
Changes from nauty 2.4 to nauty 2.5
-----------------------------------

* Add Traces.  The main files are traces.h and traces.c, but
  many changes were made to dreadnaut.c and nausparse.c also.

* Allow thread-safe storage if requested by configure --enable-tls
  and available.  This allows parallel running of nauty and Traces
  in separate threads.

* The makefile now creates static libraries like nauty.a in 
  addition to object files like nauty.o.

* Remove all uses of types permutation, nvector, np2vector, shortish.
  These are now int.

* Add schreier.h, schreier.c and the optional use of the random
  Schreier method in nauty.  These are also used in Traces, but
  are not optional there.

* Add large-file support to all programs, assuming it is available.
  Now there is no longer a 4GB limit on files read or written on
  32-bit systems.

* Use gcc extensions like __builtin_clz() if available and not
    disabled by configure --disable-clz.
  Use FIRSTBITNZ instead of FIRSTBIT if the argument is certain
    to be nonzero.

* New macros defined in nauty.h:
   COUNTER_FMT
   PRINT_COUNTER
   SETWORDSNEEDED
   ADDONEARC
   ADDONEEDGE
   EMPTYGRAPH

* The options structure has a new boolean field schreier.

* New procedures:
  densenauty()  in naugraph.c  - simplified dense graph interface
  sparsenauty() in nausparse.c - simplified sparse graph interface
  writegroupsize() in nautil.c - write two part group size
  copy_sg() in nausparse.c     - make a copy of a sparse graph

  densenauty() and sparsenauty() are now the recommended ways to
  call nauty from a program.  See the sample programs in the package.

* Use quicksort in place of shell sort in many places.  This is 
  implemented in the file sorttemplates.c that can be used in any
  applications.

* Apply the const attribute more liberally across the code.

* The sparsegraph fields nde and *v changed type from int to size_t.
  This is to allow more than 2^31 edges on 64-bit hardware.

* sparsegraph.h and sparsegraph.c:
    Corrected definition of SG_DECL in sparsegraph.h. (The erroneous
       definition would have worked but generated warnings.)
    Added DEFAULTOPTIONS_SPARSEDIGRAPH.
    Added comparelab_tr(), testcanlab_tr(), updatecan_tr() for Traces.

* gtools.h and gtools.c:
    Now gtools.h is made from gtools-h.in by configure.
    Updated G6LEN() to work for larger graphs.
    Use large-file functions fseeko(), ftello() if possible.

* Most tools now use the random number generator in naurng.c rather
  than that in rng.c.

* gutils.h, gutil1.c and gutil2.c:
    New procedures maxcliques(), indpathcount1(), indcyclecount1(),
      indcyclecount().

* Invariants:
    Corrected getbigcells(), making a small change to invariants
       celltrips, cellquins and refinvar.

* dreadnaut:
    Sparse nauty and Traces now incorported.
    New commands: A, G, F, FF, sr, O, OO, P, PP, S, V
    w command is now in units of 2*m.
    Command-line can run commands using -o.
    M command is extended; now applies to i as well as x.
    Implement ANSI controls if requested.
    File names for > and < can be given in "..." to allow spaces.
 
* Updates to utilities:
     listg:  add -b (Bliss format), -G (GRAPE format) and
          -y/-Y (dotty format), -H (HCP format)
     labelg: add -t (Traces) and -i16 (refinvar)
     countg/pickg: add -m (vertices of min degree),
         -M (vertices of max degree), -H (induced cycles),
         -K (number of maximal independent sets)
     genrang: add -t (tree)
     genbg: add -A (antichain)
        The makefile can also make genbgL which makes larger sizes
     directg: add PROCESS feature
     shortg: -S (use sparse nauty), -t (use traces), i16 (refinvar)

* New utilities:
     ranlabg: randomly relabel graphs
     linegraphg: compute linegraphs
     subdivideg: compute subdivision graphs
     watercluster2: orient edges of graphs (by Gunnar Brinkmann)

* Version 25r2 fixed a rare bug in Traces
* Version 25r3 fixed some problems in the configure script (thanks to Daniel Grayson)

Changes from nauty 2.5 to nauty 2.6
-----------------------------------

Changes to dreadnaut:
* dreadnaut now catches control-C when nauty or Traces is running.
  This uses the global variable nauty_kill_request.
* new command "vv" to display sorted degree sequence.
* new command "r&" to relabel according to the partition.
* new command "->>" to flush the output.
* new command "B" to turn on output flushing at the end of every
  command.  Command "-B" turns it off.  Default off.
* Command with short arguments now have to be all on one line.
  Most errors cause the rest of the input line to be skipped.
* The "R" command now preserves the colouring.

