Timedeltas and arrival/departure ports from MFP export - #372

Draft

j-atkins wants to merge 160 commits into

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Commits on May 20, 2026

add info on sensor configuration
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edbda0b
add list of available sensors to documentation
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cd5b523
remove redundant TODO
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4668e54
improve phrasing
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add details on sensor configurations to quickstart guide
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update sail_the_ship with sensor configuration instructions
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enahnce phrasing
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a8a4978
add testing that docs match the code for sensor options, ensure instrument column entries are consistent
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6b3628e
add check that all instruments in code are addressed in sensor table
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e23087b
update environments to pull parcels v4 alpha
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a5ff3a4
changed parcels logging api
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db44324
first wave of changes to the instrument logic with v4 logic, and particle building
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6f732d3
remove add dummy UV func, shouldn't be needed in v4 (?)
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71881cc
pull v4 from parcels/main
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62b2b1b
use AdvectionRK2
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38afc56
migrate fieldset ingestion protocol
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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d13a036

Commits on May 21, 2026

standardise variable naming for bathy data ingestion
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5c7fd29
env fixes
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ee17230
Merge branch 'main' into migrate-v4
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72161df
add ipdb for devs
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92e74bd
further changes to suit v4
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0a83437

Commits on May 22, 2026

Commits on May 26, 2026

refactor to _compute_max_depths; more changes in line with Parcels v4 API
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63122b9
depth -> z in ParticleSet's
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a6ad631

Commits on May 28, 2026

times to datetime64 and update fieldset eval output
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8e0a33f

Commits on May 29, 2026

tmp ds.load() step for v4.0
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8b76854

Commits on Jun 5, 2026

Merge branch 'main' into migrate-v4
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27c36e2
error messaging in argo floats
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81f857f
refactor _generate_fieldset()
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cd2f9ff
small tidy up
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39e63d1
from zarr -> parquet output
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0dc5975
endtime/time_origin API update
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3e52b10
no temp sampling in phase 3
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07209bf
endtimes access scalars directly
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9cb321c
fix wrong var name in kernel
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137978d
combined vector fields for instruments
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c29efe6
small tweaks/fixes
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a8242c1
cmo to pixi.toml and tweaked particleset API
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95d84b7

Commits on Jun 10, 2026

Commits on Jun 11, 2026

Revert "move to positive down API throughout virtualship"
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da86613
negate *and* reindex depth in ds before fieldset creation
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a468ade
fill land/nans with 0s
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fd2232a

Commits on Jun 12, 2026

fixes to argo kernels + some refactoring
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0be180d

Commits on Jun 16, 2026

Merge branch 'main' into migrate-v4
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c5b8378

Commits on Jul 13, 2026

Merge branch 'main' into migrate-v4
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1faf09d
switch to using .to_windowed_arrays() for performance
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c05d2f7
neater way of negating depth
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cff0240
use interpolator object
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d9df5b6

Commits on Jul 14, 2026

lat/lon/time -> y/x/t
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f89ce73
performance step: windowed arrays
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d8bd074
time -> t
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ca3ba1f

Commits on Jul 16, 2026

fix argo bug, min_depth spec to avoid immediately error out of bounds
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c740630

Commits on Jul 17, 2026

remove ds.load/to_windowed_arrays experiments
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abb5380

Commits on Jul 20, 2026

lon -> x
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583fc7b
use vertical_axis arg for depth convention
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f2becc0

Commits on Jul 22, 2026

Refactor dataset retrieval specs (#359)
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ae98059

Commits on Jul 23, 2026

add tmp file write/read step (#358)
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391b930

Commits on Jul 27, 2026

`to_windowed_arrays` only for non-underway instruments (#361)

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erikvansebille
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1ca6860

Commits on Jul 31, 2026

Update underway (#360)

j-atkins
and
erikvansebille
authored
4dfa96f

Commits on Aug 3, 2026

Add initial Field sampling for non-underway instruments (#364)

j-atkins
and
erikvansebille
authored
ebd2c0c
remove .fillna() now that it's in Parcels internals
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committed
ac43f15

Commits on Aug 4, 2026

Commits on Aug 5, 2026

update tests for v4 workflows and enhance out of bounds error checking
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de8c627
update tests for v4 workflows
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f17b43e
update drifter tests for v4 workflows
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52ff1fd
fix bugs in xbt behavious, also update particleset inspection for v4
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90bef40
update xbt tests for v4 workflows
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12d87f6
attempt to fix pixi env and CI
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4e075a2

