Merge branch 'master' into folkman

.VERSION

@@ -1 +1 @@
-1.3.1
+1.4.0

.github/workflows/ci.yml

@@ -13,33 +13,42 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: "Install dependencies . . ."
-        run: |
-          sudo pip install gaplint cpplint
-      - name: "Run gaplint + cpplint . . ."
+        name: "Check out the repository"
+      - uses: actions/setup-python@v1
+        name: "Set up Python"
+      - uses: BSFishy/pip-action@v1
+        name: "Install gaplint and cpplint with pip"
+        with:
+          packages: |
+            gaplint
+            cpplint
+      - name: "Run gaplint + cpplint"
         run: bash etc/lint.sh
   test:
-    name: "GAP ${{ matrix.gap-branch }} on ${{ matrix.os }}"
-    runs-on: ${{ matrix.os }}
+    name: "GAP ${{ matrix.gap-branch }}"
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        os:
-          - ubuntu-latest
-        digraphs-lib:
-          - digraphs-lib-0.6
         gap-branch:
           - master
           - stable-4.11
+        pkgs-to-clone:
+          - NautyTracesInterface
+
+        include:
+          - gap-branch: stable-4.10
+            pkgs-to-clone: datastructures
 
     steps:
       - uses: actions/checkout@v2
       - uses: gap-actions/setup-gap-for-packages@v1
         with:
-          GAP_PKGS_TO_CLONE: "NautyTracesInterface"
+          GAP_PKGS_TO_CLONE: "${{ matrix.pkgs-to-clone }}"
           GAP_PKGS_TO_BUILD: "io orb profiling grape NautyTracesInterface datastructures"
           GAPBRANCH: ${{ matrix.gap-branch }}
       - name: "Install digraphs-lib"
-        run: curl --retry 5 -L -O https://digraphs.github.io/Digraphs/${{ matrix.digraphs-lib }}.tar.gz
-             && tar xf ${{ matrix.digraphs-lib }}.tar.gz
+        run: DIGRAPHS_LIB="digraphs-lib-0.6"
+             && curl --retry 5 -L -O "https://digraphs.github.io/Digraphs/${DIGRAPHS_LIB}.tar.gz"
+             && tar xf "${DIGRAPHS_LIB}.tar.gz"
       - uses: gap-actions/run-test-for-packages@v1

CHANGELOG.md

@@ -4,6 +4,43 @@ Torpey, Wilf A. Wilson et al.
 
 Licensing information can be found in the `LICENSE` file.
 
+## Version 1.4.0 (released 27/01/2021)
+
+In this release there are several new features and improvements. 
+
+The following improvements and bugs have been made:
+
+* the clique finder was reimplemented in C by [Julius Jonusas][]
+* a critical bug in `CayleyDigraph` was reported and fixed by [Jan De Beule][]
+* a minor bug in `ReadDigraphs` was reported by [Wilf A. Wilson][] and
+  fixed by [James D. Mitchell][]
+* the performance of `BlissCanonicalLabelling` and `BlissAutomorphismGroup` was
+  improved for multidigraphs by Marina Anagnostopoulou-Merkouri and Sam
+  Harper.
+* a bug in `GeneratorsOfEndomorphismMonoid` that caused GAP to crash when
+  called with a multidigraph was reported by [Wilf A. Wilson][] and
+  fixed by [James D. Mitchell][] 
+*  [Wilf A. Wilson][] made some improvements to the manual.
+* the performance of `DigraphCopy` was improved by Marina
+  Anagnostopoulou-Merkouri and Sam Harper.
+
+The main new features are:
+
+* the attribute `DigraphNrLoops` was introduced by Marina
+  Anagnostopoulou-Merkouri and Sam Harper.
+* the operations 
+  * `DotColoredDigraph`
+  * `DotVertexColoredDigraph`
+  * `DotEdgeColoredDigraph`
+  * `DotSymmetricColoredDigraph`
+  * `DotSymmetricVertexColoredDigraph` 
+  * `DotSymmetricEdgeColoredDigraph` 
+  were introduced by Marina Anagnostopoulou-Merkouri and Sam Harper.
+* the operation `VerticesReachableFrom` was introduced by 
+  Marina Anagnostopoulou-Merkouri.
+* the operation `ModularProduct` was introduced by Luke Elliott and  
+  [James D. Mitchell][]
+
 ## Version 1.3.1 (released 27/11/2020)
 
