Repository: JuliaRegistries/CompatHelper.jl (julia)

Issue:
Feature request: open PRs to update compat entries for weak dependencies (`[weakdeps]`)
the compats for `weakdeps` isn't getting any update.

Pull request description:
Fixes #452

Patch:
diff --git a/Project.toml b/Project.toml
index c1ee363d..e3c325d2 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "CompatHelper"
 uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
 authors = ["Dilum Aluthge", "Brown Center for Biomedical Informatics", "contributors"]
-version = "3.10.0"
+version = "3.11.0"
 
 [deps]
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
diff --git a/src/dependencies.jl b/src/dependencies.jl
index db7d8bc6..a6c8519e 100644
--- a/src/dependencies.jl
+++ b/src/dependencies.jl
@@ -18,35 +18,39 @@ end
 
 function get_project_deps(project_file::AbstractString; include_jll::Bool=false)
     project_deps = Set{DepInfo}()
+    dep_section = Dict{DepInfo,String}()
     project = TOML.parsefile(project_file)
 
-    if haskey(project, "deps")
-        deps = project["deps"]
-        add_compat_section!(project)
-        compat = project["compat"]
-
-        for dep in deps
-            name = dep[1]
-            uuid = UUIDs.UUID(dep[2])
-
-            # Ignore JLL packages if flag set
-            # Do NOT ignore stdlib packages.
-            if !endswith(lowercase(strip(name)), "_jll") || include_jll
-                package = Package(name, uuid)
-                compat_entry = DepInfo(package)
-                dep_entry = convert(String, strip(get(compat, name, "")))
-
-                if !isempty(dep_entry)
-                    compat_entry.version_spec = semver_spec(dep_entry)
-                    compat_entry.version_verbatim = dep_entry
+    for section in ["deps", "weakdeps"]
+        if haskey(project, section)
+            deps = project[section]
+            add_compat_section!(project)
+            compat = project["compat"]
+
+            for dep in deps
+                name = dep[1]
+                uuid = UUIDs.UUID(dep[2])
+
+                # Ignore JLL packages if flag set
+                # Do NOT ignore stdlib packages.
+                if !endswith(lowercase(strip(name)), "_jll") || include_jll
+                    package = Package(name, uuid)
+                    compat_entry = DepInfo(package)
+                    dep_entry = convert(String, strip(get(compat, name, "")))
+
+                    if !isempty(dep_entry)
+                        compat_entry.version_spec = semver_spec(dep_entry)
+                        compat_entry.version_verbatim = dep_entry
+                    end
+
+                    push!(project_deps, compat_entry)
+                    get!(dep_section, compat_entry, section)
                 end
-
-                push!(project_deps, compat_entry)
             end
         end
     end
 
-    return project_deps
+    return project_deps, dep_section
 end
 
 function clone_all_registries(f::Function, registry_list::Vector{Pkg.RegistrySpec})
diff --git a/src/main.jl b/src/main.jl
index 919afca4..8a1e9a16 100644
--- a/src/main.jl
+++ b/src/main.jl
@@ -51,11 +51,12 @@ function main(
 
     for subdir in options.subdirs
         project_file = @mock joinpath(local_clone_path, subdir, "Project.toml")
-        deps = get_project_deps(project_file; include_jll=options.include_jll)
+        deps, dep_sections = get_project_deps(project_file; include_jll=options.include_jll)
 
         populate_dep_versions_from_reg!(deps; options)
 
         for dep in deps
+            dep_section = dep_sections[dep]
             pr = @mock make_pr_for_new_version(
                 api,
                 repo,
@@ -65,6 +66,7 @@ function main(
                 options,
                 subdir,
                 local_clone_path,
+                dep_section,
             )
 
             if !isnothing(pr)
diff --git a/src/utilities/new_versions.jl b/src/utilities/new_versions.jl
index 0cdba46d..664aa0af 100644
--- a/src/utilities/new_versions.jl
+++ b/src/utilities/new_versions.jl
@@ -43,9 +43,14 @@ function subdir_string(subdir::AbstractString)
     end
 end
 
