Source code for sphinx_gallery.gen_gallery

# 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.
"""


import codecs
import copy
from datetime import timedelta, datetime
from difflib import get_close_matches
from importlib import import_module
from pathlib import Path
from textwrap import indent
import re
import os
import pathlib
from xml.sax.saxutils import quoteattr, escape
from itertools import chain

from sphinx.errors import ConfigError, ExtensionError
import sphinx.util
from sphinx.util.console import blue, red, purple, bold
from . import glr_path_static, __version__ as _sg_version
from .utils import _replace_md5, _has_optipng, _has_pypandoc, _has_graphviz
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, _import_matplotlib
from .docs_resolv import embed_code_links
from .downloads import generate_zipfiles
from .sorting import NumberOfCodeLinesSortKey
from .interactive_example import (
    copy_binder_files,
    check_binder_conf,
    check_jupyterlite_conf,
)
from .interactive_example import pre_configure_jupyterlite_sphinx
from .interactive_example import post_configure_jupyterlite_sphinx
from .interactive_example import create_jupyterlite_contents
from .directives import MiniGallery, ImageSg, imagesg_addnode
from .recommender import ExampleRecommender, _write_recommendations

_KNOWN_CSS = (
    "sg_gallery",
    "sg_gallery-binder",
    "sg_gallery-dataframe",
    "sg_gallery-rendered-html",
)


[docs] class DefaultResetArgv: """Provides default 'reset_argv' callable that returns empty list.""" def __repr__(self): return "DefaultResetArgv" def __call__(self, gallery_conf, script_vars): """Return empty list.""" return []
DEFAULT_GALLERY_CONF = { "filename_pattern": re.escape(os.sep) + "plot", "ignore_pattern": r"__init__\.py", "examples_dirs": os.path.join("..", "examples"), "example_extensions": {".py"}, "filetype_parsers": {}, "notebook_extensions": {".py"}, "reset_argv": DefaultResetArgv(), "subsection_order": None, "within_subsection_order": NumberOfCodeLinesSortKey, "gallery_dirs": "auto_examples", "backreferences_dir": None, "doc_module": (), "exclude_implicit_doc": set(), "reference_url": {}, "capture_repr": ("_repr_html_", "__repr__"), "ignore_repr_types": r"", # Build options # ------------- # 'plot_gallery' also accepts strings that evaluate to a bool, e.g. "True", # "False", "1", "0" so that they can be easily set via command line # switches of sphinx-build "plot_gallery": "True", "download_all_examples": True, "abort_on_example_error": False, "only_warn_on_example_error": False, "recommender": {"enable": False}, "failing_examples": {}, "passing_examples": [], "stale_examples": [], # ones that did not need to be run due to md5sum "run_stale_examples": False, "expected_failing_examples": set(), "thumbnail_size": (400, 280), # Default CSS does 0.4 scaling (160, 112) "min_reported_time": 0, "binder": {}, "jupyterlite": {}, "promote_jupyter_magic": False, "image_scrapers": ("matplotlib",), "compress_images": (), "reset_modules": ("matplotlib", "seaborn"), "reset_modules_order": "before", "first_notebook_cell": None, "last_notebook_cell": None, "notebook_images": False, "pypandoc": False, "remove_config_comments": False, "show_memory": False, "show_signature": True, "junit": "", "log_level": {"backreference_missing": "warning"}, "inspect_global_variables": True, "css": _KNOWN_CSS, "matplotlib_animations": False, "image_srcset": [], "default_thumb_file": None, "line_numbers": False, "nested_sections": True, "prefer_full_module": set(), "api_usage_ignore": ".*__.