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lejon / TSne.jl

Julia port of L.J.P. van der Maaten and G.E. Hintons T-SNE visualisation technique.
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New Release? #25

Closed oschulz closed 3 years ago

oschulz commented 4 years ago

The current master branch seems to run on Julia v1.x, with a current set of dependencies, but the last release can't be installed (dependency trouble with ProgressMeter). Maybe make a new release, based on the current master, if you can find some time?

oschulz commented 4 years ago

CC @juliohm

grahamas commented 4 years ago

For future Googlers' sake, this leads to a wild goose chase of errors, beginning:

julia> import DifferentialEquations
[ Info: Precompiling DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa]
ERROR: LoadError: LoadError: UndefVarError: initialize_dae! not defined
Stacktrace:
 [1] getproperty(::Module, ::Symbol) at ./Base.jl:26
 [2] top-level scope at /home/graham/.julia/packages/Sundials/0yJ3G/src/common_interfa
ce/integrator_utils.jl:151
 [3] include(::Module, ::String) at ./Base.jl:377
 [4] include(::String) at /home/graham/.julia/packages/Sundials/0yJ3G/src/Sundials.jl:
3
 [5] top-level scope at /home/graham/.julia/packages/Sundials/0yJ3G/src/Sundials.jl:71
 [6] include(::Module, ::String) at ./Base.jl:377
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:449
 [10] top-level scope at ./none:3
in expression starting at /home/graham/.julia/packages/Sundials/0yJ3G/src/common_inter
face/integrator_utils.jl:151
in expression starting at /home/graham/.julia/packages/Sundials/0yJ3G/src/Sundials.jl:
71
ERROR: LoadError: Failed to precompile Sundials [c3572dad-4567-51f8-b174-8c6c989267f4]
 to /home/graham/.julia/compiled/v1.4/Sundials/j8Ppj_f4Df4.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922
 [6] include(::Module, ::String) at ./Base.jl:377
 [7] top-level scope at none:2
 [8] eval at ./boot.jl:331 [inlined]
 [9] eval(::Expr) at ./client.jl:449
 [10] top-level scope at ./none:3
in expression starting at /home/graham/.julia/packages/DifferentialEquations/xCZD1/src
/DifferentialEquations.jl:13
ERROR: Failed to precompile DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fba
a] to /home/graham/.julia/compiled/v1.4/DifferentialEquations/UQdwS_f4Df4.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922

Diligent inspection of Manifest.toml reveals that DiffEqBase is stuck at v6.19.0. Explicitly adding ]add DiffEqBase@6.29.3 gives an error that ProgressMeter is unsatisfiable, due to TSne.

My solution was to remove TSne, but you may not be able to do that.

oschulz commented 4 years ago

But how does TSne depend on DiffEqBase?

grahamas commented 4 years ago

It doesn't, but they both depend on ProgressMeter.

Starting with v6.20.0, DiffEqBase, requires ConsoleProgressMonitor which requires v1 of ProgressMeter.

On the other hand, TSne requires ProgressMeter less than v1 (implicitly, the REQUIRE file requires v0.x).

To fix this, TSne would need to move to the Project.toml setup, with

[compat]
ProgressMeter = "1"
oschulz commented 4 years ago

Oh, yes, definitly!

babaq commented 4 years ago

yes, it's broken on julia 1.4, need to make a new release, or at least update on master

submitme commented 4 years ago

Leif, time to update this to Julia 1.4. This package was mentioned in recent Julia Computing Data Science videos, but not used since it is outdated. / Prof Villani

PyDataBlog commented 4 years ago

This requires urgent attention.

juliohm commented 4 years ago

@lejon are you still with us? Can you please share an update regarding the maintenance of this package? Would you like to give others permission to maintain if you are too busy or not interested in evolving/fixing it?

lejon commented 4 years ago

Hi,

Yes I'm still here. I keep thinking that I should get back to Julia coding, because I think it is really great, but time and other prio seems to always be against it unfortunately.

Github user @alyst has previously done a great job updating the package and has in practice been the maintainer of late, but I guess he's also got alot of other stuff to do. I do not think that he would mind someone else taking over the maintainer role. Personally I'd be happy if someone wants to take that role.

Cheers! -Leif

On 15 Aug 2020, at 13:25, Júlio Hoffimann notifications@github.com wrote:



@lejon https://github.com/lejon are you still with us? Can you please share an update regarding the maintenance of this package? Would you like to give others permission to maintain if you are too busy or not interested in evolving/fixing it?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lejon/TSne.jl/issues/25#issuecomment-674385108, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA664MYIFDAPKBJ5GNPX7HDSAZWC7ANCNFSM4KGU4G6A .

alyst commented 3 years ago

Sorry, I hadn't checked this package for quite a while. I've just tagged a new version that should work with current Julia and up-to-date packages.

oschulz commented 3 years ago

Thanks!

oschulz commented 3 years ago

Maybe add https://github.com/JuliaRegistries/CompatHelper.jl to the workflows, to keep the dependency version bounds up to date?

alyst commented 3 years ago

@oschulz That's also what I would like to do (as well as installing JuliaRegistrator app). The full setup would require adding SSH deploy key, which only the owner (@lejon) can do.