Fix manifest_usage.toml and Registry process concurrency via pid locking

CHANGELOG.md

@@ -9,6 +9,8 @@ Pkg v1.9 Release Notes
   to the directory of the package being tested. Previously the `--code-coverage=user` option was used, which tracked files
   in all code outside of Core & Base, i.e. all stdlibs and all user packages, which often made running tests with
   code coverage a lot slower ([#3021]).
+- Writes to `manifest_usage.toml` and Registry downloads/updates are now protected from process concurrency clashes via
+  a pidfile lock ([#2793]).
 
 Pkg v1.8 Release Notes
 ======================
@@ -59,6 +61,7 @@ Pkg v1.7 Release Notes
 [#2580]: https://github.com/JuliaLang/Pkg.jl/issues/2580
 [#2689]: https://github.com/JuliaLang/Pkg.jl/issues/2689
 [#2702]: https://github.com/JuliaLang/Pkg.jl/issues/2702
+[#2793]: https://github.com/JuliaLang/Pkg.jl/issues/2793
 [#2815]: https://github.com/JuliaLang/Pkg.jl/issues/2815
 [#2906]: https://github.com/JuliaLang/Pkg.jl/issues/2906
 [#2933]: https://github.com/JuliaLang/Pkg.jl/issues/2933

Project.toml

@@ -9,6 +9,7 @@ version = "1.8.0"
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+FileWatching = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 LibGit2 = "76f85450-5226-5b5a-8eaa-529ad045b433"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"

ext/HistoricaStdlibGenerator/Manifest.toml

@@ -1,140 +1,160 @@
 # This file is machine-generated - editing it directly is not advised
 
-[[ArgTools]]
+julia_version = "1.9.0-DEV"
+manifest_format = "2.0"
+project_hash = "136cd253a89b81157598e253c00b82898978de50"
+
+[[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+version = "1.1.1"
 
-[[Artifacts]]
+[[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 
-[[Base64]]
+[[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
-[[Dates]]
+[[deps.Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
-[[Downloads]]
-deps = ["ArgTools", "LibCURL", "NetworkOptions"]
-git-tree-sha1 = "5a19556930ddb432b1094e0796911c16282c517f"
+[[deps.Downloads]]
+deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+version = "1.6.0"
+
+[[deps.FileWatching]]
+uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 
-[[InteractiveUtils]]
+[[deps.InteractiveUtils]]
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
-[[JSON3]]
+[[deps.JSON3]]
 deps = ["Dates", "Mmap", "Parsers", "StructTypes", "UUIDs"]
-git-tree-sha1 = "961ef1c3e5c8a595d5bec270a9007429ef12ed10"
+git-tree-sha1 = "7d58534ffb62cd947950b3aa9b993e63307a6125"
 uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
-version = "1.5.1"
+version = "1.9.2"
 
-[[LibCURL]]
+[[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
 uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+version = "0.6.3"
 
-[[LibCURL_jll]]
+[[deps.LibCURL_jll]]
 deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
 uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+version = "7.81.0+0"
 
-[[LibGit2]]
+[[deps.LibGit2]]
 deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
-[[LibSSH2_jll]]
+[[deps.LibSSH2_jll]]
 deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
 uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+version = "1.10.2+0"
 
-[[Libdl]]
+[[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[Logging]]
+[[deps.Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
-[[Markdown]]
+[[deps.Markdown]]
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
-[[MbedTLS_jll]]
+[[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.28.0+0"
 
-[[Mmap]]
+[[deps.Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
-[[MozillaCACerts_jll]]
+[[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+version = "2022.2.1"
 
-[[NetworkOptions]]
+[[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+version = "1.2.0"
 
-[[Parsers]]
+[[deps.Parsers]]
 deps = ["Dates"]
-git-tree-sha1 = "50c9a9ed8c714945e01cd53a21007ed3865ed714"
+git-tree-sha1 = "13468f237353112a01b2d6b32f3d0f80219944aa"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "1.0.15"
+version = "2.2.2"
 
-[[Pkg]]
-deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
+[[deps.Pkg]]
+deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 path = "../.."
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78e"
-version = "1.5.0"
+version = "1.8.0"
 
