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Digraphs package for GAP - CHANGELOG

Copyright (C) 2014-19 by Jan De Beule, Julius Jonušas, James D. Mitchell, Michael Torpey, Wilf A. Wilson et al.

Licensing information can be found in the LICENSE file.

Version 1.0.0 (released 31/12/2019)

Version 1.0.0! DigraphColoring (american spelling) was removed. Changed IsEulerian. QuotientDigraph is changed.

Version 0.15.4 (released 06/08/2019)

This is a minor release that fixes a few bugs.

In previous versions, the homomorphism-finding tools sometimes returned purported ‘monomoprhisms’ that were not injective. This problem was reported by Gordon Royle, see Issue #222, and fixed by James D. Mitchell in PR #223. In addition, Wilf A. Wilson fixed a bug in DigraphNrEdges. This function could previously lead to a crash when given a digraph whose OutNeighbours contained entries not in IsPlistRep.

Version 0.15.3 (released 12/06/2019)

This is a minor release that fixes a typo in the documentation of JohnsonDigraph, and contains some minor tweaks for compatibility with future versions of GAP.

Version 0.15.2 (released 17/04/2019)

This is a minor release that updates Digraphs for compatibility with the upcoming GAP 4.11, and resolves a bug in IsHamiltonianDigraph that could have lead to the boolean adjacency matrix of a digraph being accidentally modified; see Issue #191 and PR #192.

Version 0.15.1 (released 26/03/2019)

This is a minor release of the Digraphs package, which improves the compatibility of Digraphs with cygwin. In particular, in the Windows installer of the next release of GAP, Digraphs should be included in a pre-compiled and working state. See Issue #177 and PR #178 for more details.

Digraphs now requires version 4.8.2 of the orb package, or newer.

Version 0.15.0 (released 15/02/2019)

This release contains several substantial new features, and some changes to previous functionality.

The most significant change in behaviour is related to the Digraph6 format used in previous versions of the Digraphs package. This method of encoding directed graphs was developed independently from, but concurrently with, the Digraph6 format introduced by nauty; see Issue #158 for more information. The Digraphs package now uses the nauty format, although digraphs encoded using the old format can still be read in. This incompatibility was reported by Jukka Kohonen, and the changes were made by Michael Torpey in PR #162.

Other additions and changes are listed below:

  • A copy of the 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 in PR #156. The new functionality can be accessed via:
    • Is(Outer)PlanarDigraph,
    • (Outer)PlanarEmbedding,
    • Kuratowski(Outer)PlanarSubdigraph,
    • SubdigraphHomeomorphicToK(23/4/33), and
    • MaximalAntiSymmetricSubdigraph.
  • The functionality and performance for computing homomorphisms of digraphs was significantly improved by James D. Mitchell in PR #160. This PR also introduced the operations EmbeddingsDigraphs and EmbeddingsDigraphsRepresentatives.
  • The one-argument attribute DigraphColouring was renamed to DigraphGreedyColouring, and its performance was improved; it now uses the Welsh-Powell algorithm, which can be accessed directly via 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 in PR #144.
  • DigraphShortestPath was introduced by Murray Whyte in PR #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 in PR #159.
  • The attribute CharacteristcPolynomial for a digraph was added by Luke Elliott in PR #164.
  • The properties IsVertexTransitive and IsEdgeTransitive for digraphs were added by Graham Campbell in PR #165.

Version 0.14.0 (released 23/11/2018)

This release contains bugfixes and a couple of new features.

  • The operations AsSemigroup and AsMonoid for lattice and semilattice digraphs were added by Chris Russell in PR #136.
  • The operation IsDigraphColouring was added by James D. Mitchell in PR #145.
  • In previous versions of the package, the output of ArticulationPoints would sometimes contain repeated vertices (reported by Luke Elliott in Issue #140, and fixed by James D. Mitchell in PR #142).
  • In previous versions of the package, an unexpected error was sometimes caused when removing an immutable set of vertices from a digraph (reported and fixed by James D. Mitchell in PR #146).
  • The header file x86intrin.h was unnecessarily being included by the kernel module of Digraphs (reported by Wilf A. Wilson in Issue #147, and fixed by James D. Mitchell in PR #152).

Max Horn also contributed various compatibility and correctness changes to the kernel module of the package, including in PRs #149, #150, and #151.

Digraphs now requires version 4.8.1 of the orb package, or newer.

