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JOSS paper #76

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merged 175 commits into from
Oct 5, 2023
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4bb4fb7
Added flux boundary timestep adaptation
jagoosw Aug 29, 2022
1393632
First draft
jagoosw Aug 29, 2022
ce2d04a
Typo
jagoosw Aug 29, 2022
9c45059
Changed a little for oceananigans integration
jagoosw Sep 28, 2022
88781a7
Merge remote-tracking branch 'origin/main' into joss-paper
jagoosw Feb 24, 2023
ffb375e
some updates
jagoosw Feb 27, 2023
7ab12a1
added license
jagoosw Mar 15, 2023
fb8dee5
added some figures and an 'ongoing research projects' paragraph
jagoosw Mar 15, 2023
00bb2e6
Merge remote-tracking branch 'origin/main' into joss-paper
jagoosw Mar 15, 2023
429cca6
force added figures
jagoosw Mar 15, 2023
3582a8a
edited paragraph about particles to reflect recent changes
jagoosw Mar 15, 2023
96d0815
some fig caption changes
jagoosw Mar 16, 2023
a2ce262
added joss pdf compiler workflow
jagoosw Mar 18, 2023
6875ae4
fixed bibliography
jagoosw Mar 18, 2023
b833096
fixed captions
jagoosw Mar 18, 2023
d9747a9
fixed citations
jagoosw Mar 18, 2023
f25d9ea
edited acknowlegements
jagoosw Mar 18, 2023
c2094b9
fixed citations again
jagoosw Mar 18, 2023
165b0fa
fixed citations again
jagoosw Mar 18, 2023
fc1c04f
fixed NEMO citation
jagoosw Mar 18, 2023
0c12fcf
fixed NEMO citation
jagoosw Mar 18, 2023
bf4e860
fixed NEMO citation
jagoosw Mar 18, 2023
775f324
changed intro
jagoosw Mar 18, 2023
67d58a0
fixed NEMO citation
jagoosw Mar 18, 2023
b51f1a3
spelling
jagoosw Mar 18, 2023
87c7143
accidental changes from another branch
jagoosw Mar 18, 2023
9de64f9
update kelp example
jagoosw Mar 20, 2023
4862ce7
Greg -> Gregory
jagoosw Mar 20, 2023
531e8fd
Merge remote-tracking branch 'origin/main' into joss-paper
jagoosw Mar 20, 2023
99e7316
narrower version of column fig
jagoosw Mar 21, 2023
e69df03
narrower version of column fig but with C storage
jagoosw Mar 21, 2023
85eba98
Taller and less text
jagoosw Mar 21, 2023
25a4f7b
tidied fig1 caption
jagoosw Mar 21, 2023
25d7c41
tidied fig2 caption
jagoosw Mar 21, 2023
806e669
fixed Manifest (?)
jagoosw Mar 21, 2023
0a0e3fa
Slightly bigger font for eady (may still be too small)
jagoosw Mar 21, 2023
ae8fc7b
a bit bigger
jagoosw Mar 21, 2023
b116303
a bit bigger
jagoosw Mar 21, 2023
3641773
a bit bigger 3
jagoosw Mar 21, 2023
e7bffc0
edits to OceanBioME description
johnryantaylor Mar 26, 2023
a216d7f
tidied up
jagoosw May 1, 2023
a5b3b6f
Merge remote-tracking branch 'origin/joss-paper' into joss-paper
jagoosw May 3, 2023
7555c86
Update paper.md
jagoosw May 15, 2023
da416c5
Update paper.bib
jagoosw May 15, 2023
b359f87
Update paper.md
johnryantaylor May 25, 2023
a6368b6
Update paper.md
johnryantaylor May 25, 2023
b8feac4
Update paper.md
johnryantaylor May 26, 2023
6c6d43e
Merge remote-tracking branch 'origin/main' into joss-paper
jagoosw May 26, 2023
702725f
reset random src and benchmark changes to main
jagoosw May 26, 2023
f3ca7b1
removed old example, not sure how it's still here
jagoosw May 26, 2023
2964ad7
removed old stuff
jagoosw May 26, 2023
88322b1
fixed typo in figure and added figure scripts
jagoosw Jun 2, 2023
135bffe
corrected kelp density and plots
jagoosw Jun 5, 2023
fa98849
figure fixed!
