Update link to website - #215

Merged
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom
VeckoTheGecko:update-link
Oct 8, 2025
Merged

Update link to website#215
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom
VeckoTheGecko:update-link

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@VeckoTheGecko

@VeckoTheGeckoVeckoTheGecko commented Oct 7, 2025

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@VeckoTheGecko
VeckoTheGecko merged commit e4af072 into Parcels-code:mainOct 8, 2025
10 of 11 checks passed
j-atkins pushed a commit that referenced this pull request Oct 21, 2025
@VeckoTheGecko@j-atkins
Update link to website (#215)
2240b89
j-atkins added a commit that referenced this pull request Nov 21, 2025
@j-atkins@VeckoTheGecko
@pre-commit-ci@erikvansebille
v0.3 dev (#226)
3bc4324
Introduces substantial refactoring, new features, and documentation updates to VirtualShip. Overall, the changes aim to unify configuration, centralise instrument logic and overhaul data ingestion.
-----
* Unify config files to expedition.yaml (#217)
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)
* first refactoring step, parent instrument classes
* ignore refactoring notes in gitignore
* add note to remove upon completing v1 dev
* scratch inputdataset objects integration to _fetch
* add call to download_data()
* Add new instrument classes and update InputDataset to include depth parameters
* Refactor instrument handling in _fetch and update imports for consistency
* Refactor instrument classes and re-add (temporary) simulation functions across multiple files
* improve/clarify comments and notes
* Refactor ArgoFloat and XBT classes to include depth parameters and remove outdated comments
* avoid circular import issues
* make tests for InputDataset base class
* refactor instrument handling in _fetch.py and update expedition model to include get_instruments method
* refactor instrument error handling in Expedition model and remove Schedule and ShipConfig classes
* add is_underway property to InstrumentType and filter instruments in plan UI
* enhance CLI output for fetching
* general fixes and new error class
* refactor test cases to use Expedition object
* move instruments base classes out of models/ dir
* update base class imports
* make get_instruments_registry more robust with testing
* update mock reanalysis period and refactor tests to use expedition fixture
* refactor: reorganize instrument classes and update imports for clarity
* implement instrument registration and input dataset retrieval
* refactor: reorganize imports in instrument test files for consistency
* further refactoring: instrument classes to use a unified InputDataset and Instrument structure
* evaporate simulate_measurements.py; centralise run logic
* draft up check land using bathymetry
* small bug fixes
* patch copernicus product id search logic to new instrument classes, plus more debugging; verbose INFO is outstanding
* adding U and V to instruments where missing
* enhanced error messaging for XBT in too shallow regions
* bug fixes
* version U and V downloaded
* dummy U and V
* Neaten up logging output
* small bug fixes
* tidy up
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Refactor type hints and improve test coverage for instruments and utils
* Remove TODO comments and tidy up imports in test files
* Refactor bathymetry error handling, update verification methods and remove unused function
* move product id selection logic to utils
* update
* first draft direct ingestion via copernicusmarine (CTD only)
* refactor bathymetry data handling and add (temporary) timing for performance evaluation
* update instrument constructors for Copernicus Marine ingestion
* move expedition/do_expedition.py to cli/_run.py, rename Instrument.run() to Instrument.execute()
* move checkpoint class to models, move expedition_cost() to utils.py
* update imports for expedition_cost
* working with drifters (bodge), CTD_BGC not yet working
* remove fetch and all associated logic
* update docstrings/--help info
* add buffers to drifters and argos, plus depth limits for drifters
* remove _creds.py
* CTD_BGC fieldset bug fix
* fixing bugs associated with BGC data access
* update dependencies
* logic for handling copernicus credentials
* add support for taking local pre-downloaded data with --from-data optional flag in virtualship run
* update drifter to be at -1m depth, to avoid out of bounds at surface
* tidy up
* bug fixes for unnecessary copernicusmarine call when using pre-downloaded data
* remove redundant tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update tests (not yet instrument subclasses)
* update instrument tests
* test is on land tests in schedule.verify()
* Run pre-commit
* update pre-download ingestion methods to take files split by time
* fix bug
* fix bug in ingesting bgc data from disk
* tidy up
* add test for data directory structure compliance
* update docs
* edits to docs
* add more checks to docs compliance testing
* TODO in readme
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update docs/user-guide/documentation/pre_download_data.md
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Apply suggestions from code review
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Set t_min to first day of month for monthly resolution
Adjust t_min to the first day of the month based on schedule start date.
* remove redundant parameters from instrument classes
* change variable name
* make _find_files_in_timerange standalone from Instrument base class
* Update error docstring
* update plan UI logic to update space-time region dynamically
* fix xbt bug
* add warnings to ADCP max depth config if exceeds authentic limits
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* error messaging for case where measurements cause schedule to be missed
* revert to using ScheduleProblem class
* add more informative messaging on ScheduleProblem
* change test to mock using data from disk to avoid copernicus calls
* remove accidental breakpoint
---------
Co-authored-by: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
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@j-atkinsj-atkinsj-atkins approved these changes

