Merge pull request #3595 from JuliaLang/backports-release-1.9

src/API.jl

@@ -1155,7 +1155,7 @@ function precompile(ctx::Context, pkgs::Vector{PackageSpec}; internal_call::Bool
             extdep_names = extdep_names isa String ? String[extdep_names] : extdep_names
             for extdep_name in extdep_names
                 extdep_uuid = weakdeps[extdep_name]
-                if extdep_uuid in keys(ctx.env.manifest.deps)
+                if extdep_uuid in keys(ctx.env.manifest.deps) || Base.in_sysimage(Base.PkgId(extdep_uuid, extdep_name))
                     push!(ext_deps, Base.PkgId(extdep_uuid, extdep_name))
                 else
                     all_extdeps_available = false
@@ -1298,8 +1298,9 @@ function precompile(ctx::Context, pkgs::Vector{PackageSpec}; internal_call::Bool
                 println(io, " Interrupted: Exiting precompilation...")
             end
             interrupted = true
+            return true
         else
-            @error "Pkg.precompile error" exception=(err, catch_backtrace())
+            return false
         end
     end
 
@@ -1373,7 +1374,7 @@ function precompile(ctx::Context, pkgs::Vector{PackageSpec}; internal_call::Bool
                 wait(t)
             end
         catch err
-            handle_interrupt(err, true)
+            handle_interrupt(err, true) || rethrow()
         finally
             fancyprint && print(io, ansi_enablecursor)
         end
@@ -1482,7 +1483,7 @@ function precompile(ctx::Context, pkgs::Vector{PackageSpec}; internal_call::Bool
                 n_done += 1
                 notify(was_processed[pkg])
             catch err_outer
-                handle_interrupt(err_outer)
+                handle_interrupt(err_outer) || rethrow()
                 notify(was_processed[pkg])
             finally
                 filter!(!istaskdone, tasks)
@@ -1495,7 +1496,7 @@ function precompile(ctx::Context, pkgs::Vector{PackageSpec}; internal_call::Bool
     try
         wait(interrupted_or_done)
     catch err
-        handle_interrupt(err)
+        handle_interrupt(err) || rethrow()
     finally
         Base.LOADING_CACHE[] = nothing
     end
@@ -1552,7 +1553,7 @@ function precompile(ctx::Context, pkgs::Vector{PackageSpec}; internal_call::Bool
             if !isempty(stderr_outputs)
                 plural1 = length(stderr_outputs) == 1 ? "y" : "ies"
                 plural2 = length(stderr_outputs) == 1 ? "" : "s"
-                print(iostr, "\n  ", color_string("$(length(stderr_outputs))", Base.warn_color()), " dependenc$(plural1) had warnings during precompilation:")
+                print(iostr, "\n  ", color_string("$(length(stderr_outputs))", Base.warn_color()), " dependenc$(plural1) had output during precompilation:")
                 for (pkgid, err) in stderr_outputs
                     err = join(split(err, "\n"), color_string("\n│  ", Base.warn_color()))
                     print(iostr, color_string("\n┌ ", Base.warn_color()), pkgid, color_string("\n│  ", Base.warn_color()), err, color_string("\n└  ", Base.warn_color()))

src/GitTools.jl

@@ -109,7 +109,12 @@ function clone(io::IO, url, source_path; header=nothing, credentials=nothing, kw
     end
     try
         if use_cli_git()
-            run(pipeline(`git clone --quiet $url $source_path`; stdout=devnull))
+            cmd = `git clone --quiet $url $source_path`
+            try
+                run(pipeline(cmd; stdout=devnull))
+            catch err
+                Pkg.Types.pkgerror("The command $(cmd) failed, error: $err")
+            end
             return LibGit2.GitRepo(source_path)
         else
             mkpath(source_path)
@@ -161,7 +166,12 @@ function fetch(io::IO, repo::LibGit2.GitRepo, remoteurl=nothing; header=nothing,
         if use_cli_git()
             let remoteurl=remoteurl
                 cd(LibGit2.path(repo)) do
-                    run(pipeline(`git fetch -q $remoteurl $(only(refspecs))`; stdout=devnull))
+                    cmd = `git fetch -q $remoteurl $(only(refspecs))`
+                    try
+                        run(pipeline(cmd; stdout=devnull))
+                    catch err
+                        Pkg.Types.pkgerror("The command $(cmd) failed, error: $err")
+                    end
                 end
             end
         else

src/Operations.jl

@@ -922,10 +922,15 @@ end
 project_rel_path(env::EnvCache, path::String) = normpath(joinpath(dirname(env.manifest_file), path))
 
