Merge branch 'master' into lollipop

.codecov.yml

@@ -12,4 +12,10 @@ comment:
   behavior: default
 
 ignore:
- - "extern"         # Do not check coverage on the extern directory
+ - "extern/"
+ - "gap/utils.gi"
+ - "PackageInfo.g"
+ - "init.g"
+ - "makedoc.g"
+ - "read.g"
+ - "tst/testall.g"

.gitignore

@@ -53,9 +53,9 @@ planarity
 src/.deps/*
 src/.libs/*
 src/_pkgconfig.h
-extern/edge-addition-planarity-suite-Version_3.0.0.5/.libs
-extern/edge-addition-planarity-suite-Version_3.0.0.5/c/.deps
-extern/edge-addition-planarity-suite-Version_3.0.0.5/m4
+extern/edge-addition-planarity-suite-Version_*/.libs
+extern/edge-addition-planarity-suite-Version_*/c/.deps
+extern/edge-addition-planarity-suite-Version_*/m4
 src/stamp-h1
 tags
 tst/out/*
@@ -74,3 +74,4 @@ coverage
 .ipynb_checkpoints
 bliss
 *.a
+*.dylib

configure.ac

@@ -114,8 +114,8 @@ AS_IF([test "x$enable_compile_warnings" != "xno"],
 AX_CHECK_PLANARITY()
 
 if test "x$with_external_planarity" = xno ; then
-  AC_CONFIG_SUBDIRS([extern/edge-addition-planarity-suite-Version_3.0.0.5])
-  PLANARITY_SUITE_DIR=extern/edge-addition-planarity-suite-Version_3.0.0.5
+  AC_CONFIG_SUBDIRS([extern/edge-addition-planarity-suite-Version_3.0.1.0])
+  PLANARITY_SUITE_DIR=extern/edge-addition-planarity-suite-Version_3.0.1.0
   AC_SUBST(PLANARITY_SUITE_DIR)
 fi
 

doc/digraphs.bib

@@ -1,7 +1,40 @@
 % Cite keys match the cite keys that are used in the compiled GAPDoc manual
 
+@article{B12,
+   author = {John M. Boyer},
+   title = {Subgraph Homeomorphism via the Edge Addition Planarity Algorithm},
+   journal = {Journal of Graph Algorithms and Applications},
+   year = {2012},
+   volume = {16},
+   number = {2},
+   pages = {381--410},
+   doi = {10.7155/jgaa.00268}
+}
+
+@article{BM04,
+   author = {John M. Boyer and Wendy J. Myrvold},
+   title = {On the Cutting Edge: Simplified O(n) Planarity by Edge Addition},
+   journal = {Journal of Graph Algorithms and Applications},
+   year = {2004},
+   volume = {8},
+   number = {3},
+   pages = {241--273},
+   doi = {10.7155/jgaa.00091}
+}
+
+@inproceedings{B06,
+  address = {Berlin, Heidelberg},
+  author = {John M. Boyer},
+  booktitle = {Graph Drawing},
+  editor = {Healy, Patrick and Nikolov, Nikola S.},
+  isbn = {978-3-540-31667-1},
+  pages = {508--511},
+  publisher = {Springer Berlin Heidelberg},
+  title = {A New Method for Efficiently Generating Planar Graph Visibility Representations},
+  year = {2006}}
+
 @incollection{BM06,
-  Author = {John M. Boyer and Wendy J. Myrvold},
+  author = {John M. Boyer and Wendy J. Myrvold},
   Booktitle = {Graph Algorithms and Applications 5},
   Doi = {10.1142/9789812773289_0014},
   Month = {Jun},

doc/grahom.xml

@@ -798,3 +798,66 @@ false
     </Description>
   </ManSection>
 <#/GAPDoc>
+
+<#GAPDoc Label="MaximalCommonSubdigraph">
+  <ManSection>
+    <Oper Name="MaximalCommonSubdigraph" Arg="D1, D2"/>
+    <Returns>A list containing a digraph and two transformations.</Returns>
+    <Description>
+  If <A>D1</A> and <A>D2</A> are digraphs without multiple edges, then
+  <C>MaximalCommonSubdigraph</C> returns a maximal common subgraph <C>M</C> of
+  <A>D1</A> and <A>D2</A> with the maximum number of vertices. So <C>M</C> is a
+  digraph which embeds into both <A>D1</A> and <A>D2</A> and has the largest
+  number of vertices amoung such digraphs.
+
+  It returns a list <C>[M, t1, t2]</C> where <C>M</C> is the maximal common
+  subdigraph and <C>t1, t2</C> are transformations embedding <C>M</C> into
+  <A>D1</A> and <A>D2</A> respectively.
+
+<Example><![CDATA[
+gap> MaximalCommonSubdigraph(PetersenGraph(), CompleteDigraph(10));
+[ <immutable digraph with 2 vertices, 2 edges>, 
+  IdentityTransformation, IdentityTransformation ]
+gap> MaximalCommonSubdigraph(PetersenGraph(),
+> DigraphSymmetricClosure(CycleDigraph(5)));
+[ <immutable digraph with 5 vertices, 10 edges>, 
+  IdentityTransformation, IdentityTransformation ]
+gap> MaximalCommonSubdigraph(NullDigraph(0), CompleteDigraph(10));
+[ <immutable empty digraph with 0 vertices>, IdentityTransformation, 
+  IdentityTransformation ]
+]]></Example>
+    </Description>
+  </ManSection>
+<#/GAPDoc>
+
+<#GAPDoc Label="MinimalCommonSuperdigraph">
+  <ManSection>
+    <Oper Name="MinimalCommonSuperdigraph" Arg="D1, D2"/>
+    <Returns>A list containing a digraph and two transformations.</Returns>
+    <Description>
+  If <A>D1</A> and <A>D2</A> are digraphs without multiple edges, then
+  <C>MinimalCommonSuperdigraph</C> returns a minimal common superdigraph
+  <C>M</C> of <A>D1</A> and <A>D2</A> with the minimum number of vertices.
+  So <C>M</C> is a digraph into which both <A>D1</A> and <A>D2</A> embed and
+  has the smallest number of vertices amoung such digraphs.
+
+  It returns a list <C>[M, t1, t2]</C> where <C>M</C> is the minimal common 
+  superdigraph and <C>t1, t2</C> are transformations embedding <A>D1</A> and
+  <A>D2</A> respectively into <C>M</C>.
+<Example><![CDATA[
+gap> MinimalCommonSuperdigraph(PetersenGraph(), CompleteDigraph(10));
+[ <immutable digraph with 18 vertices, 118 edges>, 
+  IdentityTransformation, 
+  Transformation( [ 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 11, 12, 13,
+      14, 15, 16, 17, 18 ] ) ]
+gap> MinimalCommonSuperdigraph(PetersenGraph(),
+> DigraphSymmetricClosure(CycleDigraph(5)));
+[ <immutable digraph with 10 vertices, 30 edges>, 
+  IdentityTransformation, IdentityTransformation ]
+gap> MinimalCommonSuperdigraph(NullDigraph(0), CompleteDigraph(10));
+[ <immutable digraph with 10 vertices, 90 edges>, 
+  IdentityTransformation, IdentityTransformation ]
+]]></Example>
+    </Description>
+  </ManSection>
+<#/GAPDoc>

