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#!/usr/bin/env python3
#
# Copyright (C) 2008 Tobias Wolf <towolf@tuebingen.mpg.de>
#
# Copyright (C) 2018 Justin Ales <justin.ales@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
"""
PTB-wikify-into-files.py: Extract help strings in .m-files and write help into files
Supports markdown and mediawiki outputs.
Usage: PTB-wikify-into-files.py [options] ([m-files]|[directory])
Options:
-h, --help
-o [dir], --output-dir Output directory to write files into.
-f [format], --format Output file format, can be either markdown (default), or mediawiki
-r, --recursive Recursive mode: use only with a single directory
-m, --mexmode Mex mode: also look for .mexmaci files and post their
help strings by calling MATLAB and running them
In recursive mode both M and Mex files are posted.
(edit the source to change _mexext into one of
.mexglx, .mexmaci, or .dll)
-g, --opengl Do generate documentation for PsychOpenGL folder as well.
By default, docs for glXXX() functions in PsychOpenGL/MOGL/
are not generated, as there are too many of them for the
GitHub Wiki to handle them.
-v be verbose (massive text output)
this prints out:
- which files were skipped
- a diff of the text before submission
This script is designed to work with a GitHub wiki. GitHub exposes its wiki as
git repository with each page corresponding to a file. This script will write
out all files into a directory that can be pushed into the wiki repository to
update the wiki.
Examples:
This is currently kind of tricky to use because care must be taken with the 2
separate git repositories, the wiki and the code. The script should be run from
the Psychtoolbox root directory and give an path to an output directory outside
the psychtoolbox directory.
Example to, Clone the wiki, than extract files from PsychBasic,
than push changes back onto wiki:
cd ~/git
git clone https://github.com/Psychtoolbox-3/psychtoolbox-3.github.com.git
cd /path/to/Psychtoolbox
PTB-wikify-into-files.py -m -o ~/git/psychtoolbox-3.github.com/docs/ PsychBasic/*.m
cd ~/git/Psychtoolbox-3.wiki
git add -A
git commit -m "Update Message"
git push
Typical invocation to update the docs:
cd /path/to/Psychtoolbox
../managementtools/PTB-wikify-into-files.py -r -m -o ~/git/psychtoolbox-3.github.com/docs/ ./;
For kleinerm:
../managementtools/PTB-wikify-into-files.py -r -m -o ~/projects/OpenGLPsychtoolbox/psychtoolbox-3.github.com/docs/ ./
Alternatively recursively add all files in the directory:
PTB-wikify-into-files.py -r -m -o ~/git/psychtoolbox-3.github.com/docs/ PsychBasic/
Example script that outputs entire PTB tree:
cd /path/to/Psychtoolbox
../managementtools/PTB-wikify-into-files.py -m -o ~/git/psychtoolbox-3.github.com/docs/ *.m;
IMPORTANT!!:
Always change your working directory to the root of the
tree before running the script, e.g.,
cd Psychtoolbox
~/PTB-wikify-into-files.py -r PsychDemos/PsychExampleExperiments
(This is to figure out what the root node is supposed to be.)
"""
import sys, os, re, subprocess
import getopt
import textwrap
outputdir = "./"
_recursive = 0
_mexmode = 0
_ignoreOpenGL = 1
outputFormat = "markdown"
from sys import platform
if platform == "linux" or platform == "linux2":
# linux
_mexext = '.mexa64'
elif platform == "darwin":
# OS X
_mexext = '.mexmaci64'
elif platform == "win32":
# Windows...
_mexext = '.mexmw64'
_debug = 0
_fulldiff = 0
# This version writes files instead of directly posting onto website.
#Format a string for making a link in different markdown dialects
def formatLinkText(*args):
if len(args)==1:
label=args[0]
link=args[0]
elif len(args)==2:
label=args[0]
link=args[1]
if outputFormat == "markdown":
formattedText = "["+label + "](" + link + ")"
elif outputFormat == "mediawiki":
formattedText = "[["+link+"|"+label+"]]"
return formattedText
#Function to split a path into each different directory.