-[[Printf]]
+[[deps.Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[REPL]]
+[[deps.REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
-[[Random]]
-deps = ["Serialization"]
+[[deps.Random]]
+deps = ["SHA", "Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
-[[SHA]]
+[[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+version = "0.7.0"
 
-[[Scratch]]
+[[deps.Scratch]]
 deps = ["Dates"]
-git-tree-sha1 = "ad4b278adb62d185bbcb6864dc24959ab0627bf6"
+git-tree-sha1 = "0b4b7f1393cff97c33891da2a0bf69c6ed241fda"
 uuid = "6c6a2e73-6563-6170-7368-637461726353"
-version = "1.0.3"
+version = "1.1.0"
 
-[[Serialization]]
+[[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
-[[Sockets]]
+[[deps.Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
-[[StructTypes]]
+[[deps.StructTypes]]
 deps = ["Dates", "UUIDs"]
-git-tree-sha1 = "d94235fcdc4a09649f263365c5f7e4ed4ba6ed34"
+git-tree-sha1 = "d24a825a95a6d98c385001212dc9020d609f2d4f"
 uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
-version = "1.2.1"
+version = "1.8.1"
 
-[[TOML]]
+[[deps.TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+version = "1.0.0"
 
-[[Tar]]
+[[deps.Tar]]
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+version = "1.10.0"
 
-[[UUIDs]]
+[[deps.UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
-[[Unicode]]
+[[deps.Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
-[[Zlib_jll]]
+[[deps.Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.12+1"
 
-[[nghttp2_jll]]
+[[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+version = "1.41.0+1"
 
-[[p7zip_jll]]
+[[deps.p7zip_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
+version = "16.2.1+1"

src/Registry/Registry.jl

@@ -5,6 +5,7 @@ using ..Pkg: depots1, printpkgstyle, stderr_f, isdir_nothrow, pathrepr, pkg_serv
              GitTools, get_bool_env
 using ..Pkg.PlatformEngines: download_verify_unpack, download, download_verify, exe7z
 using UUIDs, LibGit2, TOML
+import FileWatching
 
 include("registry_instance.jl")
 
@@ -163,6 +164,8 @@ function download_registries(io::IO, regs::Vector{RegistrySpec}, depot::String=d
     populate_known_registries_with_urls!(regs)
     regdir = joinpath(depot, "registries")
     isdir(regdir) || mkpath(regdir)
+    # only allow one julia process to download and install registries at a time
+    FileWatching.mkpidlock(joinpath(regdir, ".pid"), stale_age = 10) do
     registry_urls = pkg_server_registry_urls()
     for reg in regs
         if reg.path !== nothing && reg.url !== nothing
@@ -250,6 +253,7 @@ function download_registries(io::IO, regs::Vector{RegistrySpec}, depot::String=d
             end
         end
     end
+    end # mkpidlock
     return nothing
 end
 
@@ -342,7 +346,12 @@ Pkg.Registry.update(RegistrySpec(uuid = "23338594-aafe-5451-b93e-139f81909106"))
 update(reg::Union{String,RegistrySpec}; kwargs...) = update([reg]; kwargs...)
 update(regs::Vector{String}; kwargs...) = update([RegistrySpec(name = name) for name in regs]; kwargs...)
 function update(regs::Vector{RegistrySpec} = RegistrySpec[]; io::IO=stderr_f(), force::Bool=true)
-    isempty(regs) && (regs = reachable_registries(; depots=depots1()))
+    depot = depots1()
+    isempty(regs) && (regs = reachable_registries(; depots=depot))
+    regdir = joinpath(depot, "registries")
+    isdir(regdir) || mkpath(regdir)
+    # only allow one julia process to update registries at a time
+    FileWatching.mkpidlock(joinpath(regdir, ".pid"), stale_age = 10) do
     errors = Tuple{String, String}[]
     registry_urls = pkg_server_registry_urls()
     for reg in unique(r -> r.uuid, find_installed_registries(io, regs); seen=Set{UUID}())
@@ -448,6 +457,7 @@ function update(regs::Vector{RegistrySpec} = RegistrySpec[]; io::IO=stderr_f(),
         end
         @error warn_str
     end
+    end # mkpidlock
     return
 end
 

src/Types.jl

@@ -15,6 +15,7 @@ import ..Pkg, ..Registry
 import ..Pkg: GitTools, depots, depots1, logdir, set_readonly, safe_realpath, pkg_server, stdlib_dir, stdlib_path, isurl, stderr_f, RESPECT_SYSIMAGE_VERSIONS
 import Base.BinaryPlatforms: Platform
 using ..Pkg.Versions
+import FileWatching
 
 import Base: SHA1
 using SHA
@@ -484,16 +485,31 @@ function write_env_usage(source_file::AbstractString, usage_filepath::AbstractSt
     # Ensure that log dir exists
     !ispath(logdir()) && mkpath(logdir())
 
