Migrate to Parcels v4 - #342

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j-atkins wants to merge 96 commits into
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migrate-v4
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Migrate to Parcels v4#342
j-atkins wants to merge 96 commits into
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migrate-v4

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@j-atkinsj-atkins commented May 20, 2026•
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This PR migrates to using Parcels v4 for VirtualShip.

  • Update instrument kernels
  • Update fieldset ingestion workflows
  • Update to Parquet output
  • Implement new fieldset/performance handling strategy, i.e. new v4 docs
  • Implement Refactor underway instruments #231
  • Check expedition / workflow
    • including underway instruments
    • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
  • Implement initial timestep sampling (i.e. Parcels #2622)
  • Update to work with local data / --from-data
  • Update tests
  • Add new tests for v4 specific logic(?)
  • Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]
    • Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
  • ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?

Closes#239, closes#232, closes#231, closes#323, closes#238

j-atkinsand others added 17 commits May 20, 2026 11:25
@j-atkins
add info on sensor configuration
edbda0b
@j-atkins
add list of available sensors to documentation
cd5b523
@j-atkins
remove redundant TODO
4668e54
@j-atkins
improve phrasing
ae2d528
@j-atkins
add details on sensor configurations to quickstart guide
17d5b40
@j-atkins
update sail_the_ship with sensor configuration instructions
baa982a
@j-atkins
enahnce phrasing
a8a4978
@j-atkins
add testing that docs match the code for sensor options, ensure instr…
6b3628e
…ument column entries are consistent
@j-atkins
add check that all instruments in code are addressed in sensor table
e23087b
@j-atkins
update environments to pull parcels v4 alpha
a5ff3a4
@j-atkins
changed parcels logging api
db44324
@j-atkins
first wave of changes to the instrument logic with v4 logic, and part…
6f732d3
…icle building
@j-atkins
remove add dummy UV func, shouldn't be needed in v4 (?)
71881cc
@j-atkins
pull v4 from parcels/main
62b2b1b
@j-atkins
use AdvectionRK2
38afc56
@j-atkins
migrate fieldset ingestion protocol
573da9e
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d13a036
for more information, see https://pre-commit.ci
@j-atkins
j-atkins changed the base branch from main to update-docs-sensorsMay 20, 2026 15:02
Base automatically changed from update-docs-sensors to mainMay 21, 2026 09:08
@j-atkinsj-atkins mentioned this pull request May 22, 2026
Closed
@j-atkins
j-atkins marked this pull request as ready for review August 6, 2026 11:39
@j-atkins

j-atkins commented Aug 6, 2026•
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cc @erikvansebille

This PR is now ready for review. I need to update the docs (including the post-processing tutorials to handle the new parquet data), and I will do in a separate PR, but there's enough here to go through in the meantime. Most of it has already been reviewed in previous PRs.

@j-atkinsj-atkins mentioned this pull request Aug 11, 2026
Merged
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.csv output Update numpy dependency Add support for Python 3.13/3.14 Integrate Parcels v4 into VirtualShip Refactor underway instruments

2 participants

@j-atkins@erikvansebille
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
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})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Migrate to Parcels v4 - #342
Open
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Open
Migrate to Parcels v4#342
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Conversation
@j-atkins
@j-atkinsj-atkins
commented
May 20, 2026•

edited

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This PR migrates to using Parcels v4 for VirtualShip.
  •  Update instrument kernels
  •  Update fieldset ingestion workflows
  •  Update to Parquet output
  •  Implement new fieldset/performance handling strategy, i.e. new v4 docs
  •  Implement Refactor underway instruments #231
  •  Check expedition / workflow

    •  including underway instruments
    • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
  •  Implement initial timestep sampling (i.e. Parcels #2622)
  •  Update to work with local data / --from-data
  •  Update tests
  •  Add new tests for v4 specific logic(?)
  •  Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]

