Create a gist now

Instantly share code, notes, and snippets.

What would you like to do?
Token based Fortran namelist parser. Let me know if anything does not work.
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Fortran namelist parser. Converts nameslists to python dictionaries.
Should be fairly robust. Cannot be used for verifying fortran namelists as it
is rather forgiving.
Error messages during parsing are kind of messy right now.
Usage
=====
>>> from namelist import namelist2dict
>>> namelist_dict = namelist2dict("fortran_list.txt")
Can deal with filenames, open files and file-like object (StringIO).
Works with Python 2.7 and has not further dependencies.
:copyright:
Lion Krischer (krischer@geophysik.uni-muenchen.de), 2013
:license:
GNU Lesser General Public License, Version 3
(http://www.gnu.org/copyleft/lesser.html)
"""
from StringIO import StringIO
import unittest
QUOTE_CHARS = ["'"]
class Token(object):
"""
Base class for all token types.
"""
def __str__(self):
name = self.__class__.__name__
if hasattr(self, "value"):
return "%s(%s)" % (name, str(self.value))
return name
def __repr__(self):
return self.__str__()
class StringToken(Token):
def __init__(self, value):
self.value = value
class AssignmentToken(Token):
pass
class GroupEndToken(Token):
pass
class GroupStartToken(Token):
def __init__(self, value):
self.value = value
class IntegerToken(Token):
def __init__(self, value):
self.value = int(value)
class FloatToken(Token):
def __init__(self, value):
self.value = float(value)
class BooleanToken(Token):
def __init__(self, value):
self.value = bool(value)
class NameToken(Token):
def __init__(self, value):
self.value = str(value)
class ComplexNumberToken(Token):
def __init__(self, real, imag):
self.value = complex(real, imag)
def auto_token(value):
"""
Instantiates the correct token type based on the passed value string.
"""
value = value.strip()
if value.startswith("&"):
return GroupStartToken(value[1:])
elif value.lower() == ".true.":
return BooleanToken(True)
elif value.lower() == ".false.":
return BooleanToken(False)
try:
return IntegerToken(int(value))
except:
pass
try:
return FloatToken(float(value))
except:
pass
return NameToken(value)
def tokenizer(file_object):
"""
The lexer - a generator yielding tokens.
"""
for line in file_object:
line = line.strip()
if not line:
continue
in_string = False
in_complex_number = False
current_token = []
for letter in line:
# Handle strings.
if letter in QUOTE_CHARS:
if in_string is True:
in_string = False
if current_token:
yield StringToken("".join(current_token))
current_token = []
else:
in_string = True
continue
elif in_string is True:
current_token.append(letter)
# Handle complex numbers.
elif letter == "(":
if current_token:
yield auto_token("".join(current_token))
current_token = []
in_complex_number = True
elif letter == ")":
# Parse the complex number.
real, imag = map(float, "".join(current_token).split(","))
yield ComplexNumberToken(real, imag)
current_token = []
in_complex_number = False
elif in_complex_number is True:
current_token.append(letter)
# Everything from now on is neither string nor complex number.
elif letter == "!":
break
elif not letter.strip():
if current_token:
yield auto_token("".join(current_token))
current_token = []
elif letter == ",":
if current_token:
yield auto_token("".join(current_token))
current_token = []
elif letter == "=":
if current_token:
yield auto_token("".join(current_token))
current_token = []
yield AssignmentToken()
elif letter == "/":
if current_token:
yield auto_token("".join(current_token))
current_token = []
yield GroupEndToken()
else:
current_token.append(letter)
if current_token:
yield auto_token("".join(current_token))
def group_generator(tokens):
"""
Generator yielding one dictionary per found group.
"""
current_group = {}
current_group_name = None
current_assignment = []
for token in tokens:
if isinstance(token, GroupStartToken):
if current_group_name:
msg = "Starting new group without ending old one."
raise ValueError(msg)
current_group_name = token.value
continue
elif isinstance(token, GroupEndToken):
if current_assignment:
parse_assignment(current_assignment, current_group)
current_assignment = []
if current_group and current_group_name:
yield (current_group_name, current_group)
else:
msg = "Invalid group found."
raise ValueError(msg)
current_group = {}
current_group_name = None
continue
elif isinstance(token, NameToken):
if current_assignment:
parse_assignment(current_assignment, current_group)
current_assignment = []
current_assignment.append(token)
def parse_assignment(assignment, group):
"""
Parses all tokens for one assignment. Will write the result to the passed
group dictionary.
"""
if len(assignment) < 3:
msg = "Invalid assignment."
raise ValueError(msg)
if not isinstance(assignment[0], NameToken):
msg = "Assignment must start with a name."
raise ValueError(msg)
if not isinstance(assignment[1], AssignmentToken):
msg = "Assignment must contain an AssignmentToken."
raise ValueError(msg)
values = assignment[2:]
value_types = set([type(_i) for _i in values])
if len(value_types) != 1:
msg = "All values for one assignment must have the same type."
raise ValueError(msg)
values = [_i.value for _i in values]
if len(values) == 1:
values = values[0]
group[assignment[0].value] = values
def namelist2dict(file_or_file_object):
"""
Thin wrapper to be able to deal with file-like objects and filenames.
"""
if hasattr(file_or_file_object, "read"):
return _namelist2dict(file_or_file_object)
with open(file_or_file_object, "r") as open_file:
return _namelist2dict(open_file)
def _namelist2dict(file_object):
"""
Converts a file_object containng a namelist to a dictionary.
"""
namelist_dict = {}
for group_name, group_values in group_generator(tokenizer(file_object)):
namelist_dict.setdefault(group_name, [])
namelist_dict[group_name].append(group_values)
return namelist_dict
class NameListTestCase(unittest.TestCase):
"""
Some very basic test cases.
"""
def test_simple_group(self):
"""
Test simple namelist group with values of different types.
"""
group = (
"&group\n"
" float = 0.75\n"
" integer = 700\n"
" string = 'test'\n"
" true = .TRUE.\n"
" false = .FALSE.\n"
"/")
namelist_dict = namelist2dict(StringIO(group))
self.assertEqual(namelist_dict,
{"group": [{
"float": 0.75,
"integer": 700,
"string": "test",
"true": True,
"false": False
}]})
def test_complex_single_line_group(self):
"""
Tests a rather complex single line group.
"""
group = "&list a=1, b=1,2 c='12 / !' / "
namelist_dict = namelist2dict(StringIO(group))
self.assertEqual(namelist_dict,
{"list": [{
"a": 1,
"b": [1, 2],
"c": "12 / !"
}]})
def test_complex_multiple_group(self):
"""
Same as test_complex_single_line_group() just split over lines.
"""
group = (
"&list a=1\n"
"b=1,2, c='12 / !' /")
namelist_dict = namelist2dict(StringIO(group))
self.assertEqual(namelist_dict,
{"list": [{
"a": 1,
"b": [1, 2],
"c": "12 / !"
}]})
def test_complex_numbers(self):
"""
Tests complex numbers. Complex number parsing is rather forgiving.
"""
group = (
"&complex_group\n"
" number_a = (1,2)\n"
" number_b = (1.2,3.4)\n"
" number_c = (-1.2,0.0)\n"
" number_d = (0.0, 1.0)\n"
"/")
namelist_dict = namelist2dict(StringIO(group))
self.assertEqual(namelist_dict,
{"complex_group": [{
"number_a": 1.0 + 2.0j,
"number_b": 1.2 + 3.4j,
"number_c": -1.2 + 0.0j,
"number_d": 0.0j + 1.0j
}]})
def test_group_mixed_and_lists(self):
"""
Tests a real world example.
"""
group = (
"&receiver\n"
" station ='XX02'\n"
" location = 'a'\n"
" lon = 12.51\n"
" lat = -0.01\n"
" depth = 1.0\n"
" attributes = 'vx' 'vy' 'vz'\n"
" file_name_prefix = './DATA/mess/'\n"
" override = .TRUE.\n"
"/\n")
namelist_dict = namelist2dict(StringIO(group))
self.assertEqual(namelist_dict,
{"receiver": [{
"station": "XX02",
"location": "a",
"lon": 12.51,
"lat": -0.01,
"depth": 1.0,
"attributes": ["vx", "vy", "vz"],