jagoosw Jun 5, 2023
303c85c
Update paper.md
johnryantaylor Jun 9, 2023
e014038
Update paper.md
johnryantaylor Jun 9, 2023
d36fb94
Oceananigans + author changes
jagoosw Jun 13, 2023
de29137
Typos
jagoosw Jun 13, 2023
96eef85
Bibliography mistakes
jagoosw Jun 13, 2023
ebbfff3
Update paper/paper.md
jagoosw Jun 14, 2023
f886a29
added line breaks to each sentence
jagoosw Jun 14, 2023
b55e76e
Update paper.md
johnryantaylor Jun 15, 2023
80930f9
Update paper.md
johnryantaylor Jun 15, 2023
65b3945
Used grammarly to catch some gramar mistakes
jagoosw Jun 15, 2023
abb0ddc
applied review suggesitons
jagoosw Jun 16, 2023
07ade32
added reference to figures
jagoosw Jun 16, 2023
b31d540
Apply suggestions from code review
jagoosw Jun 18, 2023
c789399
Improved figure reference wording
jagoosw Jun 18, 2023
f28fac2
Added Navid to author list
jagoosw Jun 18, 2023
604d8d7
Apply suggestions from code review
jagoosw Jun 19, 2023
f41dfcd
made package names consistent
jagoosw Jun 19, 2023
5947e65
removed repeated speed information
jagoosw Jun 19, 2023
661e615
added bullet points
jagoosw Jun 19, 2023
f550432
Apply suggestions from code review
jagoosw Jun 20, 2023
a9b2134
Implimented review suggestions
jagoosw Jun 22, 2023
5db492b
added Simone to authors
jagoosw Jun 22, 2023
044b437
fixed sentence
jagoosw Jun 22, 2023
133ce37
minor changeS
jagoosw Jun 22, 2023
41e405a
Minor edits to text
johnryantaylor Jun 22, 2023
621b917
Edited author order to alphabetical
jagoosw Jun 23, 2023
2baeede
Apply suggestions from code review
jagoosw Jun 24, 2023
994f9d2
add some doi
navidcy Jun 28, 2023
2784eac
add orcid id
navidcy Jun 28, 2023
a110755
Merge branch 'main' into joss-paper
navidcy Jul 15, 2023
2ec90fd
first attempt at restructuring for explitict statement of need
jagoosw Jul 20, 2023
7aab6fa
Spelling and grammar
jagoosw Jul 20, 2023
0ac0787
added reference
jagoosw Jul 20, 2023
d67c924
added missing doi
jagoosw Jul 20, 2023
99bfdbd
added near-global model figure
jagoosw Jul 21, 2023
a5df2de
fixed near global plot colorbar
jagoosw Jul 21, 2023
0c39115
Grammarly
jagoosw Jul 21, 2023
e2c0c71
Removed some repatition
jagoosw Jul 21, 2023
0dddb27
changed scaling on near global fig
jagoosw Jul 21, 2023
dc7b0ef
minor edits to Statement of Need
johnryantaylor Jul 21, 2023
d310a71
bib file cleanup
navidcy Jul 24, 2023
4581e05
bib file alignment
navidcy Jul 24, 2023
3db0207
capitalize Saccharina
navidcy Jul 24, 2023
c59fb68
Merge branch 'main' into joss-paper
navidcy Jul 24, 2023
e413a27
Added equal contrib flag for alphabetically listed authors
jagoosw Jul 24, 2023
2592395
added more detail to 'tracer based' models
jagoosw Aug 3, 2023
02ff1e3
added note about speedup from prescribed fields
jagoosw Aug 3, 2023
b672792
added examples table
jagoosw Aug 3, 2023
d380c64
Added more descriptive caption and panel labelling to eady example
jagoosw Aug 3, 2023
6f661fd
attempt to fix table column width
jagoosw Aug 3, 2023
df65b9d
attempted to fix table mk2
jagoosw Aug 3, 2023
51f10d0
attempted to fix table mk3
jagoosw Aug 3, 2023
ec3b155
how to make super scripts in this version of markdown
jagoosw Aug 3, 2023
96d727d
worked, now for the subscripts
jagoosw Aug 3, 2023
18537a6
updated figures scripts to latest version
jagoosw Aug 4, 2023
ef411a0
added an ORCID
jagoosw Aug 4, 2023
f129f68
improved concistency in formatting module and package names
jagoosw Aug 4, 2023
406dbf9
improved examples table
jagoosw Aug 4, 2023
7a680af
added panel labels to column fig for concistency
jagoosw Aug 4, 2023
dc2ea5d
Attempted to add a couple of sentences about the ease of implimenting…
jagoosw Aug 4, 2023
de6ff8a
JOSS can't render unicode subscript 0
jagoosw Aug 4, 2023
f5333f8
Word change
jagoosw Aug 4, 2023
598405b
Added near global example code
jagoosw Aug 6, 2023
d4bd825
Flipped phytoplankton color for concistency
jagoosw Aug 7, 2023
ead737d
added better fig 3 description and labelling + other review suggestions
jagoosw Aug 7, 2023
30e3e95
grammar
jagoosw Aug 7, 2023
a3bd6fb
Update paper.md
jagoosw Aug 23, 2023
bb09f21
fixed a citation
jagoosw Sep 5, 2023
c5cee8a
added project with compats to paper example code
jagoosw Sep 5, 2023
dbc66f2
Minor corrections
jagoosw Sep 6, 2023
16fb5bb
Updated with review suggestions
jagoosw Sep 12, 2023
038bfaf
Update paper.md
johnryantaylor Sep 14, 2023
1464028
Update paper.md
johnryantaylor Sep 14, 2023
6343f00
Update paper/paper.md
johnryantaylor Sep 14, 2023
f591649
Update paper/paper.md
johnryantaylor Sep 14, 2023
34c1574
Update paper/paper.md
johnryantaylor Sep 14, 2023
369c5bd
Update paper.bib
jagoosw Sep 14, 2023
40c88c3
add doi
jagoosw Sep 14, 2023
9ae44c5
Update paper.bib
jagoosw Sep 14, 2023
0280e20
fixed citation (?)