    •  Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
  • ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?
Closes#239, closes#232, closes#231, closes#323, closes#238
j-atkinsand others
added 17 commits
May 20, 2026 11:25
@j-atkins
add info on sensor configuration
edbda0b
@j-atkins
add list of available sensors to documentation
cd5b523
@j-atkins
remove redundant TODO
4668e54
@j-atkins
improve phrasing
ae2d528
@j-atkins
add details on sensor configurations to quickstart guide
17d5b40
@j-atkins
update sail_the_ship with sensor configuration instructions
baa982a
@j-atkins
enahnce phrasing
a8a4978
@j-atkins
add testing that docs match the code for sensor options, ensure instr…
6b3628e
…ument column entries are consistent
@j-atkins
add check that all instruments in code are addressed in sensor table
e23087b
@j-atkins
update environments to pull parcels v4 alpha
a5ff3a4
@j-atkins
changed parcels logging api
db44324
@j-atkins
first wave of changes to the instrument logic with v4 logic, and part…
6f732d3
…icle building
@j-atkins
remove add dummy UV func, shouldn't be needed in v4 (?)
71881cc
@j-atkins
pull v4 from parcels/main
62b2b1b
@j-atkins
use AdvectionRK2
38afc56
@j-atkins
migrate fieldset ingestion protocol
573da9e
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d13a036
for more information, see https://pre-commit.ci
@j-atkins
j-atkins
changed the base branch from
main
to
update-docs-sensorsMay 20, 2026 15:02

Base automatically changed from
update-docs-sensors to
mainMay 21, 2026 09:08
@j-atkinsj-atkins
mentioned this pull request
May 22, 2026
 Closed

@j-atkins
j-atkins
marked this pull request as ready for review
August 6, 2026 11:39
@j-atkins
j-atkins
commented
Aug 6, 2026•

edited

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CollaboratorAuthor
cc @erikvansebille
This PR is now ready for review. I need to update the docs (including the post-processing tutorials to handle the new parquet data), and I will do in a separate PR, but there's enough here to go through in the meantime. Most of it has already been reviewed in previous PRs.
@j-atkinsj-atkins
mentioned this pull request
Aug 11, 2026
 Merged

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@erikvansebilleerikvansebilleAwaiting requested review from erikvansebille
@VeckoTheGeckoVeckoTheGeckoAwaiting requested review from VeckoTheGecko

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Successfully merging this pull request may close these issues.

.csv output

Update numpy dependency

Add support for Python 3.13/3.14

Integrate Parcels v4 into VirtualShip

Refactor underway instruments


2 participants

@j-atkins@erikvansebille

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Migrate to Parcels v4 - #342
Open
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Open
Migrate to Parcels v4#342
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Conversation
@j-atkins
@j-atkinsj-atkins
commented
May 20, 2026•

edited

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Collaborator
This PR migrates to using Parcels v4 for VirtualShip.
  •  Update instrument kernels
  •  Update fieldset ingestion workflows
  •  Update to Parquet output
  •  Implement new fieldset/performance handling strategy, i.e. new v4 docs
  •  Implement Refactor underway instruments #231
  •  Check expedition / workflow

    •  including underway instruments
    • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
  •  Implement initial timestep sampling (i.e. Parcels #2622)
  •  Update to work with local data / --from-data
  •  Update tests
  •  Add new tests for v4 specific logic(?)
  •  Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]

    •  Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
  • ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?
Closes#239, closes#232, closes#231, closes#323, closes#238
j-atkinsand others
added 17 commits
May 20, 2026 11:25
@j-atkins
add info on sensor configuration
edbda0b
@j-atkins
add list of available sensors to documentation
cd5b523
@j-atkins
remove redundant TODO
4668e54
@j-atkins
improve phrasing
ae2d528
@j-atkins
add details on sensor configurations to quickstart guide
17d5b40
@j-atkins
update sail_the_ship with sensor configuration instructions
baa982a
@j-atkins
enahnce phrasing
a8a4978
@j-atkins
add testing that docs match the code for sensor options, ensure instr…
6b3628e
…ument column entries are consistent
@j-atkins
add check that all instruments in code are addressed in sensor table
e23087b
@j-atkins
update environments to pull parcels v4 alpha
a5ff3a4
@j-atkins
changed parcels logging api
db44324
@j-atkins
first wave of changes to the instrument logic with v4 logic, and part…
6f732d3
…icle building
@j-atkins
remove add dummy UV func, shouldn't be needed in v4 (?)
71881cc
@j-atkins
pull v4 from parcels/main
62b2b1b
@j-atkins
use AdvectionRK2
38afc56
@j-atkins
migrate fieldset ingestion protocol
573da9e
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d13a036
for more information, see https://pre-commit.ci
@j-atkins
j-atkins
changed the base branch from
main
to
update-docs-sensorsMay 20, 2026 15:02

Base automatically changed from
update-docs-sensors to
mainMay 21, 2026 09:08
@j-atkinsj-atkins
mentioned this pull request
May 22, 2026
 Closed

@j-atkins
j-atkins
marked this pull request as ready for review
August 6, 2026 11:39
@j-atkins
j-atkins
commented
Aug 6, 2026•

edited

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CollaboratorAuthor
cc @erikvansebille
This PR is now ready for review. I need to update the docs (including the post-processing tutorials to handle the new parquet data), and I will do in a separate PR, but there's enough here to go through in the meantime. Most of it has already been reviewed in previous PRs.
@j-atkinsj-atkins
mentioned this pull request
Aug 11, 2026
 Merged

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@erikvansebilleerikvansebilleAwaiting requested review from erikvansebille
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Successfully merging this pull request may close these issues.

