moved BUGS languages to seperate module

3 files changed, 302 insertions, 286 deletions

diff --git a/pygments/lexers/_mapping.py b/pygments/lexers/_mapping.py
index 00bef11b..6f342552 100644
--- a/pygments/lexers/_mapping.py
+++ b/pygments/lexers/_mapping.py
@@ -42,7 +42,7 @@ LEXERS = {
     'BooLexer': ('pygments.lexers.dotnet', 'Boo', ('boo',), ('*.boo',), ('text/x-boo',)),
     'BrainfuckLexer': ('pygments.lexers.other', 'Brainfuck', ('brainfuck', 'bf'), ('*.bf', '*.b'), ('application/x-brainfuck',)),
     'BroLexer': ('pygments.lexers.other', 'Bro', ('bro',), ('*.bro',), ()),
-    'BugsLexer': ('pygments.lexers.math', 'BUGS', ('bugs', 'winbugs', 'openbugs'), ('*.bugs',), ()),
+    'BugsLexer': ('pygments.lexers.jags', 'BUGS', ('bugs', 'winbugs', 'openbugs'), ('*.bugs',), ()),
     'CLexer': ('pygments.lexers.compiled', 'C', ('c',), ('*.c', '*.h', '*.idc'), ('text/x-chdr', 'text/x-csrc')),
     'CMakeLexer': ('pygments.lexers.text', 'CMake', ('cmake',), ('*.cmake', 'CMakeLists.txt'), ('text/x-cmake',)),
     'CObjdumpLexer': ('pygments.lexers.asm', 'c-objdump', ('c-objdump',), ('*.c-objdump',), ('text/x-c-objdump',)),
@@ -124,7 +124,7 @@ LEXERS = {
     'IokeLexer': ('pygments.lexers.jvm', 'Ioke', ('ioke', 'ik'), ('*.ik',), ('text/x-iokesrc',)),
     'IrcLogsLexer': ('pygments.lexers.text', 'IRC logs', ('irc',), ('*.weechatlog',), ('text/x-irclog',)),
     'JSONLexer': ('pygments.lexers.web', 'JSON', ('json',), ('*.json',), ('application/json',)),
-    'JagsLexer': ('pygments.lexers.math', 'JAGS', ('jags',), ('*.jags',), ()),
+    'JagsLexer': ('pygments.lexers.bugs', 'JAGS', ('jags',), ('*.jags',), ()),
     'JadeLexer': ('pygments.lexers.web', 'Jade', ('jade', 'JADE'), ('*.jade',), ('text/x-jade',)),
     'JavaLexer': ('pygments.lexers.jvm', 'Java', ('java',), ('*.java',), ('text/x-java',)),
     'JavascriptDjangoLexer': ('pygments.lexers.templates', 'JavaScript+Django/Jinja', ('js+django', 'javascript+django', 'js+jinja', 'javascript+jinja'), (), ('application/x-javascript+django', 'application/x-javascript+jinja', 'text/x-javascript+django', 'text/x-javascript+jinja', 'text/javascript+django', 'text/javascript+jinja')),
@@ -230,7 +230,7 @@ LEXERS = {
     'SqliteConsoleLexer': ('pygments.lexers.sql', 'sqlite3con', ('sqlite3',), ('*.sqlite3-console',), ('text/x-sqlite3-console',)),
     'SquidConfLexer': ('pygments.lexers.text', 'SquidConf', ('squidconf', 'squid.conf', 'squid'), ('squid.conf',), ('text/x-squidconf',)),
     'SspLexer': ('pygments.lexers.templates', 'Scalate Server Page', ('ssp',), ('*.ssp',), ('application/x-ssp',)),
-    'StanLexer': ('pygments.lexers.math', 'Stan', ('stan',), ('*.stan',), ()),
+    'StanLexer': ('pygments.lexers.bugs', 'Stan', ('stan',), ('*.stan',), ()),
     'SystemVerilogLexer': ('pygments.lexers.hdl', 'systemverilog', ('sv',), ('*.sv', '*.svh'), ('text/x-systemverilog',)),
     'TclLexer': ('pygments.lexers.agile', 'Tcl', ('tcl',), ('*.tcl',), ('text/x-tcl', 'text/x-script.tcl', 'application/x-tcl')),
     'TcshLexer': ('pygments.lexers.shell', 'Tcsh', ('tcsh', 'csh'), ('*.tcsh', '*.csh'), ('application/x-csh',)),
diff --git a/pygments/lexers/bugs.py b/pygments/lexers/bugs.py
new file mode 100644
index 00000000..584eca86
--- /dev/null
+++ b/pygments/lexers/bugs.py
@@ -0,0 +1,298 @@
+# -*- coding: utf-8 -*-
+"""
+    pygments.lexers.bugs
+    ~~~~~~~~~~~~~~~~~~~~
+
+    Lexers for BUGS-like languages for Bayesian statistical models.
