Clean-up specifing dependencies to unregistered packages with `[sourc…

…es]` (#52)

* bump compat for julia 1.11

* usage `[sources]` to separate benchmark to subproject

* use `[sources]` to specify dependency on  GraphMLReader

* specify tools deps to GraphMLReader with `[sources]`

* remove GraphML submodule

* update readme

* remove initializing submodules in CI

* remove ignoring deps

* remove unused deps

.JuliaFormatter.toml

@@ -1,4 +1,4 @@
 style = "sciml"
 yas_style_nesting = true
 
-ignore = ["deps", "data", "results"]
+ignore = ["data", "results"]

.github/workflows/test.yml

@@ -28,8 +28,6 @@ jobs:
           - 'all'
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: recursive
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "deps/GraphMLReader.jl"]
-	path = deps/GraphMLReader.jl
-	url = https://github.com/SmalRat/GraphMLReader.jl

Project.toml

@@ -5,39 +5,38 @@ version = "0.1.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
-BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 Dagger = "d58978e5-989f-55fb-8d15-ea34adc7bf54"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
-EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+GraphMLReader = "8e6830a9-644c-4485-8539-40ee18e3ca8c"
 GraphViz = "f526b714-d49f-11e8-06ff-31ed36ee7ee0"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
+[sources]
+GraphMLReader = {rev = "master", url = "https://github.com/SmalRat/GraphMLReader.jl"}
+
 [compat]
 Aqua = "0.8"
 ArgParse = "1.2"
-BenchmarkTools = "1.5"
 Dagger = "0.18.13"
 DataFrames = "1.6"
-Distributed = "1.10"
-EzXML = "1.2"
+Distributed = "1.11"
 FileIO = "1.16"
+GraphMLReader = "0.1"
 GraphViz = "0.2"
 Graphs = "1"
 JSON3 = "1.14"
-LightGraphs = "1.3"
-Logging = "1.10"
+Logging = "1.11"
 MetaGraphs = "0.7"
 Plots = "1.40"
-Printf = "1.10"
-Test = "1.10"
-julia = "1.10"
+Printf = "1.11"
+Test = "1.11"
+julia = "1.11"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"

README.md

@@ -13,7 +13,6 @@ Set-up the project:
 ```
 git clone <path>
 cd key4hep-julia-fwk
-git submodule update --init --recursive
 julia --project -e "import Pkg; Pkg.instantiate()"
 ```
 

benchmark/Project.toml

@@ -0,0 +1,18 @@
+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+FrameworkDemo = "cfbf7e84-66d2-421e-b147-9edb7a8672d2"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+GraphMLReader = "8e6830a9-644c-4485-8539-40ee18e3ca8c"
+
+[compat]
+BenchmarkTools = "1.5"
+FrameworkDemo = "0.1"
+GraphMLReader = "0.1"
+Plots = "1.40"
+Printf = "1.11"
+julia = "1.11"
+
+[sources]
+FrameworkDemo = {path = ".."}
+GraphMLReader = {rev = "master", url = "https://github.com/SmalRat/GraphMLReader.jl"}

benchmark/README.md

@@ -7,7 +7,7 @@ Run benchmarks from the project's main directory
 Run benchmark script
 
 ```
-julia --project benchmark/benchmarks.jl
+julia --project=benchmark benchmark/benchmarks.jl
 ```
 
 or benchmark with [PkgBenchmark](https://github.com/JuliaCI/PkgBenchmark.jl)

src/parsing.jl

@@ -1,6 +1,6 @@
 using Graphs
 using MetaGraphs
-include("../deps/GraphMLReader.jl/src/GraphMLReader.jl")
+import GraphMLReader
 
 function parse_graphml(filename::String)::MetaDiGraph
     return GraphMLReader.loadgraphml(filename, "G")

test/Aqua.jl

@@ -5,7 +5,6 @@ using Aqua
 @testset "Aqua.jl" begin
     Aqua.test_all(FrameworkDemo;
                   ambiguities = false,
-                  stale_deps = (;
-                                ignore = [:ArgParse, # bin/
-                                    :BenchmarkTools]))
+                  stale_deps = (; ignore = [:ArgParse]),# bin/
+                  persistent_tasks = (; broken = true)) # GraphMLReader [8e6830a9] has no known versions!
 end

tools/Project.toml

@@ -2,10 +2,8 @@
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
-Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+GraphMLReader = "8e6830a9-644c-4485-8539-40ee18e3ca8c"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
@@ -15,12 +13,13 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 ArgParse = "1.2"
 CSV = "0.10"
 DataFrames = "1.6"
-EzXML = "1.2"
-Graphs = "1"
+GraphMLReader = "0.1"
 JuliaFormatter = "1"
-LightGraphs = "1.3"
 MetaGraphs = "0.7"
 Plots = "1.40"
-julia = "1.10"
-Printf = "1.10"
-Statistics = "1.10"
+Printf = "1.11"
+Statistics = "1.11"
+julia = "1.11"
+
+[sources]
+GraphMLReader = {rev = "master", url = "https://github.com/SmalRat/GraphMLReader.jl"}

tools/format_xml.sh

@@ -1,3 +1,3 @@
 #!/usr/bin/bash
 
-find . -name "*.graphml" -type f -not -path "./deps/*" -exec xmllint --output '{}' --format '{}' \;
+find . -name "*.graphml" -type f -exec xmllint --output '{}' --format '{}' \;

tools/gaudi_alg_exec_dist.jl

@@ -1,15 +1,12 @@
 #!/usr/bin/env julia
-
+using ArgParse
 using CSV
 using DataFrames
-using Statistics
 using Plots
-using ArgParse
 using Printf
-using EzXML
+using Statistics
 using MetaGraphs
-
-include(joinpath(@__DIR__, "../deps/GraphMLReader.jl/src/GraphMLReader.jl"))
+import GraphMLReader
 
 function parse_args(args)
     s = ArgParseSettings(description =