*__", "show_api_usage": False, # if this changes, change write_api_entries, too "copyfile_regex": "", } logger = sphinx.util.logging.getLogger("sphinx-gallery") def _bool_eval(x): """Evaluate bool only configs, to allow setting via -D on the command line.""" if isinstance(x, str): try: x = eval(x) except TypeError: pass return bool(x) def _update_gallery_conf_exclude_implicit_doc(gallery_conf): """Update gallery config exclude_implicit_doc. This is separate function for better testability. """ # prepare regex for exclusions from implicit documentation exclude_regex = ( re.compile("|".join(gallery_conf["exclude_implicit_doc"])) if gallery_conf["exclude_implicit_doc"] else False ) gallery_conf["exclude_implicit_doc_regex"] = exclude_regex def _update_gallery_conf_builder_inited( sphinx_gallery_conf, src_dir, plot_gallery=True, abort_on_example_error=False, builder_name="html", ): sphinx_gallery_conf.update(plot_gallery=plot_gallery) sphinx_gallery_conf.update(abort_on_example_error=abort_on_example_error) sphinx_gallery_conf["src_dir"] = src_dir # Make it easy to know which builder we're in sphinx_gallery_conf["builder_name"] = builder_name def _fill_gallery_conf_defaults(sphinx_gallery_conf, app=None, check_keys=True): """Handle user configs and update default gallery configs.""" gallery_conf = copy.deepcopy(DEFAULT_GALLERY_CONF) options = sorted(gallery_conf) extra_keys = sorted(set(sphinx_gallery_conf) - set(options)) if extra_keys and check_keys: msg = "Unknown key(s) in sphinx_gallery_conf:\n" for key in extra_keys: options = get_close_matches(key, options, cutoff=0.66) msg += repr(key) if len(options) == 1: msg += f", did you mean {options[0]!r}?" elif len(options) > 1: msg += f", did you mean one of {options!r}?" msg += "\n" raise ConfigError(msg.strip()) gallery_conf.update(sphinx_gallery_conf) # XXX anything that can only be a bool (rather than str) should probably be # evaluated this way as it allows setting via -D on the command line for key in ( "promote_jupyter_magic", "run_stale_examples", ): gallery_conf[key] = _bool_eval(gallery_conf[key]) gallery_conf["app"] = app # Check capture_repr capture_repr = gallery_conf["capture_repr"] supported_reprs = ["__repr__", "__str__", "_repr_html_"] if isinstance(capture_repr, tuple): for rep in capture_repr: if rep not in supported_reprs: raise ConfigError( "All entries in 'capture_repr' must be one " f"of {supported_reprs}, got: {rep}" ) else: raise ConfigError(f"'capture_repr' must be a tuple, got: {type(capture_repr)}") # Check ignore_repr_types if not isinstance(gallery_conf["ignore_repr_types"], str): raise ConfigError( "'ignore_repr_types' must be a string, got: " + type(gallery_conf["ignore_repr_types"]) ) # deal with show_memory gallery_conf["memory_base"] = 0.0 if gallery_conf["show_memory"]: if not callable(gallery_conf["show_memory"]): # True-like try: from memory_profiler import memory_usage # noqa except ImportError: logger.warning( "Please install 'memory_profiler' to enable " "peak memory measurements." ) gallery_conf["show_memory"] = False else: def call_memory(func): mem, out = memory_usage( func, max_usage=True, retval=True, multiprocess=True ) try: mem = mem[0] # old MP always returned a list except TypeError: # 'float' object is not subscriptable pass return mem, out gallery_conf["call_memory"] = call_memory gallery_conf["memory_base"] = _get_memory_base(gallery_conf) else: gallery_conf["call_memory"] = gallery_conf["show_memory"] if not gallery_conf["show_memory"]: # can be set to False above def call_memory(func): return 0.0, func() gallery_conf["call_memory"] = call_memory assert callable(gallery_conf["call_memory"]) # 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 ConfigError( f"Unknown image scraper {orig_scraper!r}, got:\n{exp}" ) scrapers[si] = scraper if not callable(scraper): raise ConfigError(f"Scraper {scraper!r} was not callable") gallery_conf["image_scrapers"] = tuple(scrapers) del scrapers # Here we try to set up matplotlib but don't raise an error, # we will raise an error later when we actually try to use it # (if we do so) in scrapers.py. # In principle we could look to see if there is a matplotlib scraper # in our scrapers list, but this would be backward incompatible with # anyone using or relying on our Agg-setting behavior (e.g., for some # custom