.csv output

Update numpy dependency

Add support for Python 3.13/3.14

Integrate Parcels v4 into VirtualShip

Refactor underway instruments


2 participants

@j-atkins@erikvansebille

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Migrate to Parcels v4 - #342
Open
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Open
Migrate to Parcels v4#342
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Conversation
@j-atkins
@j-atkinsj-atkins
commented
May 20, 2026•

edited

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Collaborator
This PR migrates to using Parcels v4 for VirtualShip.
  •  Update instrument kernels
  •  Update fieldset ingestion workflows
  •  Update to Parquet output
  •  Implement new fieldset/performance handling strategy, i.e. new v4 docs
  •  Implement Refactor underway instruments #231
  •  Check expedition / workflow

    •  including underway instruments
    • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
  •  Implement initial timestep sampling (i.e. Parcels #2622)
  •  Update to work with local data / --from-data
  •  Update tests
  •  Add new tests for v4 specific logic(?)
  •  Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]

    •  Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
  • ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?
Closes#239, closes#232, closes#231, closes#323, closes#238
j-atkinsand others
added 17 commits
May 20, 2026 11:25
@j-atkins
add info on sensor configuration
edbda0b
@j-atkins
add list of available sensors to documentation
cd5b523
@j-atkins
remove redundant TODO
4668e54
@j-atkins
improve phrasing
ae2d528
@j-atkins
add details on sensor configurations to quickstart guide
17d5b40
@j-atkins
update sail_the_ship with sensor configuration instructions
baa982a
@j-atkins
enahnce phrasing
a8a4978
@j-atkins
add testing that docs match the code for sensor options, ensure instr…
6b3628e
…ument column entries are consistent
@j-atkins
add check that all instruments in code are addressed in sensor table
e23087b
@j-atkins
update environments to pull parcels v4 alpha
a5ff3a4
@j-atkins
changed parcels logging api
db44324
@j-atkins
first wave of changes to the instrument logic with v4 logic, and part…
6f732d3
…icle building
@j-atkins
remove add dummy UV func, shouldn't be needed in v4 (?)
71881cc
@j-atkins
pull v4 from parcels/main
62b2b1b
@j-atkins
use AdvectionRK2
38afc56
@j-atkins
migrate fieldset ingestion protocol
573da9e
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d13a036
for more information, see https://pre-commit.ci
@j-atkins
j-atkins
changed the base branch from
main
to
update-docs-sensorsMay 20, 2026 15:02

Base automatically changed from
update-docs-sensors to
mainMay 21, 2026 09:08
@j-atkinsj-atkins
mentioned this pull request
May 22, 2026
 Closed

@j-atkins
j-atkins
marked this pull request as ready for review
August 6, 2026 11:39
@j-atkins
j-atkins
commented
Aug 6, 2026•

edited

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CollaboratorAuthor
cc @erikvansebille
This PR is now ready for review. I need to update the docs (including the post-processing tutorials to handle the new parquet data), and I will do in a separate PR, but there's enough here to go through in the meantime. Most of it has already been reviewed in previous PRs.
@j-atkinsj-atkins
mentioned this pull request
Aug 11, 2026
 Merged

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Reviewers

@erikvansebilleerikvansebilleAwaiting requested review from erikvansebille
@VeckoTheGeckoVeckoTheGeckoAwaiting requested review from VeckoTheGecko

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Development

Successfully merging this pull request may close these issues.