 function prune_manifest(env::EnvCache)
-    # if project uses another manifest, don't prune
-    dirname(env.project_file) != dirname(env.manifest_file) && return env.manifest
-    keep = collect(values(env.project.deps))
-    env.manifest = prune_manifest(env.manifest, keep)
+    # if project uses another manifest, only prune project entry in manifest
+    if dirname(env.project_file) != dirname(env.manifest_file)
+        proj_entry = env.manifest[env.project.uuid]
+        proj_entry.deps = env.project.deps
+    else
+        keep = collect(values(env.project.deps))
+        env.manifest = prune_manifest(env.manifest, keep)
+    end
+    return env.manifest
 end
 
 function prune_manifest(manifest::Manifest, keep::Vector{UUID})

src/Pkg.jl

@@ -541,9 +541,7 @@ The logic for what path is activated is as follows:
     activate the environment at the tracked path.
   * Otherwise, `s` is interpreted as a non-existing path, which is then activated.
 
-If no argument is given to `activate`, then activate the home project.
-The home project is specified by either the `--project` command line option to
-the julia executable, or the `JULIA_PROJECT` environment variable.
+If no argument is given to `activate`, then use the first project found in `LOAD_PATH`.
 
 # Examples
 ```

src/REPLMode/command_declarations.jl

@@ -301,7 +301,7 @@ PSA[:name => "activate",
     activate [--shared] path
     activate --temp
 
-Activate the environment at the given `path`, or the home project environment if no `path` is specified.
+Activate the environment at the given `path`, or use the first project found in `LOAD_PATH` if no `path` is specified.
 The active environment is the environment that is modified by executing package commands.
 When the option `--shared` is given, `path` will be assumed to be a directory name and searched for in the
 `environments` folders of the depots in the depot stack. In case no such environment exists in any of the depots,

src/Types.jl

@@ -116,10 +116,10 @@ function PackageSpec(; name::Union{Nothing,AbstractString} = nothing,
     uuid = uuid === nothing ? nothing : UUID(uuid)
     return PackageSpec(name, uuid, version, tree_hash, repo, path, pinned, url, rev, subdir)
 end
-PackageSpec(name::AbstractString) = PackageSpec(;name=name)
-PackageSpec(name::AbstractString, uuid::UUID) = PackageSpec(;name=name, uuid=uuid)
-PackageSpec(name::AbstractString, version::VersionTypes) = PackageSpec(;name=name, version=version)
-PackageSpec(n::AbstractString, u::UUID, v::VersionTypes) = PackageSpec(;name=n, uuid=u, version=v)
+PackageSpec(name::AbstractString) = PackageSpec(;name=name)::PackageSpec
+PackageSpec(name::AbstractString, uuid::UUID) = PackageSpec(;name=name, uuid=uuid)::PackageSpec
+PackageSpec(name::AbstractString, version::VersionTypes) = PackageSpec(;name=name, version=version)::PackageSpec
+PackageSpec(n::AbstractString, u::UUID, v::VersionTypes) = PackageSpec(;name=n, uuid=u, version=v)::PackageSpec
 
 function Base.:(==)(a::PackageSpec, b::PackageSpec)
     return a.name == b.name && a.uuid == b.uuid && a.version == b.version &&

src/project.jl

@@ -179,8 +179,7 @@ function destructure(project::Project)::Dict
     entry!("uuid",     project.uuid)
     entry!("version",  project.version)
     entry!("manifest", project.manifest)
-    merge!(project.deps, project._deps_weak)
-    entry!("deps",     project.deps)
+    entry!("deps",     merge(project.deps, project._deps_weak))
     entry!("weakdeps", project.weakdeps)
     entry!("extras",   project.extras)
     entry!("compat",   Dict(name => x.str for (name, x) in project.compat))

test/api.jl

@@ -38,7 +38,7 @@ using ..Utils
         cd(mkdir("tests"))
         Pkg.activate("Foo") # activate developed Foo from another directory
         @test Base.active_project() == joinpath(path, "modules", "Foo", "Project.toml")
-        Pkg.activate() # activate home project
+        Pkg.activate() # activate LOAD_PATH project
         @test Base.ACTIVE_PROJECT[] === nothing
     end end
 end

test/misc.jl

@@ -25,4 +25,6 @@ end
     end
 end
 
+@test eltype([PackageSpec(a) for a in []]) == PackageSpec
+
 end # module

test/new.jl

@@ -53,7 +53,7 @@ Pkg._auto_gc_enabled[] = false
             source053 = pkg.source
             source053_time = mtime(pkg.source)
         end
-        # - The home project was automatically created.