+
+    :copyright: Copyright 2012 by the Pygments team, 
+    :license: BSD, see LICENSE for details.
+"""
+from pygments.lexer import RegexLexer, bygroups, include
+from pygments.token import Comment, String, Punctuation, Keyword, Name, \
+    Operator, Number, Text
+
+__all__ = ['JagsLexer', 'BugsLexer', 'StanLexer']
+
+class BugsLexer(RegexLexer):
+    """ Pygments Lexer for Stan models """
+
+    name = 'BUGS'
+    aliases = ['bugs', 'winbugs', 'openbugs']
+    filenames = ['*.bug']
+
+    _FUNCTIONS = [
+        # Scalar functions
+        'abs', 'arccos', 'arccosh', 'arcsin', 'arcsinh', 'arctan', 'arctanh',
+        'cloglog', 'cos', 'cosh', 'cumulative', 'cut', 'density', 'deviance',
+        'equals', 'expr', 'gammap', 'ilogit', 'icloglog', 'integral', 'log',
+        'logfact', 'loggam', 'logit', 'max', 'min', 'phi', 'post.p.value',
+        'pow', 'prior.p.value', 'probit', 'replicate.post', 'replicate.prior',
+        'round', 'sin', 'sinh', 'solution', 'sqrt', 'step', 'tan', 'tanh',
+        'trunc',
+        # Vector functions 
+        'inprod', 'interp.lin', 'inverse', 'logdet', 'mean', 'eigen.vals',
+        'ode', 'prod', 'p.valueM', 'rank', 'ranked', 'replicate.postM',
+        'sd', 'sort', 'sum',
+        ## Special
+        'D', 'I', 'F', 'T', 'C']
+    """ OpenBUGS built-in functions 
+
+    From http://www.openbugs.info/Manuals/ModelSpecification.html#ContentsAII
+
+    This also includes
+
+    - T, C, I : Truncation and censoring. ``T`` and ``C`` are in OpenBUGS. ``I`` in WinBUGS.
+    - D : ODE 
+    - F : Functional http://www.openbugs.info/Examples/Functionals.html
+
+    """
+
+    _DISTRIBUTIONS = ['dbern', 'dbin', 'dcat', 'dnegbin', 'dpois',
+                           'dhyper', 'dbeta', 'dchisqr', 'ddexp', 'dexp',
+                           'dflat', 'dgamma', 'dgev', 'df', 'dggamma', 'dgpar',
+                           'dloglik', 'dlnorm', 'dlogis', 'dnorm', 'dpar',
+                           'dt', 'dunif', 'dweib', 'dmulti', 'ddirch', 'dmnorm',
+                           'dmt', 'dwish']
+    """ OpenBUGS built-in distributions
+
+    Functions From http://www.openbugs.info/Manuals/ModelSpecification.html#ContentsAI
+    """
+
+
+    tokens = {
+        'whitespace' : [
+            (r"\s+", Text),
+            ],
+        'comments' : [
+            # Comments
+            (r'#.*$', Comment.Single),
+            ],
+        'root': [
+            # Comments
+            include('comments'),
+            include('whitespace'),
+            # Block start
+            (r'(?s)(model)(\s|\n)+({)',
+             bygroups(Keyword.Namespace, Text, Punctuation), 'block')
+        ],
+        'block' : [
+            include('comments'),
+            include('whitespace'),
+            # Reserved Words
+            (r'(for|in)\b', Keyword.Reserved),
+            # Built-in Functions
+            (r'(%s)(?=\s*\()'
+             % r'|'.join(_FUNCTIONS + _DISTRIBUTIONS),
+             Name.Builtin),
+            # Regular variable names
+            (r'[A-Za-z][A-Za-z0-9_.]*', Name),
+            # Number Literals
+            (r'[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?', Number),
+            # Punctuation
+            (r'(\[|\]|\(|\)|:|,)', Punctuation),
+            # Assignment operators
+            # SLexer makes these tokens Operators. 