Changes to nauty:
* nauty has an extra hook usercanonproc().
* The maximum number of vertices is now 2 billion.
* Many modern processors have instructions POPCNT and CLZ* that can
  help nauty.  The configuration script now looks for them and
  attempts to use them if possible.

New file formats (see formats.txt for definitions):
* sparse6 format is now extended with "incremental sparse6"
  format. Graphs in incremental sparse6 format specify only the
  differences from the previous graph.
  As yet, incremental sparse6 is only supported by copyg (which
  has new options -i/-I to write this format), listg, pickg and
  countg. For listg, pickg and countg, the -p switch might not work
  if the input is incremental.
* The new format digraph6 is for directed graphs.  There are
  procedures for reading and writing it in gtools.c.
  The following programs can handle digraph6 so far:
    labelg, shortg, ranlabg, directg, gentourng, amtog, complg,
    copyg, dretog, catg, listg, showg, converse, converseg, delptg,
    deledgeg, countg/pickg (partially), genrang (partially), genspecialg

New utilities:
*  converseg : take converse of a digraph
*  cubhamg : hamiltonian cycles in subcubic graphs
*  hamheuristic : heuristic for hamiltonian cycles
*  twohamg : partition quartic graphs into two hamiltonian cycles
*  genspecialg : generate special graphs like paths and cycles
*  gentreeg : generateg trees, based on a program of Li and Ruskey.
*  genquarticg : generate quartic graphs, written with Narjess Afzaly.
*  dretodot : reads one graph in dreadnaut format and writes a picture
     of it in dot format. You can use tools in the graphviz library
     to deal with it.
*  vcolg : colours the vertices of graphs in all distinct ways.
     If you choose the number of colours to be 2, this the same as
     adding loops in all distinct ways.
*  delptg : delete vertices.
As always, run the command with argument "-help" to get instructions.

Extra options in existing utilities:
* amtog now properly handles loops.  (Recall that loops are ok
    in sparse6 format but not in graph6 format.)
  amtog has a switch -o that allows selecting one colour class of
  a coloured graph, and -w to suppress the warning about loops.
* copyg has -z for writing digraph6 format. An undirected graph
  can be written as a digraph, but not vice-versa.
* directg default output format is directg6.
  directg has a new option -s for splitting into cases.
* dretog allows "d" command for digraph input.
* Option -B added to countg and pickg.
* complg has new option -R.
* genrang has new option -d that makes random regular graphs of
  any degree but does not guarantee uniform distribution.
  Also option -T for random tournaments.
  Some options now work for bipartite graphs; specify the number
  of vertices on each side like n1,n2.
* labelg has extra options -C and -W. These can help to determine
    what is different between two different programs that generate
    almost the same output.
* linegraphg has -t for making the total graph.
* Most utilities can take a single argument --version, which will
  print a message stating which nauty&traces package they belong to.

Other changes:
* Traces has substantial improvements.
* Extra argument macros SWDOUBLE, SWREALRANGE, SWSEQUENCE in gtools.h.
* girth() in gutil1.c got the wrong answer for K2.  Thanks to
  Sean Irvine for reporting it.
* gtools.c defines checkgline() to check if a graph input 
  line looks ok.
* The procedures in gtnauty.c, used by labelg and other utilities,
  had an old limit of 2^22 (4 million+) vertices.  This limit is
  now removed.  Also a new procedure setlabptn() was added to set
  lab/ptn according to an integer weight.
* planarg -p had a bug causing wrong output for n >= 65536.  Fixed.
* The structured type bigint has disappeared in favour of integer type
  nauty_counter, which is "unsigned long long" if that exists and
  "unsigned long" is only 32 bits, or "unsigned long" otherwise.
  This means that some plugins for geng/genbg/gentourng may need
  to be revised.

Changes from nauty 2.6 to nauty 2.7
-----------------------------------

* -h and -k options for independent set size and clique size were added
  to countg and pickg.  For some graphs these use the program cliquer,
  kindly provided by Sampo Nisjkanen and Patric Ostergard.

* Macros SWHIBIT, REMOVEHIBIT and ATMOSTONEBIT added to nauty.h.

* Added option -a to complg.

* Program copyg can now be used to make a simple filter.  See the
  instructions inside the source file and the example numleaves.c.