+function section_string(section::AbstractString)
+    return section == "deps" ? "" : " in [$(section)]"
+end
+
 function pr_info(
     compat_entry_verbatim::Nothing,
     name::AbstractString,
+    section_str::AbstractString,
     compat_entry_for_latest_version::AbstractString,
     compat_entry::AbstractString,
     subdir_string::AbstractString,
@@ -54,7 +59,7 @@ function pr_info(
     pr_title_prefix::String,
 )
     new_pr_title = m"""
-    $(pr_title_prefix)CompatHelper: add new compat entry for $(name) at version
+    $(pr_title_prefix)CompatHelper: add new compat entry for $(name)$(section_str) at version
     $(compat_entry_for_latest_version)$(subdir_string)$(pr_title_parenthetical)
     """
 
@@ -73,6 +78,7 @@ end
 function pr_info(
     compat_entry_verbatim::AbstractString,
     name::AbstractString,
+    section_str::AbstractString,
     compat_entry_for_latest_version::AbstractString,
     compat_entry::AbstractString,
     subdir_string::AbstractString,
@@ -81,7 +87,7 @@ function pr_info(
     pr_title_prefix::String,
 )
     new_pr_title = m"""
-    $(pr_title_prefix)CompatHelper: bump compat for $(name) to
+    $(pr_title_prefix)CompatHelper: bump compat for $(name)$(section_str) to
     $(compat_entry_for_latest_version)$(subdir_string)$(pr_title_parenthetical)
     """
 
@@ -209,6 +215,7 @@ function make_pr_for_new_version(
     options::Options,
     subdir::String,
     local_clone_path::AbstractString,
+    dep_section::String,
 )
     if !continue_with_pr(dep, options.bump_compat_containing_equality_specifier)
         return nothing
@@ -222,6 +229,7 @@ function make_pr_for_new_version(
     new_pr_title, new_pr_body = pr_info(
         dep.version_verbatim,
         dep.package.name,
+        section_string(dep_section),
         compat_entry_for_latest_version,
         brand_new_compat,
         subdir_string(subdir),


Test patch:
diff --git a/test/dependencies.jl b/test/dependencies.jl
index 755289c4..257c1bb9 100644
--- a/test/dependencies.jl
+++ b/test/dependencies.jl
@@ -14,10 +14,27 @@ end
 @testset "get_project_deps" begin
     project = joinpath(@__DIR__, "deps", "Project.toml")
 
-    deps = CompatHelper.get_project_deps(project; include_jll=true)
+    deps, dep_section = CompatHelper.get_project_deps(project; include_jll=true)
+    @test length(deps) == 5
+    @test issetequal(keys(dep_section), deps)
+    for (k, s) in pairs(dep_section)
+        if k.package.name ∈ ["Bex_jll", "Skix"]
+            @test s == "weakdeps"
+        else
+            @test s == "deps"
+        end
+    end
+
+    deps, dep_section = CompatHelper.get_project_deps(project; include_jll=false)
     @test length(deps) == 3
-    deps = CompatHelper.get_project_deps(project; include_jll=false)
-    @test length(deps) == 2
+    @test issetequal(keys(dep_section), deps)
+    for (k, s) in pairs(dep_section)
+        if k.package.name == "Skix"
+            @test s == "weakdeps"
+        else
+            @test s == "deps"
+        end
+    end
 end
 
 @testset "clone_all_registries" begin
@@ -131,7 +148,7 @@ end
     @test isfile(project_file)
     for use_existing_registries in [true, false]
         options = CompatHelper.Options(; use_existing_registries)
-        deps = CompatHelper.get_project_deps(project_file)
+        deps, _ = CompatHelper.get_project_deps(project_file)
         for dep in deps
             @test dep.latest_version === nothing
         end
diff --git a/test/deps/Project.toml b/test/deps/Project.toml
index 5b692148..ebe0127d 100644
--- a/test/deps/Project.toml
+++ b/test/deps/Project.toml
@@ -7,7 +7,16 @@ Foobar_jll = "6ca821de-e512-569d-89d9-0b16ce691416"
 Baz = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
+[weakdeps]
+Bex_jll = "3db6da90-6ed3-11ee-0779-f549c8e3e90d"
+Skix = "3db6da90-6ed3-11ee-0779-f549c8e3e90d"
+
+[extensions]
+Ext = ["Bex_jll", "Skix"]
+
 [compat]
 Foobar_jll = "1"
 Baz = "1"
+Bex_jll = "1"
+Skix = "1"
 julia = "1.6"
diff --git a/test/integration_tests.jl b/test/integration_tests.jl
index 4f87be13..48cf2b9f 100644
--- a/test/integration_tests.jl
+++ b/test/integration_tests.jl
@@ -171,6 +171,106 @@ function run_integration_tests(
         end
     end
 
