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merge Catalyst version 14 into master #830

Merged
merged 441 commits into from
May 14, 2024
Merged

merge Catalyst version 14 into master #830

merged 441 commits into from
May 14, 2024

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isaacsas
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TorkelE and others added 30 commits February 2, 2024 08:38
@TorkelE
prevents metadata to be repeated in the DSL
40985ec
@TorkelE
update history file
80e34ae
@TorkelE
use Vector{Pair{Symbol,R}} as metadata in Reactions
fcd819a
@TorkelE
up
f89d973
@TorkelE
up
3c4e252
@TorkelE
up
2215ef8
@TorkelE
up
11754dc
@TorkelE
init
7fb02c9
@TorkelE
up
1f099ab
@TorkelE
up
6b46dec
@TorkelE @isaacsas
Update docs/src/api/catalyst_api.md
6fc641d 
Co-authored-by: Sam Isaacson <[email protected]>
@TorkelE
up
829da0f
@TorkelE
Merge pull request #742 from SciML/Latexify_updates
315bc3c 
[v14 ready] Latexify improvement
@TorkelE
init
76a39b5
@isaacsas
Update src/reactionsystem.jl
8579987
@TorkelE
Merge pull request #783 from SciML/add_reaction_system_metadata
c4762dc 
Add reaction system metadata
@TorkelE
update
37096a3
@TorkelE
up
9a9d861
@TorkelE
up
08ccc68
@TorkelE
test fix
56b265e
@TorkelE
init
3238c0e
@TorkelE
fix all)unitless deprication
3c23553
@TorkelE
up MTK
4861d8e
@TorkelE @isaacsas
Update docs/src/catalyst_applications/simulation_structure_interfacin…
e802c17 
…g.md

Co-authored-by: Sam Isaacson <[email protected]>
@TorkelE @isaacsas
Update docs/src/catalyst_applications/simulation_structure_interfacin…
38ffeea 
…g.md

Co-authored-by: Sam Isaacson <[email protected]>
@TorkelE @isaacsas
Update docs/src/catalyst_applications/simulation_structure_interfacin…
0438e06 
…g.md

Co-authored-by: Sam Isaacson <[email protected]>
@TorkelE @isaacsas
Update docs/src/catalyst_functionality/network_analysis.md
f858017 
Co-authored-by: Sam Isaacson <[email protected]>
@TorkelE @isaacsas
Update src/networkapi.jl
4606337 
Co-authored-by: Sam Isaacson <[email protected]>
@TorkelE @isaacsas
Update src/networkapi.jl
f76f4be 
Co-authored-by: Sam Isaacson <[email protected]>
@TorkelE @isaacsas
Update src/networkapi.jl
8f52e12 
Co-authored-by: Sam Isaacson <[email protected]>
TorkelE and others added 22 commits May 8, 2024 17:16
@TorkelE
handle observed elimination
0dc58c8
@TorkelE
limit julia version
f72bb9c
@TorkelE
fix julia version compat
e286872
@TorkelE
Better handling of julai test version restriction
f1f116b
@TorkelE
up
19c976c
@TorkelE
revert loop
b9d573d
@TorkelE
mark test as broken (@unpack does not work on observables)
9c8e5c2
@TorkelE
up
bc93f41
@TorkelE
fix
01fcab7
@TorkelE
fix2
74a8881
@TorkelE
observabes fix
85e708e
@TorkelE
test no longer broken
8601ed1
@TorkelE
Merge pull request #801 from SciML/equations_and_events_remake
2276e1c 
Equations and events reupload
@isaacsas
start removing mutable API functions
6ccd3a6
@isaacsas
drop mutable network tests
2ea940c
@isaacsas
drop coupled equation tests as currently broken
e56ac80
@isaacsas
disable broken tests due to using Symbolics.replace
0b75921
@isaacsas
Merge pull request #823 from isaacsas/drop_mutation
8a604c4 
Drop mutating API functions and macro
@isaacsas
Merge remote-tracking branch 'origin/Catalyst_version_14' into add_co…
fcd8d6c 
…mbinatoric_ratelaws_to_dsl
@isaacsas
add combinatoric_ratelaws to DSL
4f8be29
@isaacsas
remove show
a04b527
@isaacsas
Merge pull request #828 from isaacsas/add_combinatoric_ratelaws_to_dsl
8937143 
Add `@combinatoric_ratelaws` to DSL
@isaacsas
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@TorkelE this is failing because of == equality tests between solution objects, which as I said a while back we really shouldn't be doing...

@isaacsas
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Catalyst.jl/test/miscellaneous_tests/events.jl

Line 247 in 8937143

sol_dsl = solve(SDEProblem(rn_dsl, u0, tspan, ps), ImplicitEM(); seed = 1234)
doesn't use StableRngs for the SDEProblem?

@ChrisRackauckas
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But it's relative, so both solves should change if it changes, so I think that one is okay.

@TorkelE
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TorkelE commented May 13, 2024

@TorkelE this is failing because of == equality tests between solution objects, which as I said a while back we really shouldn't be doing...

Do we know what? I can check tomorrow. Testing solutions for equality have worked for 6 years, so while moving away from it might be good, inn this case it probably suggest that something else have gone wrong as well, which we would want to know about.

doesn't use StableRngs for the SDEProblem?

SDEProblems cannot take these. I either use fixed seeds, or have these generated through StableRNGs though.

@TorkelE
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TorkelE commented May 14, 2024

Here is a previous issue in StableRNG seeds for SDEs: SciML/StochasticDiffEq.jl#569. Might be a while until it gets added though, not sure if anyone is actively working on SDEs.

@TorkelE TorkelE merged commit 1e522c6 into master May 14, 2024
3 of 8 checks passed
@TorkelE TorkelE deleted the Catalyst_version_14 branch May 15, 2024 17:37
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3 participants
@isaacsas @ChrisRackauckas @TorkelE