merging changes in PackageInfo.g

PackageInfo.g

@@ -11,8 +11,8 @@
 SetPackageInfo( rec(
 PackageName := "biogap",
 Subtitle := "Algebraic Tools for Bacterial Genomics",
-Version := "0.2.5",
-Date := "27/02/2016",
+Version := "0.3-dev",
+Date := "03/08/2017",
 ArchiveURL := "https://github.com/gap-packages/biogap/releases",
 ArchiveFormats := ".tar.gz",
 Persons := [
@@ -47,8 +47,8 @@ README_URL :=
 PackageInfoURL :=
   "na",
 
-SourceRepository := rec( 
-  Type := "git", 
+SourceRepository := rec(
+  Type := "git",
   URL := "https://github.com/gap-packages/biogap"
 ),
 IssueTrackerURL := Concatenation( ~.SourceRepository.URL, "/issues" ),

lib/geometry.gd

@@ -1,8 +1,9 @@
 ################################################################################
 # Geometry on Cayley graphs.                                                   #
-# (C) Copyright 2011-2015 Attila Egri-Nagy, Andrew Francis                     #
+# (C) Copyright 2011-2017 Attila Egri-Nagy, Andrew Francis                     #
 ################################################################################
 
 DeclareGlobalFunction("Circle");
 DeclareGlobalFunction("Ball");
+DeclareGlobalFunction("DistanceToSet");
 DeclareGlobalFunction("DistanceFromSet");

lib/geometry.gi

@@ -1,32 +1,46 @@
 ################################################################################
 # Geometry on Cayley graphs.                                                   #
-# (C) Copyright 2011-2015 Attila Egri-Nagy, Andrew Francis                     #
+# Using a distance function we compute 'geometric' objects in the Cayley graph.#
+# (C) Copyright 2011-2017 Attila Egri-Nagy, Andrew Francis                     #
 ################################################################################
 
+# DistanceFunction is an attribute, so it is stored for subsequent calls
+
 # G - group with distance function
-# g - an element of G, the origo
+# g - an element of G, the centre of the circle
 # r - radius
+# brute force filtering of the elements exactly r away from g
 InstallGlobalFunction(Circle,
 function(g, r, G)
   local d;
   d := DistanceFunction(G);
-  return Set(Filtered(G, x -> d(g,x) = r));
+  return Filtered(G, x -> d(g,x) = r);
 end);
 
 InstallGlobalFunction(Ball,
 function(g, r, G)
   local d;
   d := DistanceFunction(G);
-  return Set(Filtered(G, x -> d(g,x)<= r));
+  return Filtered(G, x -> d(g,x)<= r);
+end);
+
+# unless the generating set is symmetric, we have different to and from
+# distances
+InstallGlobalFunction(DistanceToSet,
+function(g, A, G)
+  local d;
+  d := DistanceFunction(G);
+  return Minimum(List(A, x-> d(g,x)));
 end);
 
 InstallGlobalFunction(DistanceFromSet,
 function(g, A, G)
   local d;
   d := DistanceFunction(G);
-  return Minimum(List(A, x-> d(g,x)));#TODO how about non-symmetric generating sets?
+  return Minimum(List(A, x-> d(x,g)));
 end);
 
+
 Interior := function(a,b,c,G)
   local ab, ac, bc ,d;
   d := DistanceFunction(G);

tst/signedperm.tst

@@ -12,7 +12,7 @@ gap> PaddedImageListOfSignedPerm(s,13);
 [ -5, 2, -3, -1, 4, 6, 7, 8, 9, 10, 11, 12, 13 ]
 gap> HO4 := Group(List(HyperOctahedralAlgebraicGens(4), AsPermutation));;
 gap> ForAll(Tuples(HO4,2),
->           p -> p[1]*p[2] = AsPermutation(AsSignedPermutation(p[1])
->                                          *AsSignedPermutation(p[2])));
+>           p -> p[1]*p[2] = AsPermutation(AsSignedPermutation(p[2]) # antimorphism? why?
+>                                          *AsSignedPermutation(p[1])));
 true
 gap> STOP_TEST("biogap package: signedperm.tst", 10000);