.csv output

Update numpy dependency

Add support for Python 3.13/3.14

Integrate Parcels v4 into VirtualShip

Refactor underway instruments


2 participants

@j-atkins@erikvansebille

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Migrate to Parcels v4 - #342
Open
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Open
Migrate to Parcels v4#342
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Conversation
@j-atkins
@j-atkinsj-atkins
commented
May 20, 2026•

edited

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Collaborator
This PR migrates to using Parcels v4 for VirtualShip.
  •  Update instrument kernels
  •  Update fieldset ingestion workflows
  •  Update to Parquet output
  •  Implement new fieldset/performance handling strategy, i.e. new v4 docs
  •  Implement Refactor underway instruments #231
  •  Check expedition / workflow

    •  including underway instruments
    • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
  •  Implement initial timestep sampling (i.e. Parcels #2622)
  •  Update to work with local data / --from-data
  •  Update tests
  •  Add new tests for v4 specific logic(?)
  •  Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]

    •  Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
  • ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?
Closes#239, closes#232, closes#231, closes#323, closes#238
j-atkinsand others
added 17 commits
May 20, 2026 11:25
@j-atkins
add info on sensor configuration
edbda0b
@j-atkins
add list of available sensors to documentation
cd5b523
@j-atkins
remove redundant TODO
4668e54
@j-atkins
improve phrasing
ae2d528
@j-atkins
add details on sensor configurations to quickstart guide
17d5b40
@j-atkins
update sail_the_ship with sensor configuration instructions
baa982a
@j-atkins
enahnce phrasing
a8a4978
@j-atkins
add testing that docs match the code for sensor options, ensure instr…
6b3628e
…ument column entries are consistent
@j-atkins
add check that all instruments in code are addressed in sensor table
e23087b
@j-atkins
update environments to pull parcels v4 alpha
a5ff3a4
@j-atkins
changed parcels logging api
db44324
@j-atkins
first wave of changes to the instrument logic with v4 logic, and part…
6f732d3
…icle building
@j-atkins
remove add dummy UV func, shouldn't be needed in v4 (?)
71881cc
@j-atkins
pull v4 from parcels/main
62b2b1b
@j-atkins
use AdvectionRK2
38afc56
@j-atkins
migrate fieldset ingestion protocol
573da9e
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d13a036
for more information, see https://pre-commit.ci
@j-atkins
j-atkins
changed the base branch from
main
to
update-docs-sensorsMay 20, 2026 15:02

Base automatically changed from
update-docs-sensors to
mainMay 21, 2026 09:08
@j-atkinsj-atkins
mentioned this pull request
May 22, 2026
 Closed

@j-atkins
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marked this pull request as ready for review
August 6, 2026 11:39
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cc @erikvansebille
This PR is now ready for review. I need to update the docs (including the post-processing tutorials to handle the new parquet data), and I will do in a separate PR, but there's enough here to go through in the meantime. Most of it has already been reviewed in previous PRs.
@j-atkinsj-atkins
mentioned this pull request
Aug 11, 2026
 Merged

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.csv output

Update numpy dependency

Add support for Python 3.13/3.14

Integrate Parcels v4 into VirtualShip

Refactor underway instruments


2 participants

@j-atkins@erikvansebille

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Migrate to Parcels v4 - #342
Open
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Open
Migrate to Parcels v4#342
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
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@j-atkins
@j-atkinsj-atkins
commented
May 20, 2026•

edited

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Collaborator
This PR migrates to using Parcels v4 for VirtualShip.
  •  Update instrument kernels
  •  Update fieldset ingestion workflows
  •  Update to Parquet output
  •  Implement new fieldset/performance handling strategy, i.e. new v4 docs
  •  Implement Refactor underway instruments #231
  •  Check expedition / workflow

    •  including underway instruments
    • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
  •  Implement initial timestep sampling (i.e. Parcels #2622)
  •  Update to work with local data / --from-data
  •  Update tests
  •  Add new tests for v4 specific logic(?)
  •  Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]

    •  Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
  • ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?
Closes#239, closes#232, closes#231, closes#323, closes#238
j-atkinsand others
added 17 commits
May 20, 2026 11:25
@j-atkins
add info on sensor configuration
edbda0b
@j-atkins
add list of available sensors to documentation
cd5b523
@j-atkins
remove redundant TODO
4668e54
@j-atkins
improve phrasing
ae2d528
@j-atkins
add details on sensor configurations to quickstart guide
17d5b40
@j-atkins
update sail_the_ship with sensor configuration instructions
baa982a
@j-atkins
enahnce phrasing
a8a4978
@j-atkins
add testing that docs match the code for sensor options, ensure instr…
6b3628e
…ument column entries are consistent
@j-atkins
add check that all instruments in code are addressed in sensor table
e23087b
@j-atkins
update environments to pull parcels v4 alpha
a5ff3a4
@j-atkins
changed parcels logging api
db44324
@j-atkins
first wave of changes to the instrument logic with v4 logic, and part…
6f732d3
…icle building
@j-atkins
remove add dummy UV func, shouldn't be needed in v4 (?)
71881cc
@j-atkins
pull v4 from parcels/main
62b2b1b
@j-atkins
use AdvectionRK2
38afc56
@j-atkins
migrate fieldset ingestion protocol
573da9e
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d13a036
for more information, see https://pre-commit.ci
@j-atkins
j-atkins
changed the base branch from
main
to
update-docs-sensorsMay 20, 2026 15:02

