Merge branch 'master' into chordal

Author: samuelsonric

.github/workflows/ci.yml

@@ -12,39 +12,42 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - version: '1.6'
+          - version: '1.10'
             os: ubuntu-latest
             arch: x64
           - version: '1'
             os: ubuntu-latest
             arch: x64
-          - version: '1'
-            os: ubuntu-latest
-            arch: x86
+# # See https://github.com/jump-dev/SumOfSquares.jl/pull/331
+#          - version: 'nightly'
+#            os: ubuntu-latest
+#            arch: x86
 #          - version: 'nightly'
 #            os: ubuntu-latest
 #            arch: x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v1
+      - name: MOI
+        shell: julia --project=@. {0}
+        run: |
+          using Pkg
+          Pkg.add([
+              PackageSpec(name="StarAlgebras", rev="main"),
+              PackageSpec(name="SymbolicWedderburn", rev="master"),
+              PackageSpec(name="MultivariateBases", rev="master"),
+              PackageSpec(name="MultivariateMoments", rev="master"),
+              PackageSpec(name="PolyJuMP", rev="master"),
+          ])
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
         with:
           depwarn: error
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         with:
           file: lcov.info

.github/workflows/documentation.yml

@@ -12,7 +12,7 @@ jobs:
       # Fix for Plots with GR backend, see https://github.com/JuliaPolyhedra/Polyhedra.jl/pull/265
       GKSwstype: nul
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
           # Build documentation on the latest Julia 1.x
@@ -22,6 +22,11 @@ jobs:
         run: |
           using Pkg
           Pkg.add([
+              PackageSpec(name="StarAlgebras", rev="main"),
+              PackageSpec(name="SymbolicWedderburn", rev="master"),
+              PackageSpec(name="MultivariateBases", rev="master"),
+              PackageSpec(name="MultivariateMoments", rev="master"),
+              PackageSpec(name="PolyJuMP", rev="master"),
               PackageSpec(path=pwd()),
           ])
           Pkg.instantiate()

.github/workflows/examples.yml

@@ -17,6 +17,11 @@ jobs:
         run: |
           using Pkg
           Pkg.add([
+              PackageSpec(name="StarAlgebras", rev="main"),
+              PackageSpec(name="SymbolicWedderburn", rev="master"),
+              PackageSpec(name="MultivariateBases", rev="master"),
+              PackageSpec(name="MultivariateMoments", rev="master"),
+              PackageSpec(name="PolyJuMP", rev="master"),
               PackageSpec(path=pwd()),
           ])
           Pkg.instantiate()

.github/workflows/format_check.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1'
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: Format check
         shell: julia --color=yes {0}
         run: |

Project.toml

@@ -17,6 +17,7 @@ PolyJuMP = "ddf597a6-d67e-5340-b84c-e37d84115374"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SemialgebraicSets = "8e049039-38e8-557d-ae3a-bc521ccf6204"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StarAlgebras = "0c0c59c1-dc5f-42e9-9a8b-b5dc384a6cd1"
 SymbolicWedderburn = "858aa9a9-4c7c-4c62-b466-2421203962a2"
 
 [compat]
@@ -31,5 +32,6 @@ MutableArithmetics = "1"
 PolyJuMP = "0.7"
 Reexport = "0.2, 1.0"
 SemialgebraicSets = "0.3"
-SymbolicWedderburn = "0.3"
-julia = "1.6"
+StarAlgebras = "0.3"
+SymbolicWedderburn = "0.4"
+julia = "1.10"

README.md

@@ -1,6 +1,6 @@
 # SumOfSquares.jl
 
-[![Build Status](https://github.com/jump-dev/SumOfSquares.jl/workflows/CI/badge.svg?branch=master)](https://github.com/jump-dev/SumOfSquares.jl/actions?query=workflow%3ACI)
+[![Build Status](https://github.com/jump-dev/SumOfSquares.jl/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/jump-dev/SumOfSquares.jl/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/jump-dev/SumOfSquares.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/jump-dev/SumOfSquares.jl)
 [![](https://zenodo.org/badge/DOI/10.5281/zenodo.1208672.svg)](https://doi.org/10.5281/zenodo.1208672)
 
@@ -34,7 +34,9 @@ for the in-development version of the documentation.
 Some presentations on, or using, SumOfSquares (see [blegat/SumOfSquaresSlides](https://github.com/blegat/SumOfSquaresSlides)
 for the source code of the presentations):
 
