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Open Sustainable Technology

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Recent Releases of OceanBioME.jl

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] 20 days 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 2 months 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] 3 months 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] 4 months 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] 5 months 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] 6 months 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] 6 months 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] 6 months 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] 7 months 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] 7 months 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] 7 months 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] 8 months 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] 9 months 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] 9 months 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] 10 months 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] about 1 year 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] about 1 year 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 1 year 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 1 year 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 1 year 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 1 year 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 1 year 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 1 year 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 1 year 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 1 year 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 1 year 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 almost 2 years ago

OceanBioME.jl - v0.3.0

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

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

OceanBioME.jl -

Emissions - Carbon Capture - Julia
Published by jagoosw almost 2 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 about 2 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 2 years ago