Code

JOSS paper#76

Code

Merged

jagoosw merged 175 commits intomainOceanBioME/OceanBioME.jl:mainfrom joss-paperOceanBioME/OceanBioME.jl:joss-paperCopy head branch name to clipboardOct 5, 2023

+2,925-2

Commits

Commits on Aug 29, 2022

• Added flux boundary timestep adaptation

  jagoosw

  committed
  4bb4fb7

• First draft

  jagoosw

  committed
  1393632

• Typo

  jagoosw

  committed
  ce2d04a

Commits on Sep 28, 2022

• Changed a little for oceananigans integration

  jagoosw

  authored
  9c45059

Commits on Feb 24, 2023

• Merge remote-tracking branch 'origin/main' into joss-paper

  jagoosw

  committed
  88781a7

Commits on Feb 27, 2023

• some updates

  jagoosw

  committed
  ffb375e

Commits on Mar 15, 2023

• added license

  jagoosw

  committed
  7ab12a1

• added some figures and an 'ongoing research projects' paragraph

  jagoosw

  committed
  fb8dee5

• Merge remote-tracking branch 'origin/main' into joss-paper

  jagoosw

  committed
  00bb2e6

• force added figures

  jagoosw

  committed
  429cca6

• edited paragraph about particles to reflect recent changes

  jagoosw

  committed
  3582a8a

Commits on Mar 16, 2023

• some fig caption changes

  jagoosw

  committed
  96d0815

Commits on Mar 18, 2023

• added joss pdf compiler workflow

  jagoosw

  committed
  a2ce262

• fixed bibliography

  jagoosw

  committed
  6875ae4

• fixed captions

  jagoosw

  committed
  b833096

• fixed citations

  jagoosw

  committed
  d9747a9

• edited acknowlegements

  jagoosw

  committed
  f25d9ea

• fixed citations again

  jagoosw

  committed
  c2094b9

• fixed citations again

  jagoosw

  committed
  165b0fa

• fixed NEMO citation

  jagoosw

  committed
  fc1c04f

• fixed NEMO citation

  jagoosw

  committed
  0c12fcf

• fixed NEMO citation

  jagoosw

  committed
  bf4e860

• changed intro

  jagoosw

  committed
  775f324

• fixed NEMO citation

  jagoosw

  committed
  67d58a0

• spelling

  jagoosw

  committed
  b51f1a3

• accidental changes from another branch

  jagoosw

  committed
  87c7143

Commits on Mar 20, 2023

• update kelp example

  jagoosw

  committed
  9de64f9

• Greg -> Gregory

  jagoosw

  committed
  4862ce7

• Merge remote-tracking branch 'origin/main' into joss-paper

  jagoosw

  committed
  531e8fd

Commits on Mar 21, 2023

• narrower version of column fig

  jagoosw

  committed
  99e7316

• narrower version of column fig but with C storage

  jagoosw

  committed
  e69df03

• Taller and less text

  jagoosw

  committed
  85eba98

• tidied fig1 caption

  jagoosw

  committed
  25a4f7b

• tidied fig2 caption

  jagoosw

  committed
  25d7c41

• fixed Manifest (?)

  jagoosw

  committed
  806e669

• Slightly bigger font for eady (may still be too small)