Version 0.13.0 (released 19/09/2018)

This release of Digraphs contains some bugfixes, along with the following new features:

  • The GraphViz engine used by Splash is now configurable, thanks to Markus Pfeiffer.
  • The properties IsPartialOrderDigraph, IsPreorderDigraph, and IsQuasiorderDigraph were introduced by Chris Russell, along with the following functions for visualising these kinds of digraphs:
    • DotPartialOrderDigraph
    • DotPreorderDigraph
    • DotQuasiorderDigraph
  • The following functions for transformations and permutations were added by James D. Mitchell:
    • IsDigraphHomomorphism
    • IsDigraphEpimorphism
    • IsDigraphMonomorphism
    • IsDigraphEndomorphism
    • IsDigraphEmbedding
    • IsDigraphIsomorphism

Digraphs now requires version 4.9.0 of GAP, or newer.

Version 0.12.2 (released 24/08/2018)

This is a minor release which contains some small adjustments to the build system of the package.

Version 0.12.1 (released 26/04/2018)

This is a minor release, which contains several bugfixes. The following problems were resolved by James D. Mitchell:

  • HomomorphismDigraphFinder sometimes failed to find a homomorphism when one existsed [Issue #111, reported by Gordon Royle];
  • the documentation for HomomorphismDigraphFinder was incomplete [Issue #112]; and
  • a segmentation fault could be caused when using Digraphs with NautyTracesInterface, in certain cases [Issue #114].

Version 0.12.0 (released 31/01/2018)

This release contains bugfixes and new features. In particular, it:

Digraphs now requires version 4.5.1 of the IO package.

Version 0.11.0 (released 22/11/2017)

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. This functionality requires the NautyTracesInterface package for GAP, version 0.2 or newer. However, this is not a required package, and the default engine remains bliss. It is possible to specify the engine that is used by Digraphs. These changes to Digraphs were made by James D. Mitchell].

In particular, version 0.11.0 includes the following changes:

  • BlissAutomorphismGroup and NautyAutomorphismGroup are introduced.
  • DigraphCanonicalLabelling is replaced by BlissCanonicalLabelling and NautyCanonicalLabelling.
  • BlissCanonicalDigraph and NautyCanonicalDigraph are introduced [Chris Russell and James D. Mitchell].
  • DigraphsUseNauty and DigraphsUseBliss are introduced.

The property IsHamiltonianDigraph and the attribute HamiltonianPath were added by Luke Elliott. Additionally, this release fixes several bugs, including one in DigraphSymmetricClosure and one in CompleteDigraph.

Digraphs now requires version 4.4.6 of the IO package.

Version 0.10.1 (released 16/08/2017)

This is a minor release, which contains performance improvements, and fixes a bug in Digraph that could cause a segmentation fault.

Version 0.10.0 (released 20/07/2017)

This release contains new features, bugfixes, and minor improvements to the documentation. There is a new method for ChromaticNumber, which has better performance than the previous method [Julius Jonusas and James D. Mitchell]. A bug in the code for calculating homomorphisms of digraphs, which could cause a crash, was resolved [James D. Mitchell].

New Features in Version 0.10.0

  • Vertex labelled digraphs can now be visualised in a way that displays vertex labels, by using the new operation DotVertexLabelledDigraph.
  • The attribute CliqueNumber is introduced.
  • The following new attributes for Cayley digraphs are introduced:
    • GroupOfCayleyDigraph
    • SemigroupOfCayleyDigraph
    • GeneratorsOfCayleyDigraph

All of the new features were added by James D. Mitchell.

Version 0.9.0 (released 12/07/2017)

This release introduces several new features.

New Features in Version 0.9.0

The following attributes and properties were added by James D. Mitchell:

  • ArticulationPoints (and its synonym CutVertices)
  • IsBiconnectedDigraph
  • IsCycleDigraph

The following operations related to matchings were added by Isabella Scott and Wilf A. Wilson:

  • IsMatching
  • IsPerfectMatching
  • IsMaximalMatching

Version 0.8.1 (released 18/05/2017)

This is a minor release, which updates the README file and updates the list of package authors and contributors.

Version 0.8.0 (released 17/05/2017)

This release contains new features, several minor bugfixes, and minor improvements to the documentation of the package.

New Features in Version 0.8.0

This release introduces the new operations DigraphClosure [Julius Jonusas] and BooleanAdjacencyMatrixMutableCopy [Wilf A. Wilson], along with the following properties and operations related to semilattices [Chris Russell]:

  • IsPartialOrderDigraph
  • IsMeetSemilatticeDigraph
  • IsJoinSemilatticeDigraph
  • IsLatticeDigraph
  • PartialOrderDigraphMeetOfVertices
  • PartialOrderDigraphJoinOfVertices

Version 0.7.1 (released 22/03/2017)

This is a minor release, which fixes bugs in DigraphTopologicalSort and IsAntisymmetricDigraph that could trigger segmentation faults.

Version 0.7.0 (released 14/03/2017)

This release introduces several new features, changes some existing functionality, and improves the documentation. The changes in this release were made by Wilf A. Wilson.