Commits on Aug 6, 2026

update pixi and CI to python 3.14
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dc783c0
update contribution guide for pixi instructions
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1d3955a
fix pre-commit issue
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616f5d8
sort out encoding to avoid UserWarnings
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9a53435
use fieldset.time_interval.left notation
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f37ce1d
add _handle_grounding test
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b3fe2de
Merge branch 'main' into migrate-v4
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9601783

Commits on Aug 7, 2026

remove docstring for consistency
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84db2eb
filter out parcels v4 user warning for (temporary measure)
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fb789fc
Merge branch 'migrate-v4' of github.com:OceanParcels/virtualship into migrate-v4
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d95cc5e

Commits on Aug 10, 2026

remove initial sampling from argo floats
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495c143
argo kernel: solve issue of not updating cycle_age during ascent
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26d6681

Commits on Aug 12, 2026

new Port class
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a1d0b5e
Update docs for v4 migration (#371)
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e40defd
ingest and validate mfp exports with/without (or mixture of) ports
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f6bca0f
update static expedition.yaml with ports API
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e91686b
fix timings in static expedition.yaml
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03da307
move `virtualship init` logic to new initialise.py module
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8cf91de
update init docstring
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46e7828
refactor _initialise.py
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02a1dd7

Commits on Aug 14, 2026

rename method and small update
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2f5b5e1
add Port logic to problems simulator
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ed07b42

Commits on Aug 27, 2026

`add_field` removed from Parcels API
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d756cbe
update tests for new parcels API
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81f7459
add state_date argument to init command
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a77c59e
handle timedeltas from mfp export, .xlsx only now that MFP export is .xslx only
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d8b5611
update click.echo(); no time instructions required
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b863760
add waypoint numbers (comments) to expedition.yaml
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4faa24a
add unit test: waypoint field in yaml always starts with "- instrument"
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1119153
new Port class
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6a460a4
ingest and validate mfp exports with/without (or mixture of) ports
j-atkins
committed
585d54c
update static expedition.yaml with ports API
j-atkins
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03989fb
fix timings in static expedition.yaml
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804f909
move `virtualship init` logic to new initialise.py module
j-atkins
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b2c43dc
update init docstring
j-atkins
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a8d647d
refactor _initialise.py
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33d11a9
rename method and small update
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373f4c5
add Port logic to problems simulator
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2042b4d
Merge branch 'cruise-data' of github.com:OceanParcels/virtualship into cruise-data
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fe0c5a3
remove tmp dev step
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f7ac2aa

Commits on Aug 28, 2026

Merge branch 'migrate-v4' into cruise-data
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committed
3ac7383

Commits on Aug 31, 2026

move _get_example_expedition back to utils
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60a58b4
fix datetime handling
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7946f7b
move mfp_to_yaml test to test_initialise
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92c5335

Commits on Sep 1, 2026

fix bug: UV vector field remains even after adding bathymetry
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a7b55e2

Commits on Sep 2, 2026

Commits on Sep 3, 2026

Commits on Sep 4, 2026

remove duplicate cycle age update
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538e201
clean up: unnecessary or old/stale code
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ea14cd6

Commits on Sep 7, 2026

Commits on Sep 8, 2026

add/move some structural schedule verfication checks to pydantic field validators
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4c1b9e6
add fieldsets rather than building list
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3aa1206
fieldset[particles.x, particles.y, ...] notation -> fieldset[particles]
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3ee8d04
np.where() -> boolean indexing for all kernels
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0e8cd88
remove unnecessary np.float
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dc8874f
bump pixi up from old pinnings
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c930123
prevent ctd from going out of bounds by exceeding max/min depths; update tests with more tolerance for interpolation discrepancies
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0160d44
use raw datetime objects in psets
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a7ce809
Merge branch 'main' into migrate-v4
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dfddaa0

Commits on Sep 9, 2026

fix bug when using local data: handle both depth_min and depth_max being None
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adabe91
remove broken/unnecessary warning filter
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501410d
remove tmp dev spinner skipping
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3776a6e

Commits on Sep 14, 2026

Merge branch 'migrate-v4' into cruise-data
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de539cc
Merge branch 'main' into cruise-data
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c8cbd47