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@VeckoTheGecko@j-atkins
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Update link to website - #215
Merged
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Oct 8, 2025
Merged
Update link to website#215
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Conversation
@VeckoTheGecko
@VeckoTheGeckoVeckoTheGecko
commented
Oct 7, 2025

Copy link


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  • Closes none
@VeckoTheGecko
VeckoTheGecko
merged commit e4af072
into
Parcels-code:mainOct 8, 2025

10 of 11 checks passed

j-atkins pushed a commit
that referenced
this pull request
Oct 21, 2025
@VeckoTheGecko@j-atkins
Update link to website (#215)
2240b89
j-atkins added a commit
that referenced
this pull request
Nov 21, 2025
@j-atkins@VeckoTheGecko
@pre-commit-ci@erikvansebille
v0.3 dev (#226)
3bc4324
Introduces substantial refactoring, new features, and documentation updates to VirtualShip. Overall, the changes aim to unify configuration, centralise instrument logic and overhaul data ingestion.
-----
* Unify config files to expedition.yaml (#217)
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)
* first refactoring step, parent instrument classes
* ignore refactoring notes in gitignore
* add note to remove upon completing v1 dev
* scratch inputdataset objects integration to _fetch
* add call to download_data()
* Add new instrument classes and update InputDataset to include depth parameters
* Refactor instrument handling in _fetch and update imports for consistency
* Refactor instrument classes and re-add (temporary) simulation functions across multiple files
* improve/clarify comments and notes
* Refactor ArgoFloat and XBT classes to include depth parameters and remove outdated comments
* avoid circular import issues
* make tests for InputDataset base class
* refactor instrument handling in _fetch.py and update expedition model to include get_instruments method
* refactor instrument error handling in Expedition model and remove Schedule and ShipConfig classes
* add is_underway property to InstrumentType and filter instruments in plan UI
* enhance CLI output for fetching
* general fixes and new error class
* refactor test cases to use Expedition object
* move instruments base classes out of models/ dir
* update base class imports
* make get_instruments_registry more robust with testing
* update mock reanalysis period and refactor tests to use expedition fixture
* refactor: reorganize instrument classes and update imports for clarity
* implement instrument registration and input dataset retrieval
* refactor: reorganize imports in instrument test files for consistency
* further refactoring: instrument classes to use a unified InputDataset and Instrument structure
* evaporate simulate_measurements.py; centralise run logic
* draft up check land using bathymetry
* small bug fixes
* patch copernicus product id search logic to new instrument classes, plus more debugging; verbose INFO is outstanding
* adding U and V to instruments where missing
* enhanced error messaging for XBT in too shallow regions
* bug fixes
* version U and V downloaded
* dummy U and V
* Neaten up logging output
* small bug fixes
* tidy up
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Refactor type hints and improve test coverage for instruments and utils
* Remove TODO comments and tidy up imports in test files
* Refactor bathymetry error handling, update verification methods and remove unused function
* move product id selection logic to utils
* update
* first draft direct ingestion via copernicusmarine (CTD only)
* refactor bathymetry data handling and add (temporary) timing for performance evaluation
* update instrument constructors for Copernicus Marine ingestion
* move expedition/do_expedition.py to cli/_run.py, rename Instrument.run() to Instrument.execute()
* move checkpoint class to models, move expedition_cost() to utils.py
* update imports for expedition_cost
* working with drifters (bodge), CTD_BGC not yet working
* remove fetch and all associated logic
* update docstrings/--help info
* add buffers to drifters and argos, plus depth limits for drifters
* remove _creds.py
* CTD_BGC fieldset bug fix
* fixing bugs associated with BGC data access
* update dependencies
* logic for handling copernicus credentials
* add support for taking local pre-downloaded data with --from-data optional flag in virtualship run
* update drifter to be at -1m depth, to avoid out of bounds at surface
* tidy up
* bug fixes for unnecessary copernicusmarine call when using pre-downloaded data
* remove redundant tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update tests (not yet instrument subclasses)
* update instrument tests
* test is on land tests in schedule.verify()
* Run pre-commit
* update pre-download ingestion methods to take files split by time
* fix bug
* fix bug in ingesting bgc data from disk
* tidy up
* add test for data directory structure compliance
* update docs
* edits to docs
* add more checks to docs compliance testing
* TODO in readme
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update docs/user-guide/documentation/pre_download_data.md
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Apply suggestions from code review
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Set t_min to first day of month for monthly resolution
Adjust t_min to the first day of the month based on schedule start date.
* remove redundant parameters from instrument classes
* change variable name
* make _find_files_in_timerange standalone from Instrument base class
* Update error docstring
* update plan UI logic to update space-time region dynamically
* fix xbt bug
* add warnings to ADCP max depth config if exceeds authentic limits
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* error messaging for case where measurements cause schedule to be missed
* revert to using ScheduleProblem class
* add more informative messaging on ScheduleProblem
* change test to mock using data from disk to avoid copernicus calls
* remove accidental breakpoint
---------
Co-authored-by: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers

@j-atkinsj-atkinsj-atkins approved these changes

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Milestone


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Development

Successfully merging this pull request may close these issues.