+  * Benoît Legat at [JuMP-dev 2024](https://jump.dev/meetings/jumpdev2024/) [[Slides](https://jump.dev/assets/jump-dev-workshops/2024/legat.html)] [[Video](https://youtu.be/CGPHaHxCG2w)]
   * Benoît Legat at [JuMP-dev 2023](https://pretalx.com/juliacon2023/talk/XLT8H3/) [[Slides](https://drive.google.com/file/d/1H-_Ot7tP2g7t95r0K_mTaXvGO1ChUPci/view?usp=drive_link)]
+  * Benoît Legat at [SIAM DS 2023](https://www.siam.org/conferences/cm/conference/ds23) [[Slides](https://drive.google.com/file/d/18isl8aCr_mAsLg9v3eqe-t1BxEP4_TPE/view?usp=drive_link)]
   * Benoît Legat, Marek Kaluba and Tillmann Weisser at INFORMS 2022 [[Slides](https://drive.google.com/file/d/1rlsIxgcnKWT436k4MNenjHfgH0UYRLAB/view?usp=share_link)]
   * Benoît Legat at [POEMA Learning Week 2](http://poema-network.eu/index.php/news-and-events/project-workshops/13-poema-learning-week-2)
   * Benoît Legat, Marek Kaluba and Tillmann Weisser at [JuMP-dev 2021](https://pretalx.com/juliacon2021/talk/L8DTE3/) [[Slides](https://drive.google.com/file/d/1HtArDFNMQ6IYUqRjSWR3JviJp9xLtSlB/view?usp=sharing)]

bench/sos_polynomial.jl

@@ -5,7 +5,7 @@ function sos_polynomial(n)
     @polyvar x
     monos = monomials(x, 0:2n)
     set = SumOfSquares.SOSPolynomialSet(
-        SumOfSquares.FullSpace(), monos,
+        SumOfSquares.FullSpace(), MB.SubBasis{MB.Monomial}(monos),
         SumOfSquares.Certificate.Remainder(
             SumOfSquares.SOSCone(),
             SumOfSquares.MonomialBasis,

docs/Project.toml

@@ -7,6 +7,7 @@ Cyclotomics = "da8f5974-afbb-4dc8-91d8-516d5257c83b"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 Dualization = "191a621a-6537-11e9-281d-650236a99e60"
 DynamicPolynomials = "7c1d4256-1411-5781-91ec-d7bc3513ac07"
 GroupsCore = "d5909c97-4eac-4ecc-a3dc-fdd0858a4120"
@@ -28,9 +29,11 @@ PolyJuMP = "ddf597a6-d67e-5340-b84c-e37d84115374"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 SCS = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+StarAlgebras = "0c0c59c1-dc5f-42e9-9a8b-b5dc384a6cd1"
 SumOfSquares = "4b9e565b-77fc-50a5-a571-1244f986bda1"
 SymbolicWedderburn = "858aa9a9-4c7c-4c62-b466-2421203962a2"
 TypedPolynomials = "afbbf031-7a57-5f58-a1b9-b774a0fad08d"
 
 [compat]
 Documenter = "1"
+DynamicPolynomials = "0.6"

docs/make.jl

@@ -2,6 +2,7 @@
 
 using SumOfSquares
 using Documenter, Literate
+import DocumenterCitations
 
 const _TUTORIAL_DIR = joinpath(@__DIR__, "src", "tutorials")
 const _OUTPUT_DIR   = joinpath(@__DIR__, "src", "generated")
@@ -34,12 +35,21 @@ literate_directory.(_TUTORIAL_SUBDIR)
 makedocs(
     sitename = "SumOfSquares",
     # See https://github.com/JuliaDocs/Documenter.jl/issues/868
-    format = Documenter.HTML(prettyurls = get(ENV, "CI", nothing) == "true"),
+    format = Documenter.HTML(
+        prettyurls = get(ENV, "CI", nothing) == "true",
+        assets = ["assets/citations.css"],
+    ),
     pages = [
         "Index" => "index.md",
         "Sum-of-Squares Programming" => "sumofsquares.md",
         "Variables" => "variables.md",
         "Constraints" => "constraints.md",
+        "API Reference" => [
+            "reference/standard_form.md",
+            "reference/constraints.md",
+            "reference/certificate.md",
+            "reference/internal.md",
+        ],
         "Tutorials" => map(
             subdir ->
                 subdir => map(
@@ -51,10 +61,17 @@ makedocs(
                 ),
             _TUTORIAL_SUBDIR,
         ),
+        "Bibliography" => "bibliography.md",
     ],
     # The following ensures that we only include the docstrings from
     # this module for functions define in Base that we overwrite.
-    modules = [SumOfSquares, PolyJuMP]
+    modules = [SumOfSquares, PolyJuMP],
+    plugins = [
+        DocumenterCitations.CitationBibliography(
+            joinpath(@__DIR__, "src", "references.bib");
+            style = :authoryear,
+        ),
+    ],
 )
 
 deploydocs(

docs/src/assets/citations.css

@@ -0,0 +1,17 @@
+.citation dl {
+  display: grid;
+  grid-template-columns: max-content auto; }
+.citation dt {
+  grid-column-start: 1; }
+.citation dd {
+  grid-column-start: 2;
+  margin-bottom: 0.75em; }
+.citation ul {
+ padding: 0 0 2.25em 0;
+ margin: 0;
+ list-style: none;}
+.citation ul li {
+ text-indent: -2.25em;
+ margin: 0.33em 0.5em 0.5em 2.25em;}
+.citation ol li {
+ padding-left:0.75em;}

docs/src/bibliography.md

@@ -0,0 +1,4 @@
+# Bibliography
+
+```@bibliography
+```