diff --git a/CHANGELOG.md b/CHANGELOG.md index fd1d8a2f6..2f786a3e9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,29 @@ Torpey, Wilf A. Wilson et al. Licensing information can be found in the `LICENSE` file. +## Version 1.0.1 (released 05/10/2019) + +This is a minor release of the Digraphs package. The main change in this +release is the reintroduction of the three-argument version of +`DigraphAddVertices`, which accepts a digraph, a number of vertices to add, and +a list of labels for the new vertices. The removal inadvertantly broke +backwards compatbility with some third-party pre-existing code that relied on +this functionality in the Digraphs package (see +[Issue #264](https://github.com/gap-packages/Digraphs/issues/264)). + +The second argument of the three-argument version was redundant, and so a new +two-argument version of `DigraphAddVertices`, which accepts a digraph and a list +of new vertex labels, was introduced in v1.0.0. Unfortunately, the concurrent +removal of the three-argument version of `DigraphAddVertices` was not advertised +in the `CHANGELOG`. Although the three-argument version has been reintroduced, +it will remain undocumented, since there is no good reason for any new code to +use the three-argument version. + +The author contact data on the title page of the manual was also updated. + +The changes in this version were made by [Wilf A. Wilson][]. + + ## Version 1.0.0 (released 03/10/2019) This is a major release of the Digraphs package that introduces significant new @@ -71,8 +94,8 @@ stores, and so the effect is as before. For an mutable digraph, calling `Foo` modifies the digraph in-place, which remains mutable. The majority of the changes in Digraphs relating to mutable and immutable -digraphs were made by [James D. Mitchell](http://goo.gl/ZtViV6), Finn Smith, and -[Wilf A. Wilson](http://wilf.me), with some further contributions by Reinis +digraphs were made by [James D. Mitchell][], Finn Smith, and +[Wilf A. Wilson][], with some further contributions by Reinis Cirpons, Luke Elliott, and Murray Whyte. ### New and extended functions @@ -107,9 +130,9 @@ The package now includes the following new functions: [#217](https://github.com/gap-packages/Digraphs/pull/217), respectively. * `DotHighlightedDigraph` was added by Finn Smith in [PR #169](https://github.com/gap-packages/Digraphs/pull/169). -* `IsCompleteMultipartiteDigraph` was added by [Wilf A. Wilson](http://wilf.me) +* `IsCompleteMultipartiteDigraph` was added by [Wilf A. Wilson][] in [PR #236](https://github.com/gap-packages/Digraphs/pull/236). -* `IsEquivalenceDigraph` was added by [Wilf A. Wilson](http://wilf.me) in +* `IsEquivalenceDigraph` was added by [Wilf A. Wilson][] in [PR #234](https://github.com/gap-packages/Digraphs/pull/234) as a synonym for `IsReflexiveDigraph and IsSymmetricDigraph and IsTransitiveDigraph`. * `IsVertexTransitive` and `IsEdgeTransitive` were added by Graham Campbell @@ -130,7 +153,7 @@ The package now includes the following new functions: [PR #225](https://github.com/gap-packages/Digraphs/pull/225). * The ability to compile (with the flag `--with-external-planarity`) and use the Digraphs package with the system version of the Edge Addition Planarity - Suite was added by [James D. Mitchell](http://goo.gl/ZtViV6) in + Suite was added by [James D. Mitchell][] in [PR #207](https://github.com/gap-packages/Digraphs/pull/207). @@ -142,9 +165,9 @@ 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](https://github.com/gap-packages/Digraphs/issues/222), -and fixed by [James D. Mitchell](http://goo.gl/ZtViV6) in +and fixed by [James D. Mitchell][] in [PR #223](https://github.com/gap-packages/Digraphs/pull/223). -In