gen_rst.py
# -*- 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
from distutils.version import LooseVersion
# Try Python 2 first, otherwise load from Python 3
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
# make sure that the Agg backend is set before importing any
# matplotlib
import matplotlib
matplotlib.use('agg')
matplotlib_backend = matplotlib.get_backend()
if matplotlib_backend != 'agg':
mpl_backend_msg = (
"Sphinx-Gallery relies on the matplotlib 'agg' backend to "
"render figures and write them to files. You are "
"currently using the {} backend. Sphinx-Gallery will "
"terminate the build now, because changing backends is "
"not well supported by matplotlib. We advise you to move "
"sphinx_gallery imports before any matplotlib-dependent "
"import. Moving sphinx_gallery imports at the top of "
"your conf.py file should fix this issue")
raise ValueError(mpl_backend_msg.format(matplotlib_backend))
import matplotlib.pyplot as plt
import sphinx
from . import glr_path_static
from . import sphinx_compatibility
from .backreferences import write_backreferences, _thumbnail_div
from .downloads import CODE_DOWNLOAD
from .py_source_parser import split_code_and_text_blocks
from .notebook import jupyter_notebook, save_notebook
try:
basestring
except NameError:
basestring = str
unicode = str
logger = sphinx_compatibility.getLogger('sphinx-gallery')
###############################################################################
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 <https://sphinx-gallery.readthedocs.io>`_\n"""
def codestr2rst(codestr, lang='python', lineno=None):
"""Return reStructuredText code block from code string"""
if lineno is not None:
if LooseVersion(sphinx.__version__) >= '1.3':
# Sphinx only starts numbering from the first non-empty line.
blank_lines = codestr.count('\n', 0, -len(codestr.lstrip()))
lineno = ' :lineno-start: {0}\n'.format(lineno + blank_lines)
else:
lineno = ' :linenos:\n'
else:
lineno = ''
code_directive = "\n.. code-block:: {0}\n{1}\n".format(lang, lineno)
indented_block = indent(codestr, ' ' * 4)
return code_directive + indented_block
def extract_intro(filename, docstring):
""" Extract the first paragraph of module-level docstring. max:95 char"""
# 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, 'rb') as src_data:
src_content = src_data.read()
src_md5 = hashlib.md5(src_content).hexdigest()
return src_md5
def md5sum_is_current(src_file):
"""Checks whether src_file has the same md5 hash as the one 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
-------
images_rst : str
rst code to embed the images in the document
fig_num : int
number of figures saved
"""
figure_list = []
for fig_num in plt.get_fignums():
# 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_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_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)
return figure_rst(figure_list, gallery_conf['src_dir'])
def figure_rst(figure_list, sources_dir):
"""Given a list of paths to figures generate the corresponding rst
Depending on whether we have one or more figures, we use a
single rst call to 'image' or a horizontal list.
Parameters
----------
figure_list : list of str
Strings are the figures' absolute paths
sources_dir : str
absolute path of Sphinx documentation sources
Returns
-------
images_rst : str
rst code to embed the images in the document
fig_num : int
number of figures saved
"""
figure_paths = [os.path.relpath(figure_path, sources_dir)
.replace(os.sep, '/').lstrip('/')
for figure_path in figure_list]
images_rst = ""
if len(figure_paths) == 1:
figure_name = figure_paths[0]
images_rst = SINGLE_IMAGE % figure_name
elif len(figure_paths) > 1:
images_rst = HLIST_HEADER
for figure_name in figure_paths:
images_rst += HLIST_IMAGE_TEMPLATE % figure_name
return images_rst, len(figure_list)
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:
logger.warning(
'Install optipng to reduce the size of the generated images')
def save_thumbnail(image_path_template, src_file, file_conf, gallery_conf):
"""Save the thumbnail image"""
# read specification of the figure to display as thumbnail from main text
thumbnail_number = file_conf.get('thumbnail_number', 1)
if not isinstance(thumbnail_number, int):
raise TypeError(
'sphinx_gallery_thumbnail_number setting is not a number.')
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"""
with codecs.open(os.path.join(src_dir, 'README.txt'), 'r',
encoding='utf-8') as fid:
fhindex = fid.read()
# Add empty lines to avoid bug in issue #165
fhindex += "\n\n"
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 = []
build_target_dir = os.path.relpath(target_dir, gallery_conf['src_dir'])
iterator = sphinx_compatibility.status_iterator(
sorted_listdir,
'Generating gallery for %s ' % build_target_dir,
length=len(sorted_listdir))
for fname in iterator:
intro, 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)
this_entry = _thumbnail_div(build_target_dir, fname, intro) + """
.. toctree::
:hidden:
/%s\n""" % os.path.join(build_target_dir, fname[:-3]).replace(os.sep, '/')
entries_text.append((amount_of_code, this_entry))
if gallery_conf['backreferences_dir']:
write_backreferences(seen_backrefs, gallery_conf,
target_dir, fname, intro)
# 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 handle_exception(exc_info, src_file, block_vars, gallery_conf):
etype, exc, tb = exc_info
stack = traceback.extract_tb(tb)
# Remove our code from traceback:
if isinstance(exc, SyntaxError):
