# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
Sphinx-Gallery Generator
========================
Attaches Sphinx-Gallery to Sphinx in order to generate the galleries
when building the documentation.
"""
from __future__ import division, print_function, absolute_import
import codecs
import copy
from datetime import timedelta, datetime
from importlib import import_module
import re
import os
from xml.sax.saxutils import quoteattr, escape
from sphinx.util.console import red
from . import sphinx_compatibility, glr_path_static, __version__ as _sg_version
from .utils import _replace_md5
from .backreferences import _finalize_backreferences
from .gen_rst import (generate_dir_rst, SPHX_GLR_SIG, _get_memory_base,
_get_readme)
from .scrapers import _scraper_dict, _reset_dict
from .docs_resolv import embed_code_links
from .downloads import generate_zipfiles
from .sorting import NumberOfCodeLinesSortKey
from .binder import copy_binder_files
DEFAULT_GALLERY_CONF = {
'filename_pattern': re.escape(os.sep) + 'plot',
'ignore_pattern': r'__init__\.py',
'examples_dirs': os.path.join('..', 'examples'),
'subsection_order': None,
'within_subsection_order': NumberOfCodeLinesSortKey,
'gallery_dirs': 'auto_examples',
'backreferences_dir': None,
'doc_module': (),
'reference_url': {},
'capture_repr': ('_repr_html_','__repr__'),
# Build options
# -------------
# We use a string for 'plot_gallery' rather than simply the Python boolean
# `True` as it avoids a warning about unicode when controlling this value
# via the command line switches of sphinx-build
'plot_gallery': 'True',
'download_all_examples': True,
'abort_on_example_error': False,
'failing_examples': {},
'passing_examples': [],
'stale_examples': [], # ones that did not need to be run due to md5sum
'expected_failing_examples': set(),
'thumbnail_size': (400, 280), # Default CSS does 0.4 scaling (160, 112)
'min_reported_time': 0,
'binder': {},
'image_scrapers': ('matplotlib',),
'reset_modules': ('matplotlib', 'seaborn'),
'first_notebook_cell': '%matplotlib inline',
'remove_config_comments': False,
'show_memory': False,
'junit': '',
'log_level': {'backreference_missing': 'warning'},
'inspect_global_variables': True,
}
logger = sphinx_compatibility.getLogger('sphinx-gallery')
[docs]def parse_config(app):
"""Process the Sphinx Gallery configuration"""
try:
plot_gallery = eval(app.builder.config.plot_gallery)
except TypeError:
plot_gallery = bool(app.builder.config.plot_gallery)
src_dir = app.builder.srcdir
abort_on_example_error = app.builder.config.abort_on_example_error
lang = app.builder.config.highlight_language
gallery_conf = _complete_gallery_conf(
app.config.sphinx_gallery_conf, src_dir, plot_gallery,
abort_on_example_error, lang, app.builder.name, app)
# this assures I can call the config in other places
app.config.sphinx_gallery_conf = gallery_conf
app.config.html_static_path.append(glr_path_static())
return gallery_conf
def _complete_gallery_conf(sphinx_gallery_conf, src_dir, plot_gallery,
abort_on_example_error, lang='python',
builder_name='html', app=None):
gallery_conf = copy.deepcopy(DEFAULT_GALLERY_CONF)
gallery_conf.update(sphinx_gallery_conf)
if sphinx_gallery_conf.get('find_mayavi_figures', False):
logger.warning(
"Deprecated image scraping variable `find_mayavi_figures`\n"
"detected, use `image_scrapers` instead as:\n\n"
" image_scrapers=('matplotlib', 'mayavi')",
type=DeprecationWarning)
gallery_conf['image_scrapers'] += ('mayavi',)
gallery_conf.update(plot_gallery=plot_gallery)
gallery_conf.update(abort_on_example_error=abort_on_example_error)
gallery_conf['src_dir'] = src_dir
gallery_conf['app'] = app
if gallery_conf.get("mod_example_dir", False):
backreferences_warning = """\n========
Sphinx-Gallery found the configuration key 'mod_example_dir'. This
is deprecated, and you should now use the key 'backreferences_dir'
instead. Support for 'mod_example_dir' will be removed in a subsequent
version of Sphinx-Gallery. For more details, see the backreferences
documentation:
https://sphinx-gallery.github.io/configuration.html#references-to-examples""" # noqa: E501
gallery_conf['backreferences_dir'] = gallery_conf['mod_example_dir']
logger.warning(
backreferences_warning,
type=DeprecationWarning)
# deal with show_memory
if gallery_conf['show_memory']:
try:
from memory_profiler import memory_usage # noqa, analysis:ignore
except ImportError:
logger.warning("Please install 'memory_profiler' to enable peak "
"memory measurements.")
