Hosting Docs with Documenter.jl with Dependencies / GitHub Actions with Unregistered Packages

astrobc1 · June 26, 2022, 5:25pm

I’m struggling to get the documentation for my package hosted due to external dependencies, specifically ones that are also hosted on GitHub but not the general registry. I’ve added these extra deps to both the main package and the package inside docs/ with Pkg.add(url="github_url").

The main GitHub repo: GitHub - astrobc1/Echelle.jl

Deps:

Primary error:

ERROR: expected package `EchelleReduce [6e4c0b07]` to exist at path `/home/runner/.julia/packages/EchelleReduce/kONaA`

The raw log:

2022-06-26T17:20:04.2391101Z Requested labels: ubuntu-latest
2022-06-26T17:20:04.2391147Z Job defined at: astrobc1/Echelle.jl/.github/workflows/documentation.yml@refs/heads/master
2022-06-26T17:20:04.2391170Z Waiting for a runner to pick up this job...
2022-06-26T17:20:04.8380735Z Job is waiting for a hosted runner to come online.
2022-06-26T17:20:10.1709442Z Job is about to start running on the hosted runner: Hosted Agent (hosted)
2022-06-26T17:20:14.3895605Z Current runner version: '2.293.0'
2022-06-26T17:20:14.3928579Z ##[group]Operating System
2022-06-26T17:20:14.3929517Z Ubuntu
2022-06-26T17:20:14.3929882Z 20.04.4
2022-06-26T17:20:14.3930269Z LTS
2022-06-26T17:20:14.3930636Z ##[endgroup]
2022-06-26T17:20:14.3931065Z ##[group]Virtual Environment
2022-06-26T17:20:14.3931477Z Environment: ubuntu-20.04
2022-06-26T17:20:14.3931903Z Version: 20220619.1
2022-06-26T17:20:14.3932594Z Included Software: https://github.com/actions/virtual-environments/blob/ubuntu20/20220619.1/images/linux/Ubuntu2004-Readme.md
2022-06-26T17:20:14.3933430Z Image Release: https://github.com/actions/virtual-environments/releases/tag/ubuntu20%2F20220619.1
2022-06-26T17:20:14.3933962Z ##[endgroup]
2022-06-26T17:20:14.3934422Z ##[group]Virtual Environment Provisioner
2022-06-26T17:20:14.3934914Z 1.0.0.0-main-20220531-1
2022-06-26T17:20:14.3935247Z ##[endgroup]
2022-06-26T17:20:14.3936055Z ##[group]GITHUB_TOKEN Permissions
2022-06-26T17:20:14.3936834Z Contents: write
2022-06-26T17:20:14.3937293Z Metadata: read
2022-06-26T17:20:14.3937695Z ##[endgroup]
2022-06-26T17:20:14.3941864Z Secret source: Actions
2022-06-26T17:20:14.3942399Z Prepare workflow directory
2022-06-26T17:20:14.4952365Z Prepare all required actions
2022-06-26T17:20:14.5174065Z Getting action download info
2022-06-26T17:20:14.8280859Z Download action repository 'actions/checkout@v2' (SHA:7884fcad6b5d53d10323aee724dc68d8b9096a2e)
2022-06-26T17:20:15.5379578Z Download action repository 'julia-actions/setup-julia@v1' (SHA:5113fd16e9c6c3a86d6ae9bc9155c40ce05e3acc)
2022-06-26T17:20:16.2660733Z ##[group]Run actions/checkout@v2
2022-06-26T17:20:16.2661078Z with:
2022-06-26T17:20:16.2661355Z   repository: astrobc1/Echelle.jl
2022-06-26T17:20:16.2661872Z   token: ***
2022-06-26T17:20:16.2662127Z   ssh-strict: true
2022-06-26T17:20:16.2662399Z   persist-credentials: true
2022-06-26T17:20:16.2662683Z   clean: true
2022-06-26T17:20:16.2662926Z   fetch-depth: 1
2022-06-26T17:20:16.2663156Z   lfs: false
2022-06-26T17:20:16.2663394Z   submodules: false
2022-06-26T17:20:16.2663683Z   set-safe-directory: true
2022-06-26T17:20:16.2664026Z ##[endgroup]
2022-06-26T17:20:16.5806743Z Syncing repository: astrobc1/Echelle.jl
2022-06-26T17:20:16.5809868Z ##[group]Getting Git version info
2022-06-26T17:20:16.5810503Z Working directory is '/home/runner/work/Echelle.jl/Echelle.jl'
2022-06-26T17:20:16.5811131Z [command]/usr/bin/git version
