BGC boundary and surface forcing + major refactoring (#79)

* Extract common parts of initial conditions and boundary forcing and make it mixin class

* Transpose expected test data as a result of refactor

* Update notebook with .ds data_vars moved to attributes

* Minor fixes

* Add more metadata and adapt mixin for atmospheric forcing

* Refactor boundary_forcing to work with BGC

* Mask ERA5 data as part of post processing

* Break mixin functions into smaller pieces and add docstrings

* Make ERA5Correction inherit from Dataset class

* Adapt to changes in ROMSMixin

* Add BGC boundary forcing

* Add BGC boundary forcing tests

* Update notebook that showcases BGC boundary forcing creation

* Rename mixin class

* Refactor AtmosphericForcing and automate SWR correction

* Add xarray-datatree to dependencies

* Adapt SWR tests and move them as fit

* Fix typo

* Add CESMBGCSurfaceForcingDataset and handle adding time info to Dataset

* Default climatology to True for BGC initial condition data

* Reformatting

* Add surface BGC metadata

* Add function that converts from cftime to datetime

* Download CESM surface test data

* Introduce absolute time and handle clim saving separately

* Add BGC surface forcing

* One parent class for CESM

* Surface BGC tests

* Correct filepaths

* Fix issue with time dimension

* Include units in long_name of time variable

* Add regression test for BGC clim data

* Add utils tests to github workflows

* Rename AtmosphericForcing --> SurfaceForcing

* Rename AtmosphericForcing --> SurfaceForcing

* Use tempfile with delete=True to not clutter temp space

* Write physics and BGC fields in parallel

* Change units in long name

* Merge

* Update notebooks

* Update notebooks

* Remove forcing file

* Add more docstrings to plotting function

* Fix typo for test module name

.github/workflows/tests.yaml

@@ -42,7 +42,7 @@ jobs:
         shell: bash -l {0}
         run: |
            python -V
-           coverage run --rcfile=coverage.toml -m pytest --verbose roms_tools/tests/test_datasets.py roms_tools/tests/test_grid.py roms_tools/tests/test_topography.py roms_tools/tests/test_tides.py roms_tools/tests/test_atmospheric_forcing.py roms_tools/tests/test_initial_conditions.py roms_tools/tests/test_vertical_coordinate.py roms_tools/tests/test_boundary_forcing.py
+           coverage run --rcfile=coverage.toml -m pytest --verbose roms_tools/tests/test_datasets.py roms_tools/tests/test_grid.py roms_tools/tests/test_topography.py roms_tools/tests/test_tides.py roms_tools/tests/test_surface_forcing.py roms_tools/tests/test_initial_conditions.py roms_tools/tests/test_vertical_coordinate.py roms_tools/tests/test_boundary_forcing.py roms_tools/tests/test_utils.py
 
       - name: Get coverage report
         shell: bash -l {0}

ci/environment.yml

@@ -9,6 +9,7 @@ dependencies:
   - matplotlib
   - cartopy
   - xarray
+  - xarray-datatree
   - netcdf4
   - pooch
   - packaging

docs/api.rst

@@ -26,14 +26,13 @@ Tidal Forcing
 
    roms_tools.TidalForcing
 
-Atmospheric Forcing
---------------------
+Surface Forcing
+----------------
 
 .. autosummary::
    :toctree: generated/
 
-   roms_tools.AtmosphericForcing
-   roms_tools.SWRCorrection
+   roms_tools.SurfaceForcing
 
 Initial Conditions
 --------------------