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Update package for v1.0.1 release
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139 changes: 83 additions & 56 deletions CHANGELOG.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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).


Expand All @@ -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`.
Expand Down Expand Up @@ -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:
Expand All @@ -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`.
Expand Down Expand Up @@ -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
Expand All @@ -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`
Expand All @@ -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
Expand All @@ -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].

Expand All @@ -323,15 +346,15 @@ 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:

* `BlissAutomorphismGroup` and `NautyAutomorphismGroup` are introduced.
* `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
Expand All @@ -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

Expand All @@ -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`
Expand All @@ -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]:

Expand All @@ -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
Expand Down Expand Up @@ -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]

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
8 changes: 4 additions & 4 deletions PackageInfo.g
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Expand Up @@ -9,12 +9,12 @@
##

## <#GAPDoc Label="PKGVERSIONDATA">
## <!ENTITY VERSION "1.0.0">
## <!ENTITY VERSION "1.0.1">
## <!ENTITY GAPVERS "4.9.0">
## <!ENTITY GRAPEVERS "4.8.1">
## <!ENTITY IOVERS "4.5.1">
## <!ENTITY ORBVERS "4.8.2">
## <!ENTITY ARCHIVENAME "digraphs-1.0.0">
## <!ENTITY ARCHIVENAME "digraphs-1.0.1">
## <!ENTITY COPYRIGHTYEARS "2014-19">
## <#/GAPDoc>

Expand All @@ -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",

Expand Down
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@@ -1 +1 @@
1.0.0
1.0.1
1 change: 1 addition & 0 deletions VERSIONS
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Expand Up @@ -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
Expand Down

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