2022-06-26T17:20:16.5990537Z git version 2.36.1
2022-06-26T17:20:16.5991727Z ##[endgroup]
2022-06-26T17:20:16.6016725Z Temporarily overriding HOME='/home/runner/work/_temp/ab1f4f3a-41ab-4e37-bd4d-d034548a6d05' before making global git config changes
2022-06-26T17:20:16.6017528Z Adding repository directory to the temporary git global config as a safe directory
2022-06-26T17:20:16.6025038Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/Echelle.jl/Echelle.jl
2022-06-26T17:20:16.6080424Z Deleting the contents of '/home/runner/work/Echelle.jl/Echelle.jl'
2022-06-26T17:20:16.6088076Z ##[group]Initializing the repository
2022-06-26T17:20:16.6094378Z [command]/usr/bin/git init /home/runner/work/Echelle.jl/Echelle.jl
2022-06-26T17:20:16.6176144Z hint: Using 'master' as the name for the initial branch. This default branch name
2022-06-26T17:20:16.6177056Z hint: is subject to change. To configure the initial branch name to use in all
2022-06-26T17:20:16.6178438Z hint: of your new repositories, which will suppress this warning, call:
2022-06-26T17:20:16.6178938Z hint: 
2022-06-26T17:20:16.6179607Z hint: 	git config --global init.defaultBranch <name>
2022-06-26T17:20:16.6180080Z hint: 
2022-06-26T17:20:16.6180806Z hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and
2022-06-26T17:20:16.6182164Z hint: 'development'. The just-created branch can be renamed via this command:
2022-06-26T17:20:16.6182754Z hint: 
2022-06-26T17:20:16.6183837Z hint: 	git branch -m <name>
2022-06-26T17:20:16.6188585Z Initialized empty Git repository in /home/runner/work/Echelle.jl/Echelle.jl/.git/
2022-06-26T17:20:16.6241384Z [command]/usr/bin/git remote add origin https://github.com/astrobc1/Echelle.jl
2022-06-26T17:20:16.6291743Z ##[endgroup]
2022-06-26T17:20:16.6292697Z ##[group]Disabling automatic garbage collection
2022-06-26T17:20:16.6297447Z [command]/usr/bin/git config --local gc.auto 0
2022-06-26T17:20:16.6333828Z ##[endgroup]
2022-06-26T17:20:16.6334705Z ##[group]Setting up auth
2022-06-26T17:20:16.6343649Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2022-06-26T17:20:16.6382767Z [command]/usr/bin/git submodule foreach --recursive git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :
2022-06-26T17:20:16.6813499Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2022-06-26T17:20:16.6850551Z [command]/usr/bin/git submodule foreach --recursive git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :
2022-06-26T17:20:16.7110018Z [command]/usr/bin/git config --local http.https://github.com/.extraheader AUTHORIZATION: basic ***
2022-06-26T17:20:16.7153773Z ##[endgroup]
2022-06-26T17:20:16.7154779Z ##[group]Fetching the repository
2022-06-26T17:20:16.7163354Z [command]/usr/bin/git -c protocol.version=2 fetch --no-tags --prune --progress --no-recurse-submodules --depth=1 origin +ab896342b3e50d8ae9a86c5ec719383b42b52d5b:refs/remotes/origin/master
2022-06-26T17:20:17.0061207Z remote: Enumerating objects: 88, done.        
2022-06-26T17:20:17.0066307Z remote: Counting objects:   1% (1/88)        
2022-06-26T17:20:17.0068281Z remote: Counting objects:   2% (2/88)        
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2022-06-26T17:20:17.0138090Z remote: Counting objects: 100% (88/88)        
2022-06-26T17:20:17.0138878Z remote: Counting objects: 100% (88/88), done.        
2022-06-26T17:20:17.0139580Z remote: Compressing objects:   1% (1/73)        
2022-06-26T17:20:17.0250756Z remote: Compressing objects:   2% (2/73)        
