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Recent Releases of OceanBioME.jl

OceanBioME.jl - v0.16.10

OceanBioME v0.16.10

Diff since v0.16.9

Merged pull requests:

  • Support Oceananigans v0.105 and set v0.16.10 (#339) (@ali-ramadhan)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 21 days ago

OceanBioME.jl - v0.16.9

OceanBioME v0.16.9

Diff since v0.16.8

Merged pull requests:

  • 0.16.8 Temporary allocations in scale_for_negs! kernel on a CPU (#331) (@Mikolaj-A-Kowalski)
  • (0.16.9) Bump patch (#336) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] about 2 months ago

OceanBioME.jl - v0.16.8

OceanBioME v0.16.8

Diff since v0.16.7

Merged pull requests:

  • CompatHelper: bump compat for Oceananigans to 0.104, (keep existing compat) (#332) (@github-actions[bot])

Closed issues:

  • Profiling (#260)
  • Run Nsight on the code base (#262)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] about 2 months ago

OceanBioME.jl - v0.16.7

OceanBioME v0.16.7

Diff since v0.16.6

Merged pull requests:

  • CompatHelper: bump compat for Oceananigans to 0.103, (keep existing compat) (#327) (@github-actions[bot])

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 3 months ago

OceanBioME.jl - v0.16.6

OceanBioME v0.16.6

Diff since v0.16.5

Merged pull requests:

  • Fix light, LOBSTER, and NPZD constructors to work with Float32 (#324) (@ali-ramadhan)

Closed issues:

  • MethodError when attempting to construct a Float32 LOBSTER (#273)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 3 months ago

OceanBioME.jl - v0.16.5

OceanBioME v0.16.5

Diff since v0.16.4

Merged pull requests:

  • Improves damped newton raphson peformance (#316) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 3 months ago

OceanBioME.jl - v0.16.4

OceanBioME v0.16.4

Diff since v0.16.3

Merged pull requests:

  • Reintroduce support for Julia 1.10/1.11 (#315) (@jagoosw)
  • Fix PISCES GPU issues (#322) (@jagoosw)

Closed issues:

  • Consider other profilers to use (#264)
  • Compare GPU and CPU runs (#265)
  • Investigate CPU performance (#296)
  • PISCES model does not run on GPU (#319)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 3 months ago

OceanBioME.jl - v0.16.3

OceanBioME v0.16.3

Diff since v0.16.2

Merged pull requests:

  • CompatHelper: bump compat for Oceananigans to 0.102, (keep existing compat) (#318) (@github-actions[bot])

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 4 months ago

OceanBioME.jl - v0.16.2

OceanBioME v0.16.2

Diff since v0.16.1

Merged pull requests:

  • 0.16.2 Use Julia 1.12 for Buildkite tests + fixes (#312) (@ali-ramadhan)

Closed issues:

  • Bump compat for EnsembleKalmanProcesses for docs (#213)
  • Question: What is maximum_sinking_velocity(bgc) expected behaviour? (#229)
  • Sediment models will not work with hydrostatic RK3 time stepping (#234)

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Published by github-actions[bot] 4 months ago

OceanBioME.jl - v0.16.1

OceanBioME v0.16.1

Diff since v0.16.0

Merged pull requests:

  • CompatHelper: bump compat for Oceananigans to 0.101, (keep existing compat) (#311) (@github-actions[bot])

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 4 months ago

OceanBioME.jl - v0.16.0

OceanBioME v0.16.0

Diff since v0.15.1

Breaking changes:

  • Changes LOBSTER API to take parameters for each sub-module separatly

Merged pull requests:

  • 0.16.0 Introduces iron limitation to LOBSTER and refactors for modularity (#276) (@jagoosw)

Closed issues:

  • scale_for_negs! kernel performance (#297)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 4 months ago

OceanBioME.jl - v0.15.1

OceanBioME v0.15.1

Diff since v0.15.0

  • New method for scale_for_negs! to improve peformance #297

Merged pull requests:

  • 0.15.1 Use variadic function for scale_for_negs! kernel (#306) (@Mikolaj-A-Kowalski)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 5 months ago

OceanBioME.jl - v0.15.0

OceanBioME v0.15.0

Diff since v0.14.10

Fixes a bug in CarbonChemistry

Breaking changes

  • Changes CarbonChemistry API from return_pH = true/false to output = Val(:pHᵗ) etc.

