Address review comments (#269)

* Address review comments

* up

* Fixes

* Fix cap

* Fix

paper/.vscode/ltex.dictionary.en-US.txt

@@ -0,0 +1,19 @@
+LinearAlgebra
+BenchmarkTools
+@benchmark
+mul
+BigInt
+SumOfSquares
+JuMP
+MutableArithmetics
+Dowson
+Lubin
+MultivariatePolynomials
+jl
+gcd
+num
+BangBang
+MathOptInterface
+@rewrite
+JuMP-specific
+MPZ

paper/code/axiom.jl

@@ -0,0 +1,17 @@
+function operate!!(op, args...)
+    T = typeof.(args)
+    if mutability(T[1], op, T...) isa IsMutable
+        return operate!(op, args...)
+    else
+        return op(args...)
+    end
+end
+function operate_to!!(output, op, args...)
+    O = typeof(output)
+    T = typeof.(args)
+    if mutability(O, op, T...) isa IsMutable
+        return operate_to!(output, op, args...)
+    else
+        return op(args...)
+    end
+end

paper/code/matmul.jl

@@ -0,0 +1,4 @@
+function Base.:*(A::Matrix{S}, b::Vector{T}) where {S,T}
+    c = Vector{U}(undef, size(A, 1)) # What is U ?
+    return mul_to!(c, A, b)
+end

paper/code/rational.jl

@@ -0,0 +1,4 @@
+struct Rational{T}
+    num::T
+    den::T
+end

paper/code/sum.jl

@@ -0,0 +1,7 @@
+function sum(x::Vector)
+    acc = zero(eltype(x))
+    for el in x
+        acc = acc + el
+    end
+    return acc
+end

paper/code/term.jl

@@ -0,0 +1,9 @@
+struct Term{T}
+    coef::T
+    sym::SymbolicVariable
+end
+struct Sum{T}
+    terms::Vector{Term{T}}
+end
+Base.:+(s::Sum, t::Term) = Sum(push!(copy(s.terms), t))
+Base.zero(::Type{Term{T}}) where {T} = Sum(Term{T}[])

paper/code/termsum.jl

@@ -0,0 +1,13 @@
+function sum(x)
+    acc = zero(eltype(x))
+    for el in x
+        acc = add!!(acc, el)
+    end
+    return acc
+end
+add!!(a, b) = a + b # default fallback
+add!!(a::BigInt, b::BigInt) = Base.GMP.MPZ.add!(a, b)
+function add!!(s::Sum, t::Term)
+    push!(s.terms, t)
+    return s
+end

paper/code/verify.jl

@@ -0,0 +1,10 @@
+module Verify
+using MutableArithmetics
+struct SymbolicVariable end
+for file in readdir(@__DIR__)
+    path = joinpath(@__DIR__, file)
+    if path != (@__FILE__)
+        include(file)
+    end
+end
+end

paper/header.tex

@@ -3,14 +3,13 @@
 \title{MutableArithmetics: An API for mutable operations}
 
 \author[1]{Benoît Legat}
-\affil[1]{Massachusetts Institute of Technology}
+\affil[1]{KU Leuven}
 
 \keywords{Julia, Optimization, Performance, Interface}
 
 \hypersetup{
 pdftitle = {MutableArithmetics: An API for mutable operations},
-pdfsubject = {JuliaCon 2019 Proceedings},
+pdfsubject = {JuliaCon 2021 Proceedings},
 pdfauthor = {Benoît Legat},
 pdfkeywords = {Julia, Optimization, Performance, Interface},
 }
-

paper/paper.yml

@@ -9,7 +9,7 @@ authors:
     orcid: 0000-0002-5921-368X
     affiliation: 1
 affiliations:
-  - name: Massachusetts Institute of Technology
+  - name: KU Leuven
     index: 1
 date: 29 July 2021
 bibliography: ref.bib

