The version of musixflx.lua now at

ftp://linus.cs.queensu.ca/musixflx/musixflx.lua

has been adapted to be callable from musixtex.tex. To try it out, copy
musixflx.lua and musixtex.tex into a working directory and re-define
\endmuflex (line number 4823 in version 1.15) in musixtex.tex as
follows:

\def\endmuflex{%
\immediate\closeout\outmux%
\ifx\undefined\directlua \else \directlua { 
   name_of_file = tex.jobname
   musixflx = kpse.find_file("musixflx.lua")
   dofile(musixflx)}%
\fi% 
}%

Note that there must be another closing } immediately after to close the
definition of \pass@I (starts on line 4748).

Then you can process a file basename.tex (containing a call to
\endmuflex just before the \end or \bye) as follows:

luatex --output-format=dvi basename

The --output-format=dvi option is only necessary if you're using
Postscript slurs; the default is to output pdf.

You should see that basename.mx1 is produced as usual but then
musixflx.lua is called and it will produce basename.mx2; most of the
usual musixflx output messages have been suppressed (except in debug
mode). A second call to luatex will yield a usable dvi file.

If you use a standard tex or don't have \endmuflex in your score file,
musixflx.lua won't be called and you'll have to run a separate musixflx
as usual. The newest musixflx.lua isn't really usable for this purpose
unless you assign the name_of_file variable youself.

Note that luatex is still beta and I've found that it fails to process
some examples; this has nothing to do with calling musixflx *after*
conventional processing and such issues should be reported to the luatex
developers, not to me.

Bob T.
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