[DO NOT MERGE] Parcels-v4 integration for EDITO hackathon by erikvansebille · Pull Request #220 · Parcels-code/virtualship

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 · 2026-05-22T10:49:06Z

Draft PR targeting migration to Parcels v4 has continued in #342, so I suggest we close this PR (where the Parcels v4 API is no longer up to date)

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 · 2026-05-22T10:49:06Z

Draft PR targeting migration to Parcels v4 has continued in #342, so I suggest we close this PR (where the Parcels v4 API is no longer up to date)

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 · 2026-05-22T10:49:06Z

Draft PR targeting migration to Parcels v4 has continued in #342, so I suggest we close this PR (where the Parcels v4 API is no longer up to date)

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 · 2026-05-22T10:49:06Z

Draft PR targeting migration to Parcels v4 has continued in #342, so I suggest we close this PR (where the Parcels v4 API is no longer up to date)

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 · 2026-05-22T10:49:06Z

Draft PR targeting migration to Parcels v4 has continued in #342, so I suggest we close this PR (where the Parcels v4 API is no longer up to date)

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 · 2026-05-22T10:49:06Z

Draft PR targeting migration to Parcels v4 has continued in #342, so I suggest we close this PR (where the Parcels v4 API is no longer up to date)

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 · 2026-05-22T10:49:06Z

Draft PR targeting migration to Parcels v4 has continued in #342, so I suggest we close this PR (where the Parcels v4 API is no longer up to date)

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 · 2026-05-22T10:49:06Z

Draft PR targeting migration to Parcels v4 has continued in #342, so I suggest we close this PR (where the Parcels v4 API is no longer up to date)

j-atkinsand 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' ofhttps://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#219from 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' ofhttps://github.com/Parcels-code/vir…
fbe7456
…tualship into edito-hackathon

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

VeckoTheGeckoand 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 hackathonOct 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 hackathonOct 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
Closed

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

j-atkins closed this May 22, 2026

j-atkinsand 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' ofhttps://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#219from 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' ofhttps://github.com/Parcels-code/vir…
fbe7456
…tualship into edito-hackathon

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

VeckoTheGeckoand 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 hackathonOct 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 hackathonOct 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
Closed

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

j-atkins closed this May 22, 2026

j-atkinsand 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' ofhttps://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#219from 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' ofhttps://github.com/Parcels-code/vir…
fbe7456
…tualship into edito-hackathon

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

VeckoTheGeckoand 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 hackathonOct 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 hackathonOct 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
Closed

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

j-atkins closed this May 22, 2026

j-atkinsand 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' ofhttps://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#219from 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' ofhttps://github.com/Parcels-code/vir…
fbe7456
…tualship into edito-hackathon

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

VeckoTheGeckoand 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 hackathonOct 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 hackathonOct 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
Closed

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

j-atkins closed this May 22, 2026

j-atkinsand 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' ofhttps://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#219from 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' ofhttps://github.com/Parcels-code/vir…
fbe7456
…tualship into edito-hackathon

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

VeckoTheGeckoand 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 hackathonOct 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 hackathonOct 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
Closed

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

j-atkins closed this May 22, 2026

j-atkinsand 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' ofhttps://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#219from 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' ofhttps://github.com/Parcels-code/vir…
fbe7456
…tualship into edito-hackathon

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

VeckoTheGeckoand 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 hackathonOct 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 hackathonOct 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
Closed

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

j-atkins closed this May 22, 2026

j-atkinsand 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' ofhttps://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#219from 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' ofhttps://github.com/Parcels-code/vir…
fbe7456
…tualship into edito-hackathon

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

VeckoTheGeckoand 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 hackathonOct 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 hackathonOct 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
Closed

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

j-atkins closed this May 22, 2026

j-atkinsand 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' ofhttps://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#219from 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' ofhttps://github.com/Parcels-code/vir…
fbe7456
…tualship into edito-hackathon

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

VeckoTheGeckoand 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 hackathonOct 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 hackathonOct 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
Closed

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

j-atkins closed this May 22, 2026

	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)

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