"file_name_prefix": "./DATA/mess/",
"override": True
}]})
def test_multiple_groups(self):
"""
Mixes groups from some of the previous tests.
"""
group = (
"&group\n"
" float = 0.75\n"
" integer = 700\n"
" string = 'test'\n"
" true = .TRUE.\n"
" false = .FALSE.\n"
"/\n"
"\n"
"&list a=1, b=1,2 c='12 / !' / \n"
"&list a=1\n"
"b=1,2, c='12 / !' /\n"
"&receiver\n"
" station ='XX02'\n"
" location = 'a'\n"
" lon = 12.51\n"
" lat = -0.01\n"
" depth = 1.0\n"
" attributes = 'vx' 'vy' 'vz'\n"
" file_name_prefix = './DATA/mess/'\n"
" override = .TRUE.\n"
"/\n")
namelist_dict = namelist2dict(StringIO(group))
self.assertEqual(namelist_dict,
{"group": [{
"float": 0.75,
"integer": 700,
"string": "test",
"true": True,
"false": False
}],
"list": [{
"a": 1,
"b": [1, 2],
"c": "12 / !"
}, {
"a": 1,
"b": [1, 2],
"c": "12 / !"
}],
"receiver": [{
"station": "XX02",
"location": "a",
"lon": 12.51,
"lat": -0.01,
"depth": 1.0,
"attributes": ["vx", "vy", "vz"],
"file_name_prefix": "./DATA/mess/",
"override": True
}]})
def test_real_world_example(self):
"""
Tests example from
http://owen.sj.ca.us/~rk/howto/slides/f90model/slides/namelist.html
"""
groups = (
"! can have blank lines and comments in the namelist input file\n"
"! place these comments between NAMELISTs\n"
"\n"
"!\n"
"! not every compiler supports comments within the namelist\n"
"! in particular vastf90/g77 does not\n"
"!\n"
"! some will skip NAMELISTs not directly referenced in read\n"
"!&BOGUS rko=1 /\n"
"!\n"
"&TTDATA \n"
" TTREAL = 1.,\n"
" TTINTEGER = 2,\n"
" TTCOMPLEX = (3.,4.), \n"
" TTCHAR = 'namelist', \n"
" TTBOOL = .TRUE./\n"
"&AADATA\n"
" AAREAL = 1. 1. 2. 3., \n"
" AAINTEGER = 2 2 3 4, \n"
" AACOMPLEX = (3.,4.) (3.,4.) (5.,6.) (7.,7.), \n"
" AACHAR = 'namelist' 'namelist' 'array' ' the lot', \n"
" AABOOL = .TRUE. .TRUE. .FALSE. .FALSE./\n"
"&XXDATA \n"
" XXREAL = 1., \n"
" XXINTEGER = 2, \n"
" XXCOMPLEX = (3.,4.)/")
namelist_dict = namelist2dict(StringIO(groups))
self.assertEqual(namelist_dict, {
"TTDATA": [{
"TTREAL": 1.0,
"TTINTEGER": 2,
"TTCOMPLEX": 3.0 + 4.0j,
"TTCHAR": "namelist",
"TTBOOL": True}],
"AADATA": [{
"AAREAL": [1.0, 1.0, 2.0, 3.0],
"AAINTEGER": [2, 2, 3, 4],
"AACOMPLEX": [3.0 + 4.0j, 3.0 + 4.0j, 5.0 + 6.0j, 7.0 + 7.0j],
"AACHAR": ["namelist", "namelist", "array", " the lot"],
"AABOOL": [True, True, False, False]}],
"XXDATA": [{
"XXREAL": 1.0,
"XXINTEGER": 2,
"XXCOMPLEX": 3.0 + 4.0j}]})
if __name__ == '__main__':
unittest.main()

Thanks for creating and sharing this module. I am using it (with a few modifications) to process namelists for use with the NEMO ocean modeling code (http://www.nemo-ocean.eu/).

My modifications have been pushed to my fork of this gist at https://gist.github.com/douglatornell/10020346. Each is in a separate commit. Feel free to merge any that you feel are appropriate. Details of my mods and my rationale for them are below.

  1. Handle double quoted strings - both ' and " are valid string delimiters in gfortran f90 and intel f90
  2. Handle empty string as values - empty strings are strings too :-)
  3. Handle &end as group ending token - both / and &end are valid ways of sending a namelist in gfortran f90 and intel f90
  4. Ignore empty groups instead of raising a ValueError - This is important to the way we manage our NEMO namelists, but may or may not be appropriate as a default behaviour. I suppose it could be implemented under the control of a kwarg passed into namelist2dict().
  5. Relax restriction that all elements of a list assignment must be of the same type; Python lists are heterogeneous - NEMO definitely has a use case in which the value in the namelist is a comma-separated list of values of various types, and that works fine as a Python list in the namelist dict.
  6. Add array element assignments - Assignments like foo(1) = 42 are valid in gfortran f90 and intel f90 and are a use case in NEMO namelists.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment