Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
262 lines
7.8 KiB
262 lines
7.8 KiB
#!/usr/bin/env python3
|
|
"""
|
|
|
|
process_file(filename)
|
|
|
|
takes templated file .xxx.src and produces .xxx file where .xxx
|
|
is .pyf .f90 or .f using the following template rules:
|
|
|
|
'<..>' denotes a template.
|
|
|
|
All function and subroutine blocks in a source file with names that
|
|
contain '<..>' will be replicated according to the rules in '<..>'.
|
|
|
|
The number of comma-separated words in '<..>' will determine the number of
|
|
replicates.
|
|
|
|
'<..>' may have two different forms, named and short. For example,
|
|
|
|
named:
|
|
<p=d,s,z,c> where anywhere inside a block '<p>' will be replaced with
|
|
'd', 's', 'z', and 'c' for each replicate of the block.
|
|
|
|
<_c> is already defined: <_c=s,d,c,z>
|
|
<_t> is already defined: <_t=real,double precision,complex,double complex>
|
|
|
|
short:
|
|
<s,d,c,z>, a short form of the named, useful when no <p> appears inside
|
|
a block.
|
|
|
|
In general, '<..>' contains a comma separated list of arbitrary
|
|
expressions. If these expression must contain a comma|leftarrow|rightarrow,
|
|
then prepend the comma|leftarrow|rightarrow with a backslash.
|
|
|
|
If an expression matches '\\<index>' then it will be replaced
|
|
by <index>-th expression.
|
|
|
|
Note that all '<..>' forms in a block must have the same number of
|
|
comma-separated entries.
|
|
|
|
Predefined named template rules:
|
|
<prefix=s,d,c,z>
|
|
<ftype=real,double precision,complex,double complex>
|
|
<ftypereal=real,double precision,\\0,\\1>
|
|
<ctype=float,double,complex_float,complex_double>
|
|
<ctypereal=float,double,\\0,\\1>
|
|
|
|
"""
|
|
__all__ = ['process_str', 'process_file']
|
|
|
|
import os
|
|
import sys
|
|
import re
|
|
|
|
routine_start_re = re.compile(r'(\n|\A)(( (\$|\*))|)\s*(subroutine|function)\b', re.I)
|
|
routine_end_re = re.compile(r'\n\s*end\s*(subroutine|function)\b.*(\n|\Z)', re.I)
|
|
function_start_re = re.compile(r'\n (\$|\*)\s*function\b', re.I)
|
|
|
|
def parse_structure(astr):
|
|
""" Return a list of tuples for each function or subroutine each
|
|
tuple is the start and end of a subroutine or function to be
|
|
expanded.
|
|
"""
|
|
|
|
spanlist = []
|
|
ind = 0
|
|
while True:
|
|
m = routine_start_re.search(astr, ind)
|
|
if m is None:
|
|
break
|
|
start = m.start()
|
|
if function_start_re.match(astr, start, m.end()):
|
|
while True:
|
|
i = astr.rfind('\n', ind, start)
|
|
if i==-1:
|
|
break
|
|
start = i
|
|
if astr[i:i+7]!='\n $':
|
|
break
|
|
start += 1
|
|
m = routine_end_re.search(astr, m.end())
|
|
ind = end = m and m.end()-1 or len(astr)
|
|
spanlist.append((start, end))
|
|
return spanlist
|
|
|
|
template_re = re.compile(r"<\s*(\w[\w\d]*)\s*>")
|
|
named_re = re.compile(r"<\s*(\w[\w\d]*)\s*=\s*(.*?)\s*>")
|
|
list_re = re.compile(r"<\s*((.*?))\s*>")
|
|
|
|
def find_repl_patterns(astr):
|
|
reps = named_re.findall(astr)
|
|
names = {}
|
|
for rep in reps:
|
|
name = rep[0].strip() or unique_key(names)
|
|
repl = rep[1].replace(r'\,', '@comma@')
|
|
thelist = conv(repl)
|
|
names[name] = thelist
|
|
return names
|
|
|
|
def find_and_remove_repl_patterns(astr):
|
|
names = find_repl_patterns(astr)
|
|
astr = re.subn(named_re, '', astr)[0]
|
|
return astr, names
|
|
|
|
item_re = re.compile(r"\A\\(?P<index>\d+)\Z")
|
|
def conv(astr):
|
|
b = astr.split(',')
|
|
l = [x.strip() for x in b]
|
|
for i in range(len(l)):
|
|
m = item_re.match(l[i])
|
|
if m:
|
|
j = int(m.group('index'))
|
|
l[i] = l[j]
|
|
return ','.join(l)
|
|
|
|
def unique_key(adict):
|
|
""" Obtain a unique key given a dictionary."""
