# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
==================
RST file generator
==================
Generate the rst files for the examples by iterating over the python
example files.
Files that generate images should start with 'plot'
"""
# Don't use unicode_literals here (be explicit with u"..." instead) otherwise
# tricky errors come up with exec(code_blocks, ...) calls
from __future__ import division, print_function, absolute_import
from time import time
import ast
import codecs
import hashlib
import os
import re
import shutil
import subprocess
import sys
import traceback
import warnings
from .downloads import CODE_DOWNLOAD
# Try Python 2 first, otherwise load from Python 3
from textwrap import dedent
try:
# textwrap indent only exists in python 3
from textwrap import indent
except ImportError:
def indent(text, prefix, predicate=None):
"""Adds 'prefix' to the beginning of selected lines in 'text'.
If 'predicate' is provided, 'prefix' will only be added to the lines
where 'predicate(line)' is True. If 'predicate' is not provided,
it will default to adding 'prefix' to all non-empty lines that do not
consist solely of whitespace characters.
"""
if predicate is None:
def predicate(line):
return line.strip()
def prefixed_lines():
for line in text.splitlines(True):
yield (prefix + line if predicate(line) else line)
return ''.join(prefixed_lines())
from io import StringIO
try:
# make sure that the Agg backend is set before importing any
# matplotlib
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
except ImportError:
# this script can be imported by nosetest to find tests to run: we should
# not impose the matplotlib requirement in that case.
pass
from . import glr_path_static
from .backreferences import write_backreferences, _thumbnail_div
from .notebook import Notebook
try:
basestring
except NameError:
basestring = str
unicode = str
###############################################################################
class Tee(object):
"""A tee object to redirect streams to multiple outputs"""
def __init__(self, file1, file2):
self.file1 = file1
self.file2 = file2
def write(self, data):
self.file1.write(data)
self.file2.write(data)
def flush(self):
self.file1.flush()
self.file2.flush()
# When called from a local terminal seaborn needs it in Python3
def isatty(self):
self.file1.isatty()
class MixedEncodingStringIO(StringIO):
"""Helper when both ASCII and unicode strings will be written"""
def write(self, data):
if not isinstance(data, unicode):
data = data.decode('utf-8')
StringIO.write(self, data)
###############################################################################
# The following strings are used when we have several pictures: we use
# an html div tag that our CSS uses to turn the lists into horizontal
# lists.
HLIST_HEADER = """
.. rst-class:: sphx-glr-horizontal
"""
HLIST_IMAGE_TEMPLATE = """
*
.. image:: /%s
:scale: 47
"""
SINGLE_IMAGE = """
.. image:: /%s
:align: center
"""
# This one could contain unicode
CODE_OUTPUT = u""".. rst-class:: sphx-glr-script-out
Out::
{0}\n"""
SPHX_GLR_SIG = """\n.. rst-class:: sphx-glr-signature
`Generated by Sphinx-Gallery <http://sphinx-gallery.readthedocs.io>`_\n"""
def get_docstring_and_rest(filename):
"""Separate `filename` content between docstring and the rest
Strongly inspired from ast.get_docstring.
Returns
-------
docstring: str
docstring of `filename`
rest: str
`filename` content without the docstring
"""
# can't use codecs.open(filename, 'r', 'utf-8') here b/c ast doesn't
# seem to work with unicode strings in Python2.7
# "SyntaxError: encoding declaration in Unicode string"
with open(filename, 'rb') as f:
content = f.read()
node = ast.parse(content)
if not isinstance(node, ast.Module):
raise TypeError("This function only supports modules. "
"You provided {0}".format(node.__class__.__name__))
if node.body and isinstance(node.body[0], ast.Expr) and \
isinstance(node.body[0].value, ast.Str):
docstring_node = node.body[0]
docstring = docstring_node.value.s
if hasattr(docstring, 'decode'): # python2.7
docstring = docstring.decode('utf-8')
# This get the content of the file after the docstring last line
# Note: 'maxsplit' argument is not a keyword argument in python2
rest = content.decode('utf-8').split('\n', docstring_node.lineno)[-1]
return docstring, rest
else:
raise ValueError(('Could not find docstring in file "{0}". '
'A docstring is required by sphinx-gallery')
.format(filename))
def split_code_and_text_blocks(source_file):
"""Return list with source file separated into code and text blocks.
