split up math module

1 files changed, 261 insertions, 1 deletions

diff --git a/pygments/lexers/modeling.py b/pygments/lexers/modeling.py
index 1cd1b6b1..49aca224 100644
--- a/pygments/lexers/modeling.py
+++ b/pygments/lexers/modeling.py
@@ -16,8 +16,9 @@ from pygments.token import Text, Comment, Operator, Keyword, Name, String, \
     Number, Punctuation
 
 from pygments.lexers.html import HtmlLexer
+from pygments.lexers import _stan_builtins
 
-__all__ = ['ModelicaLexer']
+__all__ = ['ModelicaLexer', 'BugsLexer', 'JagsLexer', 'StanLexer']
 
 
 class ModelicaLexer(RegexLexer):
@@ -112,3 +113,262 @@ class ModelicaLexer(RegexLexer):
             (r'.+?(?=<\s*/\s*html\s*>)', using(HtmlLexer)),
         ]
     }
+
+
+class BugsLexer(RegexLexer):
+    """
+    Pygments Lexer for `OpenBugs <http://www.openbugs.info/w/>`_ and WinBugs
+    models.
+
+    .. versionadded:: 1.6
+    """
+
+    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'(model)(\s+)({)',
+             bygroups(Keyword.Namespace, Text, Punctuation)),
+            # Reserved Words
+            (r'(for|in)(?![0-9a-zA-Z\._])', Keyword.Reserved),
+            # Built-in Functions
+            (r'(%s)(?=\s*\()'
+             % r'|'.join(_FUNCTIONS + _DISTRIBUTIONS),
+             Name.Builtin),
+            # Regular variable names
+            (r'[A-Za-z][\w.]*', 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),
+        ]
+    }
+
+    def analyse_text(text):
+        if re.search(r"^\s*model\s*{", text, re.M):
+            return 0.7
+        else:
+            return 0.0
+
+
+class JagsLexer(RegexLexer):
+    """
+    Pygments Lexer for JAGS.
+
+    .. versionadded:: 1.6
+    """
+
+    name = 'JAGS'
+    aliases = ['jags']
+    filenames = ['*.jag', '*.bug']
+
+    # 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 = tuple('[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'[a-zA-Z][\w.]*\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'(model|data)(\s+)({)',
+             bygroups(Keyword.Namespace, Text, Punctuation)),
+            (r'var(?![0-9a-zA-Z\._])', Keyword.Declaration),
+            # Reserved Words
+            (r'(for|in)(?![0-9a-zA-Z\._])', 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),
+            (r'[{}]', Punctuation),
+        ]
+    }
+
+    def analyse_text(text):
+        if re.search(r'^\s*model\s*\{', text, re.M):
+            if re.search(r'^\s*data\s*\{', text, re.M):
+                return 0.9
+            elif re.search(r'^\s*var', text, re.M):
+                return 0.9
+            else:
+                return 0.3
+        else:
+            return 0
+
+
+class StanLexer(RegexLexer):
+    """Pygments Lexer for Stan models.
+
+    The Stan modeling language is specified in the *Stan Modeling Language User's Guide and Reference Manual, v2.4.0*,
+    `pdf <https://github.com/stan-dev/stan/releases/download/v2.4.0/stan-reference-2.4.0.pdf>`__.
+
+    .. versionadded:: 1.6
+    """
+
+    name = 'Stan'
+    aliases = ['stan']
+    filenames = ['*.stan']
+
+    tokens = {
+        'whitespace': [
+            (r"\s+", Text),
+        ],
+        'comments': [
+            (r'(?s)/\*.*?\*/', Comment.Multiline),
+            # Comments
+            (r'(//|#).*$', Comment.Single),
+        ],
+        'root': [
+            # Stan is more restrictive on strings than this regex
+            (r'"[^"]*"', String),
+            # Comments
+            include('comments'),
+            # block start
+            include('whitespace'),
+            # Block start
+            (r'(%s)(\s*)({)' %
+             r'|'.join(('functions', 'data', r'transformed\s+?data',
+                        'parameters', r'transformed\s+parameters',
+                        'model', r'generated\s+quantities')),
+             bygroups(Keyword.Namespace, Text, Punctuation)),
+            # Reserved Words
+            (r'(%s)\b' % r'|'.join(_stan_builtins.KEYWORDS), Keyword),
+            # Truncation
+            (r'T(?=\s*\[)', Keyword),
+            # Data types
+            (r'(%s)\b' % r'|'.join(_stan_builtins.TYPES), Keyword.Type),
+            # Punctuation
+            (r"[;:,\[\]()]", Punctuation),
+            # Builtin
+            (r'(%s)(?=\s*\()'
+             % r'|'.join(_stan_builtins.FUNCTIONS
+                         + _stan_builtins.DISTRIBUTIONS),
+             Name.Builtin),
+            # Special names ending in __, like lp__
+            (r'[A-Za-z]\w*__\b', Name.Builtin.Pseudo),
+            (r'(%s)\b' % r'|'.join(_stan_builtins.RESERVED), Keyword.Reserved),
+            # Regular variable names
+            (r'[A-Za-z]\w*\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, prefix and postfix operators (and = )
+            (r"\+|-|\.?\*|\.?/|\\|'|\^|==?|!=?|<=?|>=?|\|\||&&", Operator),
+            # Block delimiters
+            (r'[{}]', Punctuation),
+        ]
+    }
+
+    def analyse_text(text):
+        if re.search(r'^\s*parameters\s*\{', text, re.M):
+            return 1.0
+        else:
+            return 0.0