  Show description for 0a0e3fa
  jagoosw

  committed
  0a0e3fa

• a bit bigger

  jagoosw

  committed
  ae8fc7b

• a bit bigger

  jagoosw

  committed
  b116303

• a bit bigger 3

  jagoosw

  committed
  3641773

Commits on Mar 26, 2023

• edits to OceanBioME description

  johnryantaylor

  authored
  e7bffc0

Commits on May 1, 2023

• tidied up

  jagoosw

  committed
  a216d7f

Commits on May 3, 2023

• Merge remote-tracking branch 'origin/joss-paper' into joss-paper

  jagoosw

  committed
  a5b3b6f

Commits on May 15, 2023

• Update paper.md

  jagoosw

  authored
  7555c86

• Update paper.bib

  jagoosw

  authored
  da416c5

Commits on May 25, 2023

• Update paper.md

  Show description for b359f87
  johnryantaylor

  authored
  b359f87

• Update paper.md

  Show description for a6368b6
  johnryantaylor

  authored
  a6368b6

Commits on May 26, 2023

• Update paper.md

  Show description for b8feac4
  johnryantaylor

  authored
  b8feac4

• Merge remote-tracking branch 'origin/main' into joss-paper

  jagoosw

  committed
  6c6d43e

• reset random src and benchmark changes to main

  jagoosw

  committed
  702725f

• removed old example, not sure how it's still here

  jagoosw

  committed
  f3ca7b1

• removed old stuff

  jagoosw

  committed
  2964ad7

Commits on Jun 2, 2023

• fixed typo in figure and added figure scripts

  jagoosw

  committed
  88322b1

Commits on Jun 5, 2023

• corrected kelp density and plots

  Show description for 135bffe
  jagoosw

  committed
  135bffe

• figure fixed!

