[Nauty] Announcing nauty and Traces version 2.8.6

[Brendan McKay]

This is a major release of nauty and Traces.  Please report any problems 
to us.

As usual, the files can be downloaded from these places:
https://users.cecs.anu.edu.au/~bdm/nauty/
https://pallini.di.uniroma1.it

Good luck!  Brendan & Adolfo.

Changes from nauty 2.7 to nauty 2.8.6
-----------------------------------

* New utilities: (as always, use --help to get help)
   - addptg : add additional vertices in various ways
   - ancestorg : removes a specified number of final vertices
   - productg : product of two graphs (such as Cartesian product)
   - genposetg : generate posets (mostly written by Gunnar Brinkmann)
   - dimacs2g : read files of graphs in DIMACS format

* Changes to existing utilities:
   - geng got sigificantly faster for connected graphs with a
     small number of edges.  However, if you want trees the program
     gentreeg is still much faster.  There are also new options:
       -k  generate graphs without K4
       -T  generate chordal graphs
       -S  generate split graphs
       -P  generate perfect graphs
       -F  generate claw-free graphs
     All the options can be used in combination unless the program
     complains.
     There is a program callgeng2.c that shows how geng can be
     called in multiple threads. Read the instructions at the
     start of the source file. It has a target in the makefile but
     it might not work with all operating systems and compilers.
   - countg/pickg now have an expanded set of available properties,
       using double letters. Because --eee and similar are ambiguous,
       options can be separated by commas: --e,ee or --ee,e.
       Here are all the options added since version 2.7:
        -LL  2-cycles (of digraphs)
        -ee  non-edges (including non-loops for digraphs)
        -TT  independent sets of size 3
        -x   sources
        -xx  sinks
        -W   4-cycles (undirected only so far)
        -WW  diamonds (4-cycles with diagonal), only undirected
   - gentreeg now allows a range of number of vertices.
       Example: forests on 15 vertices with no isolated vertices:
                 gentreeg 2:15 | assembleg -n15cL
       Also new option -i for no vertices of degree 2.
       Fixed output for n=1, diameter > 0.
   - genrang has an option -M# can be used in conjunction with
       -d (pseudo-random regular graphs). It runs a Markov chain
       for #*n steps. The chain has a uniform distribution as
       its limit and, although the precise rate of convergence
       is unknown, running it with a decent number of iterations
       will produce a more uniform distribution than -d alone.
   - listg has a new option -S for use with -M or -W to write
       the signless Laplacian.
   - subdivideg now works for digraphs.
   - delptg has several new options:
        -v  select which vertices to delete
        -m  lower bound on minimum degree of output graphs
        -a  delete a clique
        -b  delete an independent set
        -i  leave vertices as isolates rather than removing them
        -r  delete a random set of vertices
   - multig has a new option -V that lets it read the -T outout of
        vcolg. Also, the output code has been made faster.
   - vcolg has new options bounding the number of vertices of each
     colour and bounding the vertex degrees for each colour. Also
     the output code has been made faster.
   - directg has a new option -a for acyclic orientations

* New functions
   - gutil1.c has new procedures:
        numcomponents(g,m,n) for counting the components of an
          undirected graph, and
        sources_sinks(g,m,n,*sources,*sinks) for counting sources
          and sinks in digraphs.
   - gutil2.c has new procedures:
        digoncount(g,m,n) that counts how many cycles of length 2
          a digraph has.
        numind3sets1(g,n) for counting independent sets of size 3,
          so far only for n <= WORDSIZE.
        numsquares(g,m,n) counts 4-cycles in undirected graphs.
   - gtnauty.c has a new procedure
       breakcellwt() to split a cell according to weights on the
       vertices
   - naututil.c has new procedures
       settolist() for converting a set into a list of integers
       listtoset() for converting a list of integers into a set
   Functions nextelement(), permset(), setsize(), setinter(),
   settolist() and listtoset() now work for multi-word sets
   even if nauty is compiled with MAXN=WORDSIZE.

* Miscellaneous
   - The default "make" now creates the 16-bit libraries nautyS.a
     and nautyS1.a. There are new targets for making thread-enabled
     libraries nautyT.a, nautyT1.a, nautyTW.a, nautyTW1.a,
     nautyTL.a and nautyTL1.a; these are not built by "make all".
   - The compiler switch -march=native is omitted if the build is
     for Alpine Linux. This is due to a problem with the compiler
     issuing illegal instructions. Thanks to Gordon Royle for
     helping with this.
   - Changes were made to the configure script and nauty.h to
     support ARM64 (aarch64) architecture. So far this is only
     tested on the Apple M1 architecture.
   - Bugs were fixed in multig (if multiple edges were present,
     also combination of -V and the INPUTGRAPH hook),
     genspecialg (argument parsing for -T), pickg/countg (help
     text for -s,-S), and watercluster2 (shifting right by the
     wordsize is undefined! This only effected clang.)
   - Programs that use randomisation now initialise the random
     generator from the high-resolution realtime clock if possible.
     Specifically, it uses the first available of gettimeofday(),
     clock_gettime() and time(). This makes it much less likely
     that processes started close together will use the same seed.
   - The proceedure gtools_getline() in gtools.c, which is used by
     most utilities for reading graphs, is now faster except for
     for very small graphs.

* A new version of Traces is included, that fixes a bug reported
   by Aleksandr Krotov and makes other improvements. A side-effect
   is that the canonical labelling made by Traces has changed.

* Nauty now uses a more standard version numbering system such as
   2.8.6. Corrections will be made to the most recent version only,
   and beta versions will be released only rarely.