# -*- 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 copy
import contextlib
import ast
import codecs
from functools import partial
import gc
import pickle
import importlib
from io import StringIO
import os
import re
from textwrap import indent
import warnings
from shutil import copyfile
import subprocess
import sys
import traceback
import codeop
from sphinx.errors import ExtensionError
from .scrapers import (save_figures, ImagePathIterator, clean_modules,
_find_image_ext)
from .utils import (replace_py_ipynb, scale_image, get_md5sum, _replace_md5,
optipng)
from . import glr_path_static
from . import sphinx_compatibility
from .backreferences import (_write_backreferences, _thumbnail_div,
identify_names)
from .downloads import CODE_DOWNLOAD
from .py_source_parser import (split_code_and_text_blocks,
remove_config_comments)
from .notebook import jupyter_notebook, save_notebook
from .binder import check_binder_conf, gen_binder_rst
logger = sphinx_compatibility.getLogger('sphinx-gallery')
###############################################################################
class _LoggingTee(object):
"""A tee object to redirect streams to the logger."""
def __init__(self, src_filename):
self.logger = logger
self.src_filename = src_filename
self.logger_buffer = ''
self.set_std_and_reset_position()
def set_std_and_reset_position(self):
if not isinstance(sys.stdout, _LoggingTee):
self.origs = (sys.stdout, sys.stderr)
sys.stdout = sys.stderr = self
self.first_write = True
self.output = StringIO()
return self
def restore_std(self):
sys.stdout.flush()
sys.stderr.flush()
sys.stdout, sys.stderr = self.origs
def write(self, data):
self.output.write(data)
if self.first_write:
self.logger.verbose('Output from %s', self.src_filename,
color='brown')
self.first_write = False
data = self.logger_buffer + data
lines = data.splitlines()
if data and data[-1] not in '\r\n':
# Wait to write last line if it's incomplete. It will write next
# time or when the LoggingTee is flushed.
self.logger_buffer = lines[-1]
lines = lines[:-1]
else:
self.logger_buffer = ''
for line in lines:
self.logger.verbose('%s', line)
def flush(self):
self.output.flush()
if self.logger_buffer:
self.logger.verbose('%s', self.logger_buffer)
self.logger_buffer = ''
# When called from a local terminal seaborn needs it in Python3
def isatty(self):
return self.output.isatty()
# When called in gen_rst, conveniently use context managing
def __enter__(self):
return self
def __exit__(self, type_, value, tb):
self.restore_std()
###############################################################################
# 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
:class: sphx-glr-multi-img
"""
SINGLE_IMAGE = """
.. image:: /%s
:class: sphx-glr-single-img
"""
# This one could contain unicode
CODE_OUTPUT = u""".. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
{0}\n"""
TIMING_CONTENT = """
.. rst-class:: sphx-glr-timing
**Total running time of the script:** ({0: .0f} minutes {1: .3f} seconds)
"""
SPHX_GLR_SIG = """\n
.. only:: html
.. rst-class:: sphx-glr-signature
`Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_
"""
# Header used to include raw html
html_header = """.. raw:: html
{0}\n <br />\n <br />"""
def codestr2rst(codestr, lang='python', lineno=None):
"""Return reStructuredText code block from code string"""
if lineno is not None:
# 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 = ''
code_directive = "\n.. code-block:: {0}\n{1}\n".format(lang, lineno)
indented_block = indent(codestr, ' ' * 4)
return code_directive + indented_block
def _regroup(x):
x = x.groups()
return x[0] + x[1].split('.')[-1] + x[2]
def _sanitize_rst(string):
"""Use regex to remove at least some sphinx directives."""
# :class:`a.b.c <thing here>`, :ref:`abc <thing here>` --> thing here
p, e = r'(\s|^):[^:\s]+:`', r'`(\W|$)'
string = re.sub(p + r'\S+\s*<([^>`]+)>' + e, r'\1\2\3', string)
# :class:`~a.b.c` --> c
string = re.sub(p + r'~([^`]+)' + e, _regroup, string)
# :class:`a.b.c` --> a.b.c
string = re.sub(p + r'([^`]+)' + e, r'\1\2\3', string)
# ``whatever thing`` --> whatever thing
p = r'(\s|^)`'
string = re.sub(p + r'`([^`]+)`' + e, r'\1\2\3', string)
# `whatever thing` --> whatever thing
string = re.sub(p + r'([^`]+)' + e, r'\1\2\3', string)
return string
def extract_intro_and_title(filename, docstring):
"""Extract and clean the first paragraph of module-level docstring."""