* Programs countg and pickg can now display some parameter values
  as ranges instead of writing a separate line for each value. For
  example, countg --ne:T will write a separate line for each number
  of vertices and edges, with that line showing the range of the
  number of triangles. Everything after the ':' is shown as a range.
  There is also a switch -1 that causes output to be in a simple
  numerical table easy to read from a program and a similar switch
  -2 that omits counts.

* Program vcolg now handles digraphs and graphs with loops.

* genrang can now make random spanning trees of K(n1,n2)

* amtog has an "s" command for reading tournaments

* gentreeg made the same tree twice for n=2; thanks to Kevin Ryde
  for reporting it.

* The configure script (compiled from configure.ac) was modified to
  update some tests and remove some old code that is useless. The
  time-critical parts of nauty are now compiled with
     -march=native
  if the compiler allows those switches. Since this may result in
  a binary which does not run on older machines in the same family,
  there is a configuration option  --enable-generic  to disable
  these switches.  To work around a bug with -march-native for
  gcc version 7 on MacOSX computers (due to the linker not knowing
  some of the instructions), the extra switch -mno-avx is also added
  if it appears necessary.

* genspecialg can now make multiple special graphs at once.
  The -b option has been extended to allow removing a matching from
  a complete bipartite graph.

* watercluster2 has an option Z to write in digraph6 format.

* Problems for input of graphs with 0 vertices were fixed with help
  from Kevin Ryde.  However, note that many utilities in the package
  will not work with such graphs.  It is NOT TRUE that graphs of
  order 0 are now supported.  However, the primary function nauty()
  (but not traces()) should work for both dense and sparse versions.

* Stronger measures are taken to ensure that the sort order used by
  shortg is plain byte order. This corresponds to the C collation
  order, also known as POSIX, but it may be different from the
  collation order used by default on your command line. This means
  that utilities like sort, uniq, comm and join might consider the
  output of shortg to be out of order. To avoid this, define the
  environment variable LC_ALL to equal the string "C".
     bash:   export LC_ALL=C
     tcsh:   setenv LC_ALL C
  If LC_ALL is undefined, it will also be sufficient to define
  LC_COLLATE to equal "C".  The POSIX standard says that LC_ALL
  takes precedence over LC_COLLATE if both are defined, but this
  might not be true for older systems.  If you really don't want
  to change environment variables, you can compile shortg with
  -DKEEP_SORT_LOCALE but beware that some collation orders are
  are not even deterministic (i.e. different characters might
  compare equal).

* The bipartite graph generator genbg now has a -Y switch to
  specify the minimum number of common neighbours for two
  vertices on the second side.

* A new version of Traces (including some bug fixes) is included.
  See traces.c for more.

* New utilities: underlyingg takes the undirected graph underlying
  a graph or digraph.  assembleg combines a file of graphs (usually
  connected graphs) as components to make disconnected graphs
  of a specified size.

* geng has been modified to allow more than 32 vertices.  The
  makefile knows "geng" for up to 32 vertices, and "gengL" for
  up to 64 vertices.

* pickg and countg now have -X to reverse the selection.
  A change was made to allow these utilities to work on Windows
  computers with sizeof(long) < sizeof(void*).  Also, pickg
  now writes a header if there is one in the input file.

* listg has -L that can be used in conjunction with -W or -M to
  write the Laplacian matrix instead of the adjacency matrix.

* Fixed a possible bug in the combination "shortg -kt".

* You can change the archive manager (default "ar") by defining
  the environment variable AR at configure time.

* Some portability issues in nautycliquer.c were fixed (thanks
  to Isuru Fernando).

* The -B/--B switch of listg/countg is now isomomorphism-invariant.
  It equals 0 for non-bipartite graph, and the smallest possible
  side of a 2-colouring otherwise.  This change reflects rewriting
  of function bipartiteside() in gutil1.c.  The values can differ
  from those for nauty version <= 2.7rc1 when there are three or
  more components.

* Fixed the type of the 4th parameter of options.usercanonproc.

* Check kill requests more often. If the global int variable
  nauty_kill_request becomes nonzero, nauty and Traces will
  exit at certain key points. In dreadnaut nauty_kill_request
  is set if the user types control-C (if the operating system
  provides this facility).

* nauty.h loads <limits.h> and <stdint.h> if they exist.