2 participants

@VeckoTheGecko@j-atkins

, '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");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Update link to website - #215
Merged
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Oct 8, 2025
Merged
Update link to website#215
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Conversation
@VeckoTheGecko
@VeckoTheGeckoVeckoTheGecko
commented
Oct 7, 2025

Copy link


Copy Markdown

Collaborator
  • Closes none
@VeckoTheGecko
VeckoTheGecko
merged commit e4af072
into
Parcels-code:mainOct 8, 2025

10 of 11 checks passed

j-atkins pushed a commit
that referenced
this pull request
Oct 21, 2025
@VeckoTheGecko@j-atkins
Update link to website (#215)
2240b89
j-atkins added a commit
that referenced
this pull request
Nov 21, 2025
@j-atkins@VeckoTheGecko
@pre-commit-ci@erikvansebille
v0.3 dev (#226)
3bc4324
Introduces substantial refactoring, new features, and documentation updates to VirtualShip. Overall, the changes aim to unify configuration, centralise instrument logic and overhaul data ingestion.
-----
* Unify config files to expedition.yaml (#217)
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)
* first refactoring step, parent instrument classes
* ignore refactoring notes in gitignore
* add note to remove upon completing v1 dev
* scratch inputdataset objects integration to _fetch
* add call to download_data()
* Add new instrument classes and update InputDataset to include depth parameters
* Refactor instrument handling in _fetch and update imports for consistency
* Refactor instrument classes and re-add (temporary) simulation functions across multiple files
* improve/clarify comments and notes
* Refactor ArgoFloat and XBT classes to include depth parameters and remove outdated comments
* avoid circular import issues
* make tests for InputDataset base class
* refactor instrument handling in _fetch.py and update expedition model to include get_instruments method
* refactor instrument error handling in Expedition model and remove Schedule and ShipConfig classes
* add is_underway property to InstrumentType and filter instruments in plan UI
* enhance CLI output for fetching
* general fixes and new error class
* refactor test cases to use Expedition object
* move instruments base classes out of models/ dir
* update base class imports
* make get_instruments_registry more robust with testing
* update mock reanalysis period and refactor tests to use expedition fixture
* refactor: reorganize instrument classes and update imports for clarity
* implement instrument registration and input dataset retrieval
* refactor: reorganize imports in instrument test files for consistency
* further refactoring: instrument classes to use a unified InputDataset and Instrument structure
* evaporate simulate_measurements.py; centralise run logic
* draft up check land using bathymetry
* small bug fixes
* patch copernicus product id search logic to new instrument classes, plus more debugging; verbose INFO is outstanding
* adding U and V to instruments where missing
* enhanced error messaging for XBT in too shallow regions
* bug fixes
* version U and V downloaded
* dummy U and V
* Neaten up logging output
* small bug fixes
* tidy up
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Refactor type hints and improve test coverage for instruments and utils
* Remove TODO comments and tidy up imports in test files
* Refactor bathymetry error handling, update verification methods and remove unused function
* move product id selection logic to utils
* update
* first draft direct ingestion via copernicusmarine (CTD only)
* refactor bathymetry data handling and add (temporary) timing for performance evaluation
* update instrument constructors for Copernicus Marine ingestion
* move expedition/do_expedition.py to cli/_run.py, rename Instrument.run() to Instrument.execute()
* move checkpoint class to models, move expedition_cost() to utils.py
* update imports for expedition_cost
* working with drifters (bodge), CTD_BGC not yet working
* remove fetch and all associated logic
* update docstrings/--help info
* add buffers to drifters and argos, plus depth limits for drifters
* remove _creds.py
* CTD_BGC fieldset bug fix
* fixing bugs associated with BGC data access
* update dependencies
* logic for handling copernicus credentials
* add support for taking local pre-downloaded data with --from-data optional flag in virtualship run
* update drifter to be at -1m depth, to avoid out of bounds at surface
* tidy up
* bug fixes for unnecessary copernicusmarine call when using pre-downloaded data
* remove redundant tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update tests (not yet instrument subclasses)
* update instrument tests
* test is on land tests in schedule.verify()
* Run pre-commit
* update pre-download ingestion methods to take files split by time
* fix bug
* fix bug in ingesting bgc data from disk
* tidy up
* add test for data directory structure compliance
* update docs
* edits to docs
* add more checks to docs compliance testing
* TODO in readme
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update docs/user-guide/documentation/pre_download_data.md
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Apply suggestions from code review
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Set t_min to first day of month for monthly resolution
Adjust t_min to the first day of the month based on schedule start date.
* remove redundant parameters from instrument classes
* change variable name
* make _find_files_in_timerange standalone from Instrument base class
* Update error docstring
* update plan UI logic to update space-time region dynamically
* fix xbt bug
* add warnings to ADCP max depth config if exceeds authentic limits
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* error messaging for case where measurements cause schedule to be missed
* revert to using ScheduleProblem class
* add more informative messaging on ScheduleProblem
* change test to mock using data from disk to avoid copernicus calls
* remove accidental breakpoint
---------
Co-authored-by: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers

@j-atkinsj-atkinsj-atkins approved these changes

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Labels


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Development

Successfully merging this pull request may close these issues.