# lstrip is just in case docstring has a '\n\n' at the beginning
paragraphs = docstring.lstrip().split('\n\n')
# remove comments and other syntax like `.. _link:`
paragraphs = [p for p in paragraphs
if not p.startswith('.. ') and len(p) > 0]
if len(paragraphs) == 0:
raise ExtensionError(
"Example docstring should have a header for the example title. "
"Please check the example file:\n {}\n".format(filename))
# Title is the first paragraph with any ReSTructuredText title chars
# removed, i.e. lines that consist of (3 or more of the same) 7-bit
# non-ASCII chars.
# This conditional is not perfect but should hopefully be good enough.
title_paragraph = paragraphs[0]
match = re.search(r'^(?!([\W _])\1{3,})(.+)', title_paragraph,
re.MULTILINE)
if match is None:
raise ExtensionError(
'Could not find a title in first paragraph:\n{}'.format(
title_paragraph))
title = match.group(0).strip()
# Use the title if no other paragraphs are provided
intro_paragraph = title if len(paragraphs) < 2 else paragraphs[1]
# Concatenate all lines of the first paragraph and truncate at 95 chars
intro = re.sub('\n', ' ', intro_paragraph)
intro = _sanitize_rst(intro)
if len(intro) > 95:
intro = intro[:95] + '...'
return intro, title
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_thumbnail(image_path_template, src_file, file_conf, gallery_conf):
"""Generate and Save the thumbnail image
Parameters
----------
image_path_template : str
holds the template where to save and how to name the image
src_file : str
path to source python file
gallery_conf : dict
Sphinx-Gallery configuration dictionary
"""
thumb_dir = os.path.join(os.path.dirname(image_path_template), 'thumb')
if not os.path.exists(thumb_dir):
os.makedirs(thumb_dir)
# read specification of the figure to display as thumbnail from main text
thumbnail_number = file_conf.get('thumbnail_number', None)
thumbnail_path = file_conf.get('thumbnail_path', None)
# thumbnail_number has priority.
if thumbnail_number is None and thumbnail_path is None:
# If no number AND no path, set to default thumbnail_number
thumbnail_number = 1
if thumbnail_number is None:
image_path = os.path.join(gallery_conf['src_dir'], thumbnail_path)
else:
if not isinstance(thumbnail_number, int):
raise ExtensionError(
'sphinx_gallery_thumbnail_number setting is not a number, '
'got %r' % (thumbnail_number,))
image_path = image_path_template.format(thumbnail_number)
del thumbnail_number, thumbnail_path, image_path_template
thumbnail_image_path, ext = _find_image_ext(image_path)
base_image_name = os.path.splitext(os.path.basename(src_file))[0]
thumb_file = os.path.join(thumb_dir,
'sphx_glr_%s_thumb.%s' % (base_image_name, ext))
if src_file in gallery_conf['failing_examples']:
img = os.path.join(glr_path_static(), 'broken_example.png')
elif os.path.exists(thumbnail_image_path):
img = thumbnail_image_path
elif not os.path.exists(thumb_file):
# create something to replace the thumbnail
img = os.path.join(glr_path_static(), 'no_image.png')
img = gallery_conf.get("default_thumb_file", img)
else:
return
if ext in ('svg', 'gif'):
copyfile(img, thumb_file)
else:
scale_image(img, thumb_file, *gallery_conf["thumbnail_size"])
if 'thumbnails' in gallery_conf['compress_images']:
optipng(thumb_file, gallery_conf['compress_images_args'])
def _get_readme(dir_, gallery_conf, raise_error=True):
extensions = ['.txt'] + sorted(gallery_conf['app'].config['source_suffix'])
for ext in extensions:
for fname in ('README', 'readme'):
fpth = os.path.join(dir_, fname + ext)
if os.path.isfile(fpth):
return fpth
if raise_error:
raise ExtensionError(
"Example directory {0} does not have a README file with one "
"of the expected file extensions {1}. Please write one to "
"introduce your gallery.".format(dir_, extensions))
return None
def generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs):
"""Generate the gallery reStructuredText for an example directory."""