|
|
allkeys = list(adict.keys())
|
|
done = False
|
|
n = 1
|
|
while not done:
|
|
newkey = '__l%s' % (n)
|
|
if newkey in allkeys:
|
|
n += 1
|
|
else:
|
|
done = True
|
|
return newkey
|
|
|
|
|
|
template_name_re = re.compile(r'\A\s*(\w[\w\d]*)\s*\Z')
|
|
def expand_sub(substr, names):
|
|
substr = substr.replace(r'\>', '@rightarrow@')
|
|
substr = substr.replace(r'\<', '@leftarrow@')
|
|
lnames = find_repl_patterns(substr)
|
|
substr = named_re.sub(r"<\1>", substr) # get rid of definition templates
|
|
|
|
def listrepl(mobj):
|
|
thelist = conv(mobj.group(1).replace(r'\,', '@comma@'))
|
|
if template_name_re.match(thelist):
|
|
return "<%s>" % (thelist)
|
|
name = None
|
|
for key in lnames.keys(): # see if list is already in dictionary
|
|
if lnames[key] == thelist:
|
|
name = key
|
|
if name is None: # this list is not in the dictionary yet
|
|
name = unique_key(lnames)
|
|
lnames[name] = thelist
|
|
return "<%s>" % name
|
|
|
|
substr = list_re.sub(listrepl, substr) # convert all lists to named templates
|
|
# newnames are constructed as needed
|
|
|
|
numsubs = None
|
|
base_rule = None
|
|
rules = {}
|
|
for r in template_re.findall(substr):
|
|
if r not in rules:
|
|
thelist = lnames.get(r, names.get(r, None))
|
|
if thelist is None:
|
|
raise ValueError('No replicates found for <%s>' % (r))
|
|
if r not in names and not thelist.startswith('_'):
|
|
names[r] = thelist
|
|
rule = [i.replace('@comma@', ',') for i in thelist.split(',')]
|
|
num = len(rule)
|
|
|
|
if numsubs is None:
|
|
numsubs = num
|
|
rules[r] = rule
|
|
base_rule = r
|
|
elif num == numsubs:
|
|
rules[r] = rule
|
|
else:
|
|
print("Mismatch in number of replacements (base <%s=%s>)"
|
|
" for <%s=%s>. Ignoring." %
|
|
(base_rule, ','.join(rules[base_rule]), r, thelist))
|
|
if not rules:
|
|
return substr
|
|
|
|
def namerepl(mobj):
|
|
name = mobj.group(1)
|
|
return rules.get(name, (k+1)*[name])[k]
|
|
|
|
newstr = ''
|
|
for k in range(numsubs):
|
|
newstr += template_re.sub(namerepl, substr) + '\n\n'
|
|
|
|
newstr = newstr.replace('@rightarrow@', '>')
|
|
newstr = newstr.replace('@leftarrow@', '<')
|
|
return newstr
|
|
|
|
def process_str(allstr):
|
|
newstr = allstr
|
|
writestr = ''
|
|
|
|
struct = parse_structure(newstr)
|
|
|
|
oldend = 0
|
|
names = {}
|
|
names.update(_special_names)
|
|
for sub in struct:
|
|
cleanedstr, defs = find_and_remove_repl_patterns(newstr[oldend:sub[0]])
|
|
writestr += cleanedstr
|
|
names.update(defs)
|
|
writestr += expand_sub(newstr[sub[0]:sub[1]], names)
|
|
oldend = sub[1]
|
|
writestr += newstr[oldend:]
|
|
|
|
return writestr
|
|
|
|
include_src_re = re.compile(r"(\n|\A)\s*include\s*['\"](?P<name>[\w\d./\\]+[.]src)['\"]", re.I)
|
|
|
|
def resolve_includes(source):
|
|
d = os.path.dirname(source)
|
|
with open(source) as fid:
|
|
lines = []
|
|
for line in fid:
|
|
m = include_src_re.match(line)
|
|
if m:
|
|
fn = m.group('name')
|
|
if not os.path.isabs(fn):
|
|
fn = os.path.join(d, fn)
|
|
if os.path.isfile(fn):
|
|
print('Including file', fn)
|
|
lines.extend(resolve_includes(fn))
|
|
else:
|
|
lines.append(line)
|
|
else:
|
|
lines.append(line)
|
|
return lines
|
|
|
|
def process_file(source):
|
|
lines = resolve_includes(source)
|
|
return process_str(''.join(lines))
|
|
|
|
_special_names = find_repl_patterns('''
|
|
<_c=s,d,c,z>
|
|
<_t=real,double precision,complex,double complex>
|
|
<prefix=s,d,c,z>
|
|
<ftype=real,double precision,complex,double complex>
|
|
<ctype=float,double,complex_float,complex_double>
|
|
<ftypereal=real,double precision,\\0,\\1>
|
|
<ctypereal=float,double,\\0,\\1>
|
|
''')
|
|
|
|
def main():
|
|
try:
|
|
file = sys.argv[1]
|
|
except IndexError:
|
|
fid = sys.stdin
|
|
outfile = sys.stdout
|
|
else:
|
|
fid = open(file, 'r')
|
|
(base, ext) = os.path.splitext(file)
|
|
newname = base
|
|
outfile = open(newname, 'w')
|
|
|
|
allstr = fid.read()
|
|
writestr = process_str(allstr)
|
|
outfile.write(writestr)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|
|
|