+            (r'(<-|~)', Operator),
+            # Infix and prefix operators
+            (r'(\+|-|\*|/)', Operator),
+            # Block
+            (r'{', Punctuation, '#push'),
+            (r'}', Punctuation, '#pop'),
+            ]
+        }
+
+class JagsLexer(RegexLexer):
+    """ Pygments Lexer for JAGS """
+    name = 'JAGS'
+    aliases = ['jags']
+    filenames = ['*.jags']
+    
+    ## JAGS
+    _FUNCTIONS = [
+        'abs', 'arccos', 'arccosh', 'arcsin', 'arcsinh', 'arctan', 'arctanh',
+        'cos', 'cosh', 'cloglog',
+        'equals', 'exp', 'icloglog', 'ifelse', 'ilogit', 'log', 'logfact',
+        'loggam', 'logit', 'phi', 'pow', 'probit', 'round', 'sin', 'sinh',
+        'sqrt', 'step', 'tan', 'tanh', 'trunc', 'inprod', 'interp.lin',
+        'logdet', 'max', 'mean', 'min', 'prod', 'sum', 'sd', 'inverse', 'rank', 'sort', 't',
+        'acos', 'acosh', 'asin', 'asinh', 'atan',
+        # Truncation/Censoring (should I include)
+        'T', 'I']
+    # Distributions with density, probability and quartile functions
+    _DISTRIBUTIONS = ['[dpq]%s' % x for x in
+                           ['bern', 'beta', 'dchiqsqr', 'ddexp', 'dexp',
+                            'df', 'gamma', 'gen.gamma', 'logis', 'lnorm',
+                            'negbin', 'nchisqr', 'norm', 'par', 'pois', 'weib']]
+    # Other distributions without density and probability 
+    _OTHER_DISTRIBUTIONS = [
+        'dt', 'dunif', 'dbetabin', 'dbern', 'dbin', 'dcat', 'dhyper',
+        'ddirch', 'dmnorm', 'dwish', 'dmt', 'dmulti', 'dbinom', 'dchisq',
+        'dnbinom', 'dweibull', 'ddirich']
+
+    tokens = {
+        'whitespace' : [
+            (r"\s+", Text),
+            ],
+        'names' : [
+            # Regular variable names
+            (r'\b[A-Za-z][A-Za-z0-9_.]*\b', Name),
+            ],
+        'comments' : [
+            # do not use stateful comments
+            (r'(?s)/\*.*?\*/', Comment.Multiline),
+            # Comments
+            (r'#.*$', Comment.Single),
+            ],
+        'root': [
+            # Comments
+            include('comments'),
+            include('whitespace'),
+            # Block start
+            (r'(?s)(model|data)(\s|\n)+({)',
+             bygroups(Keyword.Namespace, Text, Punctuation), 'block'),
+            # Variable declaration (TODO: improve)
+            (r'var\b', Keyword.Declaration, 'var')
+        ],
+        'statements': [
+            include('comments'),
+            include('whitespace'),
+            # Reserved Words
+            (r'(for|in)\b', Keyword.Reserved),
+            # Builtins
+            # Need to use lookahead because . is a valid char
+            (r'(%s)(?=\s*\()' % r'|'.join(_FUNCTIONS
+                                 + _DISTRIBUTIONS
+                                 + _OTHER_DISTRIBUTIONS),
+             Name.Builtin),
+            # Names
+            include('names'),
+            # Number Literals
+            (r'[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?', Number),
+            (r'(\[|\]|\(|\)|:|,)', Punctuation),
+            # Assignment operators
+            (r'(<-|~)', Operator),
+            # # JAGS includes many more than OpenBUGS
+            # |/|\|\||\&\&|>=?|<=?|[=!]?=|!|%.*?%|^)'
+            (r'(\+|-|\*|\/|\|\|[&]{2}|[<>=]=?|\^|%.*?%)', Operator),
+            ],
+        'block' : [
+            include('statements'),
+            (r';', Punctuation),