head_ref = os.path.relpath(target_dir, gallery_conf['src_dir'])
fhindex = """\n\n.. _sphx_glr_{0}:\n\n""".format(
head_ref.replace(os.path.sep, '_'))
fname = _get_readme(src_dir, gallery_conf)
with codecs.open(fname, '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)
# get filenames
listdir = [fname for fname in os.listdir(src_dir)
if fname.endswith('.py')]
# limit which to look at based on regex (similar to filename_pattern)
listdir = [fname for fname in listdir
if re.search(gallery_conf['ignore_pattern'],
os.path.normpath(os.path.join(src_dir, fname)))
is None]
# sort them
sorted_listdir = sorted(
listdir, key=gallery_conf['within_subsection_order'](src_dir))
entries_text = []
costs = []
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, title, cost = generate_file_rst(
fname, target_dir, src_dir, gallery_conf, seen_backrefs)
src_file = os.path.normpath(os.path.join(src_dir, fname))
costs.append((cost, src_file))
this_entry = _thumbnail_div(target_dir, gallery_conf['src_dir'],
fname, intro, title) + """
.. toctree::
:hidden:
/%s\n""" % os.path.join(build_target_dir, fname[:-3]).replace(os.sep, '/')
entries_text.append(this_entry)
for entry_text in entries_text:
fhindex += entry_text
# clear at the end of the section
fhindex += """.. raw:: html\n
<div class="sphx-glr-clear"></div>\n\n"""
return fhindex, costs
def handle_exception(exc_info, src_file, script_vars, gallery_conf):
from .gen_gallery import _expected_failing_examples
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))
expected = src_file in _expected_failing_examples(gallery_conf)
if expected:
func, color = logger.info, 'blue',
else:
func, color = logger.warning, 'red'
func('%s failed to execute correctly: %s', src_file,
formatted_exception, color=color)
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
script_vars['execute_script'] = False
# Ensure it's marked as our style
except_rst = ".. rst-class:: sphx-glr-script-out\n\n" + except_rst
return except_rst
# Adapted from github.com/python/cpython/blob/3.7/Lib/warnings.py
def _showwarning(message, category, filename, lineno, file=None, line=None):
if file is None:
file = sys.stderr
if file is None:
# sys.stderr is None when run with pythonw.exe:
# warnings get lost
return
text = warnings.formatwarning(message, category, filename, lineno, line)
try:
file.write(text)
except OSError:
# the file (probably stderr) is invalid - this warning gets lost.
pass
@contextlib.contextmanager
def patch_warnings():
"""Patch warnings.showwarning to actually write out the warning."""
# Sphinx or logging or someone is patching warnings, but we want to
# capture them, so let's patch over their patch...
orig_showwarning = warnings.showwarning
try:
warnings.showwarning = _showwarning
yield
finally:
warnings.showwarning = orig_showwarning
class _exec_once(object):
"""Deal with memory_usage calling functions more than once (argh)."""
def __init__(self, code, fake_main):
self.code = code
self.fake_main = fake_main
self.run = False
def __call__(self):
if not self.run:
self.run = True
old_main = sys.modules.get('__main__', None)
with patch_warnings():
sys.modules['__main__'] = self.fake_main
try:
exec(self.code, self.fake_main.__dict__)
finally:
if old_main is not None:
sys.modules['__main__'] = old_main
def _get_memory_base(gallery_conf):
"""Get the base amount of memory used by running a Python process."""
if not gallery_conf['plot_gallery']:
return 0.
# There might be a cleaner way to do this at some point
from memory_profiler import memory_usage
if sys.platform in ('win32', 'darwin'):
sleep, timeout = (1, 2)
else:
sleep, timeout = (0.5, 1)
proc = subprocess.Popen(
[sys.executable, '-c',
'import time, sys; time.sleep(%s); sys.exit(0)' % sleep],
close_fds=True)
memories = memory_usage(proc, interval=1e-3, timeout=timeout)
kwargs = dict(timeout=timeout) if sys.version_info >= (3, 5) else {}
proc.communicate(**kwargs)
# On OSX sometimes the last entry can be None
memories = [mem for mem in memories if mem is not None] + [0.]
memory_base = max(memories)
return memory_base
def execute_code_block(compiler, block, example_globals,
script_vars, gallery_conf):
"""Execute the code block of the example file."""
