From 136ad651664092bc1418eb8a074c520eb4e3f2d3 Mon Sep 17 00:00:00 2001
From: Ricardo Fabbri <rfabbri@gmail.com>
Date: Tue, 12 Mar 2024 13:41:24 -0300
Subject: [PATCH] Fixed warnings in M2 1.23 per issue #1

Just changed variable names and double-checked with their
conflicting versions and where they are used to be sure to use the right
one. The warnings are simple but verbose.
---
 CODE/common.m2                    | 18 +++++++++---------
 CODE/monodromy_example.m2         |  2 +-
 CODE/numerical-problem-builder.m2 |  2 +-
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/CODE/common.m2 b/CODE/common.m2
index aa04951..34c2e89 100644
--- a/CODE/common.m2
+++ b/CODE/common.m2
@@ -384,8 +384,8 @@ leverageScores = M -> (
 
 
 -- indexes subsystem giving Jacobian rank
-rowSelector = method(Options=>{Threshold=>1e-4})
-rowSelector Matrix := o -> J0 -> (
+rowSelectorPLMP = method(Options=>{Threshold=>1e-4})
+rowSelectorPLMP Matrix := o -> J0 -> (
     (m , n) := size J0;
     J0' := J0^{0}; -- should technically check this is not identically zero
     i := 1;
@@ -405,7 +405,7 @@ rowSelector Matrix := o -> J0 -> (
 
 leverageScoreRowSelector = J0 -> (
     sortedRows := (leverageScores J0)/last;
-    r := rowSelector J0^(sortedRows);
+    r := rowSelectorPLMP J0^(sortedRows);
     sort(r/(i->sortedRows#i))
     )
 
@@ -493,13 +493,13 @@ cpMatrix = t -> matrix{{0,-t_(2,0),t_(1,0)},{t_(2,0),0,-t_(0,0)},{-t_(1,0),t_(0,
 
 essential = (R,t) -> R * cpMatrix t
 
-pCompose = method()
-pCompose (MutableHashTable, MutableHashTable) := (H1, H2) -> (
+pCompose2 = method()
+pCompose2 (MutableHashTable, MutableHashTable) := (H1, H2) -> (
     new MutableHashTable from apply(keys H1,k-> if H2#?(H1#k) then k=> H2#(H1#k))
     )
 
-writePermutations = method(Options=>{})
-writePermutations (HomotopyNode, String) := o -> (V, filename) -> (
+writePermutationsPLMP = method(Options=>{})
+writePermutationsPLMP (HomotopyNode, String) := o -> (V, filename) -> (
     -- assume for now that G has 2 nodes
     G := V.Graph;
     V1 := first G.Vertices;
@@ -507,10 +507,10 @@ writePermutations (HomotopyNode, String) := o -> (V, filename) -> (
     E1 := toList V1.Edges;
     -- "petal loops" based at V1
     e1 := first E1;
-    perms := apply(drop(E1,1),e->values pCompose(e1.Correspondence12,e.Correspondence21));
+    perms := apply(drop(E1,1),e->values pCompose2(e1.Correspondence12,e.Correspondence21));
     writePermutations(perms,filename);
     )
-writePermutations (List, String) := o -> (L, filename) -> (
+writePermutationsPLMP (List, String) := o -> (L, filename) -> (
     perms := L/(P->P/(i->i+1)); -- increment letters by 1 for GAP
     file := openOut (currentFileDirectory | filename);
     for i from 0 to #perms-1 do file << "p" << i << ":= PermList(" << toString(new Array from perms#i) << ");" << endl;
diff --git a/CODE/monodromy_example.m2 b/CODE/monodromy_example.m2
index 514af64..08a5a00 100644
--- a/CODE/monodromy_example.m2
+++ b/CODE/monodromy_example.m2
@@ -77,4 +77,4 @@ concatenate ts
 -- post-process the output of monodromySolver
 
 
-writePermutations(V, "example" | ".txt")
+writePermutationsPLMP(V, "example" | ".txt")
diff --git a/CODE/numerical-problem-builder.m2 b/CODE/numerical-problem-builder.m2
index f62c88c..b4af9a9 100644
--- a/CODE/numerical-problem-builder.m2
+++ b/CODE/numerical-problem-builder.m2
@@ -174,7 +174,7 @@ if (instance(Jpivots, Symbol) and JACOBIAN) then (
     (M,N) = size J;
     elapsedTime JGS = gateSystem(paramMatrix, varMatrix, transpose matrix{flatten entries J});
     elapsedTime J0 = matrix(transpose evaluate(JGS,y,c),M,N);
-    elapsedTime Jpivots = rowSelector(J0,Threshold=>1e-6);
+    elapsedTime Jpivots = rowSelectorPLMP(J0,Threshold=>1e-6);
     elapsedTime S = first SVD J0^Jpivots;
     << "pivot indices are " << toString Jpivots << endl;
     )