Version 1.0: North Atlantic Update - Tides, Curved Boundaries, Config, and More!😀🤯🥳 #193

manishvenu · 2024-10-11T19:46:33Z

Description:

Major Features:

Accepting curved boundary supergrids and bathymetry
Tides from TPXO
Import from Config Files
Major bathymetry fixes for land-sea mask
Moving experiment specific changes to MOM_override (Boundary parameters and others) and out of MOM_input
New GLORYS downloader (that can account for curved boundaries)
Additional tests (tides specific)
Changing function names to verb beginnings (initial_condition -> setup_initial_condition)
Add properties (i.e. more functional object variables) and dataset plotting

Minor Features:

Ability to code without greek letters
Removed unintentional machine-specific code
Increased print statements

Breaking Changes (for backwards compatibility):

Practically Everything. Functions changed to verb starts!

Documentation Changes (TBD):

Update README and Docs

Co-authored-by: @ashjbarnes

…CESM when parsing

Override min depth

Changes to make compatible with CESM

having mask table and layout no longer required

Fix layout requirements

fix typo in find replace

Replace minimum layers with min depth

…an depth

…nt num After talking with Ashley, the find_MOM6_orientation will likely be removed

The function names for rectangular and sinmple boundaries were changed because the tides are a kind of boundary function, the old names now give a warning and call the correct function. GFDL had rough horizontal subsetting for the tpxo dataset (probably for efficiency?), implemented in setup_tides_rectangular_boundaries.

Collapsed the *_tidal_dims functions into the encode_tides function in segment, and add citing documentation to the docstrings for now.

…l-mom6 into croc_with_req_changes

Various bathymetry improvements / bugfixes

Add angled grids to RMOM6

Update comment to reflect name change

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tests/test_angled_grids.py

navidcy · 2024-10-11T20:17:54Z

Hi @manishvenu

T H A N K S !

This is a huge PR. Is there any chance we break it into a few smaller ones? Otherwise reviewing will be hard.

~~Btw,~~
~~> Functions changed to verb starts!~~
~~what does "verb starts" mean?~~
(got it!)

navidcy · 2024-10-11T20:26:46Z

tests/test_grid_generation.py

@@ -129,7 +129,7 @@ def test_quadrilateral_areas(lat, lon, true_area):
    ],
 )
 def test_rectangular_hgrid(lat, lon):
-    assert isinstance(rectangular_hgrid(lat, lon), xr.Dataset)
+    assert isinstance(generate_rectangular_hgrid(lat, lon), xr.Dataset)


The args are reversed in the test compared to the method definition

https://github.com/CROCODILE-CESM/regional-mom6/blob/cd987f590d9346ebcb232413ee78fd3e34b86c78/regional_mom6/regional_mom6.py#L487

Probably doesn't matter for this test, but it might create confusion to users/developers.

ashjbarnes · 2024-10-12T15:43:52Z

Hi @manishvenu

T H A N K S !

This is a huge PR. Is there any chance we break it into a few smaller ones? Otherwise reviewing will be hard.

~~Btw,~~ ~~> Functions changed to verb starts!~~ ~~what does "verb starts" mean?~~ (got it!)

Yes it's a huge PR! We did have this broken down into smaller PRs on the CROCODILE fork, which we reviewed and merged one by one over the last couple of months. Unfortunately these PRs might not be useful for us to break up this big one any more, because we did need to do a lot of merging given that @manishvenu and I were working in parallel on several changes.

It's still in draft state for now while we polish it (build on the properties for each input which is WIP, add more comments, remove commented out code, review the demos etc) but thought it could be good to get the ball rolling on the review.

Is there a way you suggest that we break up the PR? Since we did a huge overhaul of the entire codebase, it's kind of hard to separate some of the changes!

…up_run_directory (#20) * Package type changes for CRR * Black Formatting * Change MOM Param * Change MOM_param to Work * black * Remvoe premade_run_dir_arg * Remove init * Black * Update MOM_param_test * Clean

* include DataReader class * within __getattr__ read data files * bug * update demo with plots * typo

ashjbarnes · 2024-10-14T20:52:38Z

BTW this PR closes #184 , #168 , and also #55 in a roundabout way since user now specifies which boundaries they want, and the MOM inputs are adjusted accordingly.

navidcy · 2024-10-14T21:26:05Z

BTW this PR closes #184 , #168 , and also #55 in a roundabout way since user now specifies which boundaries they want, and the MOM inputs are adjusted accordingly.

the closes #XYZ either needs to be in the first comment of the PR or we need to manually link the issues with the PR

navidcy · 2024-10-14T21:31:12Z

Yes it's a huge PR! We did have this broken down into smaller PRs on the CROCODILE fork, which we reviewed and merged one by one over the last couple of months. Unfortunately these PRs might not be useful for us to break up this big one any more, because we did need to do a lot of merging given that @manishvenu and I were working in parallel on several changes.

It's still in draft state for now while we polish it (build on the properties for each input which is WIP, add more comments, remove commented out code, review the demos etc) but thought it could be good to get the ball rolling on the review.

OK, when is ready to review we can talk again? Huge PRs are harder to review though and take longer...

Is there a way you suggest that we break up the PR?

Each of the major features mentioned in the first comment sounds like could be a PR? Just a suggestion..

navidcy · 2024-10-14T21:32:01Z

Ability to code without greek letters

haha, sorry if I introduced this difficulty to devs

…x __getattr__ bug (#24)

ashjbarnes and others added 30 commits August 28, 2024 14:00

included a min_depth parameter and overwite this in MOM_input

f3a220d

black

0523f1d

Remove problematic comment at top of override file. Causes issus for …

d86b147

…CESM when parsing

Merge pull request #2 from COSIMA/override-min-depth

7870d81

Override min depth

Merge pull request #3 from CROCODILE-CESM/tidy-override-file

595c4de

Changes to make compatible with CESM

having mask table and layout no longer required

3270057

Merge pull request #4 from CROCODILE-CESM/remove-masktable-requirement

a262e15

having mask table and layout no longer required

fix layout requirements

42c2840

fixed and working

005fb44

Merge pull request #5 from CROCODILE-CESM/fix-layout-requirements

9606458

Fix layout requirements

fix typo in find replace

2268c8f

Merge pull request #6 from CROCODILE-CESM/fix-layout-requirements

875549e

fix typo in find replace

Merge branch 'COSIMA:main' into main

b6fab83

replace minimum layers with min depth

6147803

black

7caae56

fix tests

718dc1c

update notebook

88938a2

Merge pull request #7 from CROCODILE-CESM/move-minimum-layers

31a6139

Replace minimum layers with min depth

bugfix setup rundir when overwriting

a21e564

fix issue where ocean mask would fail to remove values lower than oce…

2488100

…an depth

Start Setup Tides

d28a5d3

First Attempt: RM6 Tides

09a1a2f

Clean up setup_tides and adjust rect_boundaries with hard-coded segme…

d73e84a

…nt num After talking with Ashley, the find_MOM6_orientation will likely be removed

Write MOM6 Vars

5a40076

Add Docstring Cite and Merge Functions

8adb479

Collapsed the *_tidal_dims functions into the encode_tides function in segment, and add citing documentation to the docstrings for now.

Minor Path Function Changes

586832e

Merge branch 'croc_with_req_changes' of github.com:manishvenu/regiona…

89f9d1f

…l-mom6 into croc_with_req_changes

First Implementation w/ Tides

c4ff6d3

Minor Edit

ff8dc2c

ashjbarnes and others added 13 commits October 5, 2024 08:40

Merge pull request #17 from CROCODILE-CESM/bathymetry-efficiency

399e16c

Various bathymetry improvements / bugfixes

allow reading of lon lat extents from pre existing hgrid

903d329

black

69407fd

bugfixing curved boundary regridding for tracer IC and bathymetry

bb8b9ec

black

848a712

update tests

60c59b7

typo

dee8457

Update regional_mom6/regional_mom6.py

3f86a14

Black Format

ae58573

Merge branch 'main' into start_angled_boundaries

fcca7cf

Merge pull request #13 from CROCODILE-CESM/start_angled_boundaries

292ebfa

Add angled grids to RMOM6

Update regional_mom6.py

f562b1f

Update comment to reflect name change

Merge remote-tracking branch 'upstream/main'

19583c9

manishvenu changed the title ~~Version 1.0: North Atlantic Update - Tides, Curved Boundaries, Config, and More\]\]\~~ Version 1.0: North Atlantic Update - Tides, Curved Boundaries, Config, and More!😀🤯🥳 Oct 11, 2024

navidcy reviewed Oct 11, 2024

View reviewed changes

tests/test_angled_grids.py Outdated Show resolved Hide resolved

Remove unused test

cd987f5

navidcy reviewed Oct 11, 2024

View reviewed changes

manishvenu and others added 4 commits October 14, 2024 14:29

Minor Bug Fixes/Improvements to create_empty, change_MOM_param, & set…

5b1c816

…up_run_directory (#20) * Package type changes for CRR * Black Formatting * Change MOM Param * Change MOM_param to Work * black * Remvoe premade_run_dir_arg * Remove init * Black * Update MOM_param_test * Clean

allow __getattr__ to read in data arrays from disk (#23)

2ee186d

* include DataReader class * within __getattr__ read data files * bug * update demo with plots * typo

Remove the deletion of MOM_input params in change_MOM_param

61398c9

Merge branch 'main' of github.com:CROCODILE-CESM/regional-mom6

5ff128c

navidcy added the enhancement New feature or request label Oct 14, 2024

Update Config for Computer Independence, fix change_MOM_param, and fi…

7d7216e

…x __getattr__ bug (#24)

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Version 1.0: North Atlantic Update - Tides, Curved Boundaries, Config, and More!😀🤯🥳 #193

Version 1.0: North Atlantic Update - Tides, Curved Boundaries, Config, and More!😀🤯🥳 #193

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Version 1.0: North Atlantic Update - Tides, Curved Boundaries, Config, and More!😀🤯🥳 #193

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