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Issue1071/yapf (#1078)
* Issue #1071: add yapf configuration file * yapf formatting of Code directory * yapf formatting of Contrib directory * yapf formatting of Data directory * yapf formatting of Docs directory * yapf formatting of External directory * yapf formatting of Projects directory * yapf formatting of Regress directory * yapf formatting of Scripts directory * yapf formatting of Web directory * yapf formatting of rdkit directory
This commit is contained in:
gedeck
Greg Landrum
@@ -14,14 +14,18 @@ from BeautifulSoup import *
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import os
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import re
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def list_class_files(dir):
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return [name for name in os.listdir(dir)
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if (name.startswith('class_') and (not name.endswith('png')) and name.find('-members') == -1)]
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return [
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name for name in os.listdir(dir)
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if (name.startswith('class_') and (not name.endswith('png')) and name.find('-members') == -1)
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]
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def get_detail(fname):
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bs = BeautifulSoup(open(fname).read())
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det = bs.find(text='Detailed Description')
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return [bs, det]
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bs = BeautifulSoup(open(fname).read())
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det = bs.find(text='Detailed Description')
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return [bs, det]
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_example = \
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"""int RDKit::Atom::getPerturbationOrder ( INT_LIST probe ) const
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@@ -301,162 +305,168 @@ Notes:
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* the current lazy properties are implicit and explicit valence
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'''
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_renote = re.compile('^\w*(Notes?[:]?)(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL))
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_reparam = re.compile('^\w*(Param(?:eter)?s?[:]?)(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL))
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_renote = re.compile('^\w*(Notes?[:]?)(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL))
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_reparam = re.compile('^\w*(Param(?:eter)?s?[:]?)(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I |
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re.DOTALL))
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_rereturn = re.compile('^\w*(Returns[:])(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL))
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_rereturn2 = re.compile('^\w*(Returns)\s+(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL))
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_reusage = re.compile('^\w*(Usage[:]?)(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL))
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def make_method_doc(doxy_method_text, class_name):
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for f in (do_usage, do_note, do_param, do_return):
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doxy_method_text = f(doxy_method_text)
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# Create paragraphs
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doxy_method_text = doxy_method_text.replace('\n\n', '\n<p>\n')
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# But no paragraph markers just before tag
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doxy_method_text = doxy_method_text.replace('<p>@', '<p>\n@')
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# Get rid of double quotes -- note that this causes an error with initialized string parameters
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doxy_method_text = doxy_method_text.replace('"', "'")
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# Get lines
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lines = doxy_method_text.split('\n')
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# Build header -- don't want type there
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header = lines[0][lines[0].find(class_name):]
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start = 1
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while (header.find(')') < 0):
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start += 1
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header += ' ' + lines[start - 1]
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## print header
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# Or [] annotation
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header = header.replace('[inline]', '')
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header = header.replace('[virtual]', '')
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header = header.replace('[protected]', '')
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header = header.replace('[explicit]', '')
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header = '%javamethodmodifiers ' + header + '"\n/**\n'
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return header + '\n'.join(lines[start:] ) + '\n*/\npublic";\n'
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def make_class_doc(doxy_text, class_name):
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for f in (do_usage, do_note):
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doxy_text = f(doxy_text)
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# Create paragraphs
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doxy_text = doxy_text.replace('\n\n', '\n<p>\n')
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# But no paragraph markers just before tag
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doxy_text = doxy_text.replace('<p>@', '<p>\n@')
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# Get rid of double quotes
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doxy_text = doxy_text.replace('"', "'")
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# Get lines
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lines = doxy_text.split('\n')
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# Build header -- don't want type there
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header = '%typemap(javaimports) ' + class_name + ' "\n/** '
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return header + '\n'.join(lines) + ' */"\n'
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def make_method_doc(doxy_method_text, class_name):
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for f in (do_usage, do_note, do_param, do_return):
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doxy_method_text = f(doxy_method_text)
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# Create paragraphs
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doxy_method_text = doxy_method_text.replace('\n\n', '\n<p>\n')
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# But no paragraph markers just before tag
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doxy_method_text = doxy_method_text.replace('<p>@', '<p>\n@')
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# Get rid of double quotes -- note that this causes an error with initialized string parameters
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doxy_method_text = doxy_method_text.replace('"', "'")
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# Get lines
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lines = doxy_method_text.split('\n')
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# Build header -- don't want type there
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header = lines[0][lines[0].find(class_name):]
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start = 1
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while (header.find(')') < 0):
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start += 1
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header += ' ' + lines[start - 1]
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## print header