New Features in Version 0.7.0

  • This release contains a new technique for encoding a vertex-coloured multidigraph as a vertex-coloured (undirected) graph while preserving the automorphism group, in order to calculate the automorphism group and canonical labelling using bliss. This enables the following functionality:

    • the operations AutomorphismGroup and DigraphCanonicalLabelling for a digraph and a vertex-colouring now accept a multidigraph as their first argument;
    • the operations IsIsomorphicDigraph and IsomorphismDigraphs now accept multidigraphs, and they also accept vertex-colourings as optional arguments.

  • This release add new functionality related to undirected spanning trees and undirected spanning forests:

    • the property IsUndirectedForest is introduced;
    • the attributes UndirectedSpanningTree and UndirectedSpanningForest are introduced; and
    • the operations IsUndirectedSpanningTree and IsUndirectedSpanningForest are introduced.

Altered Behaviour in Version 0.7.0

  • The behaviour of IsSubdigraph is changed in the case that it is given one or two multidigraphs.
  • The one-argument version of the operation DigraphColouring (and its synonym, DigraphColoring) is now an attribute.

Version 0.6.1 (released 01/03/2017)

This is a minor release. This release fixes a bug in AsDigraph for a transformation and an integer. The operations OutNeighboursCopy and OutNeighborsCopy are renamed to OutNeighboursMutableCopy and OutNeighborsMutableCopy, respectively, and new operations InNeighboursMutableCopy and InNeighborsMutableCopy are introduced.

Version 0.6.0 (released 09/12/2016)

This is a major release, adding a variety of new operations and attributes for Digraphs, as well as improving some functions and improving the package's documentation. In this version, we welcome Luke Elliott and Markus Pfeiffer as new authors.

New Features in Version 0.6.0

  • The ability to label the edges of digraphs is introduced. [Markus Pfeiffer]
  • The operation CompleteMultipartiteDigraph is introduced. [Stuart Burrell and Wilf A. Wilson]
  • The operations ReadDIMACSDigraph and WriteDIMACSDigraph are introduced. [Wilf A. Wilson]
  • The operation ChromaticNumber is introduced. [James D. Mitchell and Wilf A. Wilson]
  • The operations IsDirectedTree and IsUndirectedTree are introduced. [Luke Elliott]
  • The operation IsEulerianDigraphis introduced. [Luke Elliott]

Version 0.5.2 (released 20/06/2016)

This is a minor release containing one bugfix and several other minor changes. Digraphs now works when it and GAP are compiled in 32 bit mode.

Version 0.5.1 (released 08/06/2016)

This release contains some bugfixes, some minor new features, and some performance improvements. The package has moved to GitHub and we welcome Finn Smith as an author.

This release contains a new technique for encoding a vertex-coloured digraph as a vertex-coloured (undirected) graph while preserving the automorphism group, in order to calculate the automorphism group using bliss. These changes were made by Finn Smith. The previous technique involved adding two intermediate vertices for every edge; on a digraph with n vertices this could add 2n(n-1) new vertices. The new technique encodes a digraph with n vertices as a graph with 3n vertices. In certain cases, this can lead to a dramatic improvement in the time taken to calculate the automorphism group.

The new reduction is based on two techniques in:

David Bremner, Mathieu Dutour Sikiric, Dmitrii V. Pasechnik, Thomas Rehn, Achill Schürmann. Computing symmetry groups of polyhedra. https://arxiv.org/abs/1210.0206v3

Namely, "Dealing with digraphs" followed by "Reduction by superposition". From the graph obtained by these techniques, n vertices which are irrelevant to automorphism finding are removed.

The actual reduction used is as follows: Given a digraph D=(V=[]1 .. n],E,c), create three copies V1, V2, V3 of the vertex set V. Colour V1 according to the colouring c of D, and V2, V3 with two distinct colours that do not occur in D. Connect each vertex in V1 to the corresponding vertices in V2, V3. For every arc (x,y) in E, put an edge between the copy of x in V2, and the copy of y in V3. Automorphisms of this graph, when restricted to V, are precisely the automorphisms of D. Because this changes the graph used to calculate automorphisms, the results sometimes nominally differ from the previous version - especially in the case of canonical labelling, where unrecognisably different results may appear. Generators also often appear in different orders.

The performance improvements are most noticeable on large, quite dense digraphs. On random digraphs with 5000 vertices and 0.5 edge probability, 200-400x speedups were common. When calculating the automorphism group of the complete digraph on 1000 vertices, with vertex i having colour i mod 2 + 1, we obtain a 66x speedup. When the vertex i is assigned colour i mod 7 + 1, this becomes a 400x speedup.