  jagoosw

  committed
  fa98849

Commits on Jun 9, 2023

• Update paper.md

  Show description for 303c85c
  johnryantaylor

  authored
  303c85c

• Update paper.md

  Show description for e014038
  johnryantaylor

  authored
  e014038

Commits on Jun 13, 2023

• Oceananigans + author changes

  Show description for d36fb94
  jagoosw

  authored
  d36fb94

• Typos

  jagoosw

  authored
  de29137

• Bibliography mistakes

  jagoosw

  authored
  96eef85

Commits on Jun 14, 2023

• Update paper/paper.md

  Show description for ebbfff3
  

  jagoosw

  and

  glwagner

  authored
  ebbfff3

• added line breaks to each sentence

  jagoosw

  authored
  f886a29

Commits on Jun 15, 2023

• Update paper.md

  Show description for b55e76e
  johnryantaylor

  authored
  b55e76e

• Update paper.md

  Show description for 80930f9
  johnryantaylor

  authored
  80930f9

• Used grammarly to catch some gramar mistakes

  jagoosw

  authored
  65b3945

Commits on Jun 16, 2023

• applied review suggesitons

  jagoosw

  committed
  abb0ddc

• added reference to figures

  jagoosw

  committed
  07ade32

Commits on Jun 18, 2023

• Apply suggestions from code review

  Show description for b31d540
  

  jagoosw

  and

  navidcy

  authored
  b31d540

• Improved figure reference wording

  jagoosw

  authored
  c789399

• Added Navid to author list

  jagoosw

  authored
  f28fac2

Commits on Jun 19, 2023

• Apply suggestions from code review

  Show description for 604d8d7
  

  jagoosw

  and

  navidcy

  authored
  604d8d7

• made package names consistent

  jagoosw

  committed
  f41dfcd

• removed repeated speed information

  jagoosw

  committed
  5947e65

• added bullet points

  jagoosw

  committed
  661e615

Commits on Jun 20, 2023

• Apply suggestions from code review

  Show description for f550432
  

  jagoosw

  and

  navidcy

  authored
  f550432

Commits on Jun 22, 2023

• Implimented review suggestions

  jagoosw

  committed
  a9b2134

• added Simone to authors

  jagoosw

  committed
  5db492b

• fixed sentence

  jagoosw

  committed
  044b437

• minor changeS

  jagoosw

  committed
  133ce37

• Minor edits to text

  johnryantaylor

  authored
  41e405a

Commits on Jun 23, 2023

• Edited author order to alphabetical

  jagoosw

  authored
  621b917

Commits on Jun 24, 2023

• Apply suggestions from code review

  Show description for 2baeede
  

  jagoosw

  and

  navidcy

  authored
  2baeede

Commits on Jun 28, 2023

• add some doi

  navidcy

  committed
  994f9d2

• add orcid id

  navidcy

  committed
  2784eac

Commits on Jul 15, 2023

• Merge branch 'main' into joss-paper

  navidcy

  authored
  a110755

Commits on Jul 20, 2023

• first attempt at restructuring for explitict statement of need

  jagoosw

  committed
  2ec90fd

• Spelling and grammar

  jagoosw

  authored
  7aab6fa

• added reference

  jagoosw

  committed
  0ac0787

• added missing doi

  jagoosw

  committed
  d67c924

Commits on Jul 21, 2023

• added near-global model figure

  jagoosw

  committed
  99bfdbd

• fixed near global plot colorbar

  jagoosw

  committed
  a5df2de

• Grammarly

  jagoosw

  authored
  0c39115

• Removed some repatition

  jagoosw

  authored
  e2c0c71

• changed scaling on near global fig

  jagoosw

  committed
  0dddb27

• minor edits to Statement of Need

  johnryantaylor

  authored
  dc7b0ef

Commits on Jul 24, 2023

• bib file cleanup

  navidcy

  committed
  d310a71

• bib file alignment

  navidcy

  committed
  4581e05

• capitalize Saccharina

  navidcy

  committed
  3db0207

• Merge branch 'main' into joss-paper

  navidcy

  authored
  c59fb68

• Added equal contrib flag for alphabetically listed authors

  Show description for e413a27
  jagoosw

  authored
  e413a27

Commits on Aug 3, 2023

• added more detail to 'tracer based' models

  jagoosw

  committed
  2592395

• added note about speedup from prescribed fields

  jagoosw

  committed
  02ff1e3

• added examples table

  jagoosw

  committed
  b672792

• Added more descriptive caption and panel labelling to eady example

  jagoosw

  committed
  d380c64

• attempt to fix table column width

  jagoosw

  committed
  6f661fd

• attempted to fix table mk2

  jagoosw

  committed
  df65b9d

• attempted to fix table mk3

  jagoosw

  committed
  51f10d0

• how to make super scripts in this version of markdown

  jagoosw

  committed
  ec3b155

• worked, now for the subscripts

  jagoosw

  committed
  96d727d

Commits on Aug 4, 2023

• updated figures scripts to latest version

  jagoosw

  committed
  18537a6

• added an ORCID

  jagoosw

  committed
  ef411a0

• improved concistency in formatting module and package names

  jagoosw

  committed
  f129f68

• improved examples table

  jagoosw

  committed
  406dbf9

• added panel labels to column fig for concistency

  jagoosw

  committed
  7a680af

• Attempted to add a couple of sentences about the ease of implimenting and modifying models

  jagoosw

  authored
  dc2ea5d

• JOSS can't render unicode subscript 0

  jagoosw

  authored
  de6ff8a

• Word change

  jagoosw

  authored
  f5333f8

Commits on Aug 6, 2023

• Added near global example code

  jagoosw

  authored
  598405b

Commits on Aug 7, 2023

• Flipped phytoplankton color for concistency

  jagoosw

  authored
  d4bd825

• added better fig 3 description and labelling + other review suggestions

  jagoosw

  committed
  ead737d

• grammar

  jagoosw

  committed
  30e3e95

Commits on Aug 23, 2023

• Update paper.md

  jagoosw

  authored
  a3bd6fb

Commits on Sep 5, 2023

• fixed a citation

  jagoosw

  committed
  bb09f21

• added project with compats to paper example code

  jagoosw

  committed
  c5cee8a

Commits on Sep 6, 2023

• Minor corrections

  jagoosw

  authored
  dbc66f2

Commits on Sep 12, 2023

• Updated with review suggestions

  jagoosw

  authored
  16fb5bb

Commits on Sep 14, 2023

• Update paper.md

  Show description for 038bfaf
  johnryantaylor

  authored
  038bfaf

• Update paper.md

  Show description for 1464028
  johnryantaylor

  authored
  1464028

• Update paper/paper.md

  Show description for 6343f00
  

  johnryantaylor

  and

  navidcy

  authored
  6343f00

• Update paper/paper.md

  Show description for f591649
  

  johnryantaylor

  and

  navidcy

  authored
  f591649

• Update paper/paper.md

  Show description for 34c1574
  

  johnryantaylor

  and

  navidcy

  authored
  34c1574

• Update paper.bib

  jagoosw

  authored
  369c5bd

• add doi

  jagoosw

  authored
  40c88c3

• Update paper.bib

  jagoosw

  authored
  9ae44c5

• fixed citation (?)