addition, [Wilf A. Wilson](http://wilf.me) +In addition, [Wilf A. Wilson][] [fixed a bug](https://github.com/gap-packages/Digraphs/commit/458a10298b08881bf7ee9207534ce431378d2c4e) in `DigraphNrEdges`. This function could previously lead to a crash when given a digraph whose `OutNeighbours` contained entries not in `IsPlistRep`. @@ -191,7 +214,7 @@ 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](https://tuhat.helsinki.fi/portal/en/persons/jukka-kohonen(a6f3f037-4918-4bf5-a114-ac417f94beb5).html), and the changes were made by -[Michael Torpey](http://www-groups.mcs.st-and.ac.uk/~mct25) in +[Michael Torpey][] in [PR #162](https://github.com/gap-packages/Digraphs/pull/162). Other additions and changes are listed below: @@ -209,7 +232,7 @@ Other additions and changes are listed below: * `SubdigraphHomeomorphicToK(23/4/33)`, and * `MaximalAntiSymmetricSubdigraph`. * The functionality and performance for computing homomorphisms of digraphs was - significantly improved by [James D. Mitchell](http://goo.gl/ZtViV6) in [PR + significantly improved by [James D. Mitchell][] in [PR #160](https://github.com/gap-packages/Digraphs/pull/160). This PR also introduced the operations `EmbeddingsDigraphs` and `EmbeddingsDigraphsRepresentatives`. @@ -247,16 +270,16 @@ This release contains bugfixes and a couple of new features. * In previous versions of the package, the output of `ArticulationPoints` would sometimes contain repeated vertices (reported by Luke Elliott in [Issue #140](https://github.com/gap-packages/Digraphs/issues/140), and fixed by - [James D. Mitchell](http://goo.gl/ZtViV6) in [PR + [James D. Mitchell][] in [PR #142](https://github.com/gap-packages/Digraphs/pull/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](http://goo.gl/ZtViV6) in [PR + by [James D. Mitchell][] in [PR #146](https://github.com/gap-packages/Digraphs/pull/146)). * The header file `x86intrin.h` was unnecessarily being included by the kernel - module of Digraphs (reported by [Wilf A. Wilson](http://wilf.me) in [Issue + module of Digraphs (reported by [Wilf A. Wilson][] in [Issue #147](https://github.com/gap-packages/Digraphs/issues/147), and fixed by - [James D. Mitchell](http://goo.gl/ZtViV6) in [PR + [James D. Mitchell][] in [PR #152](https://github.com/gap-packages/Digraphs/pull/152)). [Max Horn](https://www.quendi.de/math) also contributed various compatibility @@ -277,7 +300,7 @@ This release of Digraphs contains some bugfixes, along with the following new fe * `DotPartialOrderDigraph` * `DotPreorderDigraph` * `DotQuasiorderDigraph` -* The following functions for transformations and permutations were added by [James D. Mitchell](http://goo.gl/ZtViV6): +* The following functions for transformations and permutations were added by [James D. Mitchell][]: * `IsDigraphHomomorphism` * `IsDigraphEpimorphism` * `IsDigraphMonomorphism` @@ -295,7 +318,7 @@ 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](http://goo.gl/ZtViV6): +were resolved by [James D. Mitchell][]: * `HomomorphismDigraphFinder` sometimes failed to find a homomorphism when one existsed [[Issue #111](https://github.com/gap-packages/Digraphs/issues/111), reported by Gordon Royle]; * the documentation for `HomomorphismDigraphFinder` was @@ -307,7 +330,7 @@ were resolved by [James D. Mitchell](http://goo.gl/ZtViV6): This release contains bugfixes and new features. In particular, it: -* fixes [a bug in `ArticulationPoints` and `IsBiconnectedDigraph`](https://github.com/gap-packages/Digraphs/issues/102) [[Wilf A. Wilson](http://wilf.me)]; +* fixes [a bug in `ArticulationPoints` and `IsBiconnectedDigraph`](https://github.com/gap-packages/Digraphs/issues/102) [[Wilf