def splitall(path):
allparts = []
while 1:
parts = os.path.split(path)
if parts[0] == path: # sentinel for absolute paths
allparts.insert(0, parts[0])
break
elif parts[1] == path: # sentinel for relative paths
allparts.insert(0, parts[1])
break
else:
path = parts[0]
allparts.insert(0, parts[1])
return allparts
def parse(filename):
'''Parse helpful initial comment block from .m-file'''
docstring = []
functionellipsized = False
for line in open(filename,'r',newline=None):
# weird hack
if line.strip()[0:8] + line.strip()[-3:] == 'function...':
functionellipsized = True
if line.strip().startswith('%'): # get comment lines
docstring.append(line)
elif len(docstring): break # and stop after one block
# we allow empty lines and the function def before the block
elif len(line.strip()) > 0 \
and not line.strip().startswith('function')\
and not functionellipsized: break
# strip first two chars: '% '
return textwrap.dedent(''.join([l[1:] for l in docstring]))
def beackern(mkstring, doLinks):
'''Regex cleaning of PTB docstrings'''
# expand tabs to four spaces
mkstring = mkstring.expandtabs(4)
# Enclose text markup characters with: ""
#mkstring = re.sub(r'(\+\+|(--){2}\b|==|\'\'|@@|[^:]//|>>|<<|##)',r'""\1""',mkstring)
# escape markdown characters with \
mkstring = re.sub(r'(#|\*|_|>)',r'\\\1',mkstring)
#Double new lines for to break lines for markdown.
# mkstring = re.sub(r'(\n)',r'\n\n',mkstring)
# Replace 'Windows: ______' with headline
mkstring = re.sub(r'(?m)^(.*):\s*[_-]{3,}',r'# \1',mkstring)
# Replace long _______ with ---- i.e.<HR>
mkstring = re.sub(r'(?m)^\s*_{10,}',r'----',mkstring)
# Replace some non-WikiWord function to internal links
match = r'(\bScreen\b|' \
+ r'\bAsk\b|' \
+ r'\bBandpass\b|' \
+ r'\bBeeper\b|' \
+ r'\bCircle\b|' \
+ r'\bClose\b|' \
+ r'\bComputeDKL_M\b|' \
+ r'\bDKLDemo\b|' \
+ r'\bEllipse\b|' \
+ r'\bExpand\b|' \
+ r'\bExplode\b|' \
+ r'\bFlip\b|' \
+ r'\bGestalt\b|' \
+ r'\bGStreamer\b|' \
+ r'\bInterleave\b|' \
+ r'\bM_PToP\b|' \
+ r'\bM_PToT\b|' \
+ r'\bM_TToP\b|' \
+ r'\bM_TToT\b|' \
+ r'\bOSAUCSTest\b|' \
+ r'\bOSName\b|' \
+ r'\bPriority\b|' \
+ r'\bPsychometric\b|' \
+ r'\bQuest\b|' \
+ r'\bRandi\b|' \
+ r'\bRanint\b|' \
+ r'\bReplace\b|' \
+ r'\bResolute\b|' \
+ r'\bRush\b|' \
+ r'\bSample\b|' \
+ r'\bScale\b|' \
+ r'\bShuffle\b|' \
+ r'\bSnd\b|' \
+ r'\bStopwatch\b|' \
+ r'\bTrunc\b|' \
+ r'\bXYZTouv\b|' \
+ r'\bhexstr\b|' \
+ r'\bmoglmorpher\b|' \
+ r'\bpsychassert\b|' \
+ r'\bpsychlasterror\b|' \
+ r'\bpsychrethrow\b|' \
+ r'\bsca\b|' \
+ r'\buvTols\b|' \
+ r'\buvToxy\b|' \
+ r'\buvYToXYZ\b|' \
+ r'\bxyTouv\b|' \
+ r'\bxyYToXYZ\b|' \
+ r'\blog10nw\b|' \
+ r'\bPreference\b)'
if doLinks:
if outputFormat == "markdown":
mkstring = re.sub(match,r'[\1](\1)',mkstring)
elif outputFormat == "mediawiki":
mkstring = re.sub(match,r'[[\1|\1]]',mkstring)
#Add links for any word using UpperCamelCase: e.g. PsychHID
#BUT does NOT match any string stating wiht ' e.g. 'OpenWindow'
#Because we don't want subfunctions/strings to trigger page links
#WARNING:
#This is a pretty crazy regex to . Cobled together from lots of
#web searches and tests. Probably not very robust but gets most of the job done.