+    sleep(1)  # Prevent hitting the GH Secondary Rate Limits
+
+    @testset "master_9" begin
+        with_master_branch(templates("master_9"), url, "master") do master_9
+            withenv(env...) do
+                CompatHelper.main(
+                    ENV,
+                    ci_cfg;
+                    pr_title_prefix="$(GLOBAL_PR_TITLE_PREFIX) [test-9c] ",
+                    master_branch=master_9,
+                    entry_type=KeepEntry(),
+                )
+            end
+        end
+    end
+
+    sleep(1)  # Prevent hitting the GH Secondary Rate Limits
+
+    @testset "master_10" begin
+        with_master_branch(templates("master_10"), url, "master") do master_10
+            withenv(env...) do
+                CompatHelper.main(
+                    ENV,
+                    ci_cfg;
+                    pr_title_prefix="$(GLOBAL_PR_TITLE_PREFIX) [test-10a] ",
+                    master_branch=master_10,
+                    entry_type=DropEntry(),
+                )
+
+                sleep(1)  # Prevent hitting the GH Secondary Rate Limits
+
+                CompatHelper.main(
+                    ENV,
+                    ci_cfg;
+                    pr_title_prefix="$(GLOBAL_PR_TITLE_PREFIX) [test-10b] ",
+                    master_branch=master_10,
+                    entry_type=KeepEntry(),
+                )
+
+                sleep(1)  # Prevent hitting the GH Secondary Rate Limits
+
+                CompatHelper.main(
+                    ENV,
+                    ci_cfg;
+                    pr_title_prefix="$(GLOBAL_PR_TITLE_PREFIX) [test-10c] ",
+                    master_branch=master_10,
+                    entry_type=KeepEntry(),
+                )
+            end
+        end
+    end
+
+    sleep(1)  # Prevent hitting the GH Secondary Rate Limits
+
+    @testset "master_11" begin
+        with_master_branch(templates("master_11"), url, "master") do master_11
+            withenv(env...) do
+                CompatHelper.main(
+                    ENV,
+                    ci_cfg;
+                    pr_title_prefix="$(GLOBAL_PR_TITLE_PREFIX) [test-11c] ",
+                    master_branch=master_11,
+                    entry_type=KeepEntry(),
+                )
+            end
+        end
+    end
+
+    sleep(1)  # Prevent hitting the GH Secondary Rate Limits
+
+    @testset "master_12" begin
+        with_master_branch(templates("master_12"), url, "master") do master_12
+            withenv(env...) do
+                CompatHelper.main(
+                    ENV,
+                    ci_cfg;
+                    pr_title_prefix="$(GLOBAL_PR_TITLE_PREFIX) [test-12a] ",
+                    master_branch=master_12,
+                    entry_type=DropEntry(),
+                )
+            end
+        end
+    end
+
+    sleep(1)  # Prevent hitting the GH Secondary Rate Limits
+
+    @testset "master_13" begin
+        with_master_branch(templates("master_13"), url, "master") do master_13
+            withenv(env...) do
+                CompatHelper.main(
+                    ENV,
+                    ci_cfg;
+                    pr_title_prefix="$(GLOBAL_PR_TITLE_PREFIX) [test-13a] ",
+                    master_branch=master_13,
+                    entry_type=DropEntry(),
+                )
+            end
+        end
+    end
+
     return _cleanup_old_branches(url)
 end
 
