Releases | Open Source Science

OceanBioME.jl - v0.14.2

OceanBioME v0.14.2

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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] 11 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 1 year 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 1 year 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years ago

OceanBioME.jl - v0.10.3

OceanBioME v0.10.3

Diff since v0.10.2

Merged pull requests: - Attempt to bump compats (#176) (@jagoosw)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 2 years 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] about 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] over 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 3 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 3 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)

Scientific Software - Peer-reviewed - Julia
Published by github-actions[bot] almost 3 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).

Scientific Software - Peer-reviewed - Julia
Published by jagoosw almost 3 years ago

OceanBioME.jl - v0.3.0

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

Scientific Software - Peer-reviewed - Julia
Published by navidcy almost 3 years ago

OceanBioME.jl - v0.2.1

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

Scientific Software - Peer-reviewed - Julia
Published by navidcy almost 3 years ago

What's Changed

Docs fixes by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/79
Post process away the docs warnings by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/82
Update Oceananigans compatability by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/84

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

Scientific Software - Peer-reviewed - Julia
Published by jagoosw about 3 years ago

OceanBioME.jl - v0.1.0

What's Changed

Refactored for better flexibility by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/1
Update to README.md by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/2
Particle updating by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/6
Restructure and added box model by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/7
Change setup to better accomodate optional fields (e.g. carbonate chemistry) by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/8
Changed name, edits to Readme and box.jl example by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/11
minor edits to readme.md by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/12
added comments to box.jl example by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/13
Update box.jl by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/14
Added CCRC logo by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/15
Edits to comments in LOBSTER.jl by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/20
Added more comments to the subpolar.jl example by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/21
Generalised air sea flux boundary, added sediment model, and restructured by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/10
update to box.jl by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/25
small edits to box.jl and kelp.jl by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/33
Modified particles to conserve tracers if sinking below zero, and fixed light by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/35
Added test simulations checking nitrate conservation +other fixes by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/37
Added N conserving option for sinking tracers, timestep utility, and modified examples by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/39
Added progress messages to box.jl by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/41
Particle optional tracers by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/46
fixed kelp to conserve nitrates (hopefully) by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/53
Various fixes by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/51
Particle production from kelp model was wrong by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/54
Docs by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/52
Fixed DIC issue by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/58
Fixed error in SLatissima and Particles setup by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/59
Modified comments in box.jl by @johnryantaylor in https://github.com/OceanBioME/OceanBioME.jl/pull/61
delete duplicate code by @syou83syou83 in https://github.com/OceanBioME/OceanBioME.jl/pull/62
New Oceananigans Interface by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/60
added docs to readme by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/65
PAR halo region filling to fix #66 by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/67
Better sediment integration by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/69
Minor example tidying by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/72
Updated Oceananigans dependencies by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/74
Updating kelp particles to simplify API and make it much easier to get it working on GPU by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/73
Fix dependencies and documentation by @jagoosw in https://github.com/OceanBioME/OceanBioME.jl/pull/77

New Contributors

@johnryantaylor made their first contribution in https://github.com/OceanBioME/OceanBioME.jl/pull/2
@syou83syou83 made their first contribution in https://github.com/OceanBioME/OceanBioME.jl/pull/62

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

Scientific Software - Peer-reviewed - Julia
Published by jagoosw about 3 years ago

Recent Releases of OceanBioME.jl

OceanBioME.jl - v0.14.2

OceanBioME v0.14.2

OceanBioME.jl - v0.14.1

OceanBioME v0.14.1

OceanBioME.jl - v0.14.0

OceanBioME v0.14.0

Breaking changes

OceanBioME.jl - v0.13.6

OceanBioME v0.13.6

OceanBioME.jl - v0.13.5

OceanBioME v0.13.5

OceanBioME.jl - v0.13.4

OceanBioME v0.13.4

OceanBioME.jl - v0.13.3

OceanBioME v0.13.3

OceanBioME.jl - v0.13.2

OceanBioME v0.13.2

OceanBioME.jl - v0.13.1

OceanBioME v0.13.1

OceanBioME.jl - v0.13.0

OceanBioME v0.13.0

Breaking changes

OceanBioME.jl - v0.12.0

OceanBioME v0.12.0

OceanBioME.jl - v0.11.2

OceanBioME v0.11.2

OceanBioME.jl - v0.11.1

OceanBioME v0.11.1

OceanBioME.jl - v0.11.0

OceanBioME v0.11.0

OceanBioME.jl - v0.10.5

OceanBioME v0.10.5

OceanBioME.jl - v0.10.4

OceanBioME v0.10.4

OceanBioME.jl - v0.10.3

OceanBioME v0.10.3

OceanBioME.jl - v0.10.2

OceanBioME v0.10.2

OceanBioME.jl - v0.10.1

OceanBioME v0.10.1

OceanBioME.jl - v0.10.0

OceanBioME v0.10.0

OceanBioME.jl - v0.9.2

OceanBioME v0.9.2

OceanBioME.jl - v0.9.1

OceanBioME v0.9.1

OceanBioME.jl - v0.9.0

OceanBioME v0.9.0

OceanBioME.jl - v0.8.0

OceanBioME v0.8.0

OceanBioME.jl - v0.7.0

OceanBioME v0.7.0

OceanBioME.jl - v0.6.0

OceanBioME v0.6.0

OceanBioME.jl - v0.5.0

OceanBioME v0.5.0

OceanBioME.jl - v0.4.1

OceanBioME v0.4.1

OceanBioME.jl - v0.4.0

OceanBioME.jl - v0.3.0

OceanBioME.jl - v0.2.1

OceanBioME.jl - v0.2.0

OceanBioME.jl -

OceanBioME.jl - v0.1.1

What's Changed

OceanBioME.jl - v0.1.0

What's Changed

New Contributors