matplotlib SVG scraper as in our docs). # Eventually we can make this a config var like matplotlib_agg or something # if people need us not to set it to Agg. try: _import_matplotlib() except (ImportError, ValueError): pass # compress_images compress_images = gallery_conf["compress_images"] if isinstance(compress_images, str): compress_images = [compress_images] elif not isinstance(compress_images, (tuple, list)): raise ConfigError( "compress_images must be a tuple, list, or str, " f"got {type(compress_images)}" ) compress_images = list(compress_images) allowed_values = ("images", "thumbnails") pops = list() for ki, kind in enumerate(compress_images): if kind not in allowed_values: if kind.startswith("-"): pops.append(ki) continue raise ConfigError( "All entries in compress_images must be one of " f"{allowed_values} or a command-line switch " f'starting with "-", got {kind!r}' ) compress_images_args = [compress_images.pop(p) for p in pops[::-1]] if len(compress_images) and not _has_optipng(): logger.warning( "optipng binaries not found, PNG %s will not be optimized", " and ".join(compress_images), ) compress_images = () gallery_conf["compress_images"] = compress_images gallery_conf["compress_images_args"] = compress_images_args # 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 ConfigError(f"Unknown module resetter named {resetter!r}") resetters[ri] = _reset_dict[resetter] elif not callable(resetter): raise ConfigError(f"Module resetter {resetter!r} was not callable") gallery_conf["reset_modules"] = tuple(resetters) if not isinstance(gallery_conf["reset_modules_order"], str): raise ConfigError( "reset_modules_order must be a str, " f'got {gallery_conf["reset_modules_order"]!r}' ) if gallery_conf["reset_modules_order"] not in ["before", "after", "both"]: raise ConfigError( "reset_modules_order must be in" "['before', 'after', 'both'], " f"got {gallery_conf['reset_modules_order']!r}" ) 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 ConfigError( "The 'first_notebook_cell' parameter must be type " f"str or None, found type {type(first_cell)}" ) # Ensure the last cell text is a string if we have it last_cell = gallery_conf.get("last_notebook_cell") if (not isinstance(last_cell, str)) and (last_cell is not None): raise ConfigError( "The 'last_notebook_cell' parameter must be type str" f" or None, found type {type(last_cell)}" ) # Check pypandoc pypandoc = gallery_conf["pypandoc"] if not isinstance(pypandoc, (dict, bool)): raise ConfigError( "'pypandoc' parameter must be of type bool or dict," f"got: {type(pypandoc)}." ) gallery_conf["pypandoc"] = dict() if pypandoc is True else pypandoc has_pypandoc, version = _has_pypandoc() if isinstance(gallery_conf["pypandoc"], dict) and has_pypandoc is None: logger.warning( "'pypandoc' not available. Using Sphinx-Gallery to " "convert rst text blocks to markdown for .ipynb files." ) gallery_conf["pypandoc"] = False elif isinstance(gallery_conf["pypandoc"], dict): logger.info( "Using pandoc version: %s to convert rst text blocks to " "markdown for .ipynb files", version, ) else: logger.info( "Using Sphinx-Gallery to convert rst text blocks to " "markdown for .ipynb files." ) if isinstance(pypandoc, dict): accepted_keys = ("extra_args", "filters") for key in pypandoc: if key not in accepted_keys: raise ConfigError( "'pypandoc' only accepts the following key " f"values: {accepted_keys}, got: {key}." ) gallery_conf["titles"] = {} # Ensure 'backreferences_dir' is str, pathlib.Path or None backref = gallery_conf["backreferences_dir"] if (not isinstance(backref, (str, pathlib.Path))) and (backref is not None): raise ConfigError( "The 'backreferences_dir' parameter must be of type " "str, pathlib.Path or None, " f"found type {type(backref)}" ) # if 'backreferences_dir' is pathlib.Path, make str for Python <=3.5 # compatibility if isinstance(backref, pathlib.Path): gallery_conf["backreferences_dir"] = str(backref) # binder