Merged pull requests:

  • 0.15.0 Make CarbonChemistry be able to return pCO2 (#305) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 5 months ago

OceanBioME.jl - v0.14.10

OceanBioME v0.14.10

Diff since v0.14.9

Merged pull requests:

  • 0.14.10 Improve root finding (sugar kelp and carbon chem) by computing analytical derivatives and using newton raphson solver (#308) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 5 months ago

OceanBioME.jl - v0.14.9

OceanBioME v0.14.9

Diff since v0.14.8

Merged pull requests:

  • Fixes missing solubility factor in co2 air/sea flux (#303) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 5 months ago

OceanBioME.jl - v0.14.8

OceanBioME v0.14.8

Diff since v0.14.7

Merged pull requests:

  • Fix g_Earth import. Update Oceananigans compat. Set v0.14.8. (#300) (@ali-ramadhan)

Closed issues:

  • Cannot precompile because g_Earth does not exist anymore (#299)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 5 months ago

OceanBioME.jl - v0.14.7

OceanBioME v0.14.7

Diff since v0.14.6

Merged pull requests:

  • CompatHelper: bump compat for Oceananigans to 0.100, (keep existing compat) (#295) (@github-actions[bot])

Closed issues:

  • Define minimal profiling examples (#259)
  • Define how profiling results should be collected and structured (#263)
  • PISCES GPU error (#284)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 5 months ago

OceanBioME.jl - v0.14.6

OceanBioME v0.14.6

Diff since v0.14.5

Merged pull requests:

  • Remove redundant file (#240) (@jagoosw)
  • Make model_implementation.md less missleading (#252) (@jagoosw)
  • Add GPU section to model_implementation.md (#253) (@emmabeniston)
  • Update README.md (#254) (@jagoosw)
  • Add missing adapt methods for surface functions (#274) (@jagoosw)
  • Attempts to fix CI concurrency problem (#286) (@jagoosw)
  • Add CompatHelper workflow for dependency updates (#287) (@jagoosw)
  • Make it run only on one agent (#291) (@jagoosw)
  • CompatHelper: bump compat for JLD2 to 0.6, (keep existing compat) (#292) (@github-actions[bot])
  • CompatHelper: bump compat for Oceananigans to 0.99, (keep existing compat) (#293) (@github-actions[bot])

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 6 months ago

OceanBioME.jl - v0.14.5

OceanBioME v0.14.5

Diff since v0.14.4

Merged pull requests:

  • PISCES GPU fix (#285) (@johnryantaylor)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 6 months ago

OceanBioME.jl - v0.14.4

OceanBioME v0.14.4

Diff since v0.14.3

Merged pull requests:

  • Update Oceananigans.jl compat to include v0.98 (#283) (@ali-ramadhan)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 7 months ago

OceanBioME.jl - v0.14.3

OceanBioME v0.14.3

Diff since v0.14.2

Merged pull requests:

  • Fix precompilation warning and docs (#278) (@ali-ramadhan)

Closed issues:

  • Find out about previous profiling runs and results (#261)
  • Precompilation warning: could not import TimeSteppers.store_tendencies! into Sediments (#277)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 7 months ago

OceanBioME.jl - v0.14.2

OceanBioME v0.14.2

Diff since v0.14.1

Merged pull requests:

  • (0.14.2) Update Oceananigans compatability (#271) (@Mikolaj-A-Kowalski)

Closed issues:

  • README.md needs to add CairoMakie to make it self contained (#248)
  • ‘Implementing new models’ example doesn’t run on GPU (#251)
  • Update Oceananigans version (#270)
  • Buildkite not reporting status (#275)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 8 months ago

OceanBioME.jl - v0.14.1

OceanBioME v0.14.1

Diff since v0.14.0

Merged pull requests:

  • Makes carbon chemistry type stable made type stable attempt 2 (#255) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 11 months ago

OceanBioME.jl - v0.14.0

OceanBioME v0.14.0

Diff since v0.13.6

Breaking changes

Overhauls sediment

Merged pull requests:

  • (0.14.0) Overhauls sediment (#236) (@jagoosw)

Closed issues:

  • Sediment tendency calculations (#147)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] 12 months ago

OceanBioME.jl - v0.13.6

OceanBioME v0.13.6

Diff since v0.13.5

This PR fixes OceanBioME to work with internal changes in Oceananigans. Due to a bug in Julia before 1.10.8 which effects Oceananigans precompilation it also means OceanBioME will not work with pre 1.10.8 Julia anymore.

Merged pull requests:

  • Updated box models to be compatible with Oceananigans changes (#247) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] about 1 year ago

OceanBioME.jl - v0.13.5

OceanBioME v0.13.5

Diff since v0.13.4

Merged pull requests:

  • abstract out biogeochemical particles (#244) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] about 1 year ago

OceanBioME.jl - v0.13.4

OceanBioME v0.13.4

Diff since v0.13.3

Merged pull requests:

  • Support Oceananigans v0.95 and bump v0.13.4 (#233) (@ali-ramadhan)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] about 1 year ago

OceanBioME.jl - v0.13.3

OceanBioME v0.13.3

Diff since v0.13.2

Merged pull requests:

  • Automatically change parameter and return float types (#222) (@jagoosw)
  • adds field name to particle interpolation (#223) (@jagoosw)
  • Fix indentation in README example (#230) (@navidcy)

Closed issues:

  • Hard-coded Float64 values (#218)
  • solve_for_H in CarbonChemistry throws GPU exceptions (#228)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.13.2

OceanBioME v0.13.2

Diff since v0.13.1

Merged pull requests:

  • Update Project.toml to support Oceananigans 0.93 (#227) (@ali-ramadhan)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.13.1

OceanBioME v0.13.1

Diff since v0.13.0

Merged pull requests:

  • Update to use Oceananigans v0.92.1 (#225) (@ali-ramadhan)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.13.0

OceanBioME v0.13.0

Diff since v0.12.0

Breaking changes

  • Drastically changes BiogeochemicalParticles

Merged pull requests:

  • Make particles easier to use (#220) (@jagoosw)

Closed issues:

  • PISCES (#44)
  • PAR units (#83)
  • Model implementation example is broken (#200)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.12.0

OceanBioME v0.12.0

Diff since v0.11.2

Merged pull requests:

  • (0.12.0) Implements PISCES model (#178) (@jagoosw)

Closed issues:

  • Update gas transfer coefficients (#168)
  • Data assimilation example is broken!!! (#214)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.11.2

OceanBioME v0.11.2

Diff since v0.11.1

Merged pull requests:

  • Fixes setup_sinking_velocities and adds tests (#210) (@jagoosw)
  • Refactors to improve code clarity and make changing parameterisations easier (#212) (@jagoosw)
  • Fixs data assimilation example (#215) (@jagoosw)
  • Rewrites PISCES to be a discrete form model, I think over all this makes the implementation a lot more flexible (#217) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.11.1

OceanBioME v0.11.1

Diff since v0.11.0

Fixes bug in gas exchange for O2

Merged pull requests:

  • Adds Morel like MultiBandPhotosyntheticallyActiveRadiation (#195) (@jagoosw)
  • Hmw ct jsw/pisces (#204) (@ciadht)
  • Fixs some typos in carbon chemistry maths (#206) (@jagoosw)
  • Hmw ct jsw/pisces (#207) (@ciadht)
  • Pull Light from Jago's branch (#208) (@ciadht)
  • Hmw ct jsw/pisces (#209) (@ciadht)
  • Fixes gas exchange for partially soluble gasses like oxygen (#211) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.11.0

OceanBioME v0.11.0

Diff since v0.10.5

This PR overhauls the carbon chemistry model and changes the API to access the model.