if example_globals is None: # testing shortcut
example_globals = script_vars['fake_main'].__dict__
blabel, bcontent, lineno = block
# If example is not suitable to run, skip executing its blocks
if not script_vars['execute_script'] or blabel == 'text':
return ''
cwd = os.getcwd()
# Redirect output to stdout and
src_file = script_vars['src_file']
logging_tee = _check_reset_logging_tee(src_file)
assert isinstance(logging_tee, _LoggingTee)
# 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))
sys_path = copy.deepcopy(sys.path)
sys.path.append(os.getcwd())
try:
dont_inherit = 1
if sys.version_info >= (3, 8):
ast_Module = partial(ast.Module, type_ignores=[])
else:
ast_Module = ast.Module
code_ast = ast_Module([bcontent])
code_ast = compile(bcontent, src_file, 'exec',
ast.PyCF_ONLY_AST | compiler.flags, dont_inherit)
ast.increment_lineno(code_ast, lineno - 1)
# capture output if last line is expression
is_last_expr = False
if len(code_ast.body) and isinstance(code_ast.body[-1], ast.Expr):
is_last_expr = True
last_val = code_ast.body.pop().value
# exec body minus last expression
mem_body, _ = gallery_conf['call_memory'](
_exec_once(
compiler(code_ast, src_file, 'exec'),
script_vars['fake_main']))
# exec last expression, made into assignment
body = [ast.Assign(
targets=[ast.Name(id='___', ctx=ast.Store())], value=last_val)]
last_val_ast = ast_Module(body=body)
ast.fix_missing_locations(last_val_ast)
mem_last, _ = gallery_conf['call_memory'](
_exec_once(
compiler(last_val_ast, src_file, 'exec'),
script_vars['fake_main']))
# capture the assigned variable
___ = example_globals['___']
mem_max = max(mem_body, mem_last)
else:
mem_max, _ = gallery_conf['call_memory'](
_exec_once(
compiler(code_ast, src_file, 'exec'),
script_vars['fake_main']))
script_vars['memory_delta'].append(mem_max)
except Exception:
logging_tee.restore_std()
except_rst = handle_exception(sys.exc_info(), src_file, script_vars,
gallery_conf)
code_output = u"\n{0}\n\n\n\n".format(except_rst)
# still call this even though we won't use the images so that
# figures are closed
save_figures(block, script_vars, gallery_conf)
else:
logging_tee.restore_std()
sys.path = sys_path
os.chdir(cwd)
last_repr = None
repr_meth = None
if is_last_expr:
if gallery_conf['ignore_repr_types']:
ignore_repr = re.search(
gallery_conf['ignore_repr_types'], str(type(___))
)
else:
ignore_repr = False
if gallery_conf['capture_repr'] != () and not ignore_repr:
for meth in gallery_conf['capture_repr']:
try:
last_repr = getattr(___, meth)()
# for case when last statement is print()
if last_repr is None or last_repr == 'None':
repr_meth = None
else:
repr_meth = meth
except Exception:
pass
else:
if isinstance(last_repr, str):
break
captured_std = logging_tee.output.getvalue().expandtabs()
# normal string output
if repr_meth in ['__repr__', '__str__'] and last_repr:
captured_std = u"{0}\n{1}".format(captured_std, last_repr)
if captured_std and not captured_std.isspace():
captured_std = CODE_OUTPUT.format(indent(captured_std, u' ' * 4))
else:
captured_std = ''
images_rst = save_figures(block, script_vars, gallery_conf)
# give html output its own header
if repr_meth == '_repr_html_':
captured_html = html_header.format(indent(last_repr, u' ' * 4))
else:
captured_html = ''
code_output = u"\n{0}\n\n{1}\n{2}\n\n".format(
images_rst, captured_std, captured_html)
finally:
os.chdir(cwd)
sys.path = sys_path
logging_tee.restore_std()
return code_output
def _check_reset_logging_tee(src_file):
# Helper to deal with our tests not necessarily calling execute_script
# but rather execute_code_block directly
if isinstance(sys.stdout, _LoggingTee):
logging_tee = sys.stdout
else:
logging_tee = _LoggingTee(src_file)
logging_tee.set_std_and_reset_position()
return logging_tee
def executable_script(src_file, gallery_conf):
"""Validate if script has to be run according to gallery configuration
Parameters
----------
src_file : str
path to python script
gallery_conf : dict
Contains the configuration of Sphinx-Gallery
Returns
-------
bool
True if script has to be executed
"""
filename_pattern = gallery_conf.get('filename_pattern')
execute = re.search(filename_pattern, src_file) and gallery_conf[
'plot_gallery']
return execute
def execute_script(script_blocks, script_vars, gallery_conf):
"""Execute and capture output from python script already in block structure
Parameters
----------
script_blocks : list
(label, content, line_number)
List where each element is a tuple with the label ('text' or 'code'),
the corresponding content string of block and the leading line number
script_vars : dict
Configuration and run time variables
gallery_conf : dict
Contains the configuration of Sphinx-Gallery
Returns
-------
output_blocks : list
List of strings where each element is the restructured text
representation of the output of each block
time_elapsed : float
Time elapsed during execution
"""
