Merge branch 'stable-1.4'

.github/workflows/ci.yml

@@ -19,27 +19,30 @@ jobs:
       - 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

@@ -384,7 +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`,
@@ -403,14 +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).
@@ -426,7 +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
@@ -501,11 +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][]].
 
@@ -679,7 +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
@@ -782,7 +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][]]
@@ -801,7 +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

@@ -109,7 +109,7 @@ Persons := [
     IsAuthor      := false,
     IsMaintainer  := false,
     Email         := "[email protected]",
-    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"),

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/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

doc/digraphs.bib

@@ -26,27 +26,27 @@ @article{CK86
   Number = {2},
   Pages = {97--122},
   Title = {The geometry of two-weight codes},
-  Url = {http://dx.doi.org/10.1112/blms/18.2.97},
+  Url = {https://dx.doi.org/10.1112/blms/18.2.97},
   Volume = {18},
   Year = {1986},
-  Bdsk-Url-1 = {http://dx.doi.org/10.1112/blms/18.2.97},
+  Bdsk-Url-1 = {https://dx.doi.org/10.1112/blms/18.2.97},
 }
 
 @article{Gab00,
   Author = {Harold N. Gabow},
-  Doi = {http://dx.doi.org/10.1016/S0020-0190(00)00051-X},
+  Doi = {https://dx.doi.org/10.1016/S0020-0190(00)00051-X},
   Issn = {0020-0190},
   Journal = {Information Processing Letters},
   Keywords = {Algorithms},
   Number = {34},
   Pages = {107 - 114},
   Title = {Path-based depth-first search for strong and biconnected
            components},
-  Url = {http://www.sciencedirect.com/science/article/pii/S002001900000051X},
+  Url = {https://www.sciencedirect.com/science/article/pii/S002001900000051X},
   Volume = {74},
   Year = {2000},
-  Bdsk-Url-2 = {http://dx.doi.org/10.1016/S0020-0190(00)00051-X},
-  Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S002001900000051X},
+  Bdsk-Url-2 = {https://dx.doi.org/10.1016/S0020-0190(00)00051-X},
+  Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S002001900000051X},
 }
 
 @inproceedings{JK07,
@@ -68,17 +68,17 @@ @inproceedings{JK07
 
 @article{MP14,
   Author = {Brendan D. McKay and Adolfo Piperno},
-  Doi = {http://dx.doi.org/10.1016/j.jsc.2013.09.003},
+  Doi = {https://dx.doi.org/10.1016/j.jsc.2013.09.003},
   Issn = {0747-7171},
   Journal = {Journal of Symbolic Computation},
   Number = {0},
   Pages = {94 - 112},
   Title = {Practical graph isomorphism, {II}},
-  Url = {http://www.sciencedirect.com/science/article/pii/S0747717113001193},
+  Url = {https://www.sciencedirect.com/science/article/pii/S0747717113001193},
   Volume = {60},
   Year = {2014},
-  Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jsc.2013.09.003},
-  Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0747717113001193},
+  Bdsk-Url-2 = {https://dx.doi.org/10.1016/j.jsc.2013.09.003},
+  Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/S0747717113001193},
 }
 
 @article{vLS81,
@@ -96,10 +96,10 @@ @article{vLS81
   Pages = {63--73},
   Title = {Construction of strongly regular graphs, two-weight codes and
            partial geometries by finite fields},
-  Url = {http://dx.doi.org/10.1007/BF02579178},
+  Url = {https://dx.doi.org/10.1007/BF02579178},
   Volume = {1},
   Year = {1981},
-  Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF02579178},
+  Bdsk-Url-1 = {https://dx.doi.org/10.1007/BF02579178},
 }
 