-    # Generate entire entry as a string first
-    entry = sprint() do io
-        TOML.print(io, Dict(source_file => [Dict("time" => now())]))
-    end
-
-    # Append entry to log file in one chunk
     usage_file = joinpath(logdir(), usage_filepath)
-    open(usage_file, append=true) do io
-        write(io, entry)
+    timestamp = now()
+
+    ## Atomically write usage file using process id locking
+    FileWatching.mkpidlock(usage_file * ".pid", stale_age = 3) do
+        usage = if isfile(usage_file)
+            TOML.parsefile(usage_file)
+        else
+            Dict{String, Any}()
+        end
+
+        # record new usage
+        usage[source_file] = [Dict("time" => timestamp)]
+
+        # keep only latest usage info
+        for k in keys(usage)
+            times = map(d -> Dates.DateTime(d["time"]), usage[k])
+            usage[k] = [Dict("time" => maximum(times))]
+        end
+
+        open(usage_file, "w") do io
+            TOML.print(io, usage, sorted=true)
+        end
     end
+    return
 end
 
 function read_package(path::String)

test/pkg.jl

@@ -363,6 +363,56 @@ temp_pkg_dir() do project_path
         @test any(x -> startswith(x, manifest), keys(usage))
     end
 
+    @testset "test atomicity of write_env_usage with $(Sys.CPU_THREADS) parallel processes" begin
+        tasks = Task[]
+        iobs = IOBuffer[]
+        Sys.CPU_THREADS == 1 && error("Cannot test for atomic usage log file interaction effectively with only Sys.CPU_THREADS=1")
+        run(`$(Base.julia_cmd()) --project="$(pkgdir(Pkg))" -e "import Pkg"`) # to precompile Pkg given we're in a different depot
+        flag_start_dir = tempdir() # once n=Sys.CPU_THREADS files are in here, the processes can proceed to the concurrent test
+        flag_end_file = tempname() # use creating this file as a way to stop the processes early if an error happens
+        for i in 1:Sys.CPU_THREADS
+            iob = IOBuffer()
+            t = @async run(pipeline(`$(Base.julia_cmd()[1]) --project="$(pkgdir(Pkg))"
+                -e "import Pkg;
+                Pkg.UPDATED_REGISTRY_THIS_SESSION[] = true;
+                Pkg.activate(temp = true);
+                Pkg.add(\"Random\", io = devnull);
+                touch(tempname(raw\"$flag_start_dir\")) # file marker that first part has finished
+                while length(readdir(raw\"$flag_start_dir\")) < $(Sys.CPU_THREADS)
+                    # sync all processes to start at the same time
+                    sleep(0.1)
+                end
+                @async begin
+                    sleep(15)
+                    touch(raw\"$flag_end_file\")
+                end
+                i = 0
+                while !isfile(raw\"$flag_end_file\")
+                    global i += 1
+                    try
+                        Pkg.Types.EnvCache()
+                    catch
+                        touch(raw\"$flag_end_file\")
+                        println(stderr, \"Errored after $i iterations\")
+                        rethrow()
+                    end
+                    yield()
+                end"`,
+                stderr = iob, stdout = devnull))
+            push!(tasks, t)
+            push!(iobs, iob)
+        end
+        for i in eachindex(tasks)
+            try
+                fetch(tasks[i]) # If any of these failed it will throw when fetched
+            catch
+                print(String(take!(iobs[i])))
+                break
+            end
+        end
+        @test any(istaskfailed, tasks) == false
+    end
+
     @testset "adding nonexisting packages" begin
         nonexisting_pkg = randstring(14)
         @test_throws PkgError Pkg.add(nonexisting_pkg)