+            (r'{', Punctuation, '#push'),
+            (r'}', Punctuation, '#pop'),
+            ],
+        'var' : [
+            include('statements'),
+            (r';', Punctuation, '#pop'),
+            ]
+        }
+
+class StanLexer(RegexLexer):
+    """ Pygments Lexer for Stan models """
+    name = 'Stan'
+    aliases = ['stan']
+    filenames = ['*.stan']
+
+    _RESERVED = ('for', 'in', 'while', 'repeat', 'until', 'if',
+                'then', 'else', 'true', 'false', 'T')
+
+    _TYPES = ('int', 'real', 'vector', 'simplex', 'ordered', 'row_vector', 'matrix',
+              'corr_matrix', 'cov_matrix')
+
+    # STAN 1.0 Manual, Chapter 20
+    _CONSTANTS = ['pi', 'e', 'sqrt2', 'log2', 'log10', 'nan', 'infinity',
+                  'epsilon', 'negative_epsilon']
+    _FUNCTIONS = ['abs', 'int_step', 'min', 'max',
+                  'if_else', 'step',
+                  'fabs', 'fdim',
+                  'fmin', 'fmax',
+                  'fmod',
+                  'floor', 'ceil', 'round', 'trunc',
+                  'sqrt', 'cbrt', 'square', 'exp', 'exp2', 'expm1',
+                  'log', 'log2', 'log10', 'pow', 'logit', 'inv_logit',
+                  'inv_cloglog', 'hypot', 'cos', 'sin', 'tan', 'acos',
+                  'asin', 'atan', 'atan2', 'cosh', 'sinh', 'tanh',
+                  'acosh', 'asinh', 'atanh', 'erf', 'erfc', 'Phi',
+                  'log_loss', 'tgamma', 'lgamma', 'lmgamma', 'lbeta',
+                  'binomial_coefficient_log',
+                  'fma', 'multiply_log', 'log1p', 'log1m', 'log1p_exp',
+                  'log_sum_exp',
+                  'rows', 'cols',
+                  'dot_product', 'prod', 'mean', 'variance', 'sd',
+                  'diagonal', 'diag_matrix', 'col', 'row',
+                  'softmax', 'trace', 'determinant', 'inverse', 'eigenvalue',
+                  'eigenvalues_sym', 'cholesky', 'singular_values',
+                  '(log)?normal_p', 'exponential_p', 'gamma_p', 'weibull_p']
+    _DISTRIBUTIONS = ['bernoulli', 'bernoulli_logit', 'binomial',
+                      'beta_binomial', 'hypergeometric', 'categorical',
+                      'ordered_logistic', 'negative_binomial', 'poisson',
+                      'multinomial', 'normal', 'student_t',
+                      'cauchy', 'double_exponential', 'logistic',
+                      'lognormal', 'chi_square', 'inv_chi_square',
+                      'scaled_inv_chi_square', 'exponential',
+                      'gamma', 'inv_gamma', 'weibull', 'pareto',
+                      'beta', 'uniform', 'dirichlet', 'multi_normal',
+                      'multi_normal_cholesky', 'multi_student_t',
+                      'wishart', 'inv_wishart', 'lkj_cov',
+                      'lkj_corr_cholesky']
+
+    tokens = {
+        'whitespace' : [
+            (r"\s+", Text),
+            ],
+        'comments' : [
+            # do not use stateful comments
+            (r'(?s)/\*.*?\*/', Comment.Multiline),
+            # Comments
+            (r'(//|#).*$', Comment.Single),
+            ],
+        'root': [
+            # Comments
+            include('comments'),
+            # block start
+            include('whitespace'),
+            # Block start
+            (r'(?s)(%s)(\s*)({)' %
+             r'|'.join(('data', r'transformed\s+?data',
+                        'parameters', r'transformed\s+parameters',
+                        'model', r'generated\s+quantities')),