 % FIXME The Welsh paper is not cited in the manual!
@@ -112,8 +112,8 @@ @article{Welsh1967aa
   Pages = {85-86},
   Title = {An upper bound for the chromatic number of a graph and its
            application to timetabling problems},
-  Url = {http://dx.doi.org/10.1093/comjnl/10.1.85},
+  Url = {https://dx.doi.org/10.1093/comjnl/10.1.85},
   Volume = {10},
   Year = {1967},
-  Bdsk-Url-1 = {http://dx.doi.org/10.1093/comjnl/10.1.85}
+  Bdsk-Url-1 = {https://dx.doi.org/10.1093/comjnl/10.1.85}
 }

doc/display.xml

@@ -20,8 +20,8 @@
       The string <A>str</A> must correspond to a valid <C>dot</C> or
       <C>LaTeX</C> text file and you must have have <C>GraphViz</C> and
       <C>pdflatex</C> installed on your computer.  For details about these file
-      formats, see <URL>http://www.latex-project.org</URL> and
-      <URL>http://www.graphviz.org</URL>.<P/>
+      formats, see <URL>https://www.latex-project.org</URL> and
+      <URL>https://www.graphviz.org</URL>.<P/>
 
       This function is provided to allow convenient, immediate viewing of the
       pictures produced by the function <Ref Attr="DotDigraph"/>.<P/>
@@ -147,7 +147,7 @@ gap> Splash(DotDigraph(RandomDigraph(4)));
 
       The output is in <C>dot</C> format (also known as <C>GraphViz</C>)
       format. For details about this file format, and information about how to
-      display or edit this format see <URL>http://www.graphviz.org</URL>. <P/>
+      display or edit this format see <URL>https://www.graphviz.org</URL>. <P/>
 
       The string returned by <C>DotDigraph</C> or
       <C>DotVertexLabelledDigraph</C> can be written to a file using
@@ -411,7 +411,7 @@ gap> FileString("dot/k4.dot", DotDigraph(gr));
       The output is in <C>dot</C> format (also known as <C>GraphViz</C>)
       format. For details about this file format, and information about how
       to display or edit this format see
-      <URL>http://www.graphviz.org</URL>. <P/>
+      <URL>https://www.graphviz.org</URL>. <P/>
 
       The string returned by <C>DotSymmetricDigraph</C> can be written to a
       file using the command <Ref Func="FileString" BookName="GAPDoc"/>.<P/>
@@ -502,7 +502,7 @@ node [shape=circle]
       The output is in <C>dot</C> format (also known as <C>GraphViz</C>)
       format. For details about this file format, and information about how
       to display or edit this format see
-      <URL>http://www.graphviz.org</URL>. <P/>
+      <URL>https://www.graphviz.org</URL>. <P/>
 
       The string returned by <C>DotPartialOrderDigraph</C> can be written to a
       file using the command <Ref Func="FileString" BookName="GAPDoc"/>.<P/>
@@ -543,7 +543,7 @@ gap> FileString("dot/poset.dot", DotPartialOrderDigraph(gr));
       The output is in <C>dot</C> format (also known as <C>GraphViz</C>)
       format. For details about this file format, and information about how
       to display or edit this format see
-      <URL>http://www.graphviz.org</URL>. <P/>
+      <URL>https://www.graphviz.org</URL>. <P/>
 
       The string returned by <C>DotPreorderDigraph</C> can be written to a
       file using the command <Ref Func="FileString" BookName="GAPDoc"/>.<P/>

doc/main.xml

@@ -1,7 +1,7 @@
 <!DOCTYPE Book SYSTEM "gapdoc.dtd"
    [ <!ENTITY Digraphs "<Package>Digraphs</Package>">
      <!ENTITY Grape "<Alt Not='Text'><URL
-   Text='Grape'>http://www.maths.qmul.ac.uk/~leonard/grape/</URL></Alt><Alt
+   Text='Grape'>https://gap-packages.github.io/grape</URL></Alt><Alt
    Only='Text'><Package>Grape</Package></Alt>">
      <!ENTITY bliss "<Alt Not='Text'><URL
    Text='bliss'>http://www.tcs.tkk.fi/Software/bliss/</URL></Alt><Alt
@@ -10,16 +10,16 @@
          Text='edge-addition-planarity-suite'>https://github.com/graph-algorithms/edge-addition-planarity-suite</URL></Alt><Alt
        Only='Text'><Package>edge-addition-planarity-suite</Package></Alt>">
      <!ENTITY nauty "<Alt Not='Text'><URL
-   Text='nauty'>http://pallini.di.uniroma1.it/</URL></Alt><Alt
+   Text='nauty'>https://pallini.di.uniroma1.it/</URL></Alt><Alt
    Only='Text'><Package>nauty</Package></Alt>">
      <!ENTITY NautyTracesInterface "<Alt Not='Text'><URL
    Text='NautyTracesInterface'>https://github.com/gap-packages/NautyTracesInterface</URL></Alt><Alt
    Only='Text'><Package>NautyTracesInterface</Package></Alt>">
      <!ENTITY IO "<Alt Not='Text'><URL Text='IO'>
-     http://gap-packages.github.io/io/
+     https://gap-packages.github.io/io/
 </URL></Alt><Alt Only='Text'><Package>IO</Package></Alt>">
      <!ENTITY Orb "<Alt Not='Text'><URL Text='Orb'>
-     http://http://gap-packages.github.io/orb/</URL>
+     https://gap-packages.github.io/orb/</URL>
      </Alt><Alt Only='Text'><Package>Orb</Package></Alt>">
      <!ENTITY datastructures "<Alt Not='Text'><URL
        Text='datastructures'>https://github.com/gap-packages/datastructures</URL></Alt><Alt

