Merge branch 'pre-master'

Macaulay2 · Jun 14, 2023 · 5572c8a · 5572c8a
2 parents 8df01f4 + e08f5f1
commit 5572c8a
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diff --git a/M2/Macaulay2/packages/=distributed-packages b/M2/Macaulay2/packages/=distributed-packages
@@ -255,4 +255,4 @@ PseudomonomialPrimaryDecomposition
 PolyominoIdeals
 MatchingFields
 CellularResolutions
-SagbiGbDetection
+SagbiGbDetection
diff --git a/M2/Macaulay2/packages/DecomposableSparseSystems/examples/_solve__Decomposable__System.out b/M2/Macaulay2/packages/DecomposableSparseSystems/examples/_solve__Decomposable__System.out
@@ -102,6 +102,16 @@ The mixed volume of
  is 3
  yet we found 2 points
 Attempting to find all 3 points via monodromy.
+Found:2 solutions via monodromy
+Found:3 solutions via monodromy
+Found:3 solutions via monodromy
+Found:3 solutions via monodromy
+Found:3 solutions via monodromy
+Found:3 solutions via monodromy
+Found:3 solutions via monodromy
+Found:3 solutions via monodromy
+Found:3 solutions via monodromy
+Found:3 solutions via monodromy
 Monodromy recovery was successful
 basicSolver: Computed 3 solutions
 

diff --git a/M2/Macaulay2/packages/GraphicalModelsMLE.m2 b/M2/Macaulay2/packages/GraphicalModelsMLE.m2
@@ -44,7 +44,21 @@ newPackage(
      Headline => "maximum likelihood estimates for graphical statistical models",
      Keywords => {"Algebraic Statistics"},
      DebuggingMode => true,
-     PackageExports => {"GraphicalModels","Graphs","EigenSolver","NumericalAlgebraicGeometry","StatGraphs"}
+     PackageExports => {"GraphicalModels","Graphs","EigenSolver","NumericalAlgebraicGeometry","StatGraphs"},
+     Certification => {
+	  "journal name" => "The Journal of Software for Algebra and Geometry",
+	  "journal URI" => "http://j-sag.org/",
+	  "article title" => "Computing maximum likelihood estimates for Gaussian graphical models with Macaulay2",
+	  "acceptance date" => "14 March 2022",
+	  "published article URI" => "https://msp.org/jsag/2022/12-1/p01.xhtml",
+	  "published article DOI" => "10.2140/jsag.2022.12.1",
+	  "published code URI" => "https://msp.org/jsag/2022/12-1/jsag-v12-n1-x01-GraphicalModelsMLE.zip",
+	  "repository code URI" => "http://github.com/Macaulay2/M2/blob/master/M2/Macaulay2/packages/GraphicalModelsMLE.m2",
+	  "release at publication" => "f0aaf5e74216283f022f7773bc1116f8de6b944b",	    -- git commit number in hex
+	  "version at publication" => "1.0",
+	  "volume number" => "12",
+	  "volume URI" => "https://msp.org/jsag/2022/12-1/"
+	  }
      )
 export {
     "checkPD",

diff --git a/M2/Macaulay2/packages/Jets.m2 b/M2/Macaulay2/packages/Jets.m2
@@ -34,7 +34,21 @@ newPackage(
      Headline => "compute jets of various algebraic, geometric and combinatorial objects",
      PackageImports => {"SimpleDoc","EdgeIdeals"},
      PackageExports => {"EdgeIdeals"},
-     DebuggingMode => false
+     DebuggingMode => false,
+     Certification => {
+	  "journal name" => "The Journal of Software for Algebra and Geometry",
+	  "journal URI" => "http://j-sag.org/",
+	  "article title" => "Computing with jets",
+	  "acceptance date" => "20 October 2022",
+	  "published article URI" => "https://msp.org/jsag/2022/12-1/p06.xhtml",
+	  "published article DOI" => "10.2140/jsag.2022.12.43",
+	  "published code URI" => "https://msp.org/jsag/2022/12-1/jsag-v12-n1-x06-Jets.m2",
+	  "repository code URI" => "http://github.com/Macaulay2/M2/blob/master/M2/Macaulay2/packages/Jets.m2",
+	  "release at publication" => "b0d482205848caeda2616f4ed58be2a6783e88a2",	    -- git commit number in hex
+	  "version at publication" => "1.1",
+	  "volume number" => "12",
+	  "volume URI" => "https://msp.org/jsag/2022/12-1/"
+	  }
      )
 