+        # - The active project was automatically created.
         @test haskey(Pkg.project().dependencies, "Example")
         @test length(Pkg.project().dependencies) == 1
         # Now we install the same package at a different version:
@@ -2687,22 +2687,34 @@ end
 # # Other
 #
 # Note: these tests should be run on clean depots
-@testset "downloads" begin
-    for v in (nothing, "true")
-        withenv("JULIA_PKG_USE_CLI_GIT" => v) do
-            # libgit2 downloads
-            isolate() do
-                Pkg.add("Example"; use_git_for_all_downloads=true)
-                @test haskey(Pkg.dependencies(), exuuid)
-                @eval import $(Symbol(TEST_PKG.name))
-                @test_throws SystemError open(pathof(eval(Symbol(TEST_PKG.name))), "w") do io end  # check read-only
-                Pkg.rm(TEST_PKG.name)
-            end
+for v in (nothing, "true")
+    withenv("JULIA_PKG_USE_CLI_GIT" => v, "GIT_TERMINAL_PROMPT" => 0) do
+        @testset "downloads with JULIA_PKG_USE_CLI_GIT = $v" begin
             isolate() do
                 @testset "libgit2 downloads" begin
-                    Pkg.add(TEST_PKG.name; use_git_for_all_downloads=true)
-                    @test haskey(Pkg.dependencies(), TEST_PKG.uuid)
-                    Pkg.rm(TEST_PKG.name)
+                    @testset "via name" begin
+                        Pkg.add(TEST_PKG.name; use_git_for_all_downloads=true)
+                        @test haskey(Pkg.dependencies(), TEST_PKG.uuid)
+                        @eval import $(Symbol(TEST_PKG.name))
+                        @test_throws SystemError open(pathof(eval(Symbol(TEST_PKG.name))), "w") do io end  # check read-only
+                        Pkg.rm(TEST_PKG.name)
+                    end
+                    if (Pkg.get_bool_env("JULIA_PKG_USE_CLI_GIT", default = "false") && Sys.iswindows()) == false
+                        # TODO: fix. on GH windows runners cli git will prompt for credentials here
+                        @testset "via url" begin
+                            Pkg.add(url="https://github.com/JuliaLang/Example.jl", use_git_for_all_downloads=true)
+                            @test haskey(Pkg.dependencies(), TEST_PKG.uuid)
+                            Pkg.rm(TEST_PKG.name)
+                        end
+                    end
+                end
+                if !Sys.iswindows()
+                    # TODO: fix. on GH windows runners cli git will prompt for credentials here
+                    @testset "libgit2 failures" begin
+                        doesnotexist = "https://github.com/DoesNotExist/DoesNotExist.jl"
+                        @test_throws Pkg.Types.PkgError Pkg.add(url=doesnotexist, use_git_for_all_downloads=true)
+                        @test_throws Pkg.Types.PkgError Pkg.Registry.add(Pkg.RegistrySpec(url=doesnotexist))
+                    end
                 end
                 @testset "tarball downloads" begin
                     Pkg.add("JSON"; use_only_tarballs_for_downloads=true)

test/project_manifest.jl

@@ -1,7 +1,7 @@
 module ProjectManifestTest
 
 import ..Pkg # ensure we are using the correct Pkg
-using Test, Pkg
+using Test, Pkg, UUIDs
 using ..Utils
 
 temp_pkg_dir() do project_path
@@ -29,13 +29,33 @@ temp_pkg_dir() do project_path
                     Pkg.test()
                 end
             end
+            m = Pkg.Types.read_manifest(joinpath(dir, "monorepo", "Manifest.toml"))
+            @test haskey(m, UUID("dd0d8fba-d7c4-4f8e-a2bb-3a090b3e34f2")) # B subpackage
+            @test haskey(m, UUID("4ee78ca3-4e78-462f-a078-747ed543fa86")) # C subpackage
+            @test haskey(m, UUID("bf733257-898a-45a0-b2f2-c1c188bdd870")) # D subpackage, but no direct dependency
+            pkgC = m[UUID("4ee78ca3-4e78-462f-a078-747ed543fa86")]
+            @test haskey(pkgC.deps, "D")
             cd(joinpath(dir, "monorepo")) do
                 with_current_env() do
                     Pkg.develop(path="packages/C")
                     Pkg.add("Test")
                     Pkg.test()
                 end
             end
+            # now test removing a dependency from subpackage correctly updates root manifest
+            cd(joinpath(dir, "monorepo", "packages", "C")) do
+                with_current_env() do
+                    Pkg.rm("D")
+                    Pkg.test()
+                end
+            end