Returns
-------
blocks : list of (label, content)
List where each element is a tuple with the label ('text' or 'code'),
and content string of block.
"""
docstring, rest_of_content = get_docstring_and_rest(source_file)
blocks = [('text', docstring)]
pattern = re.compile(
r'(?P<header_line>^#{20,}.*)\s(?P<text_content>(?:^#.*\s)*)',
flags=re.M)
pos_so_far = 0
for match in re.finditer(pattern, rest_of_content):
match_start_pos, match_end_pos = match.span()
code_block_content = rest_of_content[pos_so_far:match_start_pos]
text_content = match.group('text_content')
sub_pat = re.compile('^#', flags=re.M)
text_block_content = dedent(re.sub(sub_pat, '', text_content)).lstrip()
if code_block_content.strip():
blocks.append(('code', code_block_content))
if text_block_content.strip():
blocks.append(('text', text_block_content))
pos_so_far = match_end_pos
remaining_content = rest_of_content[pos_so_far:]
if remaining_content.strip():
blocks.append(('code', remaining_content))
return blocks
def codestr2rst(codestr, lang='python'):
"""Return reStructuredText code block from code string"""
code_directive = "\n.. code-block:: {0}\n\n".format(lang)
indented_block = indent(codestr, ' ' * 4)
return code_directive + indented_block
def text2string(content):
"""Returns a string without the extra triple quotes"""
try:
return ast.literal_eval(content) + '\n'
except Exception:
return content + '\n'
def extract_thumbnail_number(text):
""" Pull out the thumbnail image number specified in the docstring. """
# check whether the user has specified a specific thumbnail image
pattr = re.compile(
r"^\s*#\s*sphinx_gallery_thumbnail_number\s*=\s*([0-9]+)\s*$", flags=re.MULTILINE)
match = pattr.search(text)
if match is None:
# by default, use the first figure created
thumbnail_number = 1
else:
thumbnail_number = int(match.groups()[0])
return thumbnail_number
def extract_intro(filename):
""" Extract the first paragraph of module-level docstring. max:95 char"""
docstring, _ = get_docstring_and_rest(filename)
# lstrip is just in case docstring has a '\n\n' at the beginning
paragraphs = docstring.lstrip().split('\n\n')
if len(paragraphs) > 1:
first_paragraph = re.sub('\n', ' ', paragraphs[1])
first_paragraph = (first_paragraph[:95] + '...'
if len(first_paragraph) > 95 else first_paragraph)
else:
raise ValueError(
"Example docstring should have a header for the example title "
"and at least a paragraph explaining what the example is about. "
"Please check the example file:\n {}\n".format(filename))
return first_paragraph
def get_md5sum(src_file):
"""Returns md5sum of file"""
with open(src_file, 'r') as src_data:
src_content = src_data.read()
# data needs to be encoded in python3 before hashing
if sys.version_info[0] == 3:
src_content = src_content.encode('utf-8')
src_md5 = hashlib.md5(src_content).hexdigest()
return src_md5
def md5sum_is_current(src_file):
"""Returns True if src_file has the same md5 hash as the one stored on disk"""
src_md5 = get_md5sum(src_file)
src_md5_file = src_file + '.md5'
if os.path.exists(src_md5_file):
with open(src_md5_file, 'r') as file_checksum:
ref_md5 = file_checksum.read()
return src_md5 == ref_md5
return False
def save_figures(image_path, fig_count, gallery_conf):
"""Save all open matplotlib figures of the example code-block
Parameters
----------
image_path : str
Path where plots are saved (format string which accepts figure number)
fig_count : int
Previous figure number count. Figure number add from this number
gallery_conf : dict
Contains the configuration of Sphinx-Gallery
Returns
-------
figure_list : list of str
strings containing the full path to each figure
images_rst : str
rst code to embed the images in the document
"""
figure_list = []
fig_managers = matplotlib._pylab_helpers.Gcf.get_all_fig_managers()
for fig_mngr in fig_managers:
# Set the fig_num figure as the current figure as we can't
# save a figure that's not the current figure.
fig = plt.figure(fig_mngr.num)
kwargs = {}
to_rgba = matplotlib.colors.colorConverter.to_rgba
for attr in ['facecolor', 'edgecolor']:
fig_attr = getattr(fig, 'get_' + attr)()
default_attr = matplotlib.rcParams['figure.' + attr]
if to_rgba(fig_attr) != to_rgba(default_attr):
kwargs[attr] = fig_attr
current_fig = image_path.format(fig_count + fig_mngr.num)
fig.savefig(current_fig, **kwargs)
figure_list.append(current_fig)
if gallery_conf.get('find_mayavi_figures', False):
from mayavi import mlab
e = mlab.get_engine()
last_matplotlib_fig_num = fig_count + len(figure_list)
total_fig_num = last_matplotlib_fig_num + len(e.scenes)
mayavi_fig_nums = range(last_matplotlib_fig_num + 1, total_fig_num + 1)
for scene, mayavi_fig_num in zip(e.scenes, mayavi_fig_nums):
current_fig = image_path.format(mayavi_fig_num)
mlab.savefig(current_fig, figure=scene)
# make sure the image is not too large
scale_image(current_fig, current_fig, 850, 999)
figure_list.append(current_fig)
mlab.close(all=True)
# Depending on whether we have one or more figures, we're using a
# horizontal list or a single rst call to 'image'.
images_rst = ""
if len(figure_list) == 1:
figure_name = figure_list[0]
images_rst = SINGLE_IMAGE % figure_name.lstrip('/')
elif len(figure_list) > 1:
images_rst = HLIST_HEADER
for figure_name in figure_list:
images_rst += HLIST_IMAGE_TEMPLATE % figure_name.lstrip('/')
return figure_list, images_rst
def scale_image(in_fname, out_fname, max_width, max_height):
"""Scales an image with the same aspect ratio centered in an
image with a given max_width and max_height
if in_fname == out_fname the image can only be scaled down
"""
# local import to avoid testing dependency on PIL:
try:
from PIL import Image
except ImportError:
import Image
img = Image.open(in_fname)
width_in, height_in = img.size
scale_w = max_width / float(width_in)
scale_h = max_height / float(height_in)
if height_in * scale_w <= max_height:
scale = scale_w
else:
scale = scale_h
if scale >= 1.0 and in_fname == out_fname:
return
width_sc = int(round(scale * width_in))
height_sc = int(round(scale * height_in))
# resize the image
img.thumbnail((width_sc, height_sc), Image.ANTIALIAS)
# insert centered
thumb = Image.new('RGB', (max_width, max_height), (255, 255, 255))
pos_insert = ((max_width - width_sc) // 2, (max_height - height_sc) // 2)
thumb.paste(img, pos_insert)
thumb.save(out_fname)
# Use optipng to perform lossless compression on the resized image if
# software is installed
if os.environ.get('SKLEARN_DOC_OPTIPNG', False):
try:
subprocess.call(["optipng", "-quiet", "-o", "9", out_fname])
except Exception:
warnings.warn('Install optipng to reduce the size of the \
generated images')
def save_thumbnail(image_path_template, src_file, gallery_conf):
"""Save the thumbnail image"""
# read specification of the figure to display as thumbnail from main text
_, content = get_docstring_and_rest(src_file)
thumbnail_number = extract_thumbnail_number(content)
thumbnail_image_path = image_path_template.format(thumbnail_number)
thumb_dir = os.path.join(os.path.dirname(thumbnail_image_path), 'thumb')
if not os.path.exists(thumb_dir):
os.makedirs(thumb_dir)
base_image_name = os.path.splitext(os.path.basename(src_file))[0]
thumb_file = os.path.join(thumb_dir,
'sphx_glr_%s_thumb.png' % base_image_name)
if src_file in gallery_conf['failing_examples']:
broken_img = os.path.join(glr_path_static(), 'broken_example.png')
scale_image(broken_img, thumb_file, 200, 140)
elif os.path.exists(thumbnail_image_path):
scale_image(thumbnail_image_path, thumb_file, 400, 280)
elif not os.path.exists(thumb_file):
# create something to replace the thumbnail
default_thumb_file = os.path.join(glr_path_static(), 'no_image.png')