2 participants

@VeckoTheGecko@j-atkins

, '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
Update link to website - #215
Merged
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Oct 8, 2025
Merged
Update link to website#215
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Conversation
@VeckoTheGecko
@VeckoTheGeckoVeckoTheGecko
commented
Oct 7, 2025

Copy link


Copy Markdown

Collaborator
  • Closes none
@VeckoTheGecko
VeckoTheGecko
merged commit e4af072
into
Parcels-code:mainOct 8, 2025

10 of 11 checks passed

j-atkins pushed a commit
that referenced
this pull request
Oct 21, 2025
@VeckoTheGecko@j-atkins
Update link to website (#215)
2240b89
j-atkins added a commit
that referenced
this pull request
Nov 21, 2025
@j-atkins@VeckoTheGecko
@pre-commit-ci@erikvansebille
v0.3 dev (#226)
3bc4324
Introduces substantial refactoring, new features, and documentation updates to VirtualShip. Overall, the changes aim to unify configuration, centralise instrument logic and overhaul data ingestion.
-----
* Unify config files to expedition.yaml (#217)
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)
* first refactoring step, parent instrument classes
* ignore refactoring notes in gitignore
* add note to remove upon completing v1 dev
* scratch inputdataset objects integration to _fetch
* add call to download_data()
* Add new instrument classes and update InputDataset to include depth parameters
* Refactor instrument handling in _fetch and update imports for consistency
* Refactor instrument classes and re-add (temporary) simulation functions across multiple files
* improve/clarify comments and notes
* Refactor ArgoFloat and XBT classes to include depth parameters and remove outdated comments
* avoid circular import issues
* make tests for InputDataset base class
* refactor instrument handling in _fetch.py and update expedition model to include get_instruments method
* refactor instrument error handling in Expedition model and remove Schedule and ShipConfig classes
* add is_underway property to InstrumentType and filter instruments in plan UI
* enhance CLI output for fetching
* general fixes and new error class
* refactor test cases to use Expedition object
* move instruments base classes out of models/ dir
* update base class imports
* make get_instruments_registry more robust with testing
* update mock reanalysis period and refactor tests to use expedition fixture
* refactor: reorganize instrument classes and update imports for clarity
* implement instrument registration and input dataset retrieval
* refactor: reorganize imports in instrument test files for consistency
* further refactoring: instrument classes to use a unified InputDataset and Instrument structure
* evaporate simulate_measurements.py; centralise run logic
* draft up check land using bathymetry
* small bug fixes
* patch copernicus product id search logic to new instrument classes, plus more debugging; verbose INFO is outstanding
* adding U and V to instruments where missing
* enhanced error messaging for XBT in too shallow regions
* bug fixes
* version U and V downloaded
* dummy U and V
* Neaten up logging output
* small bug fixes
* tidy up
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Refactor type hints and improve test coverage for instruments and utils
* Remove TODO comments and tidy up imports in test files
* Refactor bathymetry error handling, update verification methods and remove unused function
* move product id selection logic to utils
* update
* first draft direct ingestion via copernicusmarine (CTD only)
* refactor bathymetry data handling and add (temporary) timing for performance evaluation
* update instrument constructors for Copernicus Marine ingestion
* move expedition/do_expedition.py to cli/_run.py, rename Instrument.run() to Instrument.execute()
* move checkpoint class to models, move expedition_cost() to utils.py
* update imports for expedition_cost
* working with drifters (bodge), CTD_BGC not yet working
* remove fetch and all associated logic
* update docstrings/--help info
* add buffers to drifters and argos, plus depth limits for drifters
* remove _creds.py
* CTD_BGC fieldset bug fix
* fixing bugs associated with BGC data access
* update dependencies
* logic for handling copernicus credentials
* add support for taking local pre-downloaded data with --from-data optional flag in virtualship run
* update drifter to be at -1m depth, to avoid out of bounds at surface
* tidy up
* bug fixes for unnecessary copernicusmarine call when using pre-downloaded data
* remove redundant tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update tests (not yet instrument subclasses)
* update instrument tests
* test is on land tests in schedule.verify()
* Run pre-commit
* update pre-download ingestion methods to take files split by time
* fix bug
* fix bug in ingesting bgc data from disk
* tidy up
* add test for data directory structure compliance
* update docs
* edits to docs
* add more checks to docs compliance testing
* TODO in readme
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update docs/user-guide/documentation/pre_download_data.md
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Apply suggestions from code review
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Set t_min to first day of month for monthly resolution
Adjust t_min to the first day of the month based on schedule start date.
* remove redundant parameters from instrument classes
* change variable name
* make _find_files_in_timerange standalone from Instrument base class
* Update error docstring
* update plan UI logic to update space-time region dynamically
* fix xbt bug
* add warnings to ADCP max depth config if exceeds authentic limits
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* error messaging for case where measurements cause schedule to be missed
* revert to using ScheduleProblem class
* add more informative messaging on ScheduleProblem
* change test to mock using data from disk to avoid copernicus calls
* remove accidental breakpoint
---------
Co-authored-by: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
Sign up for freeto join this conversation on GitHub.
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@VeckoTheGecko@j-atkins

