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Copy pathMF_create_example_docs.py
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210 lines (127 loc) · 4.97 KB
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import os
import shutil
import shlex
import subprocess
import glob
import re
import itertools
from glob import glob as Glob
from os.path import join as Join
from Cheetah.Template import Template
import mreorg
from morphforge.core.mgrs.locmgr import LocMgr
root = os.path.normpath( os.path.join( LocMgr.get_root_path(), "..") )
examples_src_dir = os.path.join(root, "src/morphforgeexamples/")
#"/home/michael/hw/morphforge/doc"
doc_src_dir = os.path.normpath( os.path.join(root, "doc") )
examples_dst_dir = os.path.join(root, "doc/srcs_generated_examples")
examples_dst_dir_images = os.path.join(root, "doc/srcs_generated_examples/images/")
examples_build_dir = os.path.join( LocMgr.get_tmp_path(), "mf_doc_build")
examples_build_dir_image_out = os.path.join( examples_build_dir, "images/")
dirs = ['morphology', 'singlecell_simulation', 'multicell_simulation', 'advanced_examples']#, 'assorted' ]
example_subdirs = [ d for d in os.listdir(examples_src_dir) if d.startswith("""exset""") ]
dirs = sorted(example_subdirs)
example_srcs = list( itertools.chain( *[ sorted(Glob( Join(examples_src_dir, dir) + "/*.py") ) for dir in dirs] ) )
def clear_directory(d):
if os.path.exists(d):
shutil.rmtree(d)
os.mkdir(d)
def parse_src_file(filename, docstring):
d = open(filename, 'r').read()
# Remove copyright notice:
d = re.split("""[#]\s?[-]+""", d)[-1]
# Remove the docstring:
if docstring is not None:
raw_docstring = r'''"""\s*%s\s*"""''' % re.escape(docstring).strip()
d = re.sub(raw_docstring, '', d, re.MULTILINE)
return d
rstTmpl = """
$title
$titleunderline
$docstring
Code
~~~~
.. code-block:: python
$code
#if $figures
Figures
~~~~~~~~
#for $im in $figures
.. figure:: $im
:width: 3in
:figwidth: 4in
Download :download:`Figure <$im>`
#end for
#end if
Output
~~~~~~
.. code-block:: bash
$output
"""
def make_rst_output(index, examples_filename, src_code, output_images, docstring, output):
name_short = os.path.split(examples_filename)[1]
name_short = os.path.splitext(name_short)[0]
# Copy the image files accross:
im_names = []
for im in output_images:
im_newName = os.path.join(examples_dst_dir_images, "%s_%s"%(name_short, os.path.split(im)[-1]))
shutil.copyfile(im, im_newName)
im_newName_short = im_newName.replace(doc_src_dir, "") #/home/michael/hw/morphforge/doc", "")
im_names.append(im_newName_short)
title = [ l.strip() for l in docstring.split(".")[0].split("\n") if l.strip() ] [0] if docstring else None
title = title or '<Missing Docstring>'
# Prefix the title:
title = "%d. "%(index+1) +title
# Create the rst:
context = {
'title':title,
'titleunderline':"="*len(title),
'docstring': docstring,
'code' : "\n".join( ["\t"+l for l in src_code.split("\n")] ),
'figures':im_names,
'output' : "\n".join( ["\t"+l for l in output.split("\n")] ),
}
s = Template(rstTmpl, context).respond()
op_rst_filename = os.path.join( examples_dst_dir, name_short+".rst")
with open(op_rst_filename, 'w') as fOut:
fOut.write(s)
saveCodeTmpl = """
import matplotlib
import pylab
for fig_num, fig_mgr in matplotlib._pylab_helpers.Gcf.figs.iteritems():
matplotlib._pylab_helpers.Gcf.set_active(fig_mgr)
pylab.savefig("{{OUTDIR}}out%d.png" % fig_num, facecolor='lightgrey')
"""
def run_example(index, filename):
print 'Running Example:', filename
newFilename = os.path.join( examples_build_dir, os.path.split(filename)[1] )
# Clear the directory
clear_directory(examples_build_dir)
clear_directory(examples_build_dir_image_out)
#Create the python file to run:
with open(newFilename, 'w') as fOut:
fOut.write( open(filename).read() )
saveCode = saveCodeTmpl.replace("{{OUTDIR}}", examples_build_dir_image_out)
fOut.write(saveCode)
# run the file, and capture the output:
# Turn off plotting:
env = os.environ.copy()
env['MREORG_BATCHRUN'] = "True"
args = shlex.split("""python %s"""%newFilename)
#print 'Launching child process', args
result = subprocess.check_output(args, stderr=subprocess.STDOUT, env=env)
# Split the output to get at the docstring:
output = result
docstring = mreorg.utils.extract_docstring_from_fileobj( open(filename))
# Get the images:
images = glob.glob(examples_build_dir_image_out + "/*")
# Clean up the source code:
src_code = parse_src_file(filename, docstring)
# Create the Output RST File:
make_rst_output( index=index, examples_filename=filename, src_code=src_code, output_images=images, docstring=docstring, output=output)
# Start with an empty directory:
clear_directory(examples_dst_dir)
clear_directory(examples_dst_dir_images)
for index, fName in enumerate(example_srcs):
fName_full = os.path.join(examples_src_dir, fName)
run_example(index, fName_full)