default_thumb_file = gallery_conf.get("default_thumb_file",
default_thumb_file)
scale_image(default_thumb_file, thumb_file, 200, 140)
def generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs):
"""Generate the gallery reStructuredText for an example directory"""
if not os.path.exists(os.path.join(src_dir, 'README.txt')):
print(80 * '_')
print('Example directory %s does not have a README.txt file' %
src_dir)
print('Skipping this directory')
print(80 * '_')
return "", [] # because string is an expected return type
fhindex = open(os.path.join(src_dir, 'README.txt')).read()
if not os.path.exists(target_dir):
os.makedirs(target_dir)
sorted_listdir = [fname for fname in sorted(os.listdir(src_dir))
if fname.endswith('.py')]
entries_text = []
computation_times = []
for fname in sorted_listdir:
amount_of_code, time_elapsed = \
generate_file_rst(fname, target_dir, src_dir, gallery_conf)
computation_times.append((time_elapsed, fname))
new_fname = os.path.join(src_dir, fname)
intro = extract_intro(new_fname)
write_backreferences(seen_backrefs, gallery_conf,
target_dir, fname, intro)
this_entry = _thumbnail_div(target_dir, fname, intro) + """
.. toctree::
:hidden:
/%s/%s\n""" % (target_dir, fname[:-3])
entries_text.append((amount_of_code, this_entry))
# sort to have the smallest entries in the beginning
entries_text.sort()
for _, entry_text in entries_text:
fhindex += entry_text
# clear at the end of the section
fhindex += """.. raw:: html\n
<div style='clear:both'></div>\n\n"""
return fhindex, computation_times
def execute_code_block(code_block, example_globals,
block_vars, gallery_conf):
"""Executes the code block of the example file"""
time_elapsed = 0
stdout = ''
# If example is not suitable to run, skip executing its blocks
if not block_vars['execute_script']:
return stdout, time_elapsed
plt.close('all')
cwd = os.getcwd()
# Redirect output to stdout and
orig_stdout = sys.stdout
src_file = block_vars['src_file']
try:
# First cd in the original example dir, so that any file
# created by the example get created in this directory
os.chdir(os.path.dirname(src_file))
my_buffer = MixedEncodingStringIO()
my_stdout = Tee(sys.stdout, my_buffer)
sys.stdout = my_stdout
t_start = time()
# don't use unicode_literals at the top of this file or you get
# nasty errors here on Py2.7
exec(code_block, example_globals)
time_elapsed = time() - t_start
sys.stdout = orig_stdout
my_stdout = my_buffer.getvalue().strip().expandtabs()
# raise RuntimeError
if my_stdout:
stdout = CODE_OUTPUT.format(indent(my_stdout, u' ' * 4))
os.chdir(cwd)
fig_list, images_rst = save_figures(
block_vars['image_path'], block_vars['fig_count'], gallery_conf)
fig_num = len(fig_list)
except Exception:
formatted_exception = traceback.format_exc()
fail_example_warning = 80 * '_' + '\n' + \
'%s failed to execute correctly:' % src_file + \
formatted_exception + 80 * '_' + '\n'
warnings.warn(fail_example_warning)
fig_num = 0
images_rst = codestr2rst(formatted_exception, lang='pytb')
# Breaks build on first example error
# XXX This check can break during testing e.g. if you uncomment the
# `raise RuntimeError` by the `my_stdout` call, maybe use `.get()`?
if gallery_conf['abort_on_example_error']:
raise
# Stores failing file
gallery_conf['failing_examples'][src_file] = formatted_exception
block_vars['execute_script'] = False
finally:
os.chdir(cwd)
sys.stdout = orig_stdout
code_output = u"\n{0}\n\n{1}\n\n".format(images_rst, stdout)
block_vars['fig_count'] += fig_num
return code_output, time_elapsed
def clean_modules():
"""Remove "unload" seaborn from the name space
After a script is executed it can load a variety of setting that one
does not want to influence in other examples in the gallery."""