, '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
Update link to website - #215
Merged
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Oct 8, 2025
Merged
Update link to website#215
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Conversation
@VeckoTheGecko
@VeckoTheGeckoVeckoTheGecko
commented
Oct 7, 2025

Copy link


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  • Closes none
@VeckoTheGecko
VeckoTheGecko
merged commit e4af072
into
Parcels-code:mainOct 8, 2025

10 of 11 checks passed

j-atkins pushed a commit
that referenced
this pull request
Oct 21, 2025
@VeckoTheGecko@j-atkins
Update link to website (#215)
2240b89
j-atkins added a commit
that referenced
this pull request
Nov 21, 2025
@j-atkins@VeckoTheGecko
@pre-commit-ci@erikvansebille
v0.3 dev (#226)
3bc4324
Introduces substantial refactoring, new features, and documentation updates to VirtualShip. Overall, the changes aim to unify configuration, centralise instrument logic and overhaul data ingestion.
-----
* Unify config files to expedition.yaml (#217)
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)
* first refactoring step, parent instrument classes
* ignore refactoring notes in gitignore
* add note to remove upon completing v1 dev
* scratch inputdataset objects integration to _fetch
* add call to download_data()
* Add new instrument classes and update InputDataset to include depth parameters
* Refactor instrument handling in _fetch and update imports for consistency
* Refactor instrument classes and re-add (temporary) simulation functions across multiple files
* improve/clarify comments and notes
* Refactor ArgoFloat and XBT classes to include depth parameters and remove outdated comments
* avoid circular import issues
* make tests for InputDataset base class
* refactor instrument handling in _fetch.py and update expedition model to include get_instruments method
* refactor instrument error handling in Expedition model and remove Schedule and ShipConfig classes
* add is_underway property to InstrumentType and filter instruments in plan UI
* enhance CLI output for fetching
* general fixes and new error class
* refactor test cases to use Expedition object
* move instruments base classes out of models/ dir
* update base class imports
* make get_instruments_registry more robust with testing
* update mock reanalysis period and refactor tests to use expedition fixture
* refactor: reorganize instrument classes and update imports for clarity
* implement instrument registration and input dataset retrieval
* refactor: reorganize imports in instrument test files for consistency
* further refactoring: instrument classes to use a unified InputDataset and Instrument structure
* evaporate simulate_measurements.py; centralise run logic
* draft up check land using bathymetry
* small bug fixes
* patch copernicus product id search logic to new instrument classes, plus more debugging; verbose INFO is outstanding
* adding U and V to instruments where missing
* enhanced error messaging for XBT in too shallow regions
* bug fixes
* version U and V downloaded
* dummy U and V
* Neaten up logging output
* small bug fixes
* tidy up
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Refactor type hints and improve test coverage for instruments and utils
* Remove TODO comments and tidy up imports in test files
* Refactor bathymetry error handling, update verification methods and remove unused function
* move product id selection logic to utils
* update
* first draft direct ingestion via copernicusmarine (CTD only)
* refactor bathymetry data handling and add (temporary) timing for performance evaluation
* update instrument constructors for Copernicus Marine ingestion
* move expedition/do_expedition.py to cli/_run.py, rename Instrument.run() to Instrument.execute()
* move checkpoint class to models, move expedition_cost() to utils.py
* update imports for expedition_cost
* working with drifters (bodge), CTD_BGC not yet working
* remove fetch and all associated logic
* update docstrings/--help info
* add buffers to drifters and argos, plus depth limits for drifters
* remove _creds.py
* CTD_BGC fieldset bug fix
* fixing bugs associated with BGC data access
* update dependencies
* logic for handling copernicus credentials
* add support for taking local pre-downloaded data with --from-data optional flag in virtualship run
* update drifter to be at -1m depth, to avoid out of bounds at surface
* tidy up
* bug fixes for unnecessary copernicusmarine call when using pre-downloaded data
* remove redundant tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update tests (not yet instrument subclasses)
* update instrument tests
* test is on land tests in schedule.verify()
* Run pre-commit
* update pre-download ingestion methods to take files split by time
* fix bug
* fix bug in ingesting bgc data from disk
* tidy up
* add test for data directory structure compliance
* update docs
* edits to docs
* add more checks to docs compliance testing
* TODO in readme
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update docs/user-guide/documentation/pre_download_data.md
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Apply suggestions from code review
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Set t_min to first day of month for monthly resolution
Adjust t_min to the first day of the month based on schedule start date.
* remove redundant parameters from instrument classes
* change variable name
* make _find_files_in_timerange standalone from Instrument base class
* Update error docstring
* update plan UI logic to update space-time region dynamically
* fix xbt bug
* add warnings to ADCP max depth config if exceeds authentic limits
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* error messaging for case where measurements cause schedule to be missed
* revert to using ScheduleProblem class
* add more informative messaging on ScheduleProblem
* change test to mock using data from disk to avoid copernicus calls
* remove accidental breakpoint
---------
Co-authored-by: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
Sign up for freeto join this conversation on GitHub.
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Reviewers

@j-atkinsj-atkinsj-atkins approved these changes

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Development

Successfully merging this pull request may close these issues.