Base automatically changed from
update-docs-sensors to
mainMay 21, 2026 09:08
@j-atkinsj-atkins
mentioned this pull request
May 22, 2026
 Closed

@j-atkins
j-atkins
marked this pull request as ready for review
August 6, 2026 11:39
@j-atkins
j-atkins
commented
Aug 6, 2026•

edited

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CollaboratorAuthor
cc @erikvansebille
This PR is now ready for review. I need to update the docs (including the post-processing tutorials to handle the new parquet data), and I will do in a separate PR, but there's enough here to go through in the meantime. Most of it has already been reviewed in previous PRs.
@j-atkinsj-atkins
mentioned this pull request
Aug 11, 2026
 Merged

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@erikvansebilleerikvansebilleAwaiting requested review from erikvansebille
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Successfully merging this pull request may close these issues.

.csv output

Update numpy dependency

Add support for Python 3.13/3.14

Integrate Parcels v4 into VirtualShip

Refactor underway instruments


2 participants

@j-atkins@erikvansebille

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Migrate to Parcels v4 - #342
Open
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Open
Migrate to Parcels v4#342
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Conversation
@j-atkins
@j-atkinsj-atkins
commented
May 20, 2026•

edited

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Collaborator
This PR migrates to using Parcels v4 for VirtualShip.
  •  Update instrument kernels
  •  Update fieldset ingestion workflows
  •  Update to Parquet output
  •  Implement new fieldset/performance handling strategy, i.e. new v4 docs
  •  Implement Refactor underway instruments #231
  •  Check expedition / workflow

    •  including underway instruments
    • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
  •  Implement initial timestep sampling (i.e. Parcels #2622)
  •  Update to work with local data / --from-data
  •  Update tests
  •  Add new tests for v4 specific logic(?)
  •  Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]

    •  Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
  • ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?
Closes#239, closes#232, closes#231, closes#323, closes#238
j-atkinsand others
added 17 commits
May 20, 2026 11:25
@j-atkins
add info on sensor configuration
edbda0b
@j-atkins
add list of available sensors to documentation
cd5b523
@j-atkins
remove redundant TODO
4668e54
@j-atkins
improve phrasing
ae2d528
@j-atkins
add details on sensor configurations to quickstart guide
17d5b40
@j-atkins
update sail_the_ship with sensor configuration instructions
baa982a
@j-atkins
enahnce phrasing
a8a4978
@j-atkins
add testing that docs match the code for sensor options, ensure instr…
6b3628e
…ument column entries are consistent
@j-atkins
add check that all instruments in code are addressed in sensor table
e23087b
@j-atkins
update environments to pull parcels v4 alpha
a5ff3a4
@j-atkins
changed parcels logging api
db44324
@j-atkins
first wave of changes to the instrument logic with v4 logic, and part…
6f732d3
…icle building
@j-atkins
remove add dummy UV func, shouldn't be needed in v4 (?)
71881cc
@j-atkins
pull v4 from parcels/main
62b2b1b
@j-atkins
use AdvectionRK2
38afc56
@j-atkins
migrate fieldset ingestion protocol
573da9e
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d13a036
for more information, see https://pre-commit.ci
@j-atkins
j-atkins
changed the base branch from
main
to
update-docs-sensorsMay 20, 2026 15:02

Base automatically changed from
update-docs-sensors to
mainMay 21, 2026 09:08
@j-atkinsj-atkins
mentioned this pull request
May 22, 2026
 Closed

@j-atkins
j-atkins
marked this pull request as ready for review
August 6, 2026 11:39
@j-atkins
j-atkins
commented
Aug 6, 2026•

edited

Loading

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CollaboratorAuthor
cc @erikvansebille
This PR is now ready for review. I need to update the docs (including the post-processing tutorials to handle the new parquet data), and I will do in a separate PR, but there's enough here to go through in the meantime. Most of it has already been reviewed in previous PRs.
@j-atkinsj-atkins
mentioned this pull request
Aug 11, 2026
 Merged

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Reviewers

@erikvansebilleerikvansebilleAwaiting requested review from erikvansebille
@VeckoTheGeckoVeckoTheGeckoAwaiting requested review from VeckoTheGecko

At least 1 approving review is required to merge this pull request.