+            m = Pkg.Types.read_manifest(joinpath(dir, "monorepo", "Manifest.toml"))
+            # currently, we don't prune dependencies from the root manifest since when rm-ing a dep
+            # in a subpackage, we don't also do a full resolve at the root level
+            # https://github.com/JuliaLang/Pkg.jl/issues/3590
+            @test_broken !haskey(m, UUID("bf733257-898a-45a0-b2f2-c1c188bdd870")) # D subpackage, but no direct dependency
+            pkgC = m[UUID("4ee78ca3-4e78-462f-a078-747ed543fa86")]
+            @test !haskey(pkgC.deps, "D")
         end
     end
 end

test/repl.jl

@@ -260,7 +260,7 @@ temp_pkg_dir() do project_path
         pkg"activate --shared Foo" # activate existing shared Foo
         @test Base.active_project() == joinpath(tmpdir, "Project.toml")
         pop!(Base.DEPOT_PATH)
-        pkg"activate" # activate home project
+        pkg"activate" # activate LOAD_PATH project
         @test Base.ACTIVE_PROJECT[] === nothing
         # expansion of ~
         if !Sys.iswindows()

test/test_packages/ExtensionExamples/HasDepWithExtensions.jl/Manifest.toml

@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.0-DEV"
+julia_version = "1.11.0-DEV"
 manifest_format = "2.0"
-project_hash = "51e63007fdb8e0cae2b36f0e7b2acebf7b7432a5"
+project_hash = "c0b34a2f360e3789aa008772cc2c162a8e9d9850"
 
 [[deps.Adapt]]
 deps = ["LinearAlgebra"]
@@ -16,7 +16,7 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.0.1+0"
+version = "1.0.5+1"
 
 [[deps.Example]]
 git-tree-sha1 = "46e44e869b4d90b96bd8ed1fdcf32244fddfb6cc"
@@ -28,11 +28,17 @@ deps = ["Example"]
 path = "../HasExtensions.jl"
 uuid = "4d3288b3-3afc-4bb6-85f3-489fffe514c8"
 version = "0.1.0"
-weakdeps = ["OffsetArrays"]
+weakdeps = ["IndirectArrays", "OffsetArrays"]
 
     [deps.HasExtensions.extensions]
+    IndirectArraysExt = "IndirectArrays"
     OffsetArraysExt = "OffsetArrays"
 
+[[deps.IndirectArrays]]
+git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f"
+uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959"
+version = "1.0.0"
+
 [[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
@@ -49,9 +55,9 @@ version = "1.12.8"
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.21+0"
+version = "0.3.23+2"
 
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.2.0+0"
+version = "5.8.0+1"

test/test_packages/ExtensionExamples/HasDepWithExtensions.jl/Project.toml

@@ -4,10 +4,12 @@ version = "0.1.0"
 
 [deps]
 HasExtensions = "4d3288b3-3afc-4bb6-85f3-489fffe514c8"
+IndirectArrays = "9b13fd28-a010-5f03-acff-a1bbcff69959"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 
 [compat]
 HasExtensions = "0.1"
+IndirectArrays = "1.0"
 OffsetArrays = "1.12"
 
 [extras]

test/test_packages/ExtensionExamples/HasDepWithExtensions.jl/src/HasDepWithExtensions.jl

@@ -2,14 +2,20 @@ module HasDepWithExtensions
 
 using HasExtensions
 using OffsetArrays: OffsetArray
-# Loading OffsetArrays makes the extesion "OffsetArraysExt" to load
+# Loading OffsetArrays makes the extesion "OffsetArraysExt" load
+
+using IndirectArrays: IndirectArray
+# Loading IndirectArrays makes the extesion "IndirectArraysExt" load
 
 function do_something()
-    # @info "First do something with the basic array support in B"
+    # @info "First do something with the basic array support"
     HasExtensions.foo(rand(Float64, 2)) == 1 || error("Unexpected value")
 
-    # @info "Now do something with extended OffsetArray support in B"
+    # @info "Now do something with extended OffsetArray support"
     HasExtensions.foo(OffsetArray(rand(Float64, 2), 0:1)) == 2 || error("Unexpected value")
+
+    # @info "Now do something with extended IndirectArray support"
+    HasExtensions.foo(IndirectArray(rand(1:6, 32, 32), 1:6)) == 3 || error("Unexpected value")
 end
 
 end # module

test/test_packages/ExtensionExamples/HasDepWithExtensions.jl/test/runtests.jl

@@ -2,4 +2,5 @@ using HasDepWithExtensions
 using Test
 
 @test HasDepWithExtensions.HasExtensions.offsetarrays_loaded
+@test HasDepWithExtensions.HasExtensions.indirectarrays_loaded
 HasDepWithExtensions.do_something()

test/test_packages/ExtensionExamples/HasExtensions.jl/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.0-DEV"
 manifest_format = "2.0"
-project_hash = "549efd0c32255f4b8717f50f49778e183bcc0e36"
+project_hash = "8e0de0086d647967f02f7aba44b17d73156d2fee"
 
 [[deps.Example]]
 git-tree-sha1 = "46e44e869b4d90b96bd8ed1fdcf32244fddfb6cc"