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#!/usr/bin/env python
# File created on 15 Feb 2010
from __future__ import division
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Release"
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.util import make_option
import os
from string import replace
import types
import re
from sys import exit, stderr
options_lookup = get_options_lookup()
rst_text= \
'''\
.. _%s:
.. index:: %s.py
*%s.py* -- %s
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
%s
**Usage:** :file:`%s.py [options]`
**Input Arguments:**
.. note::
%s
**Output:**
%s
%s
'''
script_info={}
script_info['brief_description']="""Make Sphinx RST file"""
script_info['script_description'] = """This script will take a script file and convert the \
usage strings and options to generate a documentation .rst file."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example:""","""""","""make_qiime_rst_file.py -i make_2d_plots.py -o doc/"""))
script_info['output_description']="""This will output a Sphinx rst-formatted file."""
script_info['required_options'] = [\
# Example required option
make_option('-i','--input_script',help='This is the input script for which to \
make a .rst file'),
options_lookup['output_dir']
]
script_info['version'] = __version__
def convert_py_file_to_link(input_str):
m=re.compile('[\w]+\.py')
python_script_names=set(m.findall(input_str))
if python_script_names:
script_w_link=input_str
for i in python_script_names:
individual_script_name=os.path.splitext(i)
script_w_link=script_w_link.replace(i, '`'+ i + ' <./' + \
individual_script_name[0] + '.html>`_')
return script_w_link
else:
return input_str
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
#Determine if the input is a directory containing python scripts or a single
#file and then create a list of those scripts
if os.path.isdir(opts.input_script):
file_names = os.listdir(opts.input_script)
#Only take files which do not start with "." and end with a ".py"
file_names = [fname for fname in file_names if not \
fname.startswith('.') and fname.endswith('.py')]
elif os.path.isfile(opts.input_script):
file_names=[str(opts.input_script)]
else:
print("io error, input path not valid. Does it exist?")
exit(1)
#Identify the directory where results should be written.
dir_path = opts.output_dir
if dir_path and not dir_path.endswith('/'):
dir_path = dir_path + '/'
script={}
#Iterate through list of filenames
for file in file_names:
#Get only the name of the script and remove other path information.
file=file.split('/')[-1]
file=file.split('.')[0]
#Import the script file to get the dictionary values
try:
script=__import__(file)
except ValueError:
print "Error"
#print script.__maintainer__
#Define output file path
outf=os.path.join(dir_path,file+'.rst')
#This try block attempts to parse the dictionary and if the dictionary
#is not present, then it will write that information to stdout
try:
imported_brief_description=script.script_info['brief_description']
imported_script_description=script.script_info['script_description']
new_script_description = \
convert_py_file_to_link(imported_script_description)
#print new_script_description
inputs=''
if script.script_info.has_key('required_options') and \
script.script_info['required_options']<>[]:
inputs= '\t\n\t**[REQUIRED]**\n\t\t\n'
for i in script.script_info['required_options']:
# when no default is provided in the call to make_option,
# the value of i.default is a tuple -- this try/except
# handles the diff types that i.default can be
try:
if i.default<>'':
if i.default[0] == 'NO':
# i.default is a tuple, so defualt hasn't been
# set by the user, and it should therefore be
# None
defaults = None
else:
# i.default is a string
defaults = i.default
else:
defaults=None
except TypeError:
# i.default is not a string or a tuple (e.g., it's an
# int or None)
defaults = i.default
p=re.compile('\%default')
help_str=p.sub(str(defaults),i.help)
new_help_str=convert_py_file_to_link(help_str)
new_help_str=new_help_str[0].upper() + new_help_str[1:]
cmd_arg=str(i).replace('--','`-`-').replace('/',', ')
inputs=inputs+'\t'+str(cmd_arg)+'\n\t\t'+ new_help_str+'\n'
if script.script_info.has_key('optional_options') and \
script.script_info['optional_options']<>[]:
inputs=inputs + '\t\n\t**[OPTIONAL]**\n\t\t\n'
for i in script.script_info['optional_options']:
# when no default is provided in the call to make_option,
# the value of i.default is a tuple -- this try/except
# handles the diff types that i.default can be
try:
if i.default<>'':
if i.default[0] == 'NO':
# i.default is a tuple, so defualt hasn't been
# set by the user, and it should therefore be
# None
defaults = None
else:
# i.default is a string
defaults = i.default
else:
defaults=i.default
except TypeError:
# i.default is not a string or a tuple (e.g., it's an
# int or None)
defaults = i.default
p=re.compile('\%default')
help_str=p.sub(str(defaults),i.help)
new_help_str=convert_py_file_to_link(help_str)
new_help_str=new_help_str[0].upper() + new_help_str[1:]
cmd_arg=str(i).replace('--','`-`-').replace('/',', ')
inputs=inputs+'\t'+str(cmd_arg)+'\n\t\t'+ new_help_str+'\n'
if (not script.script_info.has_key('required_options') and not script.script_info.has_key('optional_options')) or ( script.script_info['required_options']==[] and script.script_info['optional_options']==[]):
inputs='\t\n\tNone'
script_examples=''
for ex in script.script_info['script_usage']:
example_title=ex[0].strip()
if example_title <> '':
if example_title.endswith(':'):
script_examples += '\n**' + ex[0] + '**\n'
else:
script_examples += '\n**' + ex[0] + ':**\n'
if ex[1] <> '':
script_ex=convert_py_file_to_link(ex[1])
script_examples += '\n' + script_ex + '\n'
if ex[2] <>'':
new_cmd=ex[2].replace('%prog',file+'.py')
script_examples += '\n::\n\n\t' + new_cmd + '\n'
script_out = \
script.script_info['output_description'].replace('--','`-`-')
new_script_out=convert_py_file_to_link(script_out)
output_text = rst_text % (file, file, file,
imported_brief_description,
new_script_description, file,
inputs, new_script_out,
script_examples)
###Write rst file
f = open(outf, 'w')
f.write((output_text))
f.close()
#script.close()
except ValueError:
print "%s: This file does not contain the appropriate dictionary" \
% (file)
if __name__ == "__main__":
main()
|