jagoosw Sep 14, 2023
37a0311
fix typo
navidcy Sep 15, 2023
f9d3d8c
Update paper.md
jagoosw Sep 15, 2023
9f6f5c0
Merge pull request #141 from OceanBioME/johnryantaylor-JOSS-edits
johnryantaylor Sep 16, 2023
b32322e
Update paper.md
johnryantaylor Sep 16, 2023
ac93375
added eady script and changed resolution in text
jagoosw Sep 18, 2023
1407816
Update Manifest.toml
navidcy Sep 20, 2023
6c87930
changed params from named tuple to tuple
jagoosw Sep 20, 2023
a566ab1
updated eady figure
jagoosw Sep 24, 2023
8a70f46
added sentence about color ordering
jagoosw Sep 24, 2023
526efab
added citation for KA and CUDA
jagoosw Sep 24, 2023
1257d28
corrected citation
jagoosw Sep 24, 2023
69eb822
Apply suggestions from code review
jagoosw Sep 24, 2023
c3506d2
Update src/Boundaries/Sediments/simple_multi_G.jl
jagoosw Sep 24, 2023
a7fc9e0
modified figire
jagoosw Sep 24, 2023
675d256
included Julia GPU in acknowledgements
jagoosw Sep 24, 2023
d12ee7c
Merge branch 'joss-paper' into jsw/joss-eady-fig
jagoosw Sep 24, 2023
edf470a
changed colorrange
jagoosw Sep 24, 2023
93e655d
updated eady plot file
jagoosw Sep 24, 2023
0349288
changed colorrange again
jagoosw Sep 24, 2023
591d3d2
Merge pull request #145 from OceanBioME/jsw/joss-eady-fig
jagoosw Sep 24, 2023
79a58aa
Apply suggestions from code review
jagoosw Sep 24, 2023
210951b
Apply suggestion from code review
jagoosw Sep 24, 2023
6d7a468
Merge branch 'main' into joss-paper
jagoosw Sep 24, 2023
455e885
didn't push latest figure
jagoosw Sep 24, 2023
67536a9
trying to not modify the sediment model
jagoosw Sep 24, 2023
a8bed1e
updated eady figure
jagoosw Sep 25, 2023
ed69acf
updated figure
jagoosw Sep 27, 2023
5929414
dimension correction
jagoosw Sep 27, 2023
be6b62a
Correction
jagoosw Sep 27, 2023
e4258c1
Update paper.md
johnryantaylor Sep 27, 2023
58befca
Added reviewer acknowledgements
jagoosw Oct 1, 2023
b182488
Remove draft workflow
jagoosw Oct 2, 2023
99f1906
add orcid
jagoosw Oct 3, 2023
6a5d8f8
Add orcid
jagoosw Oct 3, 2023
2ad2f3b
pin Documenter to v0.27
navidcy Oct 5, 2023
21124b2
Merge branch 'main' into joss-paper
navidcy Oct 5, 2023
59a581e
remove duplicate Documenter compat entry
navidcy Oct 5, 2023
d318121
Inconsistency in escaping of package name
jagoosw Oct 5, 2023
28aefbe
add citation.cff
navidcy Oct 5, 2023
00c1d68
Merge branch 'joss-paper' of github.com:OceanBioME/OceanBioME.jl into…
navidcy Oct 5, 2023
7e92e74
add JOSS paper doi badge
navidcy Oct 5, 2023
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1 change: 1 addition & 0 deletions docs/Project.toml
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[compat]
CairoMakie = "0.10"
Documenter = "0.27"
DocumenterCitations = "1"
Literate = "≥2.9.0"
Oceananigans = "0.84.1, 0.85, 0.86, 0.87"
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