  jagoosw

  committed
  0280e20

Commits on Sep 15, 2023

• fix typo

  navidcy

  authored
  37a0311

• Update paper.md

  jagoosw

  authored
  f9d3d8c

Commits on Sep 16, 2023

• Merge pull request #141 from OceanBioME/johnryantaylor-JOSS-edits

  Show description for 9f6f5c0
  johnryantaylor

  authored
  9f6f5c0

• Update paper.md

  Show description for b32322e
  johnryantaylor

  authored
  b32322e

Commits on Sep 18, 2023

• added eady script and changed resolution in text

  jagoosw

  committed
  ac93375

Commits on Sep 20, 2023

• Update Manifest.toml

  navidcy

  authored
  1407816

• changed params from named tuple to tuple

  jagoosw

  committed
  6c87930

Commits on Sep 24, 2023

• updated eady figure

  jagoosw

  committed
  a566ab1

• added sentence about color ordering

  jagoosw

  committed
  8a70f46

• added citation for KA and CUDA

  jagoosw

  committed
  526efab

• corrected citation

  jagoosw

  committed
  1257d28

• Apply suggestions from code review

  Show description for 69eb822
  

  jagoosw

  and

  johnryantaylor

  authored
  69eb822

• Update src/Boundaries/Sediments/simple_multi_G.jl

  Show description for c3506d2
  

  jagoosw

  and

  navidcy

  authored
  c3506d2

• modified figire

  jagoosw

  committed
  a7fc9e0

• included Julia GPU in acknowledgements

  jagoosw

  committed
  675d256

• Merge branch 'joss-paper' into jsw/joss-eady-fig

  jagoosw

  authored
  d12ee7c

• changed colorrange

  jagoosw

  committed
  edf470a

• updated eady plot file

  jagoosw

  committed
  93e655d

• changed colorrange again

  jagoosw

  committed
  0349288

• Merge pull request #145 from OceanBioME/jsw/joss-eady-fig

  Show description for 591d3d2
  jagoosw

  authored
  591d3d2

• Apply suggestions from code review

  Show description for 79a58aa
  

  jagoosw

  and

  navidcy

  authored
  79a58aa

• Apply suggestion from code review

  Show description for 210951b
  jagoosw

  authored
  210951b

• Merge branch 'main' into joss-paper

  jagoosw

  authored
  6d7a468

• didn't push latest figure

  jagoosw

  committed
  455e885

• trying to not modify the sediment model

  jagoosw

  committed
  67536a9

Commits on Sep 25, 2023

• updated eady figure

  Show description for a8bed1e
  jagoosw

  committed
  a8bed1e

Commits on Sep 27, 2023

• updated figure

  jagoosw

  committed
  ed69acf

• dimension correction

  jagoosw

  committed
  5929414

• Correction

  jagoosw

  authored
  be6b62a

• Update paper.md

  Show description for e4258c1
  johnryantaylor

  authored
  e4258c1

Commits on Oct 1, 2023

• Added reviewer acknowledgements

  jagoosw

  authored
  58befca

Commits on Oct 2, 2023

• Remove draft workflow

  jagoosw

  authored
  b182488

Commits on Oct 3, 2023

• add orcid

  jagoosw

  authored
  99f1906

• Add orcid

  jagoosw

  authored
  6a5d8f8

Commits on Oct 5, 2023

• pin Documenter to v0.27

  navidcy

  committed
  2ad2f3b

• Merge branch 'main' into joss-paper

  navidcy

  authored
  21124b2

• remove duplicate Documenter compat entry

  navidcy

  committed
  59a581e

• Inconsistency in escaping of package name

  jagoosw

  authored
  d318121

• add citation.cff

  navidcy

  committed
  28aefbe

• Merge branch 'joss-paper' of github.com:OceanBioME/OceanBioME.jl into joss-paper

  navidcy

  committed
  00c1d68

• add JOSS paper doi badge

  navidcy

  authored
  7e92e74