 

diff --git a/M2/Macaulay2/packages/LinearTruncations.m2 b/M2/Macaulay2/packages/LinearTruncations.m2
@@ -8,7 +8,21 @@ newPackage(
 	{Name => "Navid Nemati", Email => "[email protected]"}},
     Headline => "find the multigraded truncations that give linear resolutions",
     PackageExports => {"Truncations", "TateOnProducts"},
-    DebuggingMode => false
+    DebuggingMode => false,
+    Certification => {
+	 "journal name" => "The Journal of Software for Algebra and Geometry",
+	 "journal URI" => "http://j-sag.org/",
+	 "article title" => "Linear truncations package for Macaulay2",
+	 "acceptance date" => "18 May 2022",
+	 "published article URI" => "https://msp.org/jsag/2022/12-1/p02.xhtml",
+	 "published article DOI" => "10.2140/jsag.2022.12.11",
+	 "published code URI" => "https://msp.org/jsag/2022/12-1/jsag-v12-n1-x02-LinearTruncations.m2",
+	 "repository code URI" => "http://github.com/Macaulay2/M2/blob/master/M2/Macaulay2/packages/LinearTruncations.m2",
+	 "release at publication" => "c1b72330821054c17b07c574649d98ac577cb3af",	    -- git commit number in hex
+	 "version at publication" => "1.0",
+	 "volume number" => "12",
+	 "volume URI" => "https://msp.org/jsag/2022/12-1/"
+	 }
     )
 
 export{

diff --git a/M2/Macaulay2/packages/Macaulay2Doc/changes.m2 b/M2/Macaulay2/packages/Macaulay2Doc/changes.m2
@@ -6,6 +6,7 @@ document {
      Key => "changes to Macaulay2, by version",
      Subnodes => {
 	  TO "changes made for the next release",
+	  TO "changes, 1.22",
 	  TO "changes, 1.21",
 	  TO "changes, 1.20",
 	  TO "changes, 1.19.1",
@@ -44,6 +45,45 @@ document {
 document {
      Key => "changes, 1.22",
      UL {
+	  LI { "packages that have been published and certified:",
+	       UL {
+		    -- LI { star, " ", TO "::", ", a package by ... for ..., has been published." },
+		    LI { star, " ", TO "GraphicalModelsMLE::GraphicalModelsMLE", ", a package by 
+			 Carlos Amendola, Luis David Garcia Puente, Roser Homs Pons, Olga Kuznetsova, 
+			 Harshit J Motwani, Elina Robeva, and David Swinarski, for maximum likelihood
+			 estimates for graphical statistical models, has been published." },
+		    LI { star, " ", TO "LinearTruncations::LinearTruncations", ", a package by Lauren Cranton Heller,
+			  David Eisenbud, and Navid Nemati for finding multigraded truncations that give linear resolutions, 
+			  has been published."
+			  },
+	     	    LI { star, " ", TO "RationalMaps::RationalMaps", ", a package by Karl Schwede,
+			  Daniel Smolkin, S. Hamid Hassanzadeh, and C. J. Bott, for working with rational maps, has been published." },
+		    LI { star, " ", TO "PseudomonomialPrimaryDecomposition::PseudomonomialPrimaryDecomposition", ", a package by Alan 
+			 A. Veliz-Cuba for primary decomposition of square free pseudomonomial ideals, has been published."},
+		    LI { star, " ", TO "NoetherianOperators::NoetherianOperators", ", a package by Robert Krone, Justin Chen,
+			  Marc Harkonen, Yairon Cid-Ruiz, and Anton Leykin, for numerically computing local dual spaces, 
+			  Hilbert functions, and Noetherian operators, has been published." },
+		    LI { star, " ", TO "Jets::Jets", ", a package by Federico Galetto and 
+			 Nicholas Iammarino, for computing jets of various algebraic, geometric and combinatorial objects, has been published." }
+	     	    }
+	       },
+	  LI { "new packages:",
+	       UL {
+		    -- LI { TO "::", ", a package by ... for ..., has been added." },
+		    LI { TO "HolonomicSystems::HolonomicSystems", ", a package by Mahrud Sayrafi, Christine Berkesch, Anton Leykin, and 
+			 Harrison Tsai for holonomic systems, has been added.  The code was originally in the Dmodules package." },
+		    LI { TO "BernsteinSato::BernsteinSato", ", a package by Anton Leykin and Harrison Tsai for Bernstein-Sato, 
+			 has been added.  The code was originally in the Dmodules package." },
+		    LI { TO "PolyominoIdeals::PolyominoIdeals", ", a package by Carmelo Cisto, Francesco Navarra, and Rizwan Jahangir for 
+			 binomial ideals of collections of cells, has been added." },
+		    LI { TO "MatchingFields::MatchingFields", ", a package by Oliver Clarke for matching fields, has been added." },
+		    LI { TO "CellularResolutions::CellularResolutions", ", a package by Jay Yang and Aleksandra Sobieska for 
+			 cellular resolutions of monomial ideals, has been added." },
+		    LI { TO "SagbiGbDetection::SagbiGbDetection", ", a package by Viktoriia Borovik, Timothy Duff, and Elima Shehu for verifying
+			  whether the given generators of an ideal form the Gr\"obner basis or whether the given generators of a finitely 
+			  generated subalgebra of a polynomial ring are the SAGBI basis, has been added." }
+		    }
+	       },
 	  LI { "functionality added:",
 	       UL {
 		    LI { "A ", TO RingMap, " object may now be raised to the 0th power if its ", TO source, " and ", TO target, " agree." },