Merged pull requests:

  • Refactors gas exchange carbon chemistry (+ adds some complexity) (#186) (@jagoosw)
  • Hmw ct jsw/pisces (#191) (@ciadht)
  • New Box Model merge (#192) (@ciadht)
  • Hmw ct jsw/pisces (#194) (@ciadht)
  • Hmw ct jsw/pisces (#198) (@ciadht)
  • Hmw ct jsw/pisces (#199) (@ciadht)
  • Hmw ct jsw/pisces (#201) (@ciadht)
  • Changed function names (#202) (@ciadht)
  • Hmw ct jsw/pisces (#203) (@ciadht)

Closed issues:

  • Non-zero CO2 surface flux for an ocean in equilibrium (with non-zero average wind speed) (#197)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.10.5

OceanBioME v0.10.5

Diff since v0.10.4

Merged pull requests:

  • Fixs box model SpeedyOutput + adds tests for BoxModel (#188) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.10.4

OceanBioME v0.10.4

Diff since v0.10.3

Merged pull requests:

  • update index.md (#177) (@jagoosw)
  • hmw ct jsw/pisces (#181) (@ciadht)
  • Nitrates and ammonium (#182) (@hannahmw1)
  • Adds nanophytoplankton model (#183) (@ciadht)
  • Make BoxModels speedy again (+ introduce prescribed PAR) (#185) (@jagoosw)
  • Hmw ct jsw/pisces (#187) (@ciadht)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.10.3

OceanBioME v0.10.3

Diff since v0.10.2

Merged pull requests:

  • Attempt to bump compats (#176) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 1 year ago

OceanBioME.jl - v0.10.2

OceanBioME v0.10.2

Diff since v0.10.1

Merged pull requests:

  • Added invalid_fill_value to ScaleNegativeTracers (#170) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] almost 2 years ago

OceanBioME.jl - v0.10.1

OceanBioME v0.10.1

Diff since v0.10.0

Merged pull requests:

  • Use Julia v1.10 + CairoMakie v0.11 (#166) (@navidcy)
  • Add missing dois in bib file (#167) (@navidcy)
  • Update convenience constructor (NutrientPhytoplanktonZooplanktonDetritus and LOBSTER) docstrings (#169) (@jagoosw)

Closed issues:

  • Docstrings are outdated for NPZD model (#151)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] almost 2 years ago

OceanBioME.jl - v0.10.0

OceanBioME v0.10.0

Diff since v0.9.2

Merged pull requests:

  • Overhaul of box model to use more of the Clima infrastructure + data assimilation example (#164) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] about 2 years ago

OceanBioME.jl - v0.9.2

OceanBioME v0.9.2

Diff since v0.9.1

Merged pull requests:

  • Update video in readme (#160) (@jagoosw)
  • Removed old comment from example (#161) (@jagoosw)
  • Added passing of time to sediment tendency calculation (#162) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 2 years ago

OceanBioME.jl - v0.9.1

OceanBioME v0.9.1

Diff since v0.9.0

Merged pull requests:

  • Fixes a typo: No idea how we've missed this one 🫣 (#158) (@jagoosw)
  • (0.9.1) Move testing and docs to buildkite (+ minor GPU bug fix) (#159) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 2 years ago

OceanBioME.jl - v0.9.0

OceanBioME v0.9.0

Diff since v0.8.0

Merged pull requests:

  • Fix author name typo (#154) (@navidcy)
  • (0.9.0) Fix typos in code, docs, and docstrings (#155) (@pitmonticone)
  • Fixed some show methods (#156) (@jagoosw)
  • Bump Oceananigans to 0.90 (#157) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 2 years ago

OceanBioME.jl - v0.8.0

OceanBioME v0.8.0

Diff since v0.7.0

Merged pull requests:

  • JOSS paper (#76) (@jagoosw)
  • Update Documenter + some polishing (#146) (@navidcy)
  • Add citation info in README + Docs (#148) (@navidcy)
  • (0.8.0) Drop support for prescribing T and S in kelp and gas exchange models (#149) (@jagoosw)
  • Update paper.md (#150) (@johnryantaylor)
  • Accidentally deleted Oceananigans compat (#153) (@jagoosw)