gallery_conf['show_memory'] = False
gallery_conf['memory_base'] = _get_memory_base(gallery_conf)
# deal with scrapers
scrapers = gallery_conf['image_scrapers']
if not isinstance(scrapers, (tuple, list)):
scrapers = [scrapers]
scrapers = list(scrapers)
for si, scraper in enumerate(scrapers):
if isinstance(scraper, str):
if scraper in _scraper_dict:
scraper = _scraper_dict[scraper]
else:
orig_scraper = scraper
try:
scraper = import_module(scraper)
scraper = getattr(scraper, '_get_sg_image_scraper')
scraper = scraper()
except Exception as exp:
raise ValueError('Unknown image scraper %r, got:\n%s'
% (orig_scraper, exp))
scrapers[si] = scraper
if not callable(scraper):
raise ValueError('Scraper %r was not callable' % (scraper,))
gallery_conf['image_scrapers'] = tuple(scrapers)
del scrapers
# deal with resetters
resetters = gallery_conf['reset_modules']
if not isinstance(resetters, (tuple, list)):
resetters = [resetters]
resetters = list(resetters)
for ri, resetter in enumerate(resetters):
if isinstance(resetter, str):
if resetter not in _reset_dict:
raise ValueError('Unknown module resetter named %r'
% (resetter,))
resetters[ri] = _reset_dict[resetter]
elif not callable(resetter):
raise ValueError('Module resetter %r was not callable'
% (resetter,))
gallery_conf['reset_modules'] = tuple(resetters)
lang = lang if lang in ('python', 'python3', 'default') else 'python'
gallery_conf['lang'] = lang
del resetters
# Ensure the first cell text is a string if we have it
first_cell = gallery_conf.get("first_notebook_cell")
if (not isinstance(first_cell, str)) and (first_cell is not None):
raise ValueError("The 'first_notebook_cell' parameter must be type str"
"or None, found type %s" % type(first_cell))
gallery_conf['first_notebook_cell'] = first_cell
# Make it easy to know which builder we're in
gallery_conf['builder_name'] = builder_name
gallery_conf['titles'] = {}
return gallery_conf
[docs]def get_subsections(srcdir, examples_dir, gallery_conf):
"""Return the list of subsections of a gallery.
Parameters
----------
srcdir : str
absolute path to directory containing conf.py
examples_dir : str
path to the examples directory relative to conf.py
gallery_conf : dict
The gallery configuration.
Returns
-------
out : list
sorted list of gallery subsection folder names
"""
sortkey = gallery_conf['subsection_order']
subfolders = [subfolder for subfolder in os.listdir(examples_dir)
if _get_readme(os.path.join(examples_dir, subfolder),
gallery_conf, raise_error=False) is not None]
base_examples_dir_path = os.path.relpath(examples_dir, srcdir)
subfolders_with_path = [os.path.join(base_examples_dir_path, item)
for item in subfolders]
sorted_subfolders = sorted(subfolders_with_path, key=sortkey)
return [subfolders[i] for i in [subfolders_with_path.index(item)
for item in sorted_subfolders]]
def _prepare_sphx_glr_dirs(gallery_conf, srcdir):
"""Creates necessary folders for sphinx_gallery files """
examples_dirs = gallery_conf['examples_dirs']
gallery_dirs = gallery_conf['gallery_dirs']
if not isinstance(examples_dirs, list):
examples_dirs = [examples_dirs]
if not isinstance(gallery_dirs, list):
gallery_dirs = [gallery_dirs]
if bool(gallery_conf['backreferences_dir']):
backreferences_dir = os.path.join(
srcdir, gallery_conf['backreferences_dir'])
if not os.path.exists(backreferences_dir):
os.makedirs(backreferences_dir)
return list(zip(examples_dirs, gallery_dirs))
[docs]def generate_gallery_rst(app):
"""Generate the Main examples gallery reStructuredText
Start the sphinx-gallery configuration and recursively scan the examples
directories in order to populate the examples gallery
"""
logger.info('generating gallery...', color='white')
gallery_conf = parse_config(app)
seen_backrefs = set()
costs = []
workdirs = _prepare_sphx_glr_dirs(gallery_conf,
app.builder.srcdir)
# Check for duplicate filenames to make sure linking works as expected
examples_dirs = [ex_dir for ex_dir, _ in workdirs]
files = collect_gallery_files(examples_dirs)
check_duplicate_filenames(files)
for examples_dir, gallery_dir in workdirs:
examples_dir = os.path.join(app.builder.srcdir, examples_dir)
gallery_dir = os.path.join(app.builder.srcdir, gallery_dir)
# Here we don't use an os.walk, but we recurse only twice: flat is
# better than nested.
this_fhindex, this_costs = generate_dir_rst(
examples_dir, gallery_dir, gallery_conf, seen_backrefs)
costs += this_costs
write_computation_times(gallery_conf, gallery_dir, this_costs)
# we create an index.rst with all examples
index_rst_new = os.path.join(gallery_dir, 'index.rst.new')
with codecs.open(index_rst_new, 'w', encoding='utf-8') as fhindex:
# :orphan: to suppress "not included in TOCTREE" sphinx warnings
fhindex.write(":orphan:\n\n" + this_fhindex)
for subsection in get_subsections(
app.builder.srcdir, examples_dir, gallery_conf):
src_dir = os.path.join(examples_dir, subsection)
target_dir = os.path.join(gallery_dir, subsection)
this_fhindex, this_costs = \
generate_dir_rst(src_dir, target_dir, gallery_conf,
seen_backrefs)
fhindex.write(this_fhindex)
costs += this_costs
write_computation_times(gallery_conf, target_dir, this_costs)
if gallery_conf['download_all_examples']:
download_fhindex = generate_zipfiles(gallery_dir)
fhindex.write(download_fhindex)
fhindex.write(SPHX_GLR_SIG)
_replace_md5(index_rst_new)
_finalize_backreferences(seen_backrefs, gallery_conf)
if gallery_conf['plot_gallery']:
logger.info("computation time summary:", color='white')
lines, lens = _format_for_writing(
costs, os.path.normpath(gallery_conf['src_dir']), kind='console')
for name, t, m in lines:
text = (' - %s: ' % (name,)).ljust(lens[0] + 10)
if t is None:
text += '(not run)'
logger.info(text)
else:
t_float = float(t.split()[0])
if t_float >= gallery_conf['min_reported_time']:
text += t.rjust(lens[1]) + ' ' + m.rjust(lens[2])
logger.info(text)
# Also create a junit.xml file, useful e.g. on CircleCI
write_junit_xml(gallery_conf, app.builder.outdir, costs)
SPHX_GLR_COMP_TIMES = """
:orphan:
.. _{0}:
Computation times
=================
"""
def _sec_to_readable(t):
"""Convert a number of seconds to a more readable representation."""
# This will only work for < 1 day execution time
# And we reserve 2 digits for minutes because presumably
# there aren't many > 99 minute scripts, but occasionally some
# > 9 minute ones
t = datetime(1, 1, 1) + timedelta(seconds=t)
t = '{0:02d}:{1:02d}.{2:03d}'.format(
t.hour * 60 + t.minute, t.second,
int(round(t.microsecond / 1000.)))
return t
[docs]def cost_name_key(cost_name):
cost, name = cost_name
# sort by descending computation time, descending memory, alphabetical name
return (-cost[0], -cost[1], name)
def _format_for_writing(costs, path, kind='rst'):
lines = list()
for cost in sorted(costs, key=cost_name_key):
if kind == 'rst': # like in sg_execution_times
name = ':ref:`sphx_glr_{0}_{1}` (``{1}``)'.format(
path, os.path.basename(cost[1]))
t = _sec_to_readable(cost[0][0])
else: # like in generate_gallery
assert kind == 'console'
name = os.path.relpath(cost[1], path)
t = '%0.2f sec' % (cost[0][0],)
m = '{0:.1f} MB'.format(cost[0][1])
lines.append([name, t, m])
lens = [max(x) for x in zip(*[[len(l) for l in ll] for ll in lines])]
return lines, lens
[docs]def write_computation_times(gallery_conf, target_dir, costs):
total_time = sum(cost[0][0] for cost in costs)
if total_time == 0:
return
target_dir_clean = os.path.relpath(
target_dir, gallery_conf['src_dir']).replace(os.path.sep, '_')
new_ref = 'sphx_glr_%s_sg_execution_times' % target_dir_clean
with codecs.open(os.path.join(target_dir, 'sg_execution_times.rst'), 'w',
encoding='utf-8') as fid:
fid.write(SPHX_GLR_COMP_TIMES.format(new_ref))
fid.write('**{0}** total execution time for **{1}** files:\n\n'
.format(_sec_to_readable(total_time), target_dir_clean))
lines, lens = _format_for_writing(costs, target_dir_clean)
del costs
hline = ''.join(('+' + '-' * (l + 2)) for l in lens) + '+\n'
fid.write(hline)
format_str = ''.join('| {%s} ' % (ii,)
for ii in range(len(lines[0]))) + '|\n'
for line in lines:
line = [ll.ljust(len_) for ll, len_ in zip(line, lens)]
text = format_str.format(*line)
assert len(text) == len(hline)
fid.write(text)
fid.write(hline)
[docs]def write_junit_xml(gallery_conf, target_dir, costs):
if not gallery_conf['junit'] or not gallery_conf['plot_gallery']:
return
failing_as_expected, failing_unexpectedly, passing_unexpectedly = \
_parse_failures(gallery_conf)
n_tests = 0
n_failures = 0
n_skips = 0
elapsed = 0.
src_dir = gallery_conf['src_dir']
output = ''
for cost in costs:
(t, _), fname = cost
if not any(fname in x for x in (gallery_conf['passing_examples'],
failing_unexpectedly,
failing_as_expected,
passing_unexpectedly)):
continue # not subselected by our regex
title = gallery_conf['titles'][fname]
output += (
u'<testcase classname={0!s} file={1!s} line="1" '
u'name={2!s} time="{3!r}">'
.format(quoteattr(os.path.splitext(os.path.basename(fname))[0]),
quoteattr(os.path.relpath(fname, src_dir)),
quoteattr(title), t))
if fname in failing_as_expected:
output += u'<skipped message="expected example failure"></skipped>'
n_skips += 1
elif fname in failing_unexpectedly or fname in passing_unexpectedly:
if fname in failing_unexpectedly:
traceback = gallery_conf['failing_examples'][fname]
else: # fname in passing_unexpectedly
traceback = 'Passed even though it was marked to fail'
n_failures += 1
output += (u'<failure message={0!s}>{1!s}</failure>'
.format(quoteattr(traceback.splitlines()[-1].strip()),
escape(traceback)))
output += u'</testcase>'
n_tests += 1
elapsed += t
output += u'</testsuite>'
output = (u'<?xml version="1.0" encoding="utf-8"?>'
u'<testsuite errors="0" failures="{0}" name="sphinx-gallery" '
u'skipped="{1}" tests="{2}" time="{3}">'
.format(n_failures, n_skips, n_tests, elapsed)) + output
# Actually write it
fname = os.path.normpath(os.path.join(target_dir, gallery_conf['junit']))
junit_dir = os.path.dirname(fname)
if not os.path.isdir(junit_dir):
os.makedirs(junit_dir)
with codecs.open(fname, 'w', encoding='utf-8') as fid:
fid.write(output)
[docs]def touch_empty_backreferences(app, what, name, obj, options, lines):
"""Generate empty back-reference example files.
This avoids inclusion errors/warnings if there are no gallery
examples for a class / module that is being parsed by autodoc"""
if not bool(app.config.sphinx_gallery_conf['backreferences_dir']):
return
examples_path = os.path.join(app.srcdir,
app.config.sphinx_gallery_conf[
"backreferences_dir"],
"%s.examples" % name)
if not os.path.exists(examples_path):
# touch file
open(examples_path, 'w').close()
def _expected_failing_examples(gallery_conf):
return set(
os.path.normpath(os.path.join(gallery_conf['src_dir'], path))
for path in gallery_conf['expected_failing_examples'])
def _parse_failures(gallery_conf):
"""Split the failures."""
failing_examples = set(gallery_conf['failing_examples'].keys())
expected_failing_examples = _expected_failing_examples(gallery_conf)
failing_as_expected = failing_examples.intersection(
expected_failing_examples)
failing_unexpectedly = failing_examples.difference(
expected_failing_examples)
passing_unexpectedly = expected_failing_examples.difference(
failing_examples)
# filter from examples actually run
passing_unexpectedly = [
src_file for src_file in passing_unexpectedly
if re.search(gallery_conf.get('filename_pattern'), src_file)]
return failing_as_expected, failing_unexpectedly, passing_unexpectedly
[docs]def summarize_failing_examples(app, exception):
"""Collects the list of falling examples and prints them with a traceback.
Raises ValueError if there where failing examples.
"""
if exception is not None:
return
# Under no-plot Examples are not run so nothing to summarize
if not app.config.sphinx_gallery_conf['plot_gallery']:
logger.info('Sphinx-gallery gallery_conf["plot_gallery"] was '
'False, so no examples were executed.', color='brown')
return
gallery_conf = app.config.sphinx_gallery_conf
failing_as_expected, failing_unexpectedly, passing_unexpectedly = \
_parse_failures(gallery_conf)
if failing_as_expected:
logger.info("Examples failing as expected:", color='brown')
for fail_example in failing_as_expected:
logger.info('%s failed leaving traceback:', fail_example,
color='brown')
logger.info(gallery_conf['failing_examples'][fail_example],
color='brown')
fail_msgs = []
if failing_unexpectedly:
fail_msgs.append(red("Unexpected failing examples:"))
for fail_example in failing_unexpectedly:
fail_msgs.append(fail_example + ' failed leaving traceback:\n' +
gallery_conf['failing_examples'][fail_example] +
'\n')
if passing_unexpectedly:
fail_msgs.append(red("Examples expected to fail, but not failing:\n") +
"Please remove these examples from\n" +
"sphinx_gallery_conf['expected_failing_examples']\n" +
"in your conf.py file"
"\n".join(passing_unexpectedly))
# standard message
n_good = len(gallery_conf['passing_examples'])
n_tot = len(gallery_conf['failing_examples']) + n_good
n_stale = len(gallery_conf['stale_examples'])
logger.info('\nSphinx-gallery successfully executed %d out of %d '
'file%s subselected by:\n\n'
' gallery_conf["filename_pattern"] = %r\n'
' gallery_conf["ignore_pattern"] = %r\n'
'\nafter excluding %d file%s that had previously been run '
'(based on MD5).\n'
% (n_good, n_tot, 's' if n_tot != 1 else '',
gallery_conf['filename_pattern'],
gallery_conf['ignore_pattern'],
n_stale, 's' if n_stale != 1 else '',
),
color='brown')
if fail_msgs:
raise ValueError("Here is a summary of the problems encountered when "
"running the examples\n\n" + "\n".join(fail_msgs) +
"\n" + "-" * 79)
[docs]def collect_gallery_files(examples_dirs):
"""Collect python files from the gallery example directories."""
files = []
for example_dir in examples_dirs:
for root, dirnames, filenames in os.walk(example_dir):
for filename in filenames:
if filename.endswith('.py'):
files.append(os.path.join(root, filename))
return files
[docs]def check_duplicate_filenames(files):
"""Check for duplicate filenames across gallery directories."""
# Check whether we'll have duplicates
used_names = set()
dup_names = list()
for this_file in files:
this_fname = os.path.basename(this_file)
if this_fname in used_names:
dup_names.append(this_file)
else:
used_names.add(this_fname)
if len(dup_names) > 0:
logger.warning(
'Duplicate file name(s) found. Having duplicate file names will '
'break some links. List of files: {}'.format(sorted(dup_names),))
[docs]def get_default_config_value(key):
def default_getter(conf):
return conf['sphinx_gallery_conf'].get(key, DEFAULT_GALLERY_CONF[key])
return default_getter
[docs]def setup(app):
"""Setup sphinx-gallery sphinx extension"""
sphinx_compatibility._app = app
app.add_config_value('sphinx_gallery_conf', DEFAULT_GALLERY_CONF, 'html')
for key in ['plot_gallery', 'abort_on_example_error']:
app.add_config_value(key, get_default_config_value(key), 'html')
app.add_css_file('gallery.css')
if 'sphinx.ext.autodoc' in app.extensions:
app.connect('autodoc-process-docstring', touch_empty_backreferences)
app.connect('builder-inited', generate_gallery_rst)
app.connect('build-finished', copy_binder_files)
app.connect('build-finished', summarize_failing_examples)
app.connect('build-finished', embed_code_links)
metadata = {'parallel_read_safe': True,
'parallel_write_safe': True,
'version': _sg_version}
return metadata
[docs]def setup_module():
# HACK: Stop nosetests running setup() above
pass