2 participants

@VeckoTheGecko@j-atkins

, '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
Update link to website - #215
Merged
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Oct 8, 2025
Merged
Update link to website#215
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Conversation
@VeckoTheGecko
@VeckoTheGeckoVeckoTheGecko
commented
Oct 7, 2025

Copy link


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Collaborator
  • Closes none
@VeckoTheGecko
VeckoTheGecko
merged commit e4af072
into
Parcels-code:mainOct 8, 2025

10 of 11 checks passed

j-atkins pushed a commit
that referenced
this pull request
Oct 21, 2025
@VeckoTheGecko@j-atkins
Update link to website (#215)
2240b89
j-atkins added a commit
that referenced
this pull request
Nov 21, 2025
@j-atkins@VeckoTheGecko
@pre-commit-ci@erikvansebille
v0.3 dev (#226)
3bc4324
Introduces substantial refactoring, new features, and documentation updates to VirtualShip. Overall, the changes aim to unify configuration, centralise instrument logic and overhaul data ingestion.
-----
* Unify config files to expedition.yaml (#217)
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)
* first refactoring step, parent instrument classes
* ignore refactoring notes in gitignore
* add note to remove upon completing v1 dev
* scratch inputdataset objects integration to _fetch
* add call to download_data()
* Add new instrument classes and update InputDataset to include depth parameters
* Refactor instrument handling in _fetch and update imports for consistency
* Refactor instrument classes and re-add (temporary) simulation functions across multiple files
* improve/clarify comments and notes
* Refactor ArgoFloat and XBT classes to include depth parameters and remove outdated comments
* avoid circular import issues
* make tests for InputDataset base class
* refactor instrument handling in _fetch.py and update expedition model to include get_instruments method
* refactor instrument error handling in Expedition model and remove Schedule and ShipConfig classes
* add is_underway property to InstrumentType and filter instruments in plan UI
* enhance CLI output for fetching
* general fixes and new error class
* refactor test cases to use Expedition object
* move instruments base classes out of models/ dir
* update base class imports
* make get_instruments_registry more robust with testing
* update mock reanalysis period and refactor tests to use expedition fixture
* refactor: reorganize instrument classes and update imports for clarity
* implement instrument registration and input dataset retrieval
* refactor: reorganize imports in instrument test files for consistency
* further refactoring: instrument classes to use a unified InputDataset and Instrument structure
* evaporate simulate_measurements.py; centralise run logic
* draft up check land using bathymetry
* small bug fixes
* patch copernicus product id search logic to new instrument classes, plus more debugging; verbose INFO is outstanding
* adding U and V to instruments where missing
* enhanced error messaging for XBT in too shallow regions
* bug fixes
* version U and V downloaded
* dummy U and V
* Neaten up logging output
* small bug fixes
* tidy up
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Refactor type hints and improve test coverage for instruments and utils
* Remove TODO comments and tidy up imports in test files
* Refactor bathymetry error handling, update verification methods and remove unused function
* move product id selection logic to utils
* update
* first draft direct ingestion via copernicusmarine (CTD only)
* refactor bathymetry data handling and add (temporary) timing for performance evaluation
* update instrument constructors for Copernicus Marine ingestion
* move expedition/do_expedition.py to cli/_run.py, rename Instrument.run() to Instrument.execute()
* move checkpoint class to models, move expedition_cost() to utils.py
* update imports for expedition_cost
* working with drifters (bodge), CTD_BGC not yet working
* remove fetch and all associated logic
* update docstrings/--help info
* add buffers to drifters and argos, plus depth limits for drifters
* remove _creds.py
* CTD_BGC fieldset bug fix
* fixing bugs associated with BGC data access
* update dependencies
* logic for handling copernicus credentials
* add support for taking local pre-downloaded data with --from-data optional flag in virtualship run
* update drifter to be at -1m depth, to avoid out of bounds at surface
* tidy up
* bug fixes for unnecessary copernicusmarine call when using pre-downloaded data
* remove redundant tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update tests (not yet instrument subclasses)
* update instrument tests
* test is on land tests in schedule.verify()
* Run pre-commit
* update pre-download ingestion methods to take files split by time
* fix bug
* fix bug in ingesting bgc data from disk
* tidy up
* add test for data directory structure compliance
* update docs
* edits to docs
* add more checks to docs compliance testing
* TODO in readme
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update docs/user-guide/documentation/pre_download_data.md
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Apply suggestions from code review
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Set t_min to first day of month for monthly resolution
Adjust t_min to the first day of the month based on schedule start date.
* remove redundant parameters from instrument classes
* change variable name
* make _find_files_in_timerange standalone from Instrument base class
* Update error docstring
* update plan UI logic to update space-time region dynamically
* fix xbt bug
* add warnings to ADCP max depth config if exceeds authentic limits
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* error messaging for case where measurements cause schedule to be missed
* revert to using ScheduleProblem class
* add more informative messaging on ScheduleProblem
* change test to mock using data from disk to avoid copernicus calls
* remove accidental breakpoint
---------
Co-authored-by: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
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Reviewers

@j-atkinsj-atkinsj-atkins approved these changes

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Development

Successfully merging this pull request may close these issues.