Closed issues:

  • SimpleMultiG sediment models will not run on GPU (#143)
  • Negative tracer scaling raises a very confusing error message when it fails on GPU (#144)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 2 years ago

OceanBioME.jl - v0.7.0

OceanBioME v0.7.0

Diff since v0.6.0

Merged pull requests:

  • (0.7.0) Fix all the GPU bugs that have crept in (#138) (@jagoosw)
  • Update paper.md (#141) (@johnryantaylor)
  • Improve Eady figure (#145) (@jagoosw)

Closed issues:

  • Figure 1 from JOSS paper (#140)

Emissions - Carbon Capture - Julia
Published by jagoosw over 2 years ago

OceanBioME.jl - v0.6.0

OceanBioME v0.6.0

Diff since v0.5.0

Merged pull requests:

  • (0.6.0) Refactor models for more abstraction (and bumped compats) (#134) (@jagoosw)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 2 years ago

OceanBioME.jl - v0.5.0

OceanBioME v0.5.0

Diff since v0.4.1

Closed issues:

  • Hiding output for run!(simulation) in Docs (Warnings) (#80)
  • error from twoband.jl with high vertical resolution (#135)

Merged pull requests:

  • (0.5.0) Updated sediment to work with all grids and model types (#127) (@jagoosw)
  • Update model_implementation.md (#133) (@johnryantaylor)
  • Update eady.jl (#136) (@johnryantaylor)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 2 years ago

OceanBioME.jl - v0.4.1

OceanBioME v0.4.1

Diff since v0.4.0

Closed issues:

  • Add "Contributing" section to the Readme.md (#128)
  • State of the field (#129)

Merged pull requests:

  • Better References in Docs (#125) (@navidcy)
  • Various docs improvements from JOSS review (#126) (@jagoosw)
  • Update README.md (#130) (@johnryantaylor)
  • Added model implementaion page (#131) (@jagoosw)
  • Update NPZ.md (resize the image) (#132) (@iuryt)

Emissions - Carbon Capture - Julia
Published by github-actions[bot] over 2 years ago

OceanBioME.jl - v0.4.0

Breaking changes: sediment models changed from MODEL(grid) to MODEL(; grid) (#121) and testing moved from Julia v1.8 to v1.9 (#122) and thus now OceanBioME.jl requires Julia v1.9 or later.

Also adds another sediment model (#121), docs fixes (#124), and fixes light attenuation models to work on curvilinear grids (#120).

Emissions - Carbon Capture - Julia
Published by jagoosw over 2 years ago

OceanBioME.jl - v0.3.0

Breaking change: fixing typo required renaming TwoBandPhotosyntheticallyActiveRatiation -> TwoBandPhotosyntheticallyActiveRadiation (#117)

Emissions - Carbon Capture - Julia
Published by navidcy over 2 years ago

OceanBioME.jl - v0.2.1

  • Fix bug with advection; see #113
  • More docstrings in the Docs/Library

Emissions - Carbon Capture - Julia
Published by navidcy over 2 years ago

OceanBioME.jl - v0.2.0

This release:

  • updates Oceananigans and KernelAbstractions versions to latest (which includes a lot of API changes and clean up)
  • Fixed GPU particles bug
  • Tidies up examples and docs

Emissions - Carbon Capture - Julia
Published by jagoosw over 2 years ago

OceanBioME.jl -

Emissions - Carbon Capture - Julia
Published by jagoosw almost 3 years ago

OceanBioME.jl - v0.1.1

Updated oceananigans version and other minor fixes

What's Changed

Full Changelog: https://github.com/OceanBioME/OceanBioME.jl/compare/v0.1.0...v0.1.1

Emissions - Carbon Capture - Julia
Published by jagoosw almost 3 years ago

OceanBioME.jl - v0.1.0

What's Changed

New Contributors

Full Changelog: https://github.com/OceanBioME/OceanBioME.jl/commits/v0.1.0

Emissions - Carbon Capture - Julia
Published by jagoosw about 3 years ago