 This is a minor release fixing some issues, some performance improvements, and
@@ -347,7 +384,7 @@ Other additions and changes are listed below:
   Suite](https://github.com/graph-algorithms/edge-addition-planarity-suite)
   is now included in Digraphs, and so it is now possible to test digraphs for
   planarity, and to perform related computations.  This was added by [James D.
-  Mitchell](http://goo.gl/ZtViV6) in [PR
+  Mitchell][] in [PR
   #156](https://github.com/digraphs/Digraphs/pull/156).  The new
   functionality can be accessed via:
   * `Is(Outer)PlanarDigraph`,
@@ -366,14 +403,14 @@ Other additions and changes are listed below:
   `DigraphWelshPowellOrder`. The behaviour of `DigraphGreedyColouring` can be
   modified by including an optional second argument; see the
   documentation for more information. This work was done by [James D.
-  Mitchell](http://goo.gl/ZtViV6) in [PR
+  Mitchell][] in [PR
   #144](https://github.com/digraphs/Digraphs/pull/144).
 * `DigraphShortestPath` was introduced by Murray Whyte in [PR
   #148](https://github.com/digraphs/Digraphs/pull/148).
 * `IsAntiSymmetricDigraph` (with a capital S) was added as a synonym for
   `IsAntisymmetricDigraph`.
 * `RandomDigraph` now allows a float as its second argument; by [James D.
-  Mitchell](http://goo.gl/ZtViV6) in [PR
+  Mitchell][] in [PR
   #159](https://github.com/digraphs/Digraphs/pull/159).
 * The attribute `CharacteristcPolynomial` for a digraph was added by Luke
   Elliott in [PR #164](https://github.com/digraphs/Digraphs/pull/164).
@@ -389,7 +426,7 @@ This release contains bugfixes and a couple of new features.
   digraphs were added by Chris Russell in [PR
   #136](https://github.com/digraphs/Digraphs/pull/136).
 * The operation `IsDigraphColouring` was added by [James D.
-  Mitchell](http://goo.gl/ZtViV6) in [PR
+  Mitchell][] in [PR
   #145](https://github.com/digraphs/Digraphs/pull/145).
 * In previous versions of the package, the output of `ArticulationPoints` would
   sometimes contain repeated vertices (reported by Luke Elliott in [Issue
@@ -464,11 +501,11 @@ Digraphs now requires version 4.5.1 of the IO package.
 
 The principal change in Digraphs version 0.11.0 is the addition of
 support for computing automorphisms, canonical labellings, and isomorphisms of
-digraphs with [nauty](http://pallini.di.uniroma1.it/). This
+digraphs with [nauty](https://pallini.di.uniroma1.it/). This
 functionality requires the [NautyTracesInterface
 package](https://github.com/gap-packages/NautyTracesInterface) for GAP, version 0.2
 or newer. However, this is not a required package, and the default engine
-remains [bliss](http://www.tcs.hut.fi/Software/bliss/). It is possible to
+remains [bliss][]. It is possible to
 specify the engine that is used by Digraphs. These changes to Digraphs were made
 by [James D. Mitchell][]].
 
@@ -642,7 +679,7 @@ digraphs are set at creation [[Michael Torpey][]]
 
 ## Version 0.5.0 (released 03/03/2016)
 This release contains some bugfixes, as well as new and changed functionality.
-Digraphs now requires the [Orb package](http://gap-packages.github.io/orb),
+Digraphs now requires the [Orb package](https://gap-packages.github.io/orb),
 version 4.7.5 or higher.
 
 ### New Features in Version 0.5.0
@@ -745,7 +782,7 @@ This release contains a number of bugfixes and performance improvements.
 
 ### New Features in Version 0.3.0
 * The attribute `DigraphAllSimpleCircuits` based
-on the algorithm in [this paper](http://epubs.siam.org/doi/abs/10.1137/0204007?journalCode=smjcat) by Donald B. Johnson. [Stuart Burrell and [Wilf A. Wilson][]]
+on the algorithm in [this paper](https://epubs.siam.org/doi/abs/10.1137/0204007) by Donald B. Johnson. [Stuart Burrell and [Wilf A. Wilson][]]
 * Improve efficiency of the algorithm for coloring a graph with 2 colours, a method for `IsBipartiteDigraph` and `DigraphBicomponents`. [Isabella Scott and [Wilf A. Wilson][]]
 * `AutomorphismGroup` and `DigraphCanonicalLabelling` can now be used with color classes that are preserved by the permutations acting on a digraph. [[James D. Mitchell][]]
 * The `TCodeDecoder` was made more efficient. [[James D. Mitchell][]]
@@ -764,7 +801,7 @@ The first release.
 Pre-release version that was not made publicly available.
 
