Deprecated Utility Packages for Turing.jl

This repository contains deprecated utility packages for Turing.jl.
These packages have either:

• Been upstreamed into Turing.jl,
• Been superseded by new features in Turing.jl itself,
• Or replaced by other packages in the Julia ecosystem.

Planned Deprecations

Package	Status	Documentation
AdvancedPS.jl	⬜ Planned	(pending)
TuringBenchmarking.jl	✅ Merged	Documentation
TuringCallbacks.jl	⬜ Planned	(pending)
ParetoSmooth.jl	⬜ Planned	(pending)

In addition, we would like to deprecate DistributionsAD.jl when Mooncake / Enzyme replaces ReverseDiff and ForwardDiff.

Guide: Adding Packages While Preserving Commit History

The following steps describe how to migrate a standalone package into this repository while preserving its full Git history, using git subtree.

Step 1: Clone this repository

git clone https://github.com/TuringLang/deprecated.git
cd deprecated

Step 2: Create a new branch

You can always create a feature branch for each imported package.

git checkout -b migrate-<package-name>

Example:

git checkout -b migrate-advancedps

Step 3: Add the source repository as a remote

git remote add <remote-name> <url-to-original-repo>
git fetch <remote-name>

Example:

git remote add advancedps https://github.com/TuringLang/AdvancedPS.jl.git
git fetch advancedps

Step 4: Add the package using git subtree

Import the package under a subfolder while preserving history.

git subtree add --prefix=<target-folder-name> <remote-name>/<branch-name>

Example:

git subtree add --prefix=AdvancedPS advancedps/main

This will automatically create a new commit, preserving the full commit history within the subfolder.

Step 5: Check if all registered versions exist

Before opening a Pull Request, verify that all registered versions of the package are present locally. In Julia REPL, run:

using RegistryInstances, UUIDs, Git

const GENERAL_UUID = UUID("23338594-aafe-5451-b93e-139f81909106")

pretty_print_row(row) = println(row.pkg_name, ": v", row.version, " ", row.found ? "found" : "is missing")
pretty_print_table(table) = foreach(pretty_print_row, table)

function check_all_found(table)
    idx = findfirst(row -> !row.found, table)
    idx === nothing && return nothing
    row = table[idx]
    error(string("Repository missing v", row.version, " of package $(row.pkg_name)"))
end

function check_packages_versions(pkg_names, repo_url; registry_uuid=GENERAL_UUID, verbose=true, throw=true)
    if isdir(repo_url)
        dir = repo_url
    else
        dir = mktempdir()
        run(`$(git()) clone $(repo_url) $dir`)
    end

    registry = only(filter!(r -> r.uuid == registry_uuid, reachable_registries()))

    table = @NamedTuple{pkg_name::String, version::VersionNumber, found::Bool, tree_sha::Base.SHA1}[]

    for pkg_name in pkg_names
        pkg = registry.pkgs[only(uuids_from_name(registry, pkg_name))]
        versions = registry_info(pkg).version_info
        for version in sort(collect(keys(versions)))
            tree_sha = versions[version].git_tree_sha1
            found = success(`$(git()) -C $dir rev-parse -q --verify "$(tree_sha)^{tree}"`)

            push!(table, (; pkg_name, version, found, tree_sha))
        end
    end
    verbose && pretty_print_table(table)
    throw && check_all_found(table)
    return table
end

check_package_versions(pkg_name, repo_url; kw...) = check_packages_versions([pkg_name], repo_url; kw...)

Reference: JuliaRegistries/General Contributing Guide

Then check if all registered versions exist:

julia> check_package_versions("AdvancedPS", ".")

Step 6: Push your feature branch

git push origin migrate-<package-name>

Example:

git push origin migrate-advancedps

Step 7: Open a Pull Request

• Open a Pull Request from your feature branch (e.g., migrate-advancedps) into the main branch.
• Get it reviewed and merged.

Step 8: Add all versioned docs

Once the PR is merged, add all versioned docs from the gh-pages branch of the original repository to the gh-pages branch of this repository in the package folder.

git fetch origin
git checkout gh-pages
git pull origin gh-pages

Make sure that your Git is configured to allow symlinks:

git config core.symlinks true

(This should be set before cloning, but good to double-check.) Otherwise, symlinks will be cloned as plain text files.

Create a temporary folder

mkdir temp-gh-pages
cd temp-gh-pages

# Clone only the gh-pages branch of the original repo
git clone --branch gh-pages --single-branch --depth 1 <original-repo-url> .

Make sure to add these files and folders to the correct location:

• All v* folders should be added to the root of the package folder.
• versions.js should be replaced with versions.js from the original repository.
• All symlinks should be added to the root of the package folder. Ensure that your Git has symlinks enabled.

Finally, delete the temporary folder, add, commit the changes and push to the gh-pages branch of the deprecated repository:

git add -A
git commit -m "Add versioned docs for AdvancedPS"
git push origin gh-pages

Notes

• git subtree add automatically creates a commit.
• Tags from the original repository are not automatically transferred.
  If needed, important tags should be manually recreated after migration.
• Please avoid pushing directly to main. Always work via a feature branch and a Pull Request.