gallery_conf["binder"] = check_binder_conf(gallery_conf["binder"]) # jupyterlite gallery_conf["jupyterlite"] = check_jupyterlite_conf( gallery_conf.get("jupyterlite", {}), app ) if not isinstance(gallery_conf["css"], (list, tuple)): raise ConfigError( 'gallery_conf["css"] must be list or tuple, got ' f'{gallery_conf["css"]!r}' ) for css in gallery_conf["css"]: if css not in _KNOWN_CSS: raise ConfigError(f"Unknown css {css!r}, must be one of {_KNOWN_CSS!r}") if gallery_conf["app"] is not None: # can be None in testing gallery_conf["app"].add_css_file(css + ".css") # check API usage if not isinstance(gallery_conf["api_usage_ignore"], str): raise ConfigError( 'gallery_conf["api_usage_ignore"] must be str, ' f'got {type(gallery_conf["api_usage_ignore"])}' ) if ( not isinstance(gallery_conf["show_api_usage"], bool) and gallery_conf["show_api_usage"] != "unused" ): raise ConfigError( 'gallery_conf["show_api_usage"] must be True, False or "unused", ' f'got {gallery_conf["show_api_usage"]}' ) _update_gallery_conf_exclude_implicit_doc(gallery_conf) return gallery_conf
[docs] def get_subsections(srcdir, examples_dir, gallery_conf, check_for_index=True): """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[str, Any] Sphinx-Gallery configuration dictionary. check_for_index : bool only return subfolders with a ReadMe, default True 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 check_for_index: subfolders = [ subfolder for subfolder in subfolders if _get_readme( os.path.join(examples_dir, subfolder), gallery_conf, raise_error=False ) is not None ] else: # just make sure its a directory subfolders = [ subfolder for subfolder in subfolders if os.path.isdir(os.path.join(examples_dir, subfolder)) ] 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)) def _format_toctree(items, includehidden=False): """Format a toc tree.""" st = """ .. toctree:: :hidden:""" if includehidden: st += """ :includehidden: """ st += """ {}\n""".format( "\n ".join(items) ) st += "\n" return st SPHX_GLR_ORPHAN = """ :orphan: .. _{0}: """ SPHX_GLR_COMP_TIMES = ( SPHX_GLR_ORPHAN + """ 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 = "{:02d}:{:02d}.{:03d}".format( t.hour * 60 + t.minute, t.second, int(round(t.microsecond / 1000.0)) ) return t def _cost_key(cost): """Cost sorting function.""" # sort by descending computation time, descending memory, alphabetical name return (-cost["t"], -cost["mem"], cost["src_file"]) def _format_for_writing(costs, *, src_dir, kind="rst"): """Provide formatted computation summary text. Parameters ---------- costs: List[Dict] List of dicts of computation costs and paths, see gen_rst.py for details. src_dir : pathlib.Path The Sphinx source directory. kind: 'rst', 'rst-full' or 'console', default='rst' Format for printing to 'console' or for writing `sg_execution_times.rst' ('rst' for single galleries and 'rst-full' for all galleries). Returns ------- lines: List[List[str]] Formatted computation text for each example, of format: [example_file, time_elapsed, memory_used] lens: List[int] Character length of each string in `lines`. """ lines = list() for cost in sorted(costs, key=_cost_key): src_file = cost["src_file"] rel_path = os.path.relpath(src_file, src_dir) if kind in ("rst", "rst-full"): # like in sg_execution_times target_dir_clean = os.path.relpath(cost["target_dir"], src_dir).replace( os.path.sep, "_" ) paren = rel_path if kind == "rst-full" else os.path.basename(src_file) name = ":ref:`sphx_glr_{0}_{1}` (``{2}``)".format( target_dir_clean, os.path.basename(src_file), paren ) t = _sec_to_readable(cost["t"]) else: # like in generate_gallery assert kind == "console" name = rel_path t = f'{cost["t"]:0.2f} sec' m = f'{cost["mem"]:.1f} MB' lines.append([name, t, m]) lens = [max(x) for x in zip(*[[len(item) for item in cost] for cost in lines])] return lines, lens