diff --git a/...y2/packages/NCAlgebra/examples/___Basic_spoperations_spon_spnoncommutative_spalgebras.out b/...y2/packages/NCAlgebra/examples/___Basic_spoperations_spon_spnoncommutative_spalgebras.out
@@ -332,7 +332,7 @@ i45 : E' = QQ[x,y,z,w,SkewCommutative=>true]
 
 o45 = E'
 
-o45 : PolynomialRing, 4 skew commutative variables
+o45 : PolynomialRing, 4 skew commutative variable(s)
 
 i46 : E = toNCRing E'
 --Calling Bergman for NCGB calculation.
@@ -387,7 +387,7 @@ i54 : C'' = toM2Ring(C,SkewCommutative=>true)
 
 o54 = C''
 
-o54 : PolynomialRing, 4 skew commutative variables
+o54 : PolynomialRing, 4 skew commutative variable(s)
 
 i55 : y*x
 

diff --git a/M2/Macaulay2/packages/NCAlgebra/examples/_matrix_lp__N__C__Ring__Map_rp.out b/M2/Macaulay2/packages/NCAlgebra/examples/_matrix_lp__N__C__Ring__Map_rp.out
@@ -12,7 +12,7 @@ i2 : B = QQ[a,b,c,SkewCommutative=>true]
 
 o2 = B
 
-o2 : PolynomialRing, 3 skew commutative variables
+o2 : PolynomialRing, 3 skew commutative variable(s)
 
 i3 : f = ncMap(B,A,{a^3,b^2,a+b,a-b})
 

diff --git a/M2/Macaulay2/packages/NCAlgebra/examples/_to__M2__Ring.out b/M2/Macaulay2/packages/NCAlgebra/examples/_to__M2__Ring.out
@@ -44,7 +44,7 @@ i7 : C = toM2Ring(A,SkewCommutative=>true)
 
 o7 = C
 
-o7 : PolynomialRing, 4 skew commutative variables
+o7 : PolynomialRing, 4 skew commutative variable(s)
 
 i8 : x*y-y*x
 

diff --git a/M2/Macaulay2/packages/NoetherianOperators.m2 b/M2/Macaulay2/packages/NoetherianOperators.m2
@@ -20,11 +20,25 @@ newPackage(
     PackageImports => {"PrimaryDecomposition"},
     AuxiliaryFiles => false,
     DebuggingMode => false,
-    Keywords => {"Numerical Algebraic Geometry", "Commutative Algebra"}
-)
+    Keywords => {"Numerical Algebraic Geometry", "Commutative Algebra"},
+    Certification => {
+	 "journal name" => "The Journal of Software for Algebra and Geometry",
+	 "journal URI" => "http://j-sag.org/",
+	 "article title" => "Noetherian operators in Macaulay2",
+	 "acceptance date" => "26 September 2022",
+	 "published article URI" => "https://msp.org/jsag/2022/12-1/p05.xhtml",
+	 "published article DOI" => "10.2140/jsag.2022.12.33",
+	 "published code URI" => "https://msp.org/jsag/2022/12-1/jsag-v12-n1-x05-NoetherianOperators.m2",
+	 "repository code URI" => "http://github.com/Macaulay2/M2/blob/master/M2/Macaulay2/packages/NoetherianOperators.m2",
+	 "release at publication" => "28faaabb38111c186c23ef6e6a3d487b0823390e",	    -- git commit number in hex
+	 "version at publication" => "2.2.1",
+	 "volume number" => "12",
+	 "volume URI" => "https://msp.org/jsag/2022/12-1/"
+	 }
+     )
 
 debug NumericalLinearAlgebra
-
+     
 export {
     "truncatedDual",
     "zeroDimensionalDual",