 [James D. Mitchell]: https://jdbm.me
-[Wilf A. Wilson]: http://wilf.me
+[Wilf A. Wilson]: https://wilf.me
 [Michael Torpey]: https://mtorpey.github.io
 [Julius Jonusas]: http://julius.jonusas.work
 [Jan De Beule]: http://homepages.vub.ac.be/~jdbeule

LICENSE

@@ -14,4 +14,4 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
+along with this program.  If not, see <https://www.gnu.org/licenses/>.

PackageInfo.g

@@ -9,14 +9,14 @@
 ##
 
 ##  <#GAPDoc Label="PKGVERSIONDATA">
-##  <!ENTITY VERSION                  "1.3.1">
+##  <!ENTITY VERSION                  "1.4.0">
 ##  <!ENTITY GAPVERS                  "4.10.0">
 ##  <!ENTITY GRAPEVERS                "4.8.1">
 ##  <!ENTITY IOVERS                   "4.5.1">
 ##  <!ENTITY ORBVERS                  "4.8.2">
 ##  <!ENTITY DATASTRUCTURESVERS       "0.2.5">
 ##  <!ENTITY NAUTYTRACESINTERFACEVERS "0.2">
-##  <!ENTITY ARCHIVENAME    "digraphs-1.3.1">
+##  <!ENTITY ARCHIVENAME    "digraphs-1.4.0">
 ##  <!ENTITY COPYRIGHTYEARS "2014-20">
 ##  <#/GAPDoc>
 
@@ -28,8 +28,8 @@ _STANDREWSCS := Concatenation(["Jack Cole Building, North Haugh, ",
 SetPackageInfo(rec(
 PackageName := "Digraphs",
 Subtitle := "Graphs, digraphs, and multidigraphs in GAP",
-Version := "1.3.1",
-Date := "27/11/2020",  # dd/mm/yyyy format
+Version := "1.4.0",
+Date := "27/01/2021",  # dd/mm/yyyy format
 License := "GPL-3.0-or-later",
 ArchiveFormats := ".tar.gz",
 
@@ -109,7 +109,7 @@ Persons := [
     IsAuthor      := false,
     IsMaintainer  := false,
     Email         := "caj21@st-andrews.ac.uk",
-    WWWHome       := "http://caj.host.cs.st-andrews.ac.uk",
+    WWWHome       := "https://caj.host.cs.st-andrews.ac.uk",
     PostalAddress := _STANDREWSCS,
     Place         := "St Andrews",
     Institution   := "University of St Andrews"),

README.md

@@ -7,7 +7,7 @@
 
 ### Digraphs package for GAP
 
-#### Copyright (C) 2014-20 by Jan De Beule, Julius Jonušas, James D. Mitchell, Michael Torpey, Wilf A. Wilson et al.
+#### Copyright (C) 2014-21 by Jan De Beule, Julius Jonušas, James D. Mitchell, Michael Torpey, Wilf A. Wilson et al.
 ## Getting Digraphs
 
 To get the latest version of the package, download the archive file

VERSIONS

@@ -8,6 +8,7 @@
 #############################################################################
 ##
 
+release 1.4.0 - 27/01/2021
 release 1.3.1 - 27/11/2020
 release 1.3.0 - 27/06/2020
 release 1.2.1 - 27/05/2020

ci/docker-test.sh

@@ -81,7 +81,7 @@ fi
 
 if [ "$SUITE" == "conda" ]; then
   bold "Installing dependencies (conda). . ."
-  wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
   chmod +x miniconda.sh;
   ./miniconda.sh -b;
   export PATH=/home/gap/miniconda3/bin:$PATH;

doc/attr.xml

@@ -753,7 +753,7 @@ rec( comps := [ [ 1, 2 ], [ 3, 4, 5 ] ], id := [ 1, 1, 2, 2, 2 ] )
     than <M>1</M>, then this operation returns <K>fail</K>.
     <P/>
 
-    See section <Ref Subsect="Definitions" Style="Number" /> for the definition
+    See Section <Ref Subsect="Definitions" Style="Number" /> for the definition
     of a directed cycle, and the definition of a loop.
 
