changes24-27.txt

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 use 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).

* More information is provided to PRUNE/PREPRUNE plugins of geng.

* -q suppresses the "c" lines in Bliss output of listg.

* 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 a crash for digraph6 output
  over 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.

* 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 the macro 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 the compile command if the
  use has specified 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.
  (Flexible array members are declared as the last field
  in structures like x[] and the user is allowed to
  extend them.)

* 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.

* Changes to the makefile:
(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=DIR to specify a parent directory for these.
  There is still no target for dynamic libraries.
(3) Several rearrangements that most users won't notice.

* There is a new utility nbrhoodg that can extract neighbourhoods
  of vertices

* The amount of working space given to nauty was increased in a
  few places.

--- Version 2.8 changes brought forward to 2.7r4

* Fixed an obscure bug in multig that might occur if the input
  graph has loops. No example of incorrect behaviour is known.

* Fixed help text for -s and -S in pickg and countg

* Corrected argument parsing for genspecialg -T

* Fixed a problem with watercluster2 and the clang compiler.
  Note: right shift by the word size is undefined, and as an
  example BITMASK(WORDSIZE) is erroneous. The argument of
  BITMASK must be 0..WORDSIZE-1.