2 participants

@VeckoTheGecko@j-atkins

, '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
Update link to website - #215
Merged
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Oct 8, 2025
Merged
Update link to website#215
VeckoTheGecko merged 1 commit into
Parcels-code:mainfrom 
VeckoTheGecko:update-link
Conversation
@VeckoTheGecko
@VeckoTheGeckoVeckoTheGecko
commented
Oct 7, 2025

Copy link


Copy Markdown

Collaborator
  • Closes none
@VeckoTheGecko
VeckoTheGecko
merged commit e4af072
into
Parcels-code:mainOct 8, 2025

10 of 11 checks passed

j-atkins pushed a commit
that referenced
this pull request
Oct 21, 2025
@VeckoTheGecko@j-atkins
Update link to website (#215)
2240b89
j-atkins added a commit
that referenced
this pull request
Nov 21, 2025
@j-atkins@VeckoTheGecko
@pre-commit-ci@erikvansebille
v0.3 dev (#226)
3bc4324
Introduces substantial refactoring, new features, and documentation updates to VirtualShip. Overall, the changes aim to unify configuration, centralise instrument logic and overhaul data ingestion.
-----
* Unify config files to expedition.yaml (#217)
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)
* first refactoring step, parent instrument classes
* ignore refactoring notes in gitignore
* add note to remove upon completing v1 dev
* scratch inputdataset objects integration to _fetch
* add call to download_data()
* Add new instrument classes and update InputDataset to include depth parameters
* Refactor instrument handling in _fetch and update imports for consistency
* Refactor instrument classes and re-add (temporary) simulation functions across multiple files
* improve/clarify comments and notes
* Refactor ArgoFloat and XBT classes to include depth parameters and remove outdated comments
* avoid circular import issues
* make tests for InputDataset base class
* refactor instrument handling in _fetch.py and update expedition model to include get_instruments method
* refactor instrument error handling in Expedition model and remove Schedule and ShipConfig classes
* add is_underway property to InstrumentType and filter instruments in plan UI
* enhance CLI output for fetching
* general fixes and new error class
* refactor test cases to use Expedition object
* move instruments base classes out of models/ dir
* update base class imports
* make get_instruments_registry more robust with testing
* update mock reanalysis period and refactor tests to use expedition fixture
* refactor: reorganize instrument classes and update imports for clarity
* implement instrument registration and input dataset retrieval
* refactor: reorganize imports in instrument test files for consistency
* further refactoring: instrument classes to use a unified InputDataset and Instrument structure
* evaporate simulate_measurements.py; centralise run logic
* draft up check land using bathymetry
* small bug fixes
* patch copernicus product id search logic to new instrument classes, plus more debugging; verbose INFO is outstanding
* adding U and V to instruments where missing
* enhanced error messaging for XBT in too shallow regions
* bug fixes
* version U and V downloaded
* dummy U and V
* Neaten up logging output
* small bug fixes
* tidy up
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Refactor type hints and improve test coverage for instruments and utils
* Remove TODO comments and tidy up imports in test files
* Refactor bathymetry error handling, update verification methods and remove unused function
* move product id selection logic to utils
* update
* first draft direct ingestion via copernicusmarine (CTD only)
* refactor bathymetry data handling and add (temporary) timing for performance evaluation
* update instrument constructors for Copernicus Marine ingestion
* move expedition/do_expedition.py to cli/_run.py, rename Instrument.run() to Instrument.execute()
* move checkpoint class to models, move expedition_cost() to utils.py
* update imports for expedition_cost
* working with drifters (bodge), CTD_BGC not yet working
* remove fetch and all associated logic
* update docstrings/--help info
* add buffers to drifters and argos, plus depth limits for drifters
* remove _creds.py
* CTD_BGC fieldset bug fix
* fixing bugs associated with BGC data access
* update dependencies
* logic for handling copernicus credentials
* add support for taking local pre-downloaded data with --from-data optional flag in virtualship run
* update drifter to be at -1m depth, to avoid out of bounds at surface
* tidy up
* bug fixes for unnecessary copernicusmarine call when using pre-downloaded data
* remove redundant tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update tests (not yet instrument subclasses)
* update instrument tests
* test is on land tests in schedule.verify()
* Run pre-commit
* update pre-download ingestion methods to take files split by time
* fix bug
* fix bug in ingesting bgc data from disk
* tidy up
* add test for data directory structure compliance
* update docs
* edits to docs
* add more checks to docs compliance testing
* TODO in readme
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update docs/user-guide/documentation/pre_download_data.md
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Apply suggestions from code review
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Set t_min to first day of month for monthly resolution
Adjust t_min to the first day of the month based on schedule start date.
* remove redundant parameters from instrument classes
* change variable name
* make _find_files_in_timerange standalone from Instrument base class
* Update error docstring
* update plan UI logic to update space-time region dynamically
* fix xbt bug
* add warnings to ADCP max depth config if exceeds authentic limits
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* error messaging for case where measurements cause schedule to be missed
* revert to using ScheduleProblem class
* add more informative messaging on ScheduleProblem
* change test to mock using data from disk to avoid copernicus calls
* remove accidental breakpoint
---------
Co-authored-by: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
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, '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); }
})();
})();