[docs] def write_computation_times(gallery_conf, target_dir, costs): """Write computation times to `sg_execution_times.rst`. Parameters ---------- gallery_conf : Dict[str, Any] Sphinx-Gallery configuration dictionary. target_dir : str | None Path to directory where example python source file are. costs: List[Dict] List of dicts of computation costs and paths, see gen_rst.py for details. """ total_time = sum(cost["t"] for cost in costs) if target_dir is None: # all galleries together out_dir = gallery_conf["src_dir"] where = "all galleries" kind = "rst-full" ref_extra = "" else: # a single gallery out_dir = target_dir where = os.path.relpath(target_dir, gallery_conf["src_dir"]) kind = "rst" ref_extra = f'{where.replace(os.path.sep, "_")}_' new_ref = f"sphx_glr_{ref_extra}sg_execution_times" out_file = Path(out_dir) / "sg_execution_times.rst" if out_file.is_file() and total_time == 0: # a re-run return with out_file.open("w", encoding="utf-8") as fid: fid.write(SPHX_GLR_COMP_TIMES.format(new_ref)) fid.write( f"**{_sec_to_readable(total_time)}** total execution time for " f"{len(costs)} file{'s' if len(costs) != 1 else ''} **from {where}**:\n\n" ) lines, lens = _format_for_writing( costs, src_dir=gallery_conf["src_dir"], kind=kind, ) del costs # https://datatables.net/examples/styling/bootstrap5.html fid.write( # put it in a container to make the scoped style work """\ .. container:: .. raw:: html <style scoped> <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" /> <link href="https://cdn.datatables.net/1.13.6/css/dataTables.bootstrap5.min.css" rel="stylesheet" /> </style> <script src="https://code.jquery.com/jquery-3.7.0.js"></script> <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script> <script src="https://cdn.datatables.net/1.13.6/js/dataTables.bootstrap5.min.js"></script> <script type="text/javascript" class="init"> $(document).ready( function () { $('table.sg-datatable').DataTable({order: [[1, 'desc']]}); } ); </script> .. list-table:: :header-rows: 1 :class: table table-striped sg-datatable * - Example - Time - Mem (MB) """ # noqa: E501 ) # Need at least one entry or Sphinx complains for ex, t, mb in lines or [["N/A", "N/A", "N/A"]]: fid.write( f"""\ * - {ex} - {t} - {mb.rsplit(maxsplit=1)[0]} """ ) # remove the "MB" from the right
[docs] def write_api_entries(app, what, name, obj, options, lines): """Write api entries to `_sg_api_entries` configuration. To connect to `autodoc-process-docstring` event. Parameters ---------- app : The Sphinx application object. what: str The type of the object which the docstring belongs to. One of "module", "class", "exception", "function", "method", "attribute". name : The fully qualified name of the object. obj : The object itself. options : The options given to the directive: an object with attributes inherited_members, undoc_members, show_inheritance and no-index that are true if the flag option of same name was given to the auto directive. lines : The lines of the docstring, see above. """ if app.config.sphinx_gallery_conf["show_api_usage"] is False: return if "_sg_api_entries" not in app.config.sphinx_gallery_conf: app.config.sphinx_gallery_conf["_sg_api_entries"] = dict() if what not in app.config.sphinx_gallery_conf["_sg_api_entries"]: app.config.sphinx_gallery_conf["_sg_api_entries"][what] = set() app.config.sphinx_gallery_conf["_sg_api_entries"][what].add(name)
def _init_api_usage(gallery_dir): with codecs.open( os.path.join(gallery_dir, "sg_api_usage.rst"), "w", encoding="utf-8" ): pass # Colors from https://personal.sron.nl/~pault/data/colourschemes.pdf # 3 Diverging Colour Schemes, Figure 12, plus alpha=AA API_COLORS = dict( edge="#00000080", # gray (by alpha) okay="#98CAE180", # blue bad_1="#FEDA8B80", # yellow bad_2="#F67E4B80", # orange bad_3="#A5002680", # red ) def _make_graph(fname, entries, gallery_conf): """Make a graph of unused and used API entries. The used API entries themselves are documented in the list, so for the graph, we'll focus on the number of unused API entries per modules. Modules with