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Development

Successfully merging this pull request may close these issues.

.csv output

Update numpy dependency

Add support for Python 3.13/3.14

Integrate Parcels v4 into VirtualShip

Refactor underway instruments


2 participants

@j-atkins@erikvansebille

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Migrate to Parcels v4 - #342
Open
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Open
Migrate to Parcels v4#342
j-atkins wants to merge 96 commits into
mainfrom 
migrate-v4
Conversation
@j-atkins
@j-atkinsj-atkins
commented
May 20, 2026•

edited

Loading

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Collaborator
This PR migrates to using Parcels v4 for VirtualShip.
  •  Update instrument kernels
  •  Update fieldset ingestion workflows
  •  Update to Parquet output
  •  Implement new fieldset/performance handling strategy, i.e. new v4 docs
  •  Implement Refactor underway instruments #231
  •  Check expedition / workflow

    •  including underway instruments
    • Argo float bug [in kernel(s)?], immediately goes out of bounds after first timestep... likely depth convention related
  •  Implement initial timestep sampling (i.e. Parcels #2622)
  •  Update to work with local data / --from-data
  •  Update tests
  •  Add new tests for v4 specific logic(?)
  •  Update docs / tutorials (e.g. notebooks using .zarr output) [new PR]

    •  Plus new requirements for local data ingestion: depth dim has positive: down or positive: up
  • ARGO_FLOATS: Enhance performance + no need to update cycle_age during ascent?
Closes#239, closes#232, closes#231, closes#323, closes#238
j-atkinsand others
added 17 commits
May 20, 2026 11:25
@j-atkins
add info on sensor configuration
edbda0b
@j-atkins
add list of available sensors to documentation
cd5b523
@j-atkins
remove redundant TODO
4668e54
@j-atkins
improve phrasing
ae2d528
@j-atkins
add details on sensor configurations to quickstart guide
17d5b40
@j-atkins
update sail_the_ship with sensor configuration instructions
baa982a
@j-atkins
enahnce phrasing
a8a4978
@j-atkins
add testing that docs match the code for sensor options, ensure instr…
6b3628e
…ument column entries are consistent
@j-atkins
add check that all instruments in code are addressed in sensor table
e23087b
@j-atkins
update environments to pull parcels v4 alpha
a5ff3a4
@j-atkins
changed parcels logging api
db44324
@j-atkins
first wave of changes to the instrument logic with v4 logic, and part…
6f732d3
…icle building
@j-atkins
remove add dummy UV func, shouldn't be needed in v4 (?)
71881cc
@j-atkins
pull v4 from parcels/main
62b2b1b
@j-atkins
use AdvectionRK2
38afc56
@j-atkins
migrate fieldset ingestion protocol
573da9e
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d13a036
for more information, see https://pre-commit.ci
@j-atkins
j-atkins
changed the base branch from
main
to
update-docs-sensorsMay 20, 2026 15:02

Base automatically changed from
update-docs-sensors to
mainMay 21, 2026 09:08
@j-atkinsj-atkins
mentioned this pull request
May 22, 2026
 Closed

@j-atkins
j-atkins
marked this pull request as ready for review
August 6, 2026 11:39
@j-atkins
j-atkins
commented
Aug 6, 2026•

edited

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CollaboratorAuthor
cc @erikvansebille
This PR is now ready for review. I need to update the docs (including the post-processing tutorials to handle the new parquet data), and I will do in a separate PR, but there's enough here to go through in the meantime. Most of it has already been reviewed in previous PRs.
@j-atkinsj-atkins
mentioned this pull request
Aug 11, 2026
 Merged

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Reviewers

@erikvansebilleerikvansebilleAwaiting requested review from erikvansebille
@VeckoTheGeckoVeckoTheGeckoAwaiting requested review from VeckoTheGecko

At least 1 approving review is required to merge this pull request.


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Development

Successfully merging this pull request may close these issues.

.csv output

Update numpy dependency

Add support for Python 3.13/3.14

Integrate Parcels v4 into VirtualShip

Refactor underway instruments


2 participants

@j-atkins@erikvansebille