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2022-06-26T17:20:17.0275573Z remote: Compressing objects:  90% (66/73)        
2022-06-26T17:20:17.0275899Z remote: Compressing objects:  91% (67/73)        
2022-06-26T17:20:17.0276225Z remote: Compressing objects:  93% (68/73)        
2022-06-26T17:20:17.0276542Z remote: Compressing objects:  94% (69/73)        
2022-06-26T17:20:17.0276931Z remote: Compressing objects:  95% (70/73)        
2022-06-26T17:20:17.0277267Z remote: Compressing objects:  97% (71/73)        
2022-06-26T17:20:17.0277582Z remote: Compressing objects:  98% (72/73)        
2022-06-26T17:20:17.0277912Z remote: Compressing objects: 100% (73/73)        
2022-06-26T17:20:17.0278261Z remote: Compressing objects: 100% (73/73), done.        
2022-06-26T17:20:17.1367305Z remote: Total 88 (delta 19), reused 56 (delta 4), pack-reused 0        
2022-06-26T17:20:17.1587798Z From https://github.com/astrobc1/Echelle.jl
2022-06-26T17:20:17.1588899Z  * [new ref]         ab896342b3e50d8ae9a86c5ec719383b42b52d5b -> origin/master
2022-06-26T17:20:17.1628272Z ##[endgroup]
2022-06-26T17:20:17.1629496Z ##[group]Determining the checkout info
2022-06-26T17:20:17.1630875Z ##[endgroup]
2022-06-26T17:20:17.1631750Z ##[group]Checking out the ref
2022-06-26T17:20:17.1635797Z [command]/usr/bin/git checkout --progress --force -B master refs/remotes/origin/master
2022-06-26T17:20:17.1832229Z Reset branch 'master'
2022-06-26T17:20:17.1837264Z branch 'master' set up to track 'origin/master'.
2022-06-26T17:20:17.1841297Z ##[endgroup]
2022-06-26T17:20:17.1893943Z [command]/usr/bin/git log -1 --format='%H'
2022-06-26T17:20:17.1933370Z 'ab896342b3e50d8ae9a86c5ec719383b42b52d5b'
2022-06-26T17:20:17.2281288Z ##[group]Run julia-actions/setup-julia@v1
2022-06-26T17:20:17.2281619Z with:
2022-06-26T17:20:17.2281852Z   version: 1.7
2022-06-26T17:20:17.2282075Z   arch: X64
2022-06-26T17:20:17.2282339Z   show-versioninfo: false
2022-06-26T17:20:17.2282615Z ##[endgroup]
2022-06-26T17:20:18.9954721Z [command]tar xf /home/runner/work/_temp/68fc4eda-b78f-4bb0-a621-50d286c0f270 --strip-components=1 -C julia-x64-1.7.3-8HbM4O
2022-06-26T17:20:26.2849138Z [command]julia --version
2022-06-26T17:20:26.2918505Z (node:1569) [DEP0147] DeprecationWarning: In future versions of Node.js, fs.rmdir(path, { recursive: true }) will be removed. Use fs.rm(path, { recursive: true }) instead
2022-06-26T17:20:26.2919520Z (Use `node --trace-deprecation ...` to show where the warning was created)
2022-06-26T17:20:26.3303085Z julia version 1.7.3
2022-06-26T17:20:26.3477013Z ##[group]Run julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
2022-06-26T17:20:26.3477677Z e[36;1mjulia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'e[0m
2022-06-26T17:20:26.3547108Z shell: /usr/bin/bash -e {0}
2022-06-26T17:20:26.3547407Z ##[endgroup]
2022-06-26T17:20:26.9277302Z   Installing known registries into `~/.julia`
2022-06-26T17:20:29.1617375Z    Resolving package versions...
2022-06-26T17:20:30.3625226Z ERROR: expected package `EchelleReduce [6e4c0b07]` to exist at path `/home/runner/.julia/packages/EchelleReduce/kONaA`
2022-06-26T17:20:30.3625972Z Stacktrace:
2022-06-26T17:20:30.7443646Z   [1] pkgerror(msg::String)
2022-06-26T17:20:30.9200138Z     @ Pkg.Types /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/Types.jl:68
2022-06-26T17:20:30.9222693Z   [2] collect_fixed!(env::Pkg.Types.EnvCache, pkgs::Vector{Pkg.Types.PackageSpec}, names::Dict{Base.UUID, String})
2022-06-26T17:20:30.9223793Z     @ Pkg.Operations /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:258