doc/oper.xml

@@ -1374,7 +1374,7 @@ gap> VerticesReachableFrom(D, 5);
         where for each each <M>i &lt; n</M>, <M>a_i</M> is the position of
         <M>v_{i+1}</M> in
         <C>OutNeighboursOfVertex(</C><A>digraph</A><C>,</C><M>v_i</M><C>)</C>
-        corresponding to the edge <M>e_i</M>.  This is can be useful if the
+        corresponding to the edge <M>e_i</M>.  This can be useful if the
         position of a vertex in a list of out-neighours is significant, for
         example in orbit digraphs.
       </Item>

doc/z-chap1.xml

@@ -9,7 +9,7 @@
     It is assumed that you have a working copy of ⪆ with version number
     &GAPVERS; or higher. The most up-to-date version of ⪆ and instructions
     on how to install it can be obtained from the main ⪆ webpage
-    <URL>http://www.gap-system.org</URL>.<P/>
+    <URL>https://www.gap-system.org</URL>.<P/>
 
     The following is a summary of the steps that should lead to a
     successful installation of &Digraphs;:
@@ -58,7 +58,7 @@
 
       <Item>
         download the package archive <F>&ARCHIVENAME;.tar.gz</F> from
-        <URL Text="the Digraph package webpage">http://digraphs.github.io/Digraphs/</URL>.
+        <URL Text="the Digraph package webpage">https://digraphs.github.io/Digraphs/</URL>.
       </Item>
 
       <Item>

doc/z-title.xml

@@ -24,7 +24,7 @@
 
   <Author>Wilf A. Wilson
     <Email>[email protected]</Email>
-    <Homepage>http://wilf.me</Homepage>
+    <Homepage>https://wilf.me</Homepage>
   </Author>
 
   <Author>Stuart Burrell</Author>
@@ -51,7 +51,7 @@
 
     &Digraphs; is free software; you can redistribute it and/or modify it
     under the terms of the <URL Text="GNU General Public License">
-    http://www.fsf.org/licenses/gpl.html</URL> as published by the Free Software
+    https://www.fsf.org/licenses/gpl.html</URL> as published by the Free Software
     Foundation; either version 3 of the License, or (at your option) any later
     version.
   </Copyright>

gap/attr.gi

@@ -16,7 +16,7 @@ InstallMethod(OutNeighbours, "for a digraph by out-neighbours",
 
 # The next method is (yet another) DFS which simultaneously computes:
 # 1. *articulation points* as described in
-#   http://www.eecs.wsu.edu/~holder/courses/CptS223/spr08/slides/graphapps.pdf
+#   https://www.eecs.wsu.edu/~holder/courses/CptS223/spr08/slides/graphapps.pdf
 # 2. *bridges* as described in https://stackoverflow.com/q/28917290/
 #   (this is a minor adaption of the algorithm described in point 1).
 # 3. a *strong orientation* as alluded to somewhere on the internet that I can

gap/planar.gi

@@ -18,7 +18,7 @@
 
 ########################################################################
 #
-# This file is organised as follows:
+# This file is organised as follows:
 #
 # 1. Attributes
 #