+             bygroups(Keyword.Namespace, Text, Punctuation), 'block')
+        ],
+        'block' : [
+            include('comments'),
+            include('whitespace'),
+            # Reserved Words
+            (r'(%s)\b' % r'|'.join(_RESERVED), Keyword.Reserved),
+            # Data types
+            (r'(%s)\b' % r'|'.join(_TYPES), Keyword.Type),
+            # Punctuation
+            (r"[;:,\[\]()]", Punctuation),
+            # Builtin
+            (r'(%s)(?=\s*\()'
+             % r'|'.join(_FUNCTIONS
+                         + _DISTRIBUTIONS 
+                         + ['%s_log' % x for x in _DISTRIBUTIONS]),
+             Name.Builtin),
+            (r'(%s)(?=\s*\()'
+             % r'|'.join(_CONSTANTS),
+             Keyword.Constant),
+            # Special names ending in __, like lp__
+            (r'\b[A-Za-z][A-Za-z0-9_]*__\b', Name.Builtin.Pseudo),
+            # Regular variable names
+            (r'\b[A-Za-z][A-Za-z0-9_]*\b', Name),
+            # Real Literals
+            (r'-?[0-9]+(\.[0-9]+)?[eE]-?[0-9]+', Number.Float),
+            (r'-?[0-9]*\.[0-9]*', Number.Float),
+            # Integer Literals
+            (r'-?[0-9]+', Number.Integer),
+            # Assignment operators
+            # SLexer makes these tokens Operators. 
+            (r'(<-|~)', Operator),
+            # Infix and prefix operators
+            (r"(\+|-|\.?\*|\.?/|\\|')", Operator),
+            # Block
+            (r'{', Punctuation, '#push'),
+            (r'}', Punctuation, '#pop'),
+            ]
+        }
diff --git a/pygments/lexers/math.py b/pygments/lexers/math.py
index be82b2b2..a6d7a5c5 100644
--- a/pygments/lexers/math.py
+++ b/pygments/lexers/math.py
@@ -21,7 +21,7 @@ from pygments.lexers import _scilab_builtins
 
 __all__ = ['JuliaLexer', 'JuliaConsoleLexer', 'MuPADLexer', 'MatlabLexer',
            'MatlabSessionLexer', 'OctaveLexer', 'ScilabLexer', 'NumPyLexer',
-           'RConsoleLexer', 'SLexer', 'JagsLexer', 'BugsLexer', 'StanLexer']
+           'RConsoleLexer', 'SLexer']
 
 class JuliaLexer(RegexLexer):
     name = 'Julia'
@@ -1070,285 +1070,3 @@ class SLexer(RegexLexer):
     def analyse_text(text):
         return '<-' in text
 
-class BugsLexer(RegexLexer):
-    """ Pygments Lexer for Stan models """
-
-    name = 'BUGS'
-    aliases = ['bugs', 'winbugs', 'openbugs']
-    filenames = ['*.bug']
-
-    _FUNCTIONS = [
-        # Scalar functions
-        'abs', 'arccos', 'arccosh', 'arcsin', 'arcsinh', 'arctan', 'arctanh',
-        'cloglog', 'cos', 'cosh', 'cumulative', 'cut', 'density', 'deviance',
-        'equals', 'expr', 'gammap', 'ilogit', 'icloglog', 'integral', 'log',
-        'logfact', 'loggam', 'logit', 'max', 'min', 'phi', 'post.p.value',
-        'pow', 'prior.p.value', 'probit', 'replicate.post', 'replicate.prior',
-        'round', 'sin', 'sinh', 'solution', 'sqrt', 'step', 'tan', 'tanh',
-        'trunc',
-        # Vector functions 
-        'inprod', 'interp.lin', 'inverse', 'logdet', 'mean', 'eigen.vals',
-        'ode', 'prod', 'p.valueM', 'rank', 'ranked', 'replicate.postM',
-        'sd', 'sort', 'sum',
-        ## Special
-        'D', 'I', 'F', 'T', 'C']
-    """ OpenBUGS built-in functions 
-
-    From http://www.openbugs.info/Manuals/ModelSpecification.html#ContentsAII
-
-    This also includes
-
-    - T, C, I : Truncation and censoring. ``T`` and ``C`` are in OpenBUGS. ``I`` in WinBUGS.
