Merge 4041fbe into 5190225

.github/workflows/ci.yml

@@ -13,10 +13,10 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - version: '1'
+          - version: '1.9'
             os: ubuntu-latest
             arch: x64
-          - version: '1'
+          - version: '1.9'
             os: windows-latest
             arch: x64
     steps:

.github/workflows/docs.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Setup Julia
         uses: julia-actions/setup-julia@latest
         with:
-          version: '1.6'
+          version: '1.9'
       - name: Develop QUBOTools.jl
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(path=pwd())'
       - name: Build Package

.gitignore

@@ -26,5 +26,5 @@ Manifest.toml
 # VSCode
 .vscode
 
-# PythonPlots
+# PythonPlot
 .CondaPkg

Project.toml

@@ -1,19 +1,38 @@
 name = "QUBOTools"
 uuid = "60eb5b62-0a39-4ddc-84c5-97d2adff9319"
-authors = ["pedromxavier <[email protected]>", "pedroripper <[email protected]>", "AndradeTiago <[email protected]>", "joaquimg <[email protected]>", "bernalde <dbernalneira@usra.edu>"]
-version = "0.8.2"
+authors = ["pedromxavier <[email protected]>", "pedroripper <[email protected]>", "AndradeTiago <[email protected]>", "joaquimg <[email protected]>", "bernalde <dbernaln@purdue.edu>"]
+version = "0.10.0"
 
 [deps]
-InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JSONSchema = "7d188eb4-7ad8-530c-ae41-71a32a6d4692"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+PseudoBooleanOptimization = "c8fa9a04-bc42-452d-8558-dc51757be744"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[weakdeps]
+MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
+
+[extensions]
+QUBOTools_MOI = ["MathOptInterface"]
 
 [compat]
+GeometryBasics = "0.4"
+Graphs = "1"
+HDF5 = "0.16.15"
 JSON = "0.21.3"
 JSONSchema = "1"
-RecipesBase = "1.3"
-julia = "1.6"
+MathOptInterface = "1"
+NetworkLayout = "0.4.5"
+PseudoBooleanOptimization = "0.1"
+RecipesBase = "1"
+Statistics = "1"
+julia = "1.9"

README.md

@@ -51,72 +51,48 @@ where $J \in \mathbb{R}^{n \times n}$ is triangular and $\mathbf{h} \in \mathbb{
 ## Getting Started
 
 ### Installation
+
 ```julia
-julia> import Pkg
+import Pkg
 
-julia> Pkg.add("QUBOTools")
+Pkg.add("QUBOTools")
 ```
 
 ### Basic Usage
+
 ```julia
-julia> using QUBOTools
+using QUBOTools
 
-julia> model = QUBOTools.read_model("problem.json")
+model = QUBOTools.read_model("problem.json")
 
-julia> QUBOTools.write_model("problem.qubo", model)
+QUBOTools.write_model("problem.qubo", model)
 ```
 
 ## Supported Formats
+
 The `r` and `w` marks indicate that reading and writing modes are available for the corresponding file format, respectively.
 
 ### [BQPJSON](/docs/models/BQPJSON.md) `rw`
+
 The [BQPJSON](https://bqpjson.readthedocs.io) format was designed at [LANL-ANSI](https://github.com/lanl-ansi) to represent Binary Quadratic Programs in a platform-independet fashion.
 This is accomplished by using `.json` files validated using a well-defined [JSON Schema](/src/models/bqpjson.schema.json).
 
 ### [QUBO](/docs/models/QUBOTools.md) `rw`
+
 The QUBO specification appears as the input format in many of D-Wave's applications.
 A brief explanation about it can be found in [qbsolv](https://github.com/arcondello/qbsolv#qbsolv-qubo-input-file-format)'s repository README. 
 
 ### [Qubist](/docs/models/Qubist.md) `rw`
+
 This is the simplest of all current supported formats.
 
 ### [MiniZinc](/docs/models/MiniZinc.md) `rw`
+
 [MiniZinc](https://www.minizinc.org) is a constraint modelling language that can be used as input for many solvers.
 