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# Or [] annotation
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header = header.replace('[inline]', '')
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header = header.replace('[virtual]', '')
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header = header.replace('[protected]', '')
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header = header.replace('[explicit]', '')
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header = '%javamethodmodifiers ' + header + '"\n/**\n'
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return header + '\n'.join(lines[start:]) + '\n*/\npublic";\n'
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def make_class_doc(doxy_text, class_name):
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for f in (do_usage, do_note):
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doxy_text = f(doxy_text)
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# Create paragraphs
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doxy_text = doxy_text.replace('\n\n', '\n<p>\n')
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# But no paragraph markers just before tag
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doxy_text = doxy_text.replace('<p>@', '<p>\n@')
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# Get rid of double quotes
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doxy_text = doxy_text.replace('"', "'")
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# Get lines
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lines = doxy_text.split('\n')
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# Build header -- don't want type there
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header = '%typemap(javaimports) ' + class_name + ' "\n/** '
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return header + '\n'.join(lines) + ' */"\n'
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def do_note(doxy_text):
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m1 = _renote.search(doxy_text)
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if m1 != None:
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repl = m1.group(0)
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if repl[-1] != '\n':
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repl = repl[:-1]
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new_text = '<p>@notes\n'
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for line in m1.group(2).split('\n'):
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line = line.strip()
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if len(line) > 0:
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if line.startswith('*'):
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line = line[1:].strip()
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new_text = new_text + '<li>' + line + '\n'
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doxy_text = doxy_text.replace(repl, new_text)
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return doxy_text
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m1 = _renote.search(doxy_text)
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if m1 != None:
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repl = m1.group(0)
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if repl[-1] != '\n':
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repl = repl[:-1]
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new_text = '<p>@notes\n'
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for line in m1.group(2).split('\n'):
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line = line.strip()
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if len(line) > 0:
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if line.startswith('*'):
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line = line[1:].strip()
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new_text = new_text + '<li>' + line + '\n'
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doxy_text = doxy_text.replace(repl, new_text)
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return doxy_text
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def do_param(doxy_text):
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m1 = _reparam.search(doxy_text)
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if m1 != None:
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repl = m1.group(0)
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if repl[-1] != '\n':
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repl = repl[:-1]
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new_text = '<p>@param\n'
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for line in m1.group(2).split('\n'):
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line = line.strip()
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if len(line) > 0:
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new_text = new_text + line + '\n'
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doxy_text = doxy_text.replace(repl, new_text)
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return doxy_text
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m1 = _reparam.search(doxy_text)
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if m1 != None:
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repl = m1.group(0)
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if repl[-1] != '\n':
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repl = repl[:-1]
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new_text = '<p>@param\n'
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for line in m1.group(2).split('\n'):
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line = line.strip()
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if len(line) > 0:
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new_text = new_text + line + '\n'
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doxy_text = doxy_text.replace(repl, new_text)
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return doxy_text
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def do_return(doxy_text):
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m1 = _rereturn.search(doxy_text)
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if m1 == None:
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m1 = _rereturn2.search(doxy_text)
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if m1 != None:
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repl = m1.group(0)
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if repl[-1] != '\n':
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repl = repl[:-1]
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new_text = '<p>@return\n'
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for line in m1.group(2).split('\n'):
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line = line.strip()
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if len(line) > 0:
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new_text = new_text + line + '\n'
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doxy_text = doxy_text.replace(repl, new_text)
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return doxy_text
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m1 = _rereturn.search(doxy_text)
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if m1 == None:
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m1 = _rereturn2.search(doxy_text)
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if m1 != None:
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repl = m1.group(0)
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if repl[-1] != '\n':
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repl = repl[:-1]
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new_text = '<p>@return\n'
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for line in m1.group(2).split('\n'):
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line = line.strip()
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if len(line) > 0:
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new_text = new_text + line + '\n'
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doxy_text = doxy_text.replace(repl, new_text)
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return doxy_text
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def do_usage(doxy_text):
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m1 = _reusage.search(doxy_text)
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if m1 != None:
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repl = m1.group(0)
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if repl[-1] != '\n':
