When manifest =... is set, removing a dependency doesn't remove it from the Manifest.toml

[nickrobinson251]

This is an issue for packages setting the manifest = ... argument in their Project.toml

The problem we're seeing is that, if you have a package Foo with a Project.toml (at e.g. packages/Foo/Project.toml) which looks like:

name = "Foo"
uuid = "801270c1-6d38-4c07-85b6-74a2f576d89a"
manifest = "../../Manifest.toml"
version = "0.1.0"

[deps]
Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
ContextVariablesX = "6add18c4-b38d-439d-96f6-d6bc489c04c5"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
ExceptionUnwrapping = "460bff9d-24e4-43bc-9d9f-a8973cb893f4"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"

[compat]
ReTestItems = "1"

[extras]
DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
ReTestItems = "817f1d60-ba6b-4fd5-9520-3cf149f6a823"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["DeepDiffs", "JSON3", "ReTestItems", "Test"]

note the manifest = "../../Manifest.toml" entry

And then you add and then remove a package

] activate Foo
] add Example
] rm Example

which should leave the Project.toml (packages/Foo/Project.toml) and Manifest.toml (../../Manifest.toml) without any changes

But we see

(Foo) pkg> add Example
   Resolving package versions...
    Updating `~/packages/Foo/Project.toml`
  [7876af07] + Example v0.5.3
    Updating `~/Manifest.toml`
  [7876af07] + Example v0.5.3

(Foo) pkg> rm Example
    Updating `~/packages/Foo/Project.toml`
  [7876af07] - Example v0.5.3
  No Changes to `~/Manifest.toml`

And the Manifest.toml is left with a diff like:

diff --git a/Manifest.toml b/Manifest.toml
index 1311df8842..2042e8dd9d 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.9.2"
 manifest_format = "2.0"
-project_hash = "53c4ec67dcb0841eab26478fa1ef6c1836f9ee8b"
+project_hash = "c42550b13eba1529c8ab6377082cae8993859c62"
 
 [[deps.ANSIColoredPrinters]]
 git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
@@ -497,6 +497,11 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237"
 uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
 version = "1.0.4"
 
+[[deps.Example]]
+git-tree-sha1 = "46e44e869b4d90b96bd8ed1fdcf32244fddfb6cc"
+uuid = "7876af07-990d-54b4-ab0e-23690620f79a"
+version = "0.5.3"
+
 [[deps.ExceptionUnwrapping]]
 deps = ["Test"]
 git-tree-sha1 = "e90caa41f5a86296e014e148ee061bd6c3edec96"
@@ -1632,7 +1637,7 @@ uuid = "66d59315-31dc-41c8-b200-e39bcbf712f1"
 version = "0.1.0"
 
 [[deps.Foo]]
-deps = ["Compat", "ContextVariablesX", "Dates", "ExceptionUnwrapping", "JSON", "Logging"]
+deps = ["Compat", "ContextVariablesX", "Dates", "Example", "ExceptionUnwrapping", "JSON", "Logging"]
 path = "packages/Foo"
 uuid = "801270c1-6d38-4c07-85b6-74a2f576d89a"
 version = "0.1.0"

Which has the issue:

• The deps.Foo entry is left with Example in its deps (fixed by Update manifest entry of project for non-local manifests #3579)
• There is a deps.Example entry, even though nothing depends on Example (given that Foo doesn't depend on Example after the rm)

[NHDaly]

@nickrobinson251 after #3579, issue 1. is addressed, right? Should you update this ticket to only cover issue 2.?

That is, this part of the diff is no longer present after #3579, right?:

 [[deps.Foo]]
-deps = ["Compat", "ContextVariablesX", "Dates", "ExceptionUnwrapping", "JSON", "Logging"]
+deps = ["Compat", "ContextVariablesX", "Dates", "Example", "ExceptionUnwrapping", "JSON", "Logging"]
 path = "packages/Foo"
 uuid = "801270c1-6d38-4c07-85b6-74a2f576d89a"
 version = "0.1.0"

[nickrobinson251]

yeah - updated - thanks

[KristofferC]

This is a bit of an inherent drawback with the current manifest = system that exist in Pkg in that it doesn't take into account any other projects that have a manifest = entry that points to the same manifest. In order to be "safe" it therefore never removes any packages from the manifest since it could be so that other projects are using it. A full "sub project" implementation would consider that.