 ### [HFS](/docs/models/HFS.md) `w`
-HFS is a very low-level mapping of weights to D-Wave's chimera graph.
-
-### Conversion Flowchart
-**Bold arrows** indicate that a bijective (modulo rounding erros) conversion is available.
-**Regular arrows** indicate that some non-critical information might get lost in the process, such as problem metadata.
-**Dashed arrows** tell that even though a format conversion exists, important information such as scale and offset factors will be neglected.
-
-```mermaid
-flowchart TD;
-    MODEL["QUBOTools Model"];
-
-    BQPJSON["BQPJSON<br><code>Bool</code><br><code>Spin</code>"];
 
-    HFS(["HFS<br><code>Bool</code>"]);
-
-    MINIZINC(["MiniZinc<br><code>Bool</code><br><code>Spin</code>"]);
-
-    QUBO["QUBO<br><code>Bool</code>"];
-
-    QUBIST["Qubist<br><code>Spin</code>"];
-
-
-    QUBIST -.-> MODEL;
-
-    MODEL --> HFS;
-    MODEL --> QUBIST;
-
-    MODEL <==> MINIZINC;
-
-    MODEL <==> BQPJSON;
-    QUBO  <==> MODEL;
-    
-```
+HFS is a very low-level mapping of weights to D-Wave's chimera graph.
 
 <div align="center">
     <h2>PSR Quantum Optimization Toolchain</h2>

benchmark/benchmark.jl

@@ -0,0 +1,3 @@
+using BenchmarkTools
+using QUBOTools
+

docs/Project.toml

@@ -1,8 +1,10 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterDiagrams = "a106ebf2-4182-4cba-90d4-44cd3cc36e85"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 QUBOTools = "60eb5b62-0a39-4ddc-84c5-97d2adff9319"
 
 [compat]
-Documenter = "~0.27"
+Documenter = "1"
+DocumenterDiagrams = "1"
 Plots = "~1.38"

docs/make.jl

@@ -1,41 +1,43 @@
 using Documenter
+using DocumenterDiagrams
 using QUBOTools
 
 # Set up to run docstrings with jldoctest
 DocMeta.setdocmeta!(QUBOTools, :DocTestSetup, :(using QUBOTools); recursive = true)
 
 makedocs(;
-    modules = [QUBOTools],
-    doctest = true,
-    clean = true,
-    format = Documenter.HTML(
-        assets = ["assets/extra_styles.css", "assets/favicon.ico"],
-        mathengine = Documenter.KaTeX(),
-        sidebar_sitename = false,
-    ),
+    modules  = [QUBOTools, QUBOTools.PBO],
+    doctest  = true,
+    clean    = true,
     sitename = "QUBOTools.jl",
-    authors = "Pedro Xavier and and Pedro Ripper and Tiago Andrade and Joaquim Garcia and David Bernal",
-    pages = [
-        "Home"    => "index.md",
-        "Manual"  => [
+    authors  = "Pedro Maciel Xavier and Pedro Ripper and Tiago Andrade and Joaquim Garcia and David E. Bernal Neira",
+    workdir  = @__DIR__,
+    warnonly = [:missing_docs],
+    pages    = [
+        "Home" => "index.md",
+        "Manual" => [
             "Introduction"             => "manual/1-start.md",
             "Mathematical Formulation" => "manual/2-math.md",
             "Basic Usage"              => "manual/3-usage.md",
             "Models"                   => "manual/4-models.md",
             "File Formats"             => "manual/5-formats.md",
             "Solutions"                => "manual/6-solutions.md",
-            "Analysis"                 => "manual/7-analysis.md"
+            "Analysis"                 => "manual/7-analysis.md",
         ],
         "Formats" => [
             "BQPJSON"  => "formats/BQPJSON.md",
-            "HFS"      => "formats/HFS.md",
             "MiniZinc" => "formats/MiniZinc.md",
+            "QUBin"    => "formats/QUBin.md",
             "Qubist"   => "formats/Qubist.md",
             "QUBO"     => "formats/QUBO.md",
         ],
         "API Reference" => "api.md",
     ],
-    workdir = @__DIR__,
+    format   = Documenter.HTML(
+        assets           = ["assets/extra_styles.css", "assets/favicon.ico"],
+        mathengine       = Documenter.KaTeX(),
+        sidebar_sitename = false,
+    ),
 )
 
 if "--skip-deploy" ∈ ARGS