2022-06-26T17:20:30.9242738Z   [3] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber)
2022-06-26T17:20:30.9243428Z     @ Pkg.Operations /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:309
2022-06-26T17:20:30.9264538Z   [4] targeted_resolve(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
2022-06-26T17:20:30.9265301Z     @ Pkg.Operations /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1154
2022-06-26T17:20:30.9285489Z   [5] tiered_resolve(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber)
2022-06-26T17:20:30.9286173Z     @ Pkg.Operations /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1125
2022-06-26T17:20:30.9306316Z   [6] _resolve(io::Base.PipeEndpoint, env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
2022-06-26T17:20:30.9307083Z     @ Pkg.Operations /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1160
2022-06-26T17:20:30.9914561Z   [7] develop(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
2022-06-26T17:20:30.9915810Z     @ Pkg.Operations /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1198
2022-06-26T17:20:31.0386931Z   [8] develop(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; shared::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.PipeEndpoint, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.PipeEndpoint}}})
2022-06-26T17:20:31.0388429Z     @ Pkg.API /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/API.jl:215
2022-06-26T17:20:31.0583668Z   [9] develop(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
2022-06-26T17:20:31.0584725Z     @ Pkg.API /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
2022-06-26T17:20:31.0590756Z  [10] develop(pkgs::Vector{Pkg.Types.PackageSpec})
2022-06-26T17:20:31.0591541Z     @ Pkg.API /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
2022-06-26T17:20:31.0592153Z  [11] #develop#14
2022-06-26T17:20:31.0592776Z     @ /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
2022-06-26T17:20:31.0593470Z  [12] develop(pkg::Pkg.Types.PackageSpec)
2022-06-26T17:20:31.0594592Z     @ Pkg.API /opt/hostedtoolcache/julia/1.7.3/x64/share/julia/stdlib/v1.7/Pkg/src/API.jl:141
2022-06-26T17:20:31.0595571Z  [13] top-level scope
2022-06-26T17:20:31.0595981Z     @ none:1
2022-06-26T17:20:31.0751031Z ##[error]Process completed with exit code 1.
2022-06-26T17:20:31.0839345Z Post job cleanup.
2022-06-26T17:20:31.2336157Z [command]/usr/bin/git version
2022-06-26T17:20:31.2407591Z git version 2.36.1
2022-06-26T17:20:31.2419334Z Temporarily overriding HOME='/home/runner/work/_temp/bb53e454-0756-484d-921a-96c2c9549417' before making global git config changes
2022-06-26T17:20:31.2421174Z Adding repository directory to the temporary git global config as a safe directory
2022-06-26T17:20:31.2428224Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/Echelle.jl/Echelle.jl
2022-06-26T17:20:31.2477964Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2022-06-26T17:20:31.2521040Z [command]/usr/bin/git submodule foreach --recursive git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :
2022-06-26T17:20:31.2804266Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2022-06-26T17:20:31.2918850Z http.https://github.com/.extraheader
2022-06-26T17:20:31.2920198Z [command]/usr/bin/git config --local --unset-all http.https://github.com/.extraheader
2022-06-26T17:20:31.2945812Z [command]/usr/bin/git submodule foreach --recursive git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :
2022-06-26T17:20:31.3467276Z Cleaning up orphan processes

