Docs reorganise - #386

Merged

j-atkins merged 136 commits into

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docs-reorganise

Sep 21, 2026

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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ae2d528
add details on sensor configurations to quickstart guide
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17d5b40
update sail_the_ship with sensor configuration instructions
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baa982a
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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573da9e
[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
j-atkins
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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)

j-atkins
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erikvansebille
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1ca6860

Commits on Jul 31, 2026

Update underway (#360)

j-atkins
and
erikvansebille
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4dfa96f

Commits on Aug 3, 2026

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

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

Update docs for v4 migration (#371)
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e40defd

Commits on Aug 21, 2026

make train the teacher section
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d047bb4
new page for surf specific set up
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00c215f
screenshots for surf set up
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9b7eed1
additions to surf guide
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533856f
more information on file permissions on surf
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431ca68
more information on tailored support
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6ca09f4
further additions; including new documents for lesson plans and student-perspective surf set up
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e5f779c
more content to train the teacher; update the sail the ship instructions to make more generally applicable
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550cfc0

Commits on Aug 24, 2026

batch of updates to the train the teacher guide and associated docs
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30ed5f6
update user guide: reorganise to user profiles; add warning that this is docs is WIP
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912ea6a
init new directories for user profiles
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2751ea6
reorganise dir structure
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ed80f38
reorganise the educator dir
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78c0816
reorganise docs: replace teacher-content with educators
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751797d

Commits on Aug 26, 2026

further reorganisation of docs
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0457317

Commits on Aug 27, 2026

overhaul teach the trainer: use github codespaces and binder
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bfaebcd

Commits on Aug 28, 2026

tmp docs preview workflow
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1fb2f10
update workflow commit pointer
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7387c82
attempt new fix
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d628581
remove preview docs support
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ba67b81
further updates to new workspaces workflow
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4b7ab87
edit text
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4281a3b
edits to instructions
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f756262

Commits on Sep 3, 2026

use more powerful codespace for argo floats and tips for reducing memory footprint
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694f4f6

Commits on Sep 4, 2026

revert to using days for default lifetime
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c5c8912

Commits on Sep 15, 2026

Merge branch 'main' into docs-reorganise
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30d025c
revert wrong merge conflict resolutions
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43b5505
add sphinx-design
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dd93081

Commits on Sep 16, 2026

add more generalised note on codespaces performance considerations
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510b066
updated guidance on performance constraints
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78990b3
placeholders in other user-profile tabs
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20c94e7

Commits on Sep 17, 2026

further populate researchers tab
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992e825

Commits on Sep 18, 2026

remove outdated todo
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3d6a293
link to Copernicus
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e80e854
remind that using more powerful machine comes at hours cost
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2be1737
link to actual Binder environment
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2e3ae58
link to Parcels hosted workspace repo
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6832f1d
add links to guides on how to use MFP
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7a42793
add todo
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1c94a5f

Commits on Sep 21, 2026