===== New Features =====

* Faster rule parsing.  The runtime of the COBRA_TO_TIGER function on the
  iAF1260 E. coli model decreased by over 50%.

* The new parser reports helpful error messages when encountering errors
  in PARSE_STRING.  Missing parenthesis are also identified.

* A new method is included for converting GPR rules into constraints.
  The conversion uses only a single binary variable for the gene indicator,
  and continuous variables otherwise.  The GPR is also re-grouped to
  reduce the number of substitutions needed.  This feature reduces 
  complexity of the generated MILPs and can be enabled by setting the 
  'fast_gpr' parameter in COBRA_TO_TIGER to true.

* TIGER models allows for delayed indicator binding.  CMPI replaces bounds 
  on indicator variables immediately before passing the problem to the 
  solver. This feature improves runtime for MILPs.  See ADD_BINDING for 
  details.

* Expressions are represented as Matlab structures, not with a separate 
  class.  EXPR class methods are replaced with functions:

        EXPR method         Replacement function
        -----------         --------------------
        display, disp       display_expr
        iter, map           expr_map
        iterif, mapif       expr_mapif
        demorgan            demorgan_expr
        atoms               get_atoms
        AND, OR, IF, IFF    is_and, is_or, is_if, is_iff
        NULL                is_null
        cond_op             op
        is_junc, is_cond    is_junc, is_cond
        is_op, is_rule      is_op, is_rule
        is_atom             is_atom
        expr()              create_empty_expr_struct()
        copy                <none> Structures are copied automatically
                                   on assignment.

* SHOW_TIGER and SHOW_MIP display the optimization sense (max or min).

* PARSE_STRING allows the 'matlab_levels' parameter for compatibility with
  Matlab's operator order of operators ('and' binds tighter than 'or').

* Solving MIP problems with CMPI has been separated into two phases.  CMPI.PREPARE_MIP preprocesses the MIP to convert indicators, delayed bindings, and quadratic differences (Qd and Qc) into constraints in the standard form.  This MIP is then solved by CMPI.RUN_SOLVER.  CMPI.SOLVER_MIP calls both of these functions as needed, and SOLVER_TIGER is unaffected.  This feature is useful for solving a sequence of MIPs (e.g. during FVA) when repeated preprocessing is unnecessary.

===== Bug Fixes =====

* Documentation fixes for COBRA_TO_TIGER. (issue #17)

* SINGLE_GENE_KO works correctly when only given one gene name.  Also,
  status bar can be turned off with the 'status' parameter. (issue #21)

* MADE parameter 'pvalidate' parses correctly. (issue #20)

* CMPI.SET_OPTION works correctly when given [] as the only input.
  (issue #19)

* EXTRACT_TIGER now updates S to reflect changes made to the corresponding
  entries in A. (issue #16)