A. Wilson][]]; * adds the property `IsChainDigraph` [Ashley Clayton]; and * adds the operation `IsDigraphAutomorphism` [Chris Russell]. @@ -323,7 +346,7 @@ package](https://github.com/sebasguts/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 specify the engine that is used by Digraphs. These changes to Digraphs were made -by [James D. Mitchell](http://goo.gl/ZtViV6)]. +by [James D. Mitchell][]]. In particular, version 0.11.0 includes the following changes: @@ -331,7 +354,7 @@ In particular, version 0.11.0 includes the following changes: * `DigraphCanonicalLabelling` is replaced by `BlissCanonicalLabelling` and `NautyCanonicalLabelling`. * `BlissCanonicalDigraph` and `NautyCanonicalDigraph` are introduced [Chris - Russell and [James D. Mitchell](http://goo.gl/ZtViV6)]. + Russell and [James D. Mitchell][]]. * `DigraphsUseNauty` and `DigraphsUseBliss` are introduced. The property `IsHamiltonianDigraph` and the attribute `HamiltonianPath` were @@ -348,10 +371,10 @@ bug in `Digraph` that could cause a segmentation fault. 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](http://www-groups.mcs.st-and.ac.uk/~julius) -and [James D. Mitchell](http://goo.gl/ZtViV6)]. +[[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](http://goo.gl/ZtViV6)]. +a crash, was resolved [[James D. Mitchell][]]. ### New Features in Version 0.10.0 @@ -363,21 +386,21 @@ labels, by using the new operation `DotVertexLabelledDigraph`. * `SemigroupOfCayleyDigraph` * `GeneratorsOfCayleyDigraph` -All of the new features were added by [James D. Mitchell](http://goo.gl/ZtViV6). +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](http://goo.gl/ZtViV6): +[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](http://wilf.me): +[Wilf A. Wilson][]: * `IsMatching` * `IsPerfectMatching` @@ -394,9 +417,9 @@ improvements to the documentation of the package. ### New Features in Version 0.8.0 This release introduces the new operations `DigraphClosure` -[[Julius Jonusas](http://www-groups.mcs.st-and.ac.uk/~julius)] +[[Julius Jonusas][]] and `BooleanAdjacencyMatrixMutableCopy` -[[Wilf A. Wilson](http://wilf.me)], +[[Wilf A. Wilson][]], along with the following properties and operations related to semilattices [Chris Russell]: @@ -414,7 +437,7 @@ This is a minor release, which fixes bugs in `DigraphTopologicalSort` and ## 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](http://wilf.me). +made by [Wilf A. Wilson][]. ### New Features in Version 0.7.0 * This release contains a new technique for encoding a vertex-coloured @@ -455,11 +478,11 @@ 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](https://www.morphism.de/~markusp)] -* The operation `CompleteMultipartiteDigraph` is introduced. [Stuart Burrell and [Wilf A. Wilson](http://wilf.me)] +* 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](http://wilf.me)] -* The operation `ChromaticNumber` is introduced. [[James D. Mitchell](http://goo.gl/ZtViV6) and [Wilf A. Wilson](http://wilf.me)] + [[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 `IsEulerianDigraph`is introduced. [Luke Elliott] @@ -487,32 +510,31 @@ The performance improvements are most noticeable on large, quite dense digraphs. Minor changes include: -* a better method for `DigraphReverse` [[Wilf A. Wilson](http://wilf.me)] +* 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](http://www-groups.mcs.st-and.ac.uk/~mct25)] -* a minor improvement in performance in the `DigraphMaximalCliques` [[Wilf A. Wilson](http://wilf.me)] -* a new operation `AdjacencyMatrixMutableCopy` [[James D. Mitchell](http://goo.gl/ZtViV6)] +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](http://gap-packages.github.io/orb/), +Digraphs