Package won't update to most recent version

#1

Hi-

I am trying to update a package called MCMCChains to its most recent release version. For some reason, it does not work. The latest version is 0.3.7.

(v1.1) pkg> update
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
 Resolving package versions...
  Updating `~/.julia/environments/v1.1/Project.toml`
 [no changes]
  Updating `~/.julia/environments/v1.1/Manifest.toml`
 [no changes]

(v1.1) pkg> st
    Status `~/.julia/environments/v1.1/Project.toml`
  [c52e3926] Atom v0.8.5
  [593b3428] CmdStan v5.0.1
  [0c46a032] DifferentialEquations v6.3.0
  [31c24e10] Distributions v0.18.0
  [e5e0dc1b] Juno v0.7.0
  [c7f686f2] MCMCChains v0.3.6
  [429524aa] Optim v0.18.1
  [d96e819e] Parameters v0.10.3
  [91a5bcdd] Plots v0.24.0
  [295af30f] Revise v2.1.2
  [2913bbd2] StatsBase v0.29.0
  [4c63d2b9] StatsFuns v0.8.0
  [f3b207a7] StatsPlots v0.10.2
  [fce5fe82] Turing v0.6.14

(v1.1) pkg> 

I tried the following:
] gc followed by ] update
] resolve followed by ] update
] add MCMCChains @v0.3.7
adding only MCMCChains to a fresh install of Julia

0 Likes

#2

Chris, the version number in Project.toml is set to 0.3.6 so that is what will be displayed.

I would for now use add MCMCChains#master. If you want to test it, ] test MCMCChains should return:

Test Summary: | Pass  Total
MCMCChains    |  124    124
   Testing MCMCChains tests passed 

The master version by the way includes the data frame based summary updates, e.g.:

using Turing

N=50
θ = .6
k = rand(Binomial(N,θ))
@model model(N,k) = begin
    θ ~ Beta(5,5)
    k~ Binomial(N,θ)
end
Nsamples = 2000
Nadapt = 1000
δ = .85
specs = NUTS(Nsamples,Nadapt,δ)
chainarray = map(x->sample(model(N,k),specs),1:4)

x = []
for (i,ch) in enumerate(chainarray)
    print(i, " ")
    push!(x, summarize(ch[1001:end,:,:], sections=[:parameters]) )
end
println()

x[[1, 3, 4]]
0 Likes

#3

Thanks, Rob. Is there a reason 0.3.7 has been released but the Project.toml has not been updated?

0 Likes

#4

This release never made it to the registry: https://github.com/JuliaLang/METADATA.jl/pull/22777 so as far as Pkg knows 0.3.6 is the latest release.

This is not true unless you are in a checked out state (i.e. have added a branch or similar).

The maintainers forgot, and thats probably why https://github.com/JuliaLang/METADATA.jl/pull/22777 had failing tests and thus never merged.

I would file an issue with the package asking for a new release using the new system.

1 Like

#5

Thanks. That sounds like good advice. I’ll file an issue unless Rob has an objection (he is one of the maintainers).

0 Likes

#6

Over the next couple of days we will figure all of this out, but I think it might be an oversight from our side as the Pkg3 stuff was only very recently added to MCMCChains (last week). As Attobot is now gone I think we have to tag the release ourselves and, as before, update the version number, but I haven’t tried that yet.

0 Likes

#7

Would filing an issue be helpful or is this already on the agenda (I suspect)?

0 Likes

#8

Filing an issue would be great! Thanks.

0 Likes

#9

No problem. I filed the issue.

0 Likes