Don't rewrite Project.toml on resolve/instantiate

CHANGELOG.md

@@ -1,6 +1,11 @@
 Pkg v1.14 Release Notes
 =======================
 
+- `Pkg.resolve` and `Pkg.instantiate` no longer rewrite `Project.toml`. Project.toml is authored input and the
+  manifest is the derived output; these commands only produce the manifest and must not edit the project as a side
+  effect. Previously, resolving or instantiating an environment whose `Project.toml` contained a `[sources]` entry
+  (for example a top-level project in a workspace) could rewrite the file, normalizing paths and dropping comments
+  and formatting. Pass `skip_writing_project=false` to opt back into the old behavior. ([#4713])
 - `Pkg.instantiate` now accepts an `update_on_mismatch::Bool` keyword argument (and a corresponding `-u` /
   `--update_on_mismatch` REPL flag) that falls back to `Pkg.update()` when the manifest does not match the project
   or was resolved with a different Julia minor version, instead of warning or erroring. Useful for tooling and

src/API.jl

@@ -482,7 +482,7 @@ function up(
 end
 
 resolve(; io::IO = stderr_f(), kwargs...) = resolve(Context(; io); kwargs...)
-function resolve(ctx::Context; skip_writing_project::Bool = false, kwargs...)
+function resolve(ctx::Context; skip_writing_project::Bool = true, kwargs...)
     up(ctx; level = UPLEVEL_FIXED, mode = PKGMODE_MANIFEST, update_registry = false, skip_writing_project, kwargs...)
     return nothing
 end
@@ -1321,7 +1321,8 @@ function instantiate(
     if (!isfile(ctx.env.manifest_file) && manifest === nothing) || manifest == false
         # given no manifest exists, only allow invoking a registry update if there are project deps
         allow_registry_update = isfile(ctx.env.project_file) && !isempty(ctx.env.project.deps)
-        up(ctx; update_registry = update_registry && allow_registry_update)
+        # instantiate produces the manifest; it must not rewrite the authored Project.toml.
+        up(ctx; update_registry = update_registry && allow_registry_update, skip_writing_project = true)
         allow_autoprecomp && Pkg._auto_precompile(ctx, already_instantiated = true)
         return
     end
@@ -1340,7 +1341,8 @@ function instantiate(
             saved_initial_snapshot[] = true
         end
         printpkgstyle(ctx.io, :Update, "manifest does not match project or Julia version, falling back to `Pkg.update()`", color = Base.info_color())
-        up(ctx; update_registry, mode = workspace ? PKGMODE_MANIFEST : PKGMODE_PROJECT)
+        # instantiate produces the manifest; it must not rewrite the authored Project.toml.
+        up(ctx; update_registry, mode = workspace ? PKGMODE_MANIFEST : PKGMODE_PROJECT, skip_writing_project = true)
         allow_autoprecomp && Pkg._auto_precompile(ctx, already_instantiated = true)
         return
     end

test/sources.jl

@@ -11,7 +11,8 @@ temp_pkg_dir() do project_path
             path = copy_test_package(dir, "WithSources")
             cd(path) do
                 with_current_env() do
-                    Pkg.resolve()
+                    # Request project writing explicitly to sync [sources] back into Project.toml.
+                    Pkg.resolve(; skip_writing_project = false)
                     @test !isempty(Pkg.project().sources["Example"])
                     project_backup = cp("Project.toml", "Project.toml.bak"; force = true)
                     Pkg.free("Example")
@@ -21,7 +22,7 @@ temp_pkg_dir() do project_path
                     @test Pkg.project().sources["Example"] == Dict("url" => "https://github.com/JuliaLang/Example.jl/", "rev" => "78406c204b8")
                     cp("Project.toml.bak", "Project.toml"; force = true)
                     cp("BadManifest.toml", "Manifest.toml"; force = true)
-                    Pkg.resolve()
+                    Pkg.resolve(; skip_writing_project = false)
                     @test Pkg.project().sources["Example"] == Dict("rev" => "master", "url" => "https://github.com/JuliaLang/Example.jl")
                     @test Pkg.project().sources["LocalPkg"] == Dict("path" => "LocalPkg")
                 end

test/workspaces.jl

@@ -289,4 +289,89 @@ end
     end
 end
 
+# Project.toml is authored input; `resolve` and `instantiate` produce the manifest and
+# must never rewrite it. A top-level workspace [sources] entry with a deliberately
+# non-canonical path and an authored comment is the tripwire: writing the project would
+# normalize the path (`./Leaf` -> `Leaf`) and drop the comment, so any project write shows
+# up as a byte change.
+@testset "resolve/instantiate only read Project.toml" begin
+    leaf_uuid = "aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa"
+    mktempdir() do dir
+        # A local leaf package tracked by path from the top-level project.
+        mkpath(joinpath(dir, "Leaf", "src"))
+        write(
+            joinpath(dir, "Leaf", "Project.toml"),
+            """
+            name = "Leaf"
+            uuid = "$leaf_uuid"
+            version = "0.1.0"
+            """
+        )
+        write(joinpath(dir, "Leaf", "src", "Leaf.jl"), "module Leaf\nend\n")
+
+        # A workspace member, so this is a genuine workspace.
+        mkpath(joinpath(dir, "sub", "src"))
+        write(
+            joinpath(dir, "sub", "Project.toml"),
+            """
+            name = "Sub"
+            uuid = "bbbbbbbb-bbbb-bbbb-bbbb-bbbbbbbbbbbb"
+            version = "0.1.0"
+            """
+        )
+        write(joinpath(dir, "sub", "src", "Sub.jl"), "module Sub\nend\n")
+
+        # The top-level project carries [workspace] and a [sources] entry whose path is
+        # written non-canonically and is preceded by a hand-authored comment.
+        project_file = joinpath(dir, "Project.toml")
+        write(
+            project_file,
+            """
+            name = "Root"
+            uuid = "cccccccc-cccc-cccc-cccc-cccccccccccc"
+            version = "0.1.0"
+
+            [deps]
+            Leaf = "$leaf_uuid"
+
+            [workspace]
+            projects = ["sub"]
+
+            # DO-NOT-DROP: authored comment a lossy project rewrite would delete
+            [sources]
+            Leaf = {path = "./Leaf"}
+            """
+        )
+        authored = read(project_file, String)
+        manifest_file = joinpath(dir, "Manifest.toml")
+
+        cd(dir) do
+            with_current_env() do
+                Pkg.activate(".")
+
+                # `resolve` produces the manifest and must leave Project.toml untouched.
+                Pkg.resolve()
+                @test read(project_file, String) == authored
+
+                # `instantiate` with a present, consistent manifest must not rewrite it.
+                Pkg.instantiate()
+                @test read(project_file, String) == authored
+
+                # `instantiate` with no manifest falls back to `up`; still no project write.
+                rm(manifest_file; force = true)
+                Pkg.instantiate()
+                @test isfile(manifest_file)
+                @test read(project_file, String) == authored
+
+                # `instantiate(update_on_mismatch=true)` on a mismatched manifest also falls
+                # back to `up`; the manifest is refreshed but Project.toml must not change.
+                stale = replace(read(manifest_file, String), r"julia_version = \"[^\"]*\"" => "julia_version = \"0.0.0\"")
+                write(manifest_file, stale)
+                Pkg.instantiate(update_on_mismatch = true)
+                @test read(project_file, String) == authored
+            end
+        end
+    end
+end
+
 end # module