now requires the [Orb package](http://gap-packages.github.io/orb), version 4.7.5 or higher. ### New Features in Version 0.5.0 -* `DigraphFile` and `IteratorFromDigraphFile` are introduced. [[James D. Mitchell](http://goo.gl/ZtViV6)] -* `WriteDigraphs` and `ReadDigraphs` can now take a file as a first argument. [[James D. Mitchell](http://goo.gl/ZtViV6)] +* `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](http://wilf.me)] + 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](http://wilf.me)] -* The property `IsCompleteBipartiteDigraph` is introduced. [[Wilf A. Wilson](http://wilf.me)] + 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](http://wilf.me)] +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](http://goo.gl/ZtViV6)] + `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 @@ -584,10 +606,8 @@ version, we welcomed Jan De Beule to the development team. - `OutDegreeSet` - `RepresentativeOutNeighbours` -[[Jan De Beule](http://homepages.vub.ac.be/~jdbeule/), [Julius Jonusas](http://www-groups.mcs.st-and.ac.uk/~julius), -[James D. Mitchell](http://goo.gl/ZtViV6), -[Michael Torpey](http://www-groups.mcs.st-and.ac.uk/~mct25), -[Wilf A. Wilson](http://wilf.me)] +[[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 @@ -601,20 +621,27 @@ 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](http://wilf.me)] -* Improve efficiency of the algorithm for coloring a graph with 2 colours, a method for `IsBipartiteDigraph` and `DigraphBicomponents`. [Isabella Scott and [Wilf A. Wilson](http://wilf.me)] -* `AutomorphismGroup` and `DigraphCanonicalLabelling` can now be used with color classes that are preserved by the permutations acting on a digraph. [[James D. Mitchell](http://goo.gl/ZtViV6)] -* The `TCodeDecoder` was made more efficient. [[James D. Mitchell](http://goo.gl/ZtViV6)] -* `AsTransformation` is introduced for digraphs in `IsFunctionalDigraph`. [[James D. Mitchell](http://goo.gl/ZtViV6)] +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][]] +* 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](http://goo.gl/ZtViV6)] -* Some bits of code that caused compiler warnings were improved. [[James D. Mitchell](http://goo.gl/ZtViV6)] -* Some memory leaks were resolved in the Digraphs kernel module. [[Michael Torpey](http://www-groups.mcs.st-and.ac.uk/~mct25)] +* 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. + +[James D. Mitchell]: http://goo.gl/ZtViV6 +[Wilf A. Wilson]: http://wilf.me +[Michael Torpey]: https://mtorpey.github.io +[Julius Jonusas]: http://julius.jonusas.work +[Jan De Beule]: http://homepages.vub.ac.be/~jdbeule +[Markus Pfeiffer]: https://www.morphism.de/~markusp diff --git a/PackageInfo.g b/PackageInfo.g index 6ea8a5444..090a3c5c5 100644 --- a/PackageInfo.g +++ b/PackageInfo.g @@ -9,12 +9,12 @@ ## ## <#GAPDoc Label="PKGVERSIONDATA"> -## +## ## ## ## ## -## +## ## ## <#/GAPDoc> @@ -26,8 +26,8 @@ _STANDREWSCS := Concatenation(["Jack Cole Building, North Haugh, ", SetPackageInfo(rec( PackageName := "Digraphs", Subtitle := "Graphs, digraphs, and multidigraphs in GAP", -Version := "1.0.0", -Date := "03/10/2019", # dd/mm/yyyy format +Version := "1.0.1", +Date := "05/10/2019", # dd/mm/yyyy format License := "GPL-3.0-or-later", ArchiveFormats := ".tar.gz", diff --git a/VERSION b/VERSION index 3eefcb9dd..7dea76edb 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.0.0 +1.0.1 diff --git a/VERSIONS b/VERSIONS index 558dee347..814f89894 100644 --- a/VERSIONS +++ b/VERSIONS @@ -8,6 +8,7 @@ ############################################################################# ## +release 1.0.1 - 05/10/2019 release 1.0.0 - 03/10/2019 release 0.15.4 - 06/08/2019 release 0.15.3 - 12/06/2019