# Remove one extra level through ast.parse.
stack = stack[2:]
else:
stack = stack[1:]
formatted_exception = 'Traceback (most recent call last):\n' + ''.join(
traceback.format_list(stack) +
traceback.format_exception_only(etype, exc))
logger.warning('%s failed to execute correctly: %s', src_file,
formatted_exception)
except_rst = codestr2rst(formatted_exception, lang='pytb')
# Breaks build on first example error
if gallery_conf['abort_on_example_error']:
raise
# Stores failing file
gallery_conf['failing_examples'][src_file] = formatted_exception
block_vars['execute_script'] = False
return except_rst
def execute_code_block(src_file, code_block, lineno, example_globals,
block_vars, gallery_conf):
"""Executes the code block of the example file"""
time_elapsed = 0
# If example is not suitable to run, skip executing its blocks
if not block_vars['execute_script']:
return '', time_elapsed
plt.close('all')
cwd = os.getcwd()
# Redirect output to stdout and
orig_stdout = sys.stdout
src_file = block_vars['src_file']
# First cd in the original example dir, so that any file
# created by the example get created in this directory
my_stdout = MixedEncodingStringIO()
os.chdir(os.path.dirname(src_file))
sys.stdout = my_stdout
try:
code_ast = ast.parse(code_block, src_file)
ast.increment_lineno(code_ast, lineno - 1)
t_start = time()
# don't use unicode_literals at the top of this file or you get
# nasty errors here on Py2.7
exec(compile(code_ast, src_file, 'exec'), example_globals)
time_elapsed = time() - t_start
except Exception:
sys.stdout = orig_stdout
except_rst = handle_exception(sys.exc_info(), src_file, block_vars,
gallery_conf)
code_output = u"\n{0}\n\n\n\n".format(except_rst)
else:
sys.stdout = orig_stdout
os.chdir(cwd)
my_stdout = my_stdout.getvalue().strip().expandtabs()
if my_stdout:
stdout = CODE_OUTPUT.format(indent(my_stdout, u' ' * 4))
logger.verbose('Output from %s', src_file, color='brown')
logger.verbose(my_stdout)
else:
stdout = ''
images_rst, fig_num = save_figures(block_vars['image_path'],
block_vars['fig_count'],
gallery_conf)
block_vars['fig_count'] += fig_num
code_output = u"\n{0}\n\n{1}\n\n".format(images_rst, stdout)
finally:
os.chdir(cwd)
sys.stdout = orig_stdout
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
-------
intro: str
The introduction of the example
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.normpath(os.path.join(src_dir, fname))
example_file = os.path.join(target_dir, fname)
shutil.copyfile(src_file, example_file)
file_conf, script_blocks = split_code_and_text_blocks(src_file)
amount_of_code = sum([len(bcontent)
for blabel, bcontent, lineno in script_blocks
if blabel == 'code'])
intro = extract_intro(fname, script_blocks[0][1])
if md5sum_is_current(example_file):
return intro, 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'
build_image_dir = os.path.relpath(image_dir, gallery_conf['src_dir'])
image_path_template = os.path.join(image_dir, image_fname)
ref_fname = os.path.relpath(example_file, gallery_conf['src_dir'])
ref_fname = ref_fname.replace(os.path.sep, '_')
example_rst = """\n\n.. _sphx_glr_{0}:\n\n""".format(ref_fname)
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__',
# Don't ever support __file__: Issues #166 #212
}
# 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}
argv_orig = sys.argv[:]
if block_vars['execute_script']:
# We want to run the example without arguments. See
# https://github.com/sphinx-gallery/sphinx-gallery/pull/252
# for more details.
sys.argv[0] = src_file
sys.argv[1:] = []
for blabel, bcontent, lineno in script_blocks:
if blabel == 'code':
code_output, rtime = execute_code_block(src_file, bcontent, lineno,
example_globals,
block_vars, gallery_conf)
time_elapsed += rtime
if not file_conf.get('line_numbers',
gallery_conf.get('line_numbers', False)):
lineno = None
if is_example_notebook_like:
example_rst += codestr2rst(bcontent, lineno=lineno) + '\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, lineno=lineno) + '\n'
else:
example_rst += bcontent + '\n\n'
sys.argv = argv_orig
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, file_conf, gallery_conf)
time_m, time_s = divmod(time_elapsed, 60)
example_nb = jupyter_notebook(script_blocks)
save_notebook(example_nb, example_file.replace('.py', '.ipynb'))
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,
fname.replace('.py', '.ipynb'))
example_rst += SPHX_GLR_SIG
f.write(example_rst)
if block_vars['execute_script']:
logger.debug("%s ran in : %.2g seconds", src_file, time_elapsed)
return intro, amount_of_code, time_elapsed