UpperCamelMatch = r'(?<!\')(?:\(|\b)[A-Z]([A-Z0-9]*[a-z][a-z0-9]*[A-Z]|[a-z0-9]*[A-Z][A-Z0-9]*[a-z])[A-Za-z0-9]*(?:\)|\b)(?!\')'
#r'(?<!\')[A-Z]([A-Z0-9]*[a-z][a-z0-9]*[A-Z]|[a-z0-9]*[A-Z][A-Z0-9]*[a-z])[A-Za-z0-9]*'
if outputFormat == "markdown":
mkstring = re.sub(UpperCamelMatch,r'[\g<0>](\g<0>)',mkstring)
elif outputFormat == "mediawiki":
mkstring = re.sub(UpperCamelMatch,r'[[\g<0>|\g<0>]]',mkstring)
# purge useless help lines
mkstring = re.sub(r'(?m)^.*triple-click me & hit enter.*$\n','',mkstring)
# Generate more headlines (Word:$, CAPITAL LETTERS$, etc)
mkstring = re.sub(r'(?m)((?<=\n\n).+:((?=\s*\n\n)+))', r'### \1',mkstring)
mkstring = re.sub('(?m)((?<=\n\n)\ *[A-Z][A-Z :!-]+\ *(?=\n))', r'### \1',mkstring)
#media wiki interprets whitespace at beggining of line as code block
if outputFormat == "mediawiki":
mkstring = re.sub(r'^\s+','',mkstring,flags=re.M)
if outputFormat == "markdown":
# Add double space after lines for markdown to keep paragraph togethr
mkstring = re.sub(r'(\n)',r' \n',mkstring)
elif outputFormat == "mediawiki":
#Add manual linebreaks to preserve formatting
mkstring = re.sub(r'(\n)',r'<br />\n',mkstring)
return mkstring
def writeFiles(outputDir,files):
''' create pages for all files in there and link to the category'''
for name in files:
from pathlib import Path
#Get absolute path for checking file parent.
absPath = os.path.abspath(name)
category = Path(Path(absPath).parent).stem
# single out some names
head, basename = os.path.split(name)
root = os.path.join(os.path.basename(os.getcwd()))
path = os.path.normpath(os.path.join(root,head))
funcname, ext = os.path.splitext(basename)
cattext = ''
mexname = os.path.join(os.path.split(absPath)[0],funcname+_mexext)
mexSuccess = True
if not os.path.exists(name) or not ext=='.m':
if _mexmode and ext == _mexext:
mexSuccess = mexhelpextract(outputDir,[funcname])
if mexSuccess:
continue
else:
name = os.path.join(head,funcname + '.m')
if os.path.exists(name):
print('No help in mexfile. Trying m file: ' + name )
else:
print('Skipping because cannot find help in mex or mfile for: ' + os.path.join(head, basename))
continue
#If mexmode is on and mex file exists skip the .m file
if mexSuccess and (_mexmode and os.path.exists(mexname)):
print('Mex file exists. skipping m file: ' + name )
continue
if basename=='Contents.m' or basename=='contents.m':