* Some features were added to assist installation on non-POSIX
  systems or where 'configure' can't be easily run, such as
  Microsoft Visual Studio. These changes are mostly in nauty.h.
  1. The predefined names _MSC_VER, _WIN32 and _WIN64 are examined.
  2. HAVE_HWLZCNT and HAVE_HWPOPCNT can be defined at compile time
     (to 0 or 1) to indicate the presence of hardware lzcnt and
     popcnt instructions.
  3. The FIRSTBITNZ, FIRSTBIT and POPCOUNT macros can be defined
     at compile time (though it is unlikely you will be able to do
     much better than the default versions). FIRSTBIT is defined
     in terms of FIRSTBITNZ if it isn't defined separately.
  4. Loading of unavailable header files can be disabled by
     predefining macros: AVOID_SYS_TYPES_H, AVOID_UNISTD_H,
     AVOID_STRINGS_H and AVOID_SYS_WAIT_H.
  There is more to do here; there are lots of variations in
  different software versions and documentation is inconsistent.
  Thanks to Andy Mercier for discussions so far.

* Bug fixed in directg that caused crash when digraphg6 output
  was selected for more than WORDSIZE vertices.

* The external variables labelorg and nauty_kill_request were
  moved into the "C" block of nauty.h for C++ compatibility.

* Identical BUGS in naugraph.c and sparsegraph.c.
  The static sizes of dnwork[] and snwork[] were too small.
  This bug first crept into version 2.6 beta 10.  To meet this
  bug, all of the following must be true:
  (a) called densenauty() or sparsenauty() rather than calling
      nauty() directly.
  (b) processed graphs with 20 or more vertices.
  (c) compiled naugraph.c or sparsegraph.c with an explicit
      value of MAXN, rather than the default MAXN=0.
      This includes using the libraries nauty1.a, nautyW1.a
      or nautyL1.a. However nauty.a, nautyW.a and nautyL.a
      were safe.  Likewise, the utilities distributed with
      nauty were also safe.
  Thanks to James Trimble and Chris Jefferson for uncovering this.
  Versions 2.6r12 and 2.7rc5 were fixed.

* A bug in nauty.h caused compilation failure on some hardware
  without popcnt instructions. You didn't encounter this if you
  didn't get compile-time error messages about POPCOUNT.  Thanks
  to Anthony Matos for reporting this error.

* Tweak the configure script to more reliably detect standard
  function declarations and to improve the test for the POPCNT
  instruction.

* Don't define INFINITY even if it isn't defined in math.h.
  Note that nauty's infinity is NAUTY_INFINITY and plain
  INFINITY is a required macro in the C standard.

* A bug prevented a filtering version of copyg (needs special
  compilation, see copyg.c) from playing nice with incremental
  sparse6 input. You didn't meet this bug unless you saw an
  error message like "readg_inc: missing prior".  Another
  bug in the same facility caused the number of outputs to
  be reported as the same as the number of inputs even if some
  of them had been filtered out.  The outputs themselves were
  correct.

* -march=native is not added to compiles if the user has
  provided an architecture via CC or CFLAGS.

* traces.h has extern "C" { } for function declarations to
  assist calling from C++.

* nauty.h defines FLEX_ARRAY_OK to 1 if flexible array
  members of structures are allowed, and 0 otherwise.

* Compiling with preprocessor variable USE_TLS defined will
  have the same effect as configuring with --enable-tls.
  (a) If either --enable-tls or USE_TLS is defined then:
     USE_TLS is defined, HAVE_TLS is defined as 1, and
     TLS_ATTR is defined to be the attribute for thread-local
     memory (either thread_local, _Thread_local, __thread or
     __declspec(thread)).
     If the compiler doesn't support thread-local memory at
     all, an error is issued.
  (b) If --enable-tls is not used and USE_TLS is not defined,
     then USE_TLS is not defined, HAVE_TLS is defined as 0,
     and TLS_ATTR is defined as empty.

(1) The line "AR?=ar" in the makefile violated the Posix standard, see
  https://pubs.opengroup.org/onlinepubs/9699919799/utilities/make.html
  It is now gone. This shouldn't be a problem since the variable AR
  is used instead and its default value is "ar" unless a different
  value is specified on the make command line.
(2) There is an install target.  It puts executables into ${bindir},
  include files into ${includedir}, static libraries into ${libdir},
  and pkg-config configuration files into ${pkgconfigexecdir}.
  Configure with --prefix=PATH to specify a parent directory for these.
  There is still no target for dynamic libraries.
(3) Several rearrangements that most users won't notice.

* New utility nbrhoodg can extract neighbourhoods of vertices

Changes from nauty 2.7 to nauty 2.8
-----------------------------------

* 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.), assembleg
    found by Szabolcs Horvát.
  - 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.

----- Now 2.8.6