# Examples may contain if __name__ == '__main__' guards
# for in example scikit-learn if the example uses multiprocessing.
# Here we create a new __main__ module, and temporarily change
# sys.modules when running our example
fake_main = importlib.util.module_from_spec(
importlib.util.spec_from_loader('__main__', None))
example_globals = fake_main.__dict__
example_globals.update({
# 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__': '',
# Don't ever support __file__: Issues #166 #212
})
script_vars['example_globals'] = example_globals
argv_orig = sys.argv[:]
if script_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] = script_vars['src_file']
sys.argv[1:] = []
gc.collect()
memory_start, _ = gallery_conf['call_memory'](lambda: None)
else:
memory_start = 0.
t_start = time()
compiler = codeop.Compile()
# include at least one entry to avoid max() ever failing
script_vars['memory_delta'] = [memory_start]
script_vars['fake_main'] = fake_main
output_blocks = list()
with _LoggingTee(script_vars.get('src_file', '')) as logging_tee:
for block in script_blocks:
logging_tee.set_std_and_reset_position()
output_blocks.append(execute_code_block(
compiler, block, example_globals, script_vars, gallery_conf))
time_elapsed = time() - t_start
sys.argv = argv_orig
script_vars['memory_delta'] = max(script_vars['memory_delta'])
if script_vars['execute_script']:
script_vars['memory_delta'] -= memory_start
# Write md5 checksum if the example was meant to run (no-plot
# shall not cache md5sum) and has built correctly
with open(script_vars['target_file'] + '.md5', 'w') as file_checksum:
file_checksum.write(get_md5sum(script_vars['target_file']))
gallery_conf['passing_examples'].append(script_vars['src_file'])
return output_blocks, time_elapsed
def generate_file_rst(fname, target_dir, src_dir, gallery_conf,
seen_backrefs=None):
"""Generate the rst file for a given example.
Parameters
----------
fname : str
Filename of python script
target_dir : str
Absolute path to directory in documentation where examples are saved
src_dir : str
Absolute path to directory where source examples are stored
gallery_conf : dict
Contains the configuration of Sphinx-Gallery
seen_backrefs : set
The seen backreferences.
Returns
-------
intro: str
The introduction of the example
cost : tuple
A tuple containing the ``(time, memory)`` required to run the script.
"""
seen_backrefs = set() if seen_backrefs is None else seen_backrefs
src_file = os.path.normpath(os.path.join(src_dir, fname))
target_file = os.path.join(target_dir, fname)
_replace_md5(src_file, target_file, 'copy')
file_conf, script_blocks, node = split_code_and_text_blocks(
src_file, return_node=True)
intro, title = extract_intro_and_title(fname, script_blocks[0][1])
gallery_conf['titles'][src_file] = title
executable = executable_script(src_file, gallery_conf)
if md5sum_is_current(target_file):
if executable:
gallery_conf['stale_examples'].append(target_file)
return intro, title, (0, 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)
script_vars = {
'execute_script': executable,
'image_path_iterator': ImagePathIterator(image_path_template),
'src_file': src_file,
'target_file': target_file}
if gallery_conf['remove_config_comments']:
script_blocks = [
(label, remove_config_comments(content), line_number)
for label, content, line_number in script_blocks
]
if executable:
clean_modules(gallery_conf, fname)
output_blocks, time_elapsed = execute_script(script_blocks,
script_vars,
gallery_conf)
logger.debug("%s ran in : %.2g seconds\n", src_file, time_elapsed)
example_rst = rst_blocks(script_blocks, output_blocks,
file_conf, gallery_conf)
memory_used = gallery_conf['memory_base'] + script_vars['memory_delta']
if not executable:
time_elapsed = memory_used = 0. # don't let the output change
save_rst_example(example_rst, target_file, time_elapsed, memory_used,
gallery_conf)
save_thumbnail(image_path_template, src_file, file_conf, gallery_conf)
example_nb = jupyter_notebook(script_blocks, gallery_conf)
ipy_fname = replace_py_ipynb(target_file) + '.new'
save_notebook(example_nb, ipy_fname)