-    - D : ODE 
-    - F : Functional http://www.openbugs.info/Examples/Functionals.html
-
-    """
-
-    _DISTRIBUTIONS = ['dbern', 'dbin', 'dcat', 'dnegbin', 'dpois',
-                           'dhyper', 'dbeta', 'dchisqr', 'ddexp', 'dexp',
-                           'dflat', 'dgamma', 'dgev', 'df', 'dggamma', 'dgpar',
-                           'dloglik', 'dlnorm', 'dlogis', 'dnorm', 'dpar',
-                           'dt', 'dunif', 'dweib', 'dmulti', 'ddirch', 'dmnorm',
-                           'dmt', 'dwish']
-    """ OpenBUGS built-in distributions
-
-    Functions From http://www.openbugs.info/Manuals/ModelSpecification.html#ContentsAI
-    """
-
-
-    tokens = {
-        'whitespace' : [
-            (r"\s+", Text),
-            ],
-        'comments' : [
-            # Comments
-            (r'#.*$', Comment.Single),
-            ],
-        'root': [
-            # Comments
-            include('comments'),
-            include('whitespace'),
-            # Block start
-            (r'(?s)(model)(\s|\n)+({)',
-             bygroups(Keyword.Namespace, Text, Punctuation), 'block')
-        ],
-        'block' : [
-            include('comments'),
-            include('whitespace'),
-            # Reserved Words
-            (r'(for|in)\b', Keyword.Reserved),
-            # Built-in Functions
-            (r'(%s)(?=\s*\()'
-             % r'|'.join(_FUNCTIONS + _DISTRIBUTIONS),
-             Name.Builtin),
-            # Regular variable names
-            (r'[A-Za-z][A-Za-z0-9_.]*', Name),
-            # Number Literals
-            (r'[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?', Number),
-            # Punctuation
-            (r'(\[|\]|\(|\)|:|,)', Punctuation),
-            # Assignment operators
-            # SLexer makes these tokens Operators. 
-            (r'(<-|~)', Operator),
-            # Infix and prefix operators
-            (r'(\+|-|\*|/)', Operator),
-            # Block
-            (r'{', Punctuation, '#push'),
-            (r'}', Punctuation, '#pop'),
-            ]
-        }
-
-class JagsLexer(RegexLexer):
-    """ Pygments Lexer for JAGS """
-    name = 'JAGS'
-    aliases = ['jags']
-    filenames = ['*.jags']
-    
-    ## JAGS
-    _FUNCTIONS = [
-        'abs', 'arccos', 'arccosh', 'arcsin', 'arcsinh', 'arctan', 'arctanh',
-        'cos', 'cosh', 'cloglog',
-        'equals', 'exp', 'icloglog', 'ifelse', 'ilogit', 'log', 'logfact',
-        'loggam', 'logit', 'phi', 'pow', 'probit', 'round', 'sin', 'sinh',
-        'sqrt', 'step', 'tan', 'tanh', 'trunc', 'inprod', 'interp.lin',
-        'logdet', 'max', 'mean', 'min', 'prod', 'sum', 'sd', 'inverse', 'rank', 'sort', 't',
-        'acos', 'acosh', 'asin', 'asinh', 'atan',
-        # Truncation/Censoring (should I include)
-        'T', 'I']
-    # Distributions with density, probability and quartile functions
-    _DISTRIBUTIONS = ['[dpq]%s' % x for x in
-                           ['bern', 'beta', 'dchiqsqr', 'ddexp', 'dexp',
-                            'df', 'gamma', 'gen.gamma', 'logis', 'lnorm',
-                            'negbin', 'nchisqr', 'norm', 'par', 'pois', 'weib']]
-    # Other distributions without density and probability 
-    _OTHER_DISTRIBUTIONS = [
-        'dt', 'dunif', 'dbetabin', 'dbern', 'dbin', 'dcat', 'dhyper',
-        'ddirch', 'dmnorm', 'dwish', 'dmt', 'dmulti', 'dbinom', 'dchisq',
-        'dnbinom', 'dweibull', 'ddirich']