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repl = repl[:-1]
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new_text = '<p>@example\n<pre><code>\n'
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for line in m1.group(2).split('\n'):
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new_text = new_text + line + '\n'
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## doxy_text = _reusage.sub(new_text, doxy_text) + '</code></pre>\n'
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new_text += '</code></pre>\n'
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doxy_text = doxy_text.replace(repl, new_text)
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return doxy_text
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m1 = _reusage.search(doxy_text)
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if m1 != None:
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repl = m1.group(0)
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if repl[-1] != '\n':
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repl = repl[:-1]
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new_text = '<p>@example\n<pre><code>\n'
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for line in m1.group(2).split('\n'):
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new_text = new_text + line + '\n'
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## doxy_text = _reusage.sub(new_text, doxy_text) + '</code></pre>\n'
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new_text += '</code></pre>\n'
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doxy_text = doxy_text.replace(repl, new_text)
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return doxy_text
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def do_methods(doxy_text, class_name):
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methods = []
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method_lines = []
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in_method_region = False
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for line in doxy_text.split('\n'):
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if line.find('Function Documentation') >= 0:
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in_method_region = True
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elif in_method_region:
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if line.find(class_name) >= 0 or line.find('Member Data') >= 0:
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if len(method_lines) > 0:
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methods.append(make_method_doc('\n'.join(method_lines), class_name))
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if line.find('Member Data') >= 0:
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in_method_region = False
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else:
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method_lines = [line]
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else:
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method_lines.append(line)
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if len(method_lines) > 0:
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methods.append(make_method_doc('\n'.join(method_lines), class_name))
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method_lines = [line]
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return methods
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def do_class(doxy_text, class_name):
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in_class_region = False
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class_doc = ''
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for line in doxy_text.split('\n'):
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if line.find('Detailed Description') >= 0:
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in_class_region = True
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class_lines = []
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elif in_class_region:
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if line.strip().endswith('Documentation') :
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if len(class_lines) > 0:
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class_doc = make_class_doc('\n'.join(class_lines), class_name)
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in_class_region = False
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else:
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class_lines.append(line)
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return class_doc
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def do_methods(doxy_text, class_name):
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methods = []
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method_lines = []
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in_method_region = False
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for line in doxy_text.split('\n'):
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if line.find('Function Documentation') >= 0:
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in_method_region = True
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elif in_method_region:
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if line.find(class_name) >= 0 or line.find('Member Data') >= 0:
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if len(method_lines) > 0:
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methods.append(make_method_doc('\n'.join(method_lines), class_name))
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if line.find('Member Data') >= 0:
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in_method_region = False
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else:
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method_lines = [line]
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else:
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method_lines.append(line)
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if len(method_lines) > 0:
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methods.append(make_method_doc('\n'.join(method_lines), class_name))
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method_lines = [line]
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return methods
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def do_class(doxy_text, class_name):
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in_class_region = False
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class_doc = ''
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for line in doxy_text.split('\n'):
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if line.find('Detailed Description') >= 0:
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in_class_region = True
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class_lines = []
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elif in_class_region:
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if line.strip().endswith('Documentation'):
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if len(class_lines) > 0:
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class_doc = make_class_doc('\n'.join(class_lines), class_name)
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in_class_region = False
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else:
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class_lines.append(line)
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return class_doc
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if __name__ == '__main__':
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import sys
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text = open(sys.argv[1]).read()
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class_name = sys.argv[2]
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print(do_class(text, class_name))
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docs = do_methods(text, class_name)
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for doc in docs:
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print(doc)
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import sys
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text = open(sys.argv[1]).read()
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class_name = sys.argv[2]
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print(do_class(text, class_name))
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docs = do_methods(text, class_name)
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for doc in docs:
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print(doc)
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