Minor changes include:

  • a better method for DigraphReverse [Wilf A. Wilson]
  • automorphism groups of complete, empty, cycle, chain, and complete bipartite digraphs are set at creation [Michael Torpey]
  • a minor improvement in performance in the DigraphMaximalCliques [Wilf A. Wilson]
  • a new operation AdjacencyMatrixMutableCopy [James D. Mitchell]

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, version 4.7.5 or higher.

New Features in Version 0.5.0

  • DigraphFile and IteratorFromDigraphFile are introduced. [James D. Mitchell]
  • WriteDigraphs and ReadDigraphs can now take a file as a first argument. [James D. Mitchell]
  • The operation DigraphPath is introduced to find a path between two vertices in a digraph. [Wilf A. Wilson]
  • The operation IteratorOfPaths is introduced to iterate over the paths between two vertices in a digraph. [Wilf A. Wilson]
  • The property IsCompleteBipartiteDigraph is introduced. [Wilf A. Wilson]

Issues Resolved in Version 0.5.0

Several bugs related to clique finding have been resolved. [Wilf A. Wilson]

  • Files with extension bz2 were previously not (un)compressed when used with ReadDigraphs and WriteDigraphs. [James D. Mitchell]
  • The documentation in Chapter 8 "Finding cliques and independent sets" has been corrected to accurately reflect the functionality of the package.
  • A bug which led to too few cliques and independent sets being found for some digraphs has been resolved.
  • A bug which led to duplicate cliques and independent sets being found for some digraphs has been resolved.

Version 0.4.2 (released 28/01/2016)

This is a minor release to fix a bug in DigraphAllSimpleCircuits that failed to return all simple circuits in some cases Issue 13. Some documentation was also updated.

Version 0.4.1 (released 22/01/2016)

This is a very minor release to change the version of GAP required.

Version 0.4.0 (released 19/01/2016)

This is a major release, primarily aimed at incorporating more of the functionality of Grape into Digraphs, as well as fixing some bugs. In this version, we welcomed Jan De Beule to the development team.

New Features in Version 0.4.0

  • Functionality to calculate cliques and independent sets
  • New methods for the constructor function Digraph
  • ReadDigraphs and WriteDigraphs now have a new output format .p or .pickle, which allows known automorphisms to be stored with the digraph
  • The following functions now use known automorphisms:
    • DigraphDiameter
    • DigraphDual
    • DigraphShortestDistances
    • Digraph method for a Grape graph
    • Graph
    • InDegreeSequence
    • OutDegreeSequence
  • The following new functions were added:
    • BipartiteDoubleDigraph
    • BooleanAdjacencyMatrix
    • CayleyDigraph
    • DigraphAddAllLoops
    • DigraphAddEdgeOrbit
    • DigraphAdjacencyFunction
    • DigraphColoring for a digraph
    • DigraphDegeneracyOrdering
    • DigraphDegeneracy
    • DigraphDistanceSet
    • DigraphGirth
    • DigraphGroup
    • DigraphLayers
    • DigraphLongestSimpleCircuit
    • DigraphOrbitReps
    • DigraphOrbits
    • DigraphRemoveEdgeOrbit
    • DigraphSchreierVector
    • DigraphShortestDistance
    • DigraphStabilizer
    • DigraphUndirectedGirth
    • DistanceDigraph
    • DoubleDigraph
    • EdgeOrbitsDigraph
    • InDegreeSet
    • IsDigraphEdge for a digraph and a list
    • IsDistanceRegularDigraph
    • IsInRegularDigraph
    • IsOutRegularDigraph
    • IsRegularDigraph
    • JohnsonDigraph
    • LineDigraph
    • LineUndirectedDigraph
    • MaximalSymmetricSubdigraphWithoutLoops
    • MaximalSymmetricSubdigraph
    • OutDegreeSet
    • RepresentativeOutNeighbours

[Jan De Beule, Julius Jonusas, James D. Mitchell, Michael Torpey, Wilf A. Wilson]

Version 0.3.2 (released 14/01/2016)

This is another minor release due to some missing build files in the Version 0.3.1 archive.

Version 0.3.1 (released 13/01/2016)

This is a minor release due to some missing build files in the Version 0.3 archive.

Version 0.3.0 (released 12/01/2016)

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 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]
  • AsTransformation is introduced for digraphs in IsFunctionalDigraph. [James D. Mitchell]
  • The tests and their code coverage were improved.

Issues Resolved in Version 0.3.0

  • There was a memory leak in bliss-0.73, which is fixed in the copy of bliss included with Digraphs, but not in the official release of bliss. [James D. Mitchell]
  • Some bits of code that caused compiler warnings were improved. [James D. Mitchell]
  • Some memory leaks were resolved in the Digraphs kernel module. [Michael Torpey]

Version 0.2.0 (released 04/09/2015)

The first release.

Version 0.1.0

Pre-release version that was not made publicly available.