_replace_md5(ipy_fname)
# Write names
if gallery_conf['inspect_global_variables']:
global_variables = script_vars['example_globals']
else:
global_variables = None
example_code_obj = identify_names(script_blocks, global_variables, node)
if example_code_obj:
codeobj_fname = target_file[:-3] + '_codeobj.pickle.new'
with open(codeobj_fname, 'wb') as fid:
pickle.dump(example_code_obj, fid, pickle.HIGHEST_PROTOCOL)
_replace_md5(codeobj_fname)
backrefs = set('{module_short}.{name}'.format(**cobj)
for cobjs in example_code_obj.values()
for cobj in cobjs
if cobj['module'].startswith(gallery_conf['doc_module']))
# Write backreferences
_write_backreferences(backrefs, seen_backrefs, gallery_conf, target_dir,
fname, intro, title)
return intro, title, (time_elapsed, memory_used)
def rst_blocks(script_blocks, output_blocks, file_conf, gallery_conf):
"""Generates the rst string containing the script prose, code and output
Parameters
----------
script_blocks : list
(label, content, line_number)
List where each element is a tuple with the label ('text' or 'code'),
the corresponding content string of block and the leading line number
output_blocks : list
List of strings where each element is the restructured text
representation of the output of each block
file_conf : dict
File-specific settings given in source file comments as:
``# sphinx_gallery_<name> = <value>``
gallery_conf : dict
Contains the configuration of Sphinx-Gallery
Returns
-------
out : str
rst notebook
"""
# 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
example_rst = u"" # there can be unicode content
for (blabel, bcontent, lineno), code_output in \
zip(script_blocks, output_blocks):
if blabel == 'code':
if not file_conf.get('line_numbers',
gallery_conf.get('line_numbers', False)):
lineno = None
code_rst = codestr2rst(bcontent, lang=gallery_conf['lang'],
lineno=lineno) + '\n'
if is_example_notebook_like:
example_rst += code_rst
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 += code_rst
else:
block_separator = '\n\n' if not bcontent.endswith('\n') else '\n'
example_rst += bcontent + block_separator
return example_rst
def save_rst_example(example_rst, example_file, time_elapsed,
memory_used, gallery_conf):
"""Saves the rst notebook to example_file including header & footer
Parameters
----------
example_rst : str
rst containing the executed file content
example_file : str
Filename with full path of python example file in documentation folder
time_elapsed : float
Time elapsed in seconds while executing file
memory_used : float
Additional memory used during the run.
gallery_conf : dict
Sphinx-Gallery configuration dictionary
"""
ref_fname = os.path.relpath(example_file, gallery_conf['src_dir'])
ref_fname = ref_fname.replace(os.path.sep, "_")
binder_conf = check_binder_conf(gallery_conf.get('binder'))
binder_text = (" or to run this example in your browser via Binder"
if len(binder_conf) else "")
example_rst = (".. only:: html\n\n"
" .. note::\n"
" :class: sphx-glr-download-link-note\n\n"
" Click :ref:`here <sphx_glr_download_{0}>` "
" to download the full example code{1}\n"
" .. rst-class:: sphx-glr-example-title\n\n"
" .. _sphx_glr_{0}:\n\n"
).format(ref_fname, binder_text) + example_rst
if time_elapsed >= gallery_conf["min_reported_time"]:
time_m, time_s = divmod(time_elapsed, 60)
example_rst += TIMING_CONTENT.format(time_m, time_s)
if gallery_conf['show_memory']:
example_rst += ("**Estimated memory usage:** {0: .0f} MB\n\n"
.format(memory_used))
# Generate a binder URL if specified
binder_badge_rst = ''
if len(binder_conf) > 0:
binder_badge_rst += gen_binder_rst(example_file, binder_conf,
gallery_conf)
fname = os.path.basename(example_file)
example_rst += CODE_DOWNLOAD.format(fname,
replace_py_ipynb(fname),
binder_badge_rst,
ref_fname)
example_rst += SPHX_GLR_SIG
write_file_new = re.sub(r'\.py$', '.rst.new', example_file)
with codecs.open(write_file_new, 'w', encoding="utf-8") as f:
f.write(example_rst)
# in case it wasn't in our pattern, only replace the file if it's
# still stale.
_replace_md5(write_file_new)
