Pkg.add updates other packages too?

  1. I installed Julia 1.6
  2. I installed the latest MLJ 0.16
  3. I installed NaiveBayes.jl but got downgraded to MLJ 0.15.2 without my consent!
    Is this non-consentual downgrading intended?
  4. If this is the wrong place please redirect me to the appropriate thread …

julia> Pkg.add("NaiveBayes")
   Resolving package versions...
   Installed GPUCompiler ─ v0.9.2
   Installed CUDA ──────── v2.6.0
    Updating `~/.julia/environments/v1.6/Project.toml`
  [f6006082] ↓ EvoTrees v0.7.0 ⇒ v0.5.3
  [add582a8] ↓ MLJ v0.16.0 ⇒ v0.15.2
  [d491faf4] ↓ MLJModels v0.14.1 ⇒ v0.13.3
  [9bbee03b] + NaiveBayes v0.5.0

Yes, it is intended, and it is consensual: you executed a function (Pkg.add) without reading the documentation. You can pass a keyword parameter to the function to force it to avoid any downgrading.

julia> using Pkg

help?> Pkg.add
  Pkg.add(pkg::Union{String, Vector{String}}; preserve=PRESERVE_TIERED)
  Pkg.add(pkg::Union{PackageSpec, Vector{PackageSpec}}; preserve=PRESERVE_TIERED)

  Add a package to the current project. This package will be available by using the
  import and using keywords in the Julia REPL, and if the current project is a
  package, also inside that package.

  Resolution Tiers

  Pkg resolves the set of packages in your environment using a tiered algorithm. The
  preserve keyword argument allows you to key into a specific tier in the resolve
  algorithm. The following table describes the argument values for preserve (in
  order of strictness):

  Value           Description                                                                        
  ––––––––––––––– –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
  PRESERVE_ALL    Preserve the state of all existing dependencies (including recursive dependencies) 
  PRESERVE_DIRECT Preserve the state of all existing direct dependencies                             
  PRESERVE_SEMVER Preserve semver-compatible versions of direct dependencies                         
  PRESERVE_NONE   Do not attempt to preserve any version information                                 
  PRESERVE_TIERED Use the tier which will preserve the most version information (this is the default)


  Pkg.add("Example") # Add a package from registry
  Pkg.add("Example"; preserve=Pkg.PRESERVE_ALL) # Add the `Example` package and preserve existing dependencies
  Pkg.add(name="Example", version="0.3") # Specify version; latest release in the 0.3 series
  Pkg.add(name="Example", version="0.3.1") # Specify version; exact release
  Pkg.add(url="", rev="master") # From url to remote gitrepo
  Pkg.add(url="/remote/mycompany/juliapackages/OurPackage") # From path to local gitrepo
  Pkg.add(url="", subdir="juliapkgs/Package.jl)") # With subdir

  See also PackageSpec.

Thanks for referring me to the docs.

The current default option is: preserve=PRESERVE_TIERED
By “consent” I mean avoiding a default option for package resolution and instead asking the user to select an option in REPL.

Or maybe keep the default option in Pkg.add as is (with current warnings), but tell the user in Pkg.status() which package version is in the current environment and which version is the latest:

(@v1.6) pkg> status
      Status `C:\Users\azevelev\.julia\environments\v1.6\Project.toml`
              Package    Current   Latest
  [f6006082] `EvoTrees   v0.5.3    v0.7.0`
  [9bbee03b]  NaiveBayes v0.5.0    v0.5.0
  [add582a8] `MLJ        v0.15.2   v0.16.0`
  [d491faf4] `MLJModels  v0.13.3   v0.14.1` 

And highlight (in a different color?) which packages in the current environment are not the latest.

I think package resolution is one of the most common challenges faced by newcomers to Julia.

It would help if there was a standard parsimonious tutorial introducing package management to newcomers.