-
-    tokens = {
-        'whitespace' : [
-            (r"\s+", Text),
-            ],
-        'names' : [
-            # Regular variable names
-            (r'\b[A-Za-z][A-Za-z0-9_.]*\b', Name),
-            ],
-        'comments' : [
-            # do not use stateful comments
-            (r'(?s)/\*.*?\*/', Comment.Multiline),
-            # Comments
-            (r'#.*$', Comment.Single),
-            ],
-        'root': [
-            # Comments
-            include('comments'),
-            include('whitespace'),
-            # Block start
-            (r'(?s)(model|data)(\s|\n)+({)',
-             bygroups(Keyword.Namespace, Text, Punctuation), 'block'),
-            # Variable declaration (TODO: improve)
-            (r'var\b', Keyword.Declaration, 'var')
-        ],
-        'statements': [
-            include('comments'),
-            include('whitespace'),
-            # Reserved Words
-            (r'(for|in)\b', Keyword.Reserved),
-            # Builtins
-            # Need to use lookahead because . is a valid char
-            (r'(%s)(?=\s*\()' % r'|'.join(_FUNCTIONS
-                                 + _DISTRIBUTIONS
-                                 + _OTHER_DISTRIBUTIONS),
-             Name.Builtin),
-            # Names
-            include('names'),
-            # Number Literals
-            (r'[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?', Number),
-            (r'(\[|\]|\(|\)|:|,)', Punctuation),
-            # Assignment operators
-            (r'(<-|~)', Operator),
-            # # JAGS includes many more than OpenBUGS
-            # |/|\|\||\&\&|>=?|<=?|[=!]?=|!|%.*?%|^)'
-            (r'(\+|-|\*|\/|\|\|[&]{2}|[<>=]=?|\^|%.*?%)', Operator),
-            ],
-        'block' : [
-            include('statements'),
-            (r';', Punctuation),
-            (r'{', Punctuation, '#push'),
-            (r'}', Punctuation, '#pop'),
-            ],
-        'var' : [
-            include('statements'),
-            (r';', Punctuation, '#pop'),
-            ]
-        }
-
-class StanLexer(RegexLexer):
-    """ Pygments Lexer for Stan models """
-    name = 'Stan'
-    aliases = ['stan']
-    filenames = ['*.stan']
-
-    _RESERVED = ('for', 'in', 'while', 'repeat', 'until', 'if',
-                'then', 'else', 'true', 'false', 'T')
-
-    _TYPES = ('int', 'real', 'vector', 'simplex', 'ordered', 'row_vector', 'matrix',
-              'corr_matrix', 'cov_matrix')
-
-    # STAN 1.0 Manual, Chapter 20
-    _CONSTANTS = ['pi', 'e', 'sqrt2', 'log2', 'log10', 'nan', 'infinity',
-                  'epsilon', 'negative_epsilon']
-    _FUNCTIONS = ['abs', 'int_step', 'min', 'max',
-                  'if_else', 'step',
-                  'fabs', 'fdim',
-                  'fmin', 'fmax',
-                  'fmod',
-                  'floor', 'ceil', 'round', 'trunc',
-                  'sqrt', 'cbrt', 'square', 'exp', 'exp2', 'expm1',
-                  'log', 'log2', 'log10', 'pow', 'logit', 'inv_logit',
-                  'inv_cloglog', 'hypot', 'cos', 'sin', 'tan', 'acos',
-                  'asin', 'atan', 'atan2', 'cosh', 'sinh', 'tanh',
-                  'acosh', 'asinh', 'atanh', 'erf', 'erfc', 'Phi',
-                  'log_loss', 'tgamma', 'lgamma', 'lmgamma', 'lbeta',
-                  'binomial_coefficient_log',
-                  'fma', 'multiply_log', 'log1p', 'log1m', 'log1p_exp',
-                  'log_sum_exp',