funcname = category
# path = os.path.dirname(path)
# #Sooo Kludgy. SHould update directory parsing.
# if len(path) < 3:
# funcname = 'Psychtoolbox'
cattext = '{{category}}'
# load and build the text for the page
headline = "# " + formatLinkText(funcname)+ "\n"
breadcrumb = "##### "
dirnames = splitall(path)
for dirname in dirnames:
breadcrumb = breadcrumb + ">" + formatLinkText(dirname)
breadcrumb = breadcrumb + "\n\n"
# read the .m-file and strip all the crap
docstring = parse(name)
# scrub the text real good, to get us some nice wiki formatting
if docstring:
body = beackern(docstring, 1)
else:
body = 'This function is not yet documented.\n\n\n MissingDocs'
pathlinks = """
<div class="code_header" style="text-align:right;">
<span style="float:left;">Path </span> <span class="counter">Retrieve <a href=
"https://raw.github.com/Psychtoolbox-3/Psychtoolbox-3/beta/%s">current version from GitHub</a> | View <a href=
"https://github.com/Psychtoolbox-3/Psychtoolbox-3/commits/beta/%s">changelog</a></span>
</div>
<div class="code">
<code>%s</code>
</div>
"""% tuple([os.path.join(path,basename)]*3)
text = headline \
+ breadcrumb \
+ body \
+ '\n\n\n' \
+ textwrap.dedent(pathlinks) \
+ '\n' \
+ cattext
if outputFormat == "markdown":
suffix = '.md'
elif outputFormat == "mediawiki":
suffix = '.wiki'
wikiFileName = os.path.join(outputDir,funcname + suffix)
print("writing file %s"%wikiFileName)
f = open(wikiFileName,"w+")
f.write(text)
def parseMexExtract(filename):
from collections import defaultdict
sectionPattern = re.compile(r'\[section:(.*?)\]')
keyPattern = re.compile(r'\[key:(.*?)\]')
extractedText = defaultdict(lambda: defaultdict(str))
with open(filename) as toParse:
for line in toParse:
sectionMatch = sectionPattern.match(line)
keyMatch = keyPattern.match(line)
if sectionMatch:
sectionName = sectionMatch.groups()[0]
elif keyMatch:
keyName = keyMatch.groups()[0]
else:
extractedText[sectionName][keyName]=extractedText[sectionName][keyName]+line
return extractedText
def formatUsage(usage,mexname,subfunctions):
if outputFormat == "markdown":
# Add double space after lines for markdown to keep paragraph togethr
usage = re.sub(r'(\n)',r' \n',usage)
elif outputFormat == "mediawiki":
#Add manual linebreaks to preserve formatting
usage = re.sub(r'(\n)',r'<br />\n',usage)
#Now parse the usage block to add links to sub function help
#Looking for pattern: mexfile('subfunc'
for subFuncName,subFuncText in subfunctions.items():
if outputFormat == "markdown":
usage = re.sub( \
mexname+'\(\'' +subFuncName + '\'', \
mexname+'(\'[' + subFuncName + '](' + mexname + '-' + subFuncName + ')\'', \
usage)
elif outputFormat == "mediawiki":
usage = re.sub( \
mexname+'\(\'' +subFuncName + '\'', \
mexname+'(\'[[' + mexname + '-' + subFuncName + '|' + subFuncName + ']]\'', \
usage)
return usage
def mexhelpextract(outputDir,mexnames):
#print 'processing mex files: ' + mexnames.__repr__()
mexHelpSuccess = True
for mexname in mexnames:
# First build help text for mex.
# assemble command line for matlab
matlabcmd = 'addpath(\'%s\');%s(\'%s\',\'%s\'); exit' % \
(_tmpdir, \
os.path.splitext(os.path.basename(_mexscript))[0], \
mexname, \
_tmpdir)
# and execute Octave or Matlab w/ the temporary script we wrote earlier
try:
# Try Octave first:
cmd = 'octave --no-history --no-window-system --silent --no-gui --eval "%s" > /dev/null' % matlabcmd
print('running OCTAVE for %s in %s' % (mexname,_tmpdir))
p = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE,
stderr=subprocess.STDOUT, close_fds=True)
stderr = p.communicate()[1]
if stderr: print(stderr)
except:
# Failed: Try Matlab:
try:
cmd = 'matlab -nojvm -nodisplay -r "%s" > /dev/null' % matlabcmd
print('running MATLAB for %s in %s' % (mexname,_tmpdir))
p = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE,
stderr=subprocess.STDOUT, close_fds=True)
stderr = p.communicate()[1]
if stderr: print(stderr)
except:
print('could not dump help for %s into %s.' % (mexname,_tmpdir))
mexDumpName = os.path.join(_tmpdir,mexname);
if not os.path.isfile(mexDumpName):
print("skipping " + mexname + " (no output)")
mexHelpSuccess = False
continue
# Parse the mex dumped file using the following format:
# [Section:SubFunction]
# [key:usage]
# usage text
# [key:help]
# help text
# [key:seealso]
# see also text
subfunctions = parseMexExtract(mexDumpName)
subFuncList = ''
for key in subfunctions:
subFuncList = subFuncList + ', ' + key
print('processing subfunctions: ' + subFuncList)
for subFuncName,subFuncText in subfunctions.items():
# read in the strings for this subfunction
usage = subFuncText['usage']
help = subFuncText['help']
seealso = subFuncText['seealso']
headline = '# ['+mexname+'(\''+subFuncName+'\')](' \
+ mexname + '-' + subFuncName + ') ' + '\n'
breadcrumb = "##### " + formatLinkText('Psychtoolbox','Psychtoolbox') + ">" \
+ formatLinkText(mexname) + ".{mex*} subfunction\n\n"
if subFuncName == '__main__':
usage = formatUsage(usage,mexname,subfunctions)
headline = "# " + formatLinkText(mexname,mexname) + "\n"
breadcrumb = "##### " + formatLinkText('Psychtoolbox','Psychtoolbox') + ">" \
+ formatLinkText(mexname) + "\n\n"
# Scrub the text for main help text of mex file only - without keyword substitution for main function help:
body = beackern(help, 0)
else:
# Scrub the text for main help text of subfunction only - with keyword substitution:
body = beackern(help, 1)
# docstring = '' \
# + '%%(matlab;Usage)' \
# + usage \
# + '%%\n' \
# + body \
# + '\n\n'
docstring = '' \
+ usage \
+ '\n' \
+ body \
+ '\n\n'
if seealso:
#Add links for any word using UpperCamelCase: e.g. PsychHID
#BUT does NOT match any string stating wiht ' e.g. 'OpenWindow'
#Because we don't want subfunctions/strings to trigger page links
#WARNING:
#This is a pretty crazy regex to . Cobled together from lots of
#web searches and tests. Probably not very robust but gets most of the job done.
UpperCamelMatch = r'(?<!\')(?:\(|\b)[A-Z]([A-Z0-9]*[a-z][a-z0-9]*[A-Z]|[a-z0-9]*[A-Z][A-Z0-9]*[a-z])[A-Za-z0-9]*(?:\)|\b)(?!\')'
#r'(?<!\')[A-Z]([A-Z0-9]*[a-z][a-z0-9]*[A-Z]|[a-z0-9]*[A-Z][A-Z0-9]*[a-z])[A-Za-z0-9]*'
if outputFormat == "markdown":
seealso = re.sub(UpperCamelMatch,r'[\g<0>]('+mexname + '-\g<0>)',seealso)
elif outputFormat == "mediawiki":
seealso = re.sub(UpperCamelMatch,r'[['+mexname + '-\g<0>|\g<0>]]',seealso)
docstring = docstring + '###See also:\n' + seealso
text = headline \
+ breadcrumb \
+ docstring
if outputFormat == "markdown":
suffix = '.md'
elif outputFormat == "mediawiki":
suffix = '.wiki'
outputFilename = os.path.join(outputDir,mexname + '-' + subFuncName + suffix)
if subFuncName == '__main__':
outputFilename = os.path.join(outputDir,mexname + suffix)
print("writing mex help to file: " + outputFilename)
f = open(outputFilename,"w+")
f.write(text)
return mexHelpSuccess
def recursivewalk(outputDir,rootfolder):
'''traverse the root directory and post all .m-files'''
for root, dirs, files in os.walk(rootfolder):
if re.search(os.sep+'\.svn|'+os.sep+'private',root):
continue
if _ignoreOpenGL and re.search(os.sep+'MOGL',root):
continue
print('Entering folder ' + root)
# .m-files are processed with postsinglefiles
mfiles = [os.path.join(root,f) for f in files \
if f.endswith(('.m','.M',_mexext))]
writeFiles(outputDir,mfiles)
print("Exiting: Done with this tree.")