diff --git a/test/main.jl b/test/main.jl
index 3742ba1d..80800658 100644
--- a/test/main.jl
+++ b/test/main.jl
@@ -62,8 +62,9 @@
                     "GITHUB_REPOSITORY" => "CompatHelper.jl", "GITHUB_TOKEN" => "token"
                 ) do
                     prs = CompatHelper.main()
-                    @test length(prs) == 2
+                    @test length(prs) == 3
                     @test prs[1] isa GitHub.PullRequest
+                    @test prs[2] isa GitHub.PullRequest
                 end
             end
         end
@@ -96,8 +97,9 @@
                     ) do
                         delete!(ENV, "GITHUB_REPOSITORY")
                         prs = CompatHelper.main()
-                        @test length(prs) == 2
+                        @test length(prs) == 3
                         @test prs[1] isa GitLab.MergeRequest
+                        @test prs[2] isa GitLab.MergeRequest
                     end
                 end
             end
diff --git a/test/templates/master_10/Project.toml b/test/templates/master_10/Project.toml
new file mode 100644
index 00000000..cd68aced
--- /dev/null
+++ b/test/templates/master_10/Project.toml
@@ -0,0 +1,28 @@
+name = "compathelper_integration_test_repo"
+uuid = "0e97b93d-f6aa-40c8-b749-d2f6bf239ed7"
+authors = ["Brown Center for Biomedical Informatics"]
+description = "Test Project.toml with both dependencies and weak dependencies, compat entries; major ver, ~"
+version = "0.1.0"
+
+[weakdeps]
+BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+IterableTables = "1c8ee90f-4401-5389-894e-7a04a3dc0f4d"
+Nettle_jll = "4c82536e-c426-54e4-b420-14f461c4ed8b"
+PGFPlotsX = "8314cec4-20b6-5062-9cdb-752b83310925"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[extensions]
+Ext = ["BioSequences", "DataFrames", "Flux", "IterableTables", "Nettle_jll", "PGFPlotsX"]
+
+[compat]
+IterableTables = "1"
+PGFPlotsX = "~1.0.0"
+julia = "1.2"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/test/templates/master_11/Project.toml b/test/templates/master_11/Project.toml
new file mode 100644
index 00000000..4b939ca5
--- /dev/null
+++ b/test/templates/master_11/Project.toml
@@ -0,0 +1,20 @@
+name = "compathelper_integration_test_repo"
+uuid = "0e97b93d-f6aa-40c8-b749-d2f6bf239ed7"
+authors = ["Brown Center for Biomedical Informatics"]
+description = "Test Project.toml with weak dependency where package does not exist"
+version = "0.1.0"
+
+[weakdeps]
+ThisPackageDoesNotExist = "2c58d03c-75de-479c-aa0b-96bf0b358d76"
+
+[extensions]
+Ext = "ThisPackageDoesNotExist"
+
+[compat]
+julia = "1.2"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/test/templates/master_12/Project.toml b/test/templates/master_12/Project.toml
new file mode 100644
index 00000000..965933a3
--- /dev/null
+++ b/test/templates/master_12/Project.toml
@@ -0,0 +1,21 @@
+name = "compathelper_integration_test_repo"
+uuid = "0e97b93d-f6aa-40c8-b749-d2f6bf239ed7"
+authors = ["Brown Center for Biomedical Informatics"]
+description = "Test Project.toml with weak dependency and compat entry for it"
+version = "0.1.0"
+
+[weakdeps]
+PGFPlotsX = "8314cec4-20b6-5062-9cdb-752b83310925"
+
+[extensions]
+Ext = "PGFPlotsX"
+
+[compat]
+PGFPlotsX = "~1.0.0"
+julia = "1.2"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/test/templates/master_13/Project.toml b/test/templates/master_13/Project.toml
new file mode 100644
index 00000000..c6f611d9
--- /dev/null
+++ b/test/templates/master_13/Project.toml
@@ -0,0 +1,25 @@
+name = "compathelper_integration_test_repo"
+uuid = "0e97b93d-f6aa-40c8-b749-d2f6bf239ed7"
+authors = ["Brown Center for Biomedical Informatics"]
+description = "Test Project.toml with dependency and weak dependency and compat entries for them"
+version = "0.1.0"
+
+[deps]
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+
+[weakdeps]
+PGFPlotsX = "8314cec4-20b6-5062-9cdb-752b83310925"
+
+[extensions]
+Ext = "PGFPlotsX"
+
+[compat]
+PGFPlotsX = "~1.0.0"
+Plots = "1"
+julia = "1.2"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/test/templates/master_2/Project.toml b/test/templates/master_2/Project.toml
index 1fbfec26..7428ec16 100644
--- a/test/templates/master_2/Project.toml
+++ b/test/templates/master_2/Project.toml
@@ -1,14 +1,17 @@
 name = "compathelper_integration_test_repo"
 uuid = "0e97b93d-f6aa-40c8-b749-d2f6bf239ed7"
 authors = ["Brown Center for Biomedical Informatics"]
-description = "Test Project.toml with dependencies and no compat entries"
+description = "Test Project.toml with weak dependencies and no compat entries"
 version = "0.1.0"
 
