Import Debian changes 3a1-4.2debian/3a1-4.2

slib (3a1-4.2) unstable; urgency=low

  * Non-maintainer upload.
  * Add guile.init.local for use within the build dir, since otherwise we
    have an (earlier unnoticed) circular build-dep due to a difference
    between scm and guile.

slib (3a1-4.1) unstable; urgency=low

  * Non-maintainer upload.
  * Build-depend on guile-1.6 instead of scm, since the new version of
    scm is wedged in unstable (closes: #281809).

slib (3a1-4) unstable; urgency=low

  * Also check for expected creation on slibcat. (Closes: #240096)

slib (3a1-3) unstable; urgency=low

  * Also check for /usr/share/guile/1.6/slib before installing for guile
    1.6. (Closes: #239267)

slib (3a1-2) unstable; urgency=low

  * Add format.scm back into slib until gnucash stops using it.
  * Call guile-1.6 new-catalog (Closes: #238231)

slib (3a1-1) unstable; urgency=low

  * New upstream release
  * Remove Info section from doc-base file (Closes: #186950)
  * Remove period from end of description (linda, lintian)
  * html gen fixed upstream (Closes: #111778)

slib (2d4-2) unstable; urgency=low

  * Fix url for upstream source (Closes: #144981)
  * Fix typo in slib.texi (enquque->enqueue) (Closes: #147475)
  * Add build depends.

slib (2d4-1) unstable; urgency=low

  * New upstream.

slib (2d3-1) unstable; urgency=low

  * New upstream.
  * Remove texi2html call in debian/rules.  Now done upstream.  Add make
    html instead.
  * Changes to rules and doc-base to conform to upstream html gen
  * Clean up upstream makefile to make sure it cleans up after itself.

1 files changed, 50 insertions, 40 deletions

diff --git a/differ.txi b/differ.txi
index f7b1f75..c46fc2a 100644
--- a/differ.txi
+++ b/differ.txi
@@ -1,5 +1,5 @@
 @noindent
-This package implements the algorithm:
+@code{diff:edit-length} implements the algorithm:
 
 @ifinfo
 @example
@@ -18,6 +18,18 @@ Information Processing Letters 35, 6 (1990), 317-323.
 @end ifset
 
 @noindent
+The values returned by @code{diff:edit-length} can be used to gauge
+the degree of match between two sequences.
+
+@noindent
+Surprisingly, "An O(NP) Sequence Comparison Algorithm" does not
+derive the edit sequence; only the sequence length.  Developing this
+linear-space sub-quadratic-time algorithm for computing the edit
+sequence required hundreds of hours of work.  I have submitted a
+paper describing the algorithm to the Journal of Computational
+Biology.
+
+@noindent
 If the items being sequenced are text lines, then the computed
 edit-list is equivalent to the output of the @dfn{diff} utility
 @cindex diff
@@ -25,71 +37,69 @@ program.  If the items being sequenced are words, then it is like the
 lesser known @dfn{spiff} program.
 @cindex spiff
 
-@noindent
-The values returned by @code{diff:edit-length} can be used to gauge
-the degree of match between two sequences.
 
-@noindent
-I believe that this algorithm is currently the fastest for these
-tasks, but genome sequencing applications fuel extensive research in
-this area.
+@defun diff:longest-common-subsequence array1 array2 =? p-lim
 
 
-@defun diff:longest-common-subsequence array1 array2 =?
+@defunx diff:longest-common-subsequence array1 array2 =?
+@var{array1} and @var{array2} are one-dimensional arrays.  The procedure @var{=?} is used
+to compare sequence tokens for equality.
 
+The non-negative integer @var{p-lim}, if provided, is maximum number of
+deletions of the shorter sequence to allow.  @code{diff:longest-common-subsequence} will return @code{#f}
+if more deletions would be necessary.
 