-                  'rows', 'cols',
-                  'dot_product', 'prod', 'mean', 'variance', 'sd',
-                  'diagonal', 'diag_matrix', 'col', 'row',
-                  'softmax', 'trace', 'determinant', 'inverse', 'eigenvalue',
-                  'eigenvalues_sym', 'cholesky', 'singular_values',
-                  '(log)?normal_p', 'exponential_p', 'gamma_p', 'weibull_p']
-    _DISTRIBUTIONS = ['bernoulli', 'bernoulli_logit', 'binomial',
-                      'beta_binomial', 'hypergeometric', 'categorical',
-                      'ordered_logistic', 'negative_binomial', 'poisson',
-                      'multinomial', 'normal', 'student_t',
-                      'cauchy', 'double_exponential', 'logistic',
-                      'lognormal', 'chi_square', 'inv_chi_square',
-                      'scaled_inv_chi_square', 'exponential',
-                      'gamma', 'inv_gamma', 'weibull', 'pareto',
-                      'beta', 'uniform', 'dirichlet', 'multi_normal',
-                      'multi_normal_cholesky', 'multi_student_t',
-                      'wishart', 'inv_wishart', 'lkj_cov',
-                      'lkj_corr_cholesky']
-
-    tokens = {
-        'whitespace' : [
-            (r"\s+", Text),
-            ],
-        'comments' : [
-            # do not use stateful comments
-            (r'(?s)/\*.*?\*/', Comment.Multiline),
-            # Comments
-            (r'(//|#).*$', Comment.Single),
-            ],
-        'root': [
-            # Comments
-            include('comments'),
-            # block start
-            include('whitespace'),
-            # Block start
-            (r'(?s)(%s)(\s*)({)' %
-             r'|'.join(('data', r'transformed\s+?data',
-                        'parameters', r'transformed\s+parameters',
-                        'model', r'generated\s+quantities')),
-             bygroups(Keyword.Namespace, Text, Punctuation), 'block')
-        ],
-        'block' : [
-            include('comments'),
-            include('whitespace'),
-            # Reserved Words
-            (r'(%s)\b' % r'|'.join(_RESERVED), Keyword.Reserved),
-            # Data types
-            (r'(%s)\b' % r'|'.join(_TYPES), Keyword.Type),
-            # Punctuation
-            (r"[;:,\[\]()]", Punctuation),
-            # Builtin
-            (r'(%s)(?=\s*\()'
-             % r'|'.join(_FUNCTIONS
-                         + _DISTRIBUTIONS 
-                         + ['%s_log' % x for x in _DISTRIBUTIONS]),
-             Name.Builtin),
-            (r'(%s)(?=\s*\()'
-             % r'|'.join(_CONSTANTS),
-             Keyword.Constant),
-            # Special names ending in __, like lp__
-            (r'\b[A-Za-z][A-Za-z0-9_]*__\b', Name.Builtin.Pseudo),
-            # Regular variable names
-            (r'\b[A-Za-z][A-Za-z0-9_]*\b', Name),
-            # Real Literals
-            (r'-?[0-9]+(\.[0-9]+)?[eE]-?[0-9]+', Number.Float),
-            (r'-?[0-9]*\.[0-9]*', Number.Float),
-            # Integer Literals
-            (r'-?[0-9]+', Number.Integer),
-            # Assignment operators
-            # SLexer makes these tokens Operators. 
-            (r'(<-|~)', Operator),
-            # Infix and prefix operators
-            (r"(\+|-|\.?\*|\.?/|\\|')", Operator),
-            # Block
-            (r'{', Punctuation, '#push'),
-            (r'}', Punctuation, '#pop'),
-            ]
-        }