     <P/>
@@ -930,7 +930,7 @@ gap> DigraphDiameter(D);
   <Description>
     This attribute returns the <E>girth</E> of the digraph <A>digraph</A>.
     The <E>girth</E> of a digraph is the length of its shortest simple circuit.
-    See section <Ref Subsect="Definitions" Style="Number" /> for the definitions
+    See Section <Ref Subsect="Definitions" Style="Number" /> for the definitions
     of simple circuit, directed cycle, and loop.
     <P/>
 
@@ -1204,7 +1204,7 @@ gap> ArticulationPoints(ChainDigraph(2));
     If <A>digraph</A> is a digraph, then <C>DigraphAllSimpleCircuits</C>
     returns a list of the <E>simple circuits</E> in <A>digraph</A>. <P/>
 
-    See section <Ref Subsect="Definitions" Style="Number" /> for the definition
+    See Section <Ref Subsect="Definitions" Style="Number" /> for the definition
     of a simple circuit, and related notions. Note that a loop is a simple
     circuit. <P/>
 
@@ -1256,7 +1256,7 @@ gap> DigraphAllSimpleCircuits(D);
   <Returns>A list of vertices, or <K>fail</K>.</Returns>
   <Description>
     If <A>digraph</A> is a digraph, then <C>DigraphLongestSimpleCircuit</C>
-    returns the longest <E>simple circuit</E> in <A>digraph</A>. See section
+    returns the longest <E>simple circuit</E> in <A>digraph</A>. See Section
     <Ref Subsect="Definitions" Style="Number" /> for the definition of simple
     circuit, and the definition of length for a simple circuit.<P/>
 
@@ -1342,7 +1342,7 @@ fail
     If a digraph <A>digraph</A> has at least one directed cycle, then the period
     is the greatest positive integer which divides the lengths of all directed
     cycles of <A>digraph</A>.  If <A>digraph</A> has no directed cycles, then
-    this function returns <M>0</M>.  See section <Ref Subsect="Definitions"
+    this function returns <M>0</M>.  See Section <Ref Subsect="Definitions"
       Style="Number" /> for the definition of a directed cycle. <P/>
 
     A digraph with a period of <M>1</M> is said to be <E>aperiodic</E>.  See

doc/cliques.xml

@@ -145,14 +145,14 @@ true]]></Example>
       <Item>
         If one or two arguments are supplied, then <C>DigraphClique</C> and
         <C>DigraphMaximalClique</C> greedily enlarge the clique <A>include</A>
-        until it can not continue.  The result is guaranteed to be a maximal
+        until it cannot continue.  The result is guaranteed to be a maximal
         clique. This may or may not return an answer more quickly than using
         <Ref Func="DigraphMaximalCliques"/>.  with a limit of 1.
       </Item>
       <Mark>Three arguments</Mark>
       <Item>
         If three arguments are supplied, then <C>DigraphClique</C> greedily
-        enlarges the clique <A>include</A> until it can not continue, although
+        enlarges the clique <A>include</A> until it cannot continue, although
         this clique may not be maximal.<P/>
 
         Given three arguments, <C>DigraphMaximalClique</C> returns the maximal
@@ -345,15 +345,15 @@ gap> DigraphMaximalCliques(D);
       <Item>
         If one or two arguments are supplied, then <C>DigraphIndependentSet</C>
         and <C>DigraphMaximalIndependentSet</C> greedily enlarge the
-        independent set <A>include</A> until it can not continue.  The result
+        independent set <A>include</A> until it cannot continue.  The result
         is guaranteed to be a maximal independent set. This may or may not
         return an answer more quickly than using <Ref
           Func="DigraphMaximalIndependentSets"/>.  with a limit of 1.
       </Item>
       <Mark>Three arguments</Mark>
       <Item>
         If three arguments are supplied, then <C>DigraphIndependentSet</C>
-        greedily enlarges the independent set <A>include</A> until it can not
+        greedily enlarges the independent set <A>include</A> until it cannot
         continue, although this independent set may not be maximal.<P/>
 
         Given three arguments, <C>DigraphMaximalIndependentSet</C> returns the