halleysfifthinc · June 27, 2022, 2:37pm

Based on one of my own packages depending on another personal and unregistered package, I think the repo-url might need to be a git link (i.e. the GitHub link with '.git' at the end). You would need to fix that in the environment of your main package and in the docs environment.

astrobc1 · June 27, 2022, 4:45pm

Thanks for the advice! Are you recommending I manually edit the Manifest.toml file by adding .git to the end of any repo-urls? The Project.toml file doesn’t explicitly contain repo urls from what I can see, regardless of where the package is registered. I tried this and it resulted in the same error, although this time it took much longer to fail.

[[deps.EchelleBase]]
deps = ["DataFrames", "FITSIO", "Infiltrator", "LinearAlgebra", "LoopVectorization", "NaNStatistics", "Pkg", "Polynomials", "PyCall", "Reexport", "Statistics", "StatsBase"]
git-tree-sha1 = "40ead7c6e8a3247ad18f8da5a5ad4d6bdf9d09d7"
repo-rev = "master"
repo-url = "https://github.com/astrobc1/EchelleBase.jl" <-- Added .git to the end
uuid = "fb2f92b1-9968-41b4-8835-2765b866fa7d"
version = "0.1.0"

I also don’t need to do anything special with these external package deps to use the package itself -I just use, e.g., Pkg.add(url="https://github.com/astrobc1/EchelleBase.jl") to make them visible in any other package.

halleysfifthinc · June 27, 2022, 4:57pm

No you should not edit the Manifest file manually, as it is automatically generated and your edits would be overwritten. I suggest you try e.g. Pkg.add(Pkg.add(url="https://github.com/JuliaLang/Example.jl", rev="master") (or use a particular tag instead of your master/main branch).

astrobc1 · June 27, 2022, 5:19pm

Right ok, that’s what I thought.

So I think then I’ve already added the deps for both the main package and sub-package within docs/ as you’ve instructed. The only difference is that I didn’t add .git onto the end of the repo url. I tried re-adding the relevant deps in both the main package and docs sub-package with .git on the end of the url, again resulting in the same error.

astrobc1 · June 30, 2022, 2:39pm

One thing I now realize is that the dependency it’s failing on (EchelleReduce) is unlikely the first unregistered dep it would run into (EchelleBase). So I suspect it successfully managed to find the EchelleBase dep without problems, but I’m really not sure what the difference is, if any.

astrobc1 · July 4, 2022, 9:36pm

Another update: I’ve narrowed down the problem to have little if anything to do with Documenter.jl, but rather the available registries when the GitHub actions are run. I had tested adding the package EchelleBase to the general registry, which is why it doesn’t fail on that dependency.

Instead, it fails at Pkg.develop(PackageSpec(path=pwd()));

So, is there a way in my documentation.yml file to tell Julia in the the GitHub actions where to locate these dependencies?

name: Documentation

on:
  push:
    branches:
      - master # update to match your development branch (master, main, dev, trunk, ...)
    tags: '*'
  pull_request:

jobs:
  build:
    permissions:
      contents: write
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - uses: julia-actions/setup-julia@v1
        with:
          version: '1.7'
      - name: Install dependencies
        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); println("Hello"); Pkg.instantiate()'
      - name: Build and deploy
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
        run: julia --project=docs/ docs/make.jl

filchristou · November 11, 2022, 6:03pm

I have the same problem with some forks of mine. I am getting the same error. I substituted the forked packages with the registered ones and it just worked without changing anything (Manifests.toml were also uploaded). I am not sure what the problem is.

j-fu · November 11, 2022, 8:50pm

You could register (with the help of LocalRegistry.jl) the package in your own registry (may be with version 0.0.x if you later want to register in General starting with 0.1.0.).

Then you can add that registry during CI.
See e.g. this ci file and a julia script called therein
to add another registry during CI.

Oleg_Soloviev · June 23, 2023, 3:31pm

I’ve just met the same problem. The workaround I use now is to add the dependencies not using Project.toml, but in github action file documentation.yaml. So now its section Install dependencies reads for me

run: julia --project=docs/ -e 'using Pkg; Pkg.add(url = "https://github.com/olejorik/AlternatingProjections.jl", rev= "develop"); Pkg.add(url = "https://github.com/olejorik/SampledDomains.jl"); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'

The packages AlternatingProjections.jl and SampledDomains.jl are unregistered and removed from Project.toml.

The whole github action file is available here.