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Update link to website - #215
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VeckoTheGecko merged 1 commit into
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VeckoTheGecko:update-link
Oct 8, 2025
Merged
Update link to website#215
VeckoTheGecko merged 1 commit into
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@VeckoTheGecko@j-atkins
Update link to website (#215)
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j-atkins added a commit
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Nov 21, 2025
@j-atkins@VeckoTheGecko
@pre-commit-ci@erikvansebille
v0.3 dev (#226)
3bc4324
Introduces substantial refactoring, new features, and documentation updates to VirtualShip. Overall, the changes aim to unify configuration, centralise instrument logic and overhaul data ingestion.
-----
* Unify config files to expedition.yaml (#217)
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)
* first refactoring step, parent instrument classes
* ignore refactoring notes in gitignore
* add note to remove upon completing v1 dev
* scratch inputdataset objects integration to _fetch
* add call to download_data()
* Add new instrument classes and update InputDataset to include depth parameters
* Refactor instrument handling in _fetch and update imports for consistency
* Refactor instrument classes and re-add (temporary) simulation functions across multiple files
* improve/clarify comments and notes
* Refactor ArgoFloat and XBT classes to include depth parameters and remove outdated comments
* avoid circular import issues
* make tests for InputDataset base class
* refactor instrument handling in _fetch.py and update expedition model to include get_instruments method
* refactor instrument error handling in Expedition model and remove Schedule and ShipConfig classes
* add is_underway property to InstrumentType and filter instruments in plan UI
* enhance CLI output for fetching
* general fixes and new error class
* refactor test cases to use Expedition object
* move instruments base classes out of models/ dir
* update base class imports
* make get_instruments_registry more robust with testing
* update mock reanalysis period and refactor tests to use expedition fixture
* refactor: reorganize instrument classes and update imports for clarity
* implement instrument registration and input dataset retrieval
* refactor: reorganize imports in instrument test files for consistency
* further refactoring: instrument classes to use a unified InputDataset and Instrument structure
* evaporate simulate_measurements.py; centralise run logic
* draft up check land using bathymetry
* small bug fixes
* patch copernicus product id search logic to new instrument classes, plus more debugging; verbose INFO is outstanding
* adding U and V to instruments where missing
* enhanced error messaging for XBT in too shallow regions
* bug fixes
* version U and V downloaded
* dummy U and V
* Neaten up logging output
* small bug fixes
* tidy up
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Refactor type hints and improve test coverage for instruments and utils
* Remove TODO comments and tidy up imports in test files
* Refactor bathymetry error handling, update verification methods and remove unused function
* move product id selection logic to utils
* update
* first draft direct ingestion via copernicusmarine (CTD only)
* refactor bathymetry data handling and add (temporary) timing for performance evaluation
* update instrument constructors for Copernicus Marine ingestion
* move expedition/do_expedition.py to cli/_run.py, rename Instrument.run() to Instrument.execute()
* move checkpoint class to models, move expedition_cost() to utils.py
* update imports for expedition_cost
* working with drifters (bodge), CTD_BGC not yet working
* remove fetch and all associated logic
* update docstrings/--help info
* add buffers to drifters and argos, plus depth limits for drifters
* remove _creds.py
* CTD_BGC fieldset bug fix
* fixing bugs associated with BGC data access
* update dependencies
* logic for handling copernicus credentials
* add support for taking local pre-downloaded data with --from-data optional flag in virtualship run
* update drifter to be at -1m depth, to avoid out of bounds at surface
* tidy up
* bug fixes for unnecessary copernicusmarine call when using pre-downloaded data
* remove redundant tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update tests (not yet instrument subclasses)
* update instrument tests
* test is on land tests in schedule.verify()
* Run pre-commit
* update pre-download ingestion methods to take files split by time
* fix bug
* fix bug in ingesting bgc data from disk
* tidy up
* add test for data directory structure compliance
* update docs
* edits to docs
* add more checks to docs compliance testing
* TODO in readme
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update docs/user-guide/documentation/pre_download_data.md
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Apply suggestions from code review
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
* Set t_min to first day of month for monthly resolution
Adjust t_min to the first day of the month based on schedule start date.
* remove redundant parameters from instrument classes
* change variable name
* make _find_files_in_timerange standalone from Instrument base class
* Update error docstring
* update plan UI logic to update space-time region dynamically
* fix xbt bug
* add warnings to ADCP max depth config if exceeds authentic limits
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* error messaging for case where measurements cause schedule to be missed
* revert to using ScheduleProblem class
* add more informative messaging on ScheduleProblem
* change test to mock using data from disk to avoid copernicus calls
* remove accidental breakpoint
---------
Co-authored-by: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Erik van Sebille <erikvansebille@gmail.com>
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