-@defunx diff:longest-common-subsequence array1 array2
-@var{array1} and @var{array2} are one-dimensional arrays.  The procedure @var{=?} is used
-to compare sequence tokens for equality.  @var{=?} defaults to @code{eqv?}.
 @code{diff:longest-common-subsequence} returns a one-dimensional array of length @code{(quotient (- (+
-len1 len2) (fp:edit-length @var{array1} @var{array2})) 2)} holding the longest sequence
+len1 len2) (diff:edit-length @var{array1} @var{array2})) 2)} holding the longest sequence
 common to both @var{array}s.
 @end defun
 
-@defun diff:edits array1 array2 =?
+@defun diff:edits array1 array2 =? p-lim
 
 
-@defunx diff:edits array1 array2
+@defunx diff:edits array1 array2 =?
 @var{array1} and @var{array2} are one-dimensional arrays.  The procedure @var{=?} is used
-to compare sequence tokens for equality.  @var{=?} defaults to @code{eqv?}.
-@code{diff:edits} returns a list of length @code{(fp:edit-length @var{array1} @var{array2})} composed of
-a shortest sequence of edits transformaing @var{array1} to @var{array2}.
+to compare sequence tokens for equality.
 
-Each edit is a list of an integer and a symbol:
+The non-negative integer @var{p-lim}, if provided, is maximum number of
+deletions of the shorter sequence to allow.  @code{diff:edits} will return @code{#f}
+if more deletions would be necessary.
+
+@code{diff:edits} returns a vector of length @code{(diff:edit-length @var{array1} @var{array2})} composed
+of a shortest sequence of edits transformaing @var{array1} to @var{array2}.
+
+Each edit is an integer:
 @table @asis
-@item (@var{j} insert)
-Inserts @code{(array-ref @var{array1} @var{j})} into the sequence.
-@item (@var{k} delete)
-Deletes @code{(array-ref @var{array2} @var{k})} from the sequence.
+@item @var{k} > 0
+Inserts @code{(array-ref @var{array1} (+ -1 @var{j}))} into the sequence.
+@item @var{k} < 0
+Deletes @code{(array-ref @var{array2} (- -1 @var{k}))} from the sequence.
 @end table
 @end defun
 
-@defun diff:edit-length array1 array2 =?
+@defun diff:edit-length array1 array2 =? p-lim
 
 
-@defunx diff:edit-length array1 array2
+@defunx diff:edit-length array1 array2 =?
 @var{array1} and @var{array2} are one-dimensional arrays.  The procedure @var{=?} is used
-to compare sequence tokens for equality.  @var{=?} defaults to @code{eqv?}.
+to compare sequence tokens for equality.
+
+The non-negative integer @var{p-lim}, if provided, is maximum number of
+deletions of the shorter sequence to allow.  @code{diff:edit-length} will return @code{#f}
+if more deletions would be necessary.
+
 @code{diff:edit-length} returns the length of the shortest sequence of edits transformaing
 @var{array1} to @var{array2}.
 @end defun
 @example
-(diff:longest-common-subsequence '#(f g h i e j c k l m)
-                                 '#(f g e h i j k p q r l m))
-                                 @result{} #(f g h i j k l m)
+(diff:longest-common-subsequence "fghiejcklm" "fgehijkpqrlm" eqv?)
+@result{} "fghijklm"
 
-(diff:edit-length '#(f g h i e j c k l m)
-                  '#(f g e h i j k p q r l m))
+(diff:edit-length "fghiejcklm" "fgehijkpqrlm" eqv?)
 @result{} 6
 
-(pretty-print (diff:edits '#(f g h i e j c k l m)
-                          '#(f g e h i j k p q r l m)))
-@print{}
-((3 insert)                           ; e
- (4 delete)                           ; c
- (6 delete)                           ; h
- (7 insert)                           ; p
- (8 insert)                           ; q
- (9 insert))                          ; r
+(diff:edits "fghiejcklm" "fgehijkpqrlm" eqv?)
+@result{} #As32(3 -5 -7 8 9 10)
+       ; e  c  h p q  r
 @end example