-[deps]
+[weakdeps]
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 
+[extensions]
+Ext = ["BioSequences", "DataFrames", "Flux"]
+
 [compat]
 DataFrames = "0.19"
 julia = "1.2"
diff --git a/test/templates/master_9/Project.toml b/test/templates/master_9/Project.toml
new file mode 100644
index 00000000..1fbfec26
--- /dev/null
+++ b/test/templates/master_9/Project.toml
@@ -0,0 +1,20 @@
+name = "compathelper_integration_test_repo"
+uuid = "0e97b93d-f6aa-40c8-b749-d2f6bf239ed7"
+authors = ["Brown Center for Biomedical Informatics"]
+description = "Test Project.toml with dependencies and no compat entries"
+version = "0.1.0"
+
+[deps]
+BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+
+[compat]
+DataFrames = "0.19"
+julia = "1.2"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/test/utilities/new_versions.jl b/test/utilities/new_versions.jl
index dae87779..e6596487 100644
--- a/test/utilities/new_versions.jl
+++ b/test/utilities/new_versions.jl
@@ -89,6 +89,11 @@ end
     end
 end
 
+@testset "section_string -- $(section)" for (section, expected) in
+                                            [("deps", ""), ("weakdeps", " in [weakdeps]")]
+    @test CompatHelper.section_string(section) == expected
+end
+
 @testset "skip_equality_specifiers" begin
     cases = [
         (false, "=", true)
@@ -108,13 +113,15 @@ end
 end
 
 @testset "pr_info -- $(typeof(case[1]))" for case in [
-    (nothing, "add new compat entry for", "pull request sets the compat")
-    ("", "bump compat for", "pull request changes the compat")
+    (nothing, "add new compat entry for", "pull request sets the compat", "deps")
+    ("", "bump compat for", "pull request changes the compat", "weakdeps")
 ]
-    verbatim, expected_title, expected_body = case
-    title, body = CompatHelper.pr_info(verbatim, "", "", "", "", "", "", "")
+    verbatim, expected_title, expected_body, section = case
+    section_str = section == "deps" ? "" : " in [$section]"
+    title, body = CompatHelper.pr_info(verbatim, "", section_str, "", "", "", "", "", "")
 
     @test contains(title, expected_title)
+    section === "weakdeps" && @test contains(title, section_str)
     @test contains(body, expected_body)
 end
 
@@ -436,6 +443,7 @@ end
                 options,
                 subdir,
                 local_clone_path=mktempdir(),
+                dep_section="deps",
             ),
         )
     end
@@ -458,6 +466,7 @@ end
                     options,
                     subdir,
                     local_clone_path=mktempdir(),
+                    dep_section="deps",
                 ),
             )
         end
@@ -512,6 +521,7 @@ end
                         options,
                         subdir,
                         local_clone_path=tmpdir,
+                        dep_section="deps",
                     )
                     @test pr isa GitHub.PullRequest
 
@@ -534,6 +544,7 @@ end
                             options,
                             subdir,
                             local_clone_path=tmpdir,
+                            dep_section="deps",
                         )
                         @test pr isa GitHub.PullRequest
                     end