengzhuzhang, I would appreciate a PR review to ensure my code changes look good to you as well.
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The main of file of interest to add support for glob of .nc files.
tomvothecoder
commented
Oct 17, 2024
tomvothecoder
commented
Oct 21, 2024
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@tomvothecoder, to follow up our discussion this morning, for the file path pattern, if there is a e3sm_diags/e3sm_diags/driver/utils/dataset_xr.py Lines 1087 to 1092 in 80b62a0 |
Just noting that this logic has been verified to work in previous regression testing and there are units tests that cover it. |
tomvothecoder
commented
Oct 22, 2024
tomvothecoder
changed the title
enso_diags, streamflow, tc_analysisenso_diags set, various smaller fixes
tomvothecoder
changed the title
enso_diags set, various smaller fixesenso_diags set, and raise exception for non-existent or empty TE stitch file
- This function was working correctly before
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tomvothecoder
changed the title
enso_diags set, and raise exception for non-existent or empty TE stitch fileenso_diags set
tomvothecoder
commented
Oct 28, 2024
Comment on lines
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-372
| if self.is_climo: | ||
| ds = self._get_climo_dataset(season) | ||
| return ds | ||
| elif self.is_time_series: | ||
| if self.is_time_series: | ||
| ds = self.get_time_series_dataset(var) | ||
| ds_climo = climo(ds, self.var, season).to_dataset() | ||
|
|
||
| return ds_climo | ||
| else: | ||
| raise RuntimeError( | ||
| "This Dataset object could not be identified as either a climatology " | ||
| "(`self.is_climo`) or time series dataset (`self.is_time_series`)." | ||
| ) |
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Removed else statement because this condition will never be met (always climo or time series)
| # filename if the season is in ["ANN", "DJF", "MAM", "JJA", "SON"]. | ||
| if season in ["ANN", "DJF", "MAM", "JJA", "SON"]: | ||
| # filename. This is a more general pattern for model only data. | ||
| if season in MODEL_ONLY_SEASONS: |
|
Regression tests show same results as before. @forsyth2 I just merged this PR to |
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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 <[email protected]> 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 <[email protected]> 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 <[email protected]> [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 <[email protected]> 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 <[email protected]> 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)
tomvothecoder
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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 <[email protected]> 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 <[email protected]> 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 <[email protected]> [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 <[email protected]> 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 <[email protected]> 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)
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@tomvothecoder Following up on #866 (comment) and #866 (comment):
Has this actually caused an error or is it more a readability issue? I'm not sure if I missed that above. pre- CDAT migration
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Correct me if I'm wrong, but isn't CDAT-based e3sm_diags BehaviorIn the CDAT-based version of the CDAT-free e3sm_diags BehaviorIn the CDAT-free version of Limitations of Directory Structure HandlingThe file-matching logic in the CDAT-free code is limited in terms of how many subdirectories it can handle, and this number can vary depending on the |
In That means that line is essentially: Now, let's jump up a level: So, Now, that code block is run after That means that line is essentially: Now, we have
@golaz @chengzhuzhang What was the original purpose of the On but these lines just create symbolic links: So, it occurs to me that the changes in https://github.com/E3SM-Project/zppy/pull/651/files#top should have been to symoblic links, not copies. In any case, we're clearly still creating copies/links to pass into Diags. Are these symbolic links still necessary in the CDAT-migrated E3SM Diags? I can't seem to recall why it was implemented this way. From what @tomvothecoder says, it seems like it would be better to just pass in the directories directly. (In any case, the |
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Hi @forsyth2 , creating symbolic links for For monthly time-series files, for the pre-CDAT-migration, we need to create xml files that essentially concatenate ts files from multiple files. In CDAT-migrated diags, time slicing is handled withing E3SM Diags, I think that's why @tomvothecoder suggested to pass in directoreis directly without symbolic links or copying files around. |
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Ah ok, thanks for the info.
Great, I'll integrate that into E3SM-Project/zppy#651 and test that along with the changes that #907 introduces. |
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Jan 15, 2025
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 <[email protected]> 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 <[email protected]> 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 <[email protected]> [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 <[email protected]> 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 <[email protected]> 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)
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Description
Summary of changes
globfilepathopen_dataset()withopen_mfdataset()in_get_time_series_dataset_obj()_get_time_series_filepathsand_get_matching_time_series_filepathsto return a list of filepath(s) or None if no filepaths found_subset_and_load_vars()with time series datasetsareatotal2,lat, andlonforarm_diagsset_get_time_slice()to support parsing a list of filepath(s) for start and end years via_parse_years_from_filepaths()enso_diags(related errors)calculate_nino_index_model()not catching the correctIOErrormessage before trying to get thesstdataset using the"TS"variable.load()with time series dataset for downstream operationstc_analysis/lcrc/group/e3sm/ac.forsyth2/zppy_min_case_e3sm_diags_cdat_migrated_output/test-diags-no-cdat-20240917/v3.LR.historical_0051/post/atm/tc-analysis_1987_1988/cyclones_stitch_v3.LR.historical_0051_1987_1988.datstreamflow.ncfiles usinggloband regex under nested directories -- not sure if this will work because how will e3sm_diags know which.ncfiles to use if there are multiple sub-directories with the same matching files?zppyto use exact filepath for root directory containing file/lcrc/group/e3sm/ac.forsyth2/zppy_min_case_e3sm_diags_cdat_migrated_output/test-diags-no-cdat-20240917/v3.LR.historical_0051/post/rof/native/ts/monthly/2yr/Checklist
If applicable: