[DO NOT MERGE] Parcels-v4 integration for EDITO hackathon #220

erikvansebille · 2025-10-23T09:13:38Z

This PR implements some changes needed to get virtualshipcode to run with parcels v4, as part of the EDITO Model Lab hackathon. It is not aligned with the v1-refactoring/development though, so better to not merge. Also, better to manually copy some of the changes here to a new PR for proper v4-integration later, when Parcels-v4 is out of alpha stage

Perhaps the most important aspect is the creation of the FieldSet, which is surprisingly clean:

virtualship/src/virtualship/expedition/input_data.py

Lines 101 to 111 in 46a1ed6

    
           dso = xr.open_mfdataset([filenames["U"], filenames["T"], filenames["S"]]) 
        
           dso["depth"] = -dso["depth"] 
        
           dso = dso.reindex(depth=dso.depth[::-1]) 
        
           dso = dso.rename({"so": "S", "thetao": "T"}) 
        
           dso.time.attrs["axis"] = "T" 
        
           dsb = xr.open_dataset(filenames["bathymetry"]).rename_vars({"deptho": "bathymetry"}) 
        
           dsb["bathymetry"] = -dsb["bathymetry"] 
        
           ds = xr.merge([dso, dsb], join="inner") 
        
           fieldset = FieldSet.from_copernicusmarine(ds)

Also note that, during this attempt to integrate virtualship and Parcels-v4, we also found some bugs/issues in Parcels-v4 itself: Parcels-code/Parcels#2348

Consolidates/unifies the old dual ship_config.yaml and schedule.yaml config files into one expedition.yaml file, in line with v1 dev objectives.

Fix unnecessarily divergent branches.

…ls dependency from parcels-v4 branch on github

for more information, see https://pre-commit.ci

into parcels-v4

for more information, see https://pre-commit.ci

- Define workspace with VirtualShip name and pixi-build preview - Configure multiple test environments (py310, py311, py312) - Set up feature environments for docs, typing, and pre-commit - Define pixi tasks for tests, docs, linting, and type checking - Align dependencies with existing pyproject.toml

- Replace mamba-org/setup-micromamba with prefix-dev/setup-pixi - Update test job to use pixi environments (test-py310, test-py312) - Update typechecking job to use pixi run typing - Enable pixi caching for faster CI runs - Simplify workflow by removing manual dependency installation

- Replace Conda-based development setup with Pixi - Add comprehensive Pixi workflows section with examples - Document testing, docs, and code quality commands - Include tips for environment management and CI reproduction - Update dependency management instructions to reference pixi.toml

Add Pixi badge to indicate project uses Pixi for environment management

Environment management is now handled by pixi.toml. The environment.yml file is no longer needed as all dependencies are defined in pixi.toml.

v4 of Parcels is 3.11+

for more information, see https://pre-commit.ci

…tualship into edito-hackathon

Requires Parcels-code/Parcels#2348 to work

j-atkins and others added 30 commits October 21, 2025 13:38

Unify config files to expedition.yaml (#217)

a4f9deb

Consolidates/unifies the old dual ship_config.yaml and schedule.yaml config files into one expedition.yaml file, in line with v1 dev objectives.

Update link to website (#215)

2240b89

Merge branch 'main' into v1-dev

8c08b45

Fix unnecessarily divergent branches.

update environment configuration for ship_parcelsv4 and specify parce…

fa1a04c

…ls dependency from parcels-v4 branch on github

update all instrument kernels to parcels v4

fab164d

Fixing parcels inputs and warnings

c8ec729

Fixing test_drifter

9fee385

[pre-commit.ci] auto fixes from pre-commit.com hooks

27b8f62

for more information, see https://pre-commit.ci

Porting CTD and test to v4

9ebeda3

Merge branch 'parcels-v4' of https://github.com/Parcels-code/virtualship

f9a0844

into parcels-v4

[pre-commit.ci] auto fixes from pre-commit.com hooks

a008053

for more information, see https://pre-commit.ci

Attempt to port test_expedition to v4

ec7b76c

Using np.datetime64 in pset

e5726cd

renaming temperature and salinity variables

5af08cf

Fixing bathymetry sampling

30b32e4

Add Pixi badge to README

01465ab

Add Pixi badge to indicate project uses Pixi for environment management

Remove environment.yml

e0a1608

Environment management is now handled by pixi.toml. The environment.yml file is no longer needed as all dependencies are defined in pixi.toml.