# Horrible code to 'unload' seaborn, so that it resets
# its default when is load
# Python does not support unloading of modules
# https://bugs.python.org/issue9072
for module in list(sys.modules.keys()):
if 'seaborn' in module:
del sys.modules[module]
# Reset Matplotlib to default
plt.rcdefaults()
def generate_file_rst(fname, target_dir, src_dir, gallery_conf):
"""Generate the rst file for a given example.
Returns
-------
amount_of_code : int
character count of the corresponding python script in file
time_elapsed : float
seconds required to run the script
"""
src_file = os.path.join(src_dir, fname)
example_file = os.path.join(target_dir, fname)
shutil.copyfile(src_file, example_file)
script_blocks = split_code_and_text_blocks(src_file)
amount_of_code = sum([len(bcontent)
for blabel, bcontent in script_blocks
if blabel == 'code'])
if md5sum_is_current(example_file):
return amount_of_code, 0
image_dir = os.path.join(target_dir, 'images')
if not os.path.exists(image_dir):
os.makedirs(image_dir)
base_image_name = os.path.splitext(fname)[0]
image_fname = 'sphx_glr_' + base_image_name + '_{0:03}.png'
image_path_template = os.path.join(image_dir, image_fname)
ref_fname = example_file.replace(os.path.sep, '_')
example_rst = """\n\n.. _sphx_glr_{0}:\n\n""".format(ref_fname)
example_nb = Notebook(fname, target_dir)
filename_pattern = gallery_conf.get('filename_pattern')
execute_script = re.search(filename_pattern, src_file) and gallery_conf[
'plot_gallery']
example_globals = {
# A lot of examples contains 'print(__doc__)' for example in
# scikit-learn so that running the example prints some useful
# information. Because the docstring has been separated from
# the code blocks in sphinx-gallery, __doc__ is actually
# __builtin__.__doc__ in the execution context and we do not
# want to print it
'__doc__': '',
# Examples may contain if __name__ == '__main__' guards
# for in example scikit-learn if the example uses multiprocessing
'__name__': '__main__',
}
# A simple example has two blocks: one for the
# example introduction/explanation and one for the code
is_example_notebook_like = len(script_blocks) > 2
time_elapsed = 0
block_vars = {'execute_script': execute_script, 'fig_count': 0,
'image_path': image_path_template, 'src_file': src_file}
print('Executing file %s' % src_file)
for blabel, bcontent in script_blocks:
if blabel == 'code':
code_output, rtime = execute_code_block(bcontent,
example_globals,
block_vars,
gallery_conf)
time_elapsed += rtime
example_nb.add_code_cell(bcontent)
if is_example_notebook_like:
example_rst += codestr2rst(bcontent) + '\n'
example_rst += code_output
else:
example_rst += code_output
if 'sphx-glr-script-out' in code_output:
# Add some vertical space after output
example_rst += "\n\n|\n\n"
example_rst += codestr2rst(bcontent) + '\n'
else:
example_rst += text2string(bcontent) + '\n'
example_nb.add_markdown_cell(text2string(bcontent))
clean_modules()
# Writes md5 checksum if example has build correctly
# not failed and was initially meant to run(no-plot shall not cache md5sum)
if block_vars['execute_script']:
with open(example_file + '.md5', 'w') as file_checksum:
file_checksum.write(get_md5sum(example_file))
save_thumbnail(image_path_template, src_file, gallery_conf)
time_m, time_s = divmod(time_elapsed, 60)
example_nb.save_file()
with codecs.open(os.path.join(target_dir, base_image_name + '.rst'),
mode='w', encoding='utf-8') as f:
example_rst += "**Total running time of the script:**" \
" ({0: .0f} minutes {1: .3f} seconds)\n\n".format(
time_m, time_s)
example_rst += CODE_DOWNLOAD.format(fname, example_nb.file_name)
example_rst += SPHX_GLR_SIG
f.write(example_rst)
print("{0} ran in : {1:.2g} seconds\n".format(src_file, time_elapsed))
return amount_of_code, time_elapsed