paper/ref.bib

@@ -39,49 +39,54 @@ @Article{dunning2017jump
   publisher = {SIAM},
 }
 
-@Article{legat2021mathoptinterface,
-  author  = {Legat, Beno\^{\i}t and Dowson, Oscar and Garcia, Joaquim Dias and Lubin, Miles},
-  journal = {INFORMS Journal on Computing},
-  title   = {{MathOptInterface}: a data structure for mathematical optimization problems},
-  year    = {2021},
-  note    = {In press},
-}
-
-@software{legat2021multivariatepolynomials,
-  author       = {Benoît Legat and
-                  Sascha Timme and
-                  Robin Deits},
-  title        = {{JuliaAlgebra/MultivariatePolynomials.jl: v0.3.18}},
-  month        = jul,
-  year         = 2021,
-  publisher    = {Zenodo},
-  version      = {v0.3.18},
-  doi          = {10.5281/zenodo.5083796},
-  url          = {https://doi.org/10.5281/zenodo.5083796}
+@article{legat2021mathoptinterface,
+    title={{MathOptInterface}: a data structure for mathematical optimization problems},
+    author={Legat, Beno{\^\i}t and Dowson, Oscar and Dias Garcia, Joaquim and Lubin, Miles},
+    journal={INFORMS Journal on Computing},
+    year={2021},
+    volume={34},
+    number={2},
+    pages={672--689},
+    doi={10.1287/ijoc.2021.1067},
+    publisher={INFORMS}
 }
 
 @software{verzani2021polynomials,
   author       = {John Verzani and
                   Miles Lucas and
                   Zdeněk Hurák and
                   Jameson Nash},
-  title        = {{JuliaMath/Polynomials.jl: v2.0.14}},
-  version      = {v2.0.14},
+  title        = {{JuliaMath/Polynomials.jl: v4.0.5}},
+  version      = {v4.0.5},
   url          = {https://github.com/JuliaMath/Polynomials.jl}
 }
 
 @software{takafumi2021bangbang,
   author       = {Takafumi Arakaki},
-  title        = {{JuliaFolds/BangBang.jl: v0.3.31}},
-  version      = {v0.3.31},
-  url          = {https://github.com/JuliaFolds/BangBang.jl}
+  title        = {{JuliaFolds2/BangBang.jl: v0.4.1}},
+  version      = {v0.4.1},
+  url          = {https://github.com/JuliaFolds2/BangBang.jl}
 }
 
 @article{gowda2021high,
-  title={High-performance symbolic-numerics via multiple dispatch},
-  author={Gowda, Shashi and Ma, Yingbo and Cheli, Alessandro and Gwozdz, Maja and Shah, Viral B and Edelman, Alan and Rackauckas, Christopher},
-  journal={arXiv preprint arXiv:2105.03949},
-  year={2021}
+  author       = {Shashi Gowda and
+                  Yingbo Ma and
+                  Alessandro Cheli and
+                  Maja Gw{\'{o}}zdz and
+                  Viral B. Shah and
+                  Alan Edelman and
+                  Christopher Rackauckas},
+  title        = {High-performance symbolic-numerics via multiple dispatch},
+  journal      = {{ACM} Commun. Comput. Algebra},
+  volume       = {55},
+  number       = {3},
+  pages        = {92--96},
+  year         = {2021},
+  url          = {https://doi.org/10.1145/3511528.3511535},
+  doi          = {10.1145/3511528.3511535},
+  timestamp    = {Sat, 28 Jan 2023 18:54:19 +0100},
+  biburl       = {https://dblp.org/rec/journals/cca/GowdaMCGSER21.bib},
+  bibsource    = {dblp computer science bibliography, https://dblp.org}
 }
 
 @inproceedings{AbstractAlgebra.jl-2017,
@@ -113,9 +118,20 @@ @ARTICLE{BenchmarkTools.jl-2016
   adsnote =	 {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@Conference{legat2020sumofsquares,
-  author    = {Legat, Beno{\^\i}t and Weisser, Tillmann},
-  title     = {SumOfSquares: A Julia package for Polynomial Optimization},
-  booktitle = {INFORMS Annual Meeting},
-  year      = {2020},
+@Conference{weisser2019polynomial,
+  author    = {Weisser, Tillmann and Legat, Beno{\^\i}t and Coey, Chris and Kapelevich, Lea and Vielma, Juan Pablo},
+  title     = {Polynomial and Moment Optimization in Julia and JuMP},
+  booktitle = {JuliaCon},
+  year      = {2019},
+  url       = {https://pretalx.com/juliacon2019/talk/QZBKAU/},
 }
+
+@Conference{legat2023multivariate,
+  author       = {Legat, Beno{\^\i}t},
+  title        = {Multivariate polynomials in {Julia}},
+  month        = jul,
+  year         = 2022,
+  booktitle    = {JuliaCon},
+  year         = {2022},
+  url          = {https://pretalx.com/juliacon-2022/talk/TRFSJY/},
+}