doc/grape.xml

@@ -1,7 +1,7 @@
 #############################################################################
 ##
 #W  grape.xml
-#Y  Copyright (C) 2014-19                               James D. Mitchell
+#Y  Copyright (C) 2014-21                               James D. Mitchell
 ##
 ##  Licensing information can be found in the README file of this package.
 ##
@@ -51,12 +51,19 @@ true]]></Example>
   <Description>
     Let <A>G</A> be any group and let <A>gens</A> be a list of elements of
     <A>G</A>. This operation returns an immutable digraph that corresponds to
-    the Cayley graph of <A>G</A> with respect
-    <A>gens</A>. The vertices are the elements of <A>G</A>. There exists an edge
-    from the vertex <C>u</C> to the vertex <C>v</C> if and only if there exists
-    a generator <C>g</C> in <A>gens</A> such that <C>x * g = y</C>. <P/>
+    the Cayley graph of <A>G</A> with respect to <A>gens</A>. <P/>
 
-    <!-- FIXME What is the correspondence between vertices and elements? -->
+    The vertices of the digraph correspond to the elements of <A>G</A>,
+    in the order given by <C>AsList(<A>G</A>)</C>.
+    There exists an edge from vertex <C>u</C> to vertex <C>v</C>
+    if and only if there exists a generator <C>g</C> in <A>gens</A>
+    such that <C>AsList(<A>G</A>)[u] * g = AsList(<A>G</A>)[v]</C>. <P/>
+
+    The labels of the vertices <C>u</C>, <C>v</C>, and the edge <C>[u, v]</C>
+    are the corresponding elements <C>AsList(<A>G</A>)[u]</C>,
+    <C>AsList(<A>G</A>)[v]</C>, and generator <C>g</C>, respectively;
+    see <Ref Oper="DigraphVertexLabel"/> and <Ref Oper="DigraphEdgeLabel"/>.
+    <P/>
 
     If the optional second argument <A>gens</A> is not present, then the
     generators of <A>G</A> are used by default.<P/>

doc/z-chap0.xml

@@ -50,6 +50,14 @@
   <Ref Sect="Isomorphisms and canonical labellings"/> for more details.  
   <P/>
 
+  The &edge-addition-planarity-suite; is also included in &Digraphs;; see
+  <Cite Key="BM04"/>, <Cite Key="B06"/>, <Cite Key="BM06"/>, and <Cite
+  Key="B12"/> .  The &edge-addition-planarity-suite; is an open-source
+  implementation of the edge addition planar graph embedding algorithm and
+  related algorithms by John M. Boyer. See Section <Ref Sect="Planarity"/> for
+  more details.
+  <P/>
+
   From version 1.0.0 of this package, digraphs can be either mutable or immutable.
   Mutable digraphs can be changed in-place by many of the methods in the
   package, which avoids unnecessary copying. Immutable digraphs cannot be

doc/z-chap5.xml

@@ -42,7 +42,7 @@
     <#Include Label="IsCycleDigraph">
   </Section>
 
-  <Section><Heading>Planarity</Heading>
+  <Section Label="Planarity"><Heading>Planarity</Heading>
     <#Include Label="IsPlanarDigraph">
     <#Include Label="IsOuterPlanarDigraph">
   </Section>

doc/z-chap6.xml

@@ -42,6 +42,8 @@ from} $E_a$ \emph{to} $E_b$. In this case we say that $E_a$ and $E_b$ are
     <#Include Label="RepresentativeOutNeighbours">
     <#Include Label="IsDigraphAutomorphism">
     <#Include Label="IsDigraphColouring">
+    <#Include Label="MaximalCommonSubdigraph">
+    <#Include Label="MinimalCommonSuperdigraph">
   </Section>
 
   <Section><Heading>Homomorphisms of digraphs</Heading>