sys.exit(0)
def usage():
print(__doc__)
def main(argv):
try:
opts, args = getopt.getopt(argv, "o:f:hrmvg", \
["help", "output-dir=", "format=", "opengl", "recursive", "mexmode"])
except getopt.GetoptError:
usage()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"):
usage()
sys.exit()
elif opt in ("-o", "--output-dir"):
global outputDir
outputDir = arg
elif opt in ("-f", "--format"):
global outputFormat
print(arg)
if arg.lower() not in ('markdown','mediawiki'):
print('Error: output format must be either markdown or mediawiki\n\n')
sys.exit(1)
outputFormat = arg.lower()
elif opt in ("-r", "--recursive"):
global _recursive
_recursive = 1
elif opt in ("-g", "--opengl"):
global _ignoreOpenGL
_ignoreOpenGL = 0
elif opt in ("-m", "--mexmode"):
import tempfile
global _mexmode, _mexext, _tmpdir, _mexscript
_mexmode = 1
_tmpdir = tempfile.mkdtemp(prefix="PTB-doc-mexfunctionhelp-")
_mexscript = os.path.join(_tmpdir, 'PsychtoolboxMexhelpextract.m')
fid = open(_mexscript, 'w')
script = '''\
function PsychtoolboxMexhelpextract(mexname,tmpdir)
try
subfunctions=eval([mexname '(''DescribeModulefunctionshelper'')']);
catch
subfunctions = [];
end
fid = fopen(fullfile(tmpdir,mexname),'wt');
if fid == -1
return;
end
try
% First extract help for main function, including subfunction list
fprintf(fid,'[section:__main__]\\n');
synopsisText = evalc([mexname ';']);
helpText = help([mexname '.m']);
fprintf(fid,'[key:usage]\\n%s\\n',synopsisText);
fprintf(fid,'[key:help]\\n%s\\n',helpText);
fprintf(fid,'[key:seealso]\\n');
if iscell(subfunctions) && ~isempty(subfunctions)
for i=1:size(subfunctions,2)
fprintf(fid,'[section:%s]\\n',subfunctions{i});
docs = eval([mexname '(''DescribeModulefunctionshelper'',1,subfunctions{i})']);
fprintf(fid,'[key:usage]:\\n%s\\n',docs{1});
fprintf(fid,'[key:help]\\n%s\\n',docs{2});
fprintf(fid,'[key:seealso]\\n%s\\n',docs{3});
end
end
catch
fclose(fid);
return;
end
fclose(fid);
return
'''
fid.write(textwrap.dedent(script))
fid.close()
elif opt == '-v':
global _debug
_debug = 1
if args:
if _recursive:
if len(args) == 1 and os.path.isdir(args[0]):
recursivewalk(outputDir,args[0])
else:
usage()
print('Error: Recursive mode works with one directory only\n\n')
sys.exit(1)
else:
print("Parsing Input: " + str(args[0]) + " writing to: " + outputDir)
writeFiles(outputDir,args)
else:
usage()
print('Error: No files specified to submit to Wiki\n\n')
sys.exit(1)
if __name__ == "__main__":
main(sys.argv[1:])
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