Add virtualship source dependency

6fc2c58

Move pytest args to CI call

a08d964

Update RTD config

5a8624b

Update virtualship to drop Python 3.10

daa4be9

v4 of Parcels is 3.11+

Add Parcels as submodule and source installation

49280cb

[pre-commit.ci] auto fixes from pre-commit.com hooks

e038774

for more information, see https://pre-commit.ci

Add caching of Pixi lock

f3ef01b

Update ci.yml to checkout submodules

cdfe1e6

Update cache-pixi-lock workflow to recurse submodules

31c7bbb

Merge pull request #219 from VeckoTheGecko/pixi-for-edito

7204e25

erikvansebille added 2 commits October 23, 2025 11:12

test CTD BGC support for v4

921631f

Merge branch 'edito-hackathon' of https://github.com/Parcels-code/vir…

fbe7456

…tualship into edito-hackathon

erikvansebille changed the base branch from main to v1-dev October 23, 2025 09:14

VeckoTheGecko and others added 12 commits October 23, 2025 11:33

Fix submodule definition (#221)

f41e24d

Adding Parcels dependencies to virtualship pixi.toml

57f73b0

Move openpyxl to be a core dep (#222)

805547a

Add setup script for installing Pixi on EDITO

576285f

Add readme for pixi on EDITO

245ab25

Update CI environments

546625c

Setting axis metadata for time

12f6eb9

Using for-loop for ctd raising and lowering kernels

6f3307d

Fixing ctd unit test

e2e5401

Requires Parcels-code/Parcels#2348 to work

removing decode_cf=False now that it's fixed in v4-dev

84ac211

Change field.eval output to single float

282aa4d

Swapping depth-axis order to be strictly increasing

44b724e

j-atkins changed the title ~~Edito hackathon~~ Edito hackathon (Parcels v4) Oct 27, 2025

Fixing CTD dataset ingestion

46a1ed6

erikvansebille changed the title ~~Edito hackathon (Parcels v4)~~ [DP NOT MERGE] Parcels-v4 integration for EDITO hackathon Oct 27, 2025

erikvansebille marked this pull request as draft October 27, 2025 15:45

erikvansebille changed the title ~~[DP NOT MERGE] Parcels-v4 integration for EDITO hackathon~~ [DO NOT MERGE] Parcels-v4 integration for EDITO hackathon Oct 27, 2025

erikvansebille added 2 commits November 3, 2025 07:57

Fixing depth sampling to throw OutofBounds error

9cf830c

Using XLinearInvdistLandTracer interpolation

14c6021

erikvansebille mentioned this pull request Nov 19, 2025

Integrate Parcels v4 into VirtualShip #232

Open

j-atkins mentioned this pull request Nov 19, 2025

Pixi integration #240

Open

Base automatically changed from v1-dev to main November 21, 2025 09:10

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[DO NOT MERGE] Parcels-v4 integration for EDITO hackathon #220

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erikvansebille commented Oct 23, 2025 •

edited

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	dso = xr.open_mfdataset([filenames["U"], filenames["T"], filenames["S"]])
	dso["depth"] = -dso["depth"]
	dso = dso.reindex(depth=dso.depth[::-1])
	dso = dso.rename({"so": "S", "thetao": "T"})
	dso.time.attrs["axis"] = "T"

	dsb = xr.open_dataset(filenames["bathymetry"]).rename_vars({"deptho": "bathymetry"})
	dsb["bathymetry"] = -dsb["bathymetry"]

	ds = xr.merge([dso, dsb], join="inner")
	fieldset = FieldSet.from_copernicusmarine(ds)

[DO NOT MERGE] Parcels-v4 integration for EDITO hackathon #220

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erikvansebille commented Oct 23, 2025 •

edited

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