lots of unused entries (11+) will be colored red, those with less (6+) will be colored orange, those with only a few (1-5) will be colored yellow and those with no unused entries will be colored blue. The API entries that are used are shown with one graph per module. That way you can see the examples that each API entry is used in for that module (if this was done for the whole project at once, the graph would get too large very large quickly). Parameters ---------- fname: str Path to '*sg_api_unused.dot' file. entries: Dict[str, List] or List[str] Used (List) or unused (Dict) API entries. gallery_conf : Dict[str, Any] Sphinx-Gallery configuration dictionary. """ import graphviz dg = graphviz.Digraph( filename=fname, graph_attr={ "overlap": "scale", "pad": "0.5", }, node_attr={ "color": API_COLORS["okay"], "style": "filled", "fontsize": "20", "shape": "box", "fontname": "Open Sans,Arial", }, ) if isinstance(entries, list): connections = set() lut = dict() # look up table for connections so they don't repeat structs = [entry.split(".") for entry in entries] for struct in sorted(structs, key=len): for level in range(len(struct) - 2): if (struct[level], struct[level + 1]) in connections: continue connections.add((struct[level], struct[level + 1])) node_from = ( lut[struct[level]] if struct[level] in lut else struct[level] ) dg.node(node_from) node_to = struct[level + 1] node_kwargs = dict() # count, don't show leaves if len(struct) - 3 == level: leaf_count = 0 for struct2 in structs: # find structures of the same length as struct if len(struct2) != level + 3: continue # find structures with two entries before # the leaf that are the same as struct if all( [ struct2[level2] == struct[level2] for level2 in range(level + 2) ] ): leaf_count += 1 node_to += f" ({leaf_count})" lut[struct[level + 1]] = node_to if leaf_count > 10: color_key = "bad_3" elif leaf_count > 5: color_key = "bad_2" else: color_key = "bad_1" node_kwargs["color"] = API_COLORS[color_key] dg.node(node_to, **node_kwargs) dg.edge(node_from, node_to, color=API_COLORS["edge"]) # add modules with all API entries for module in gallery_conf["_sg_api_entries"]["module"]: struct = module.split(".") for i in range(len(struct) - 1): if struct[i + 1] not in lut: dg.edge(struct[i], struct[i + 1]) else: assert isinstance(entries, dict) for entry, refs in entries.items(): dg.node(entry) for ref in refs: dg.node(ref, color=API_COLORS["bad_1"]) dg.edge(entry, ref, color=API_COLORS["edge"]) dg.save()
[docs] def write_api_entry_usage(app, docname, source): """Write an html page describing which API entries are used and unused. To document and graph only those API entries that are used by autodoc, we have to wait for autodoc to finish and hook into the ``source-read`` event. This intercepts the text from the rst such that it can be modified. Since, we only touched an empty file, we have to add 1) a list of all the API entries that are unused and a graph of the number of unused API entries per module and 2) a list of API entries that are used in examples, each with a sub-list of which examples that API entry is used in, and a graph that connects all of the API entries in a module to the examples that they are used in. Parameters ---------- app : The Sphinx application object. docname : Docname of the document currently being parsed. source : List whose single element is the contents of the source file """ docname = docname or "" # can be None on Sphinx 7.2 if docname != "sg_api_usage": return gallery_conf = app.config.sphinx_gallery_conf if gallery_conf["show_api_usage"] is False: return # since this is done at the gallery directory level (as opposed # to in a gallery directory, e.g. auto_examples), it runs last # which means that all the api entries will be in gallery_conf # Always write at least the title source[0] = SPHX_GLR_ORPHAN.format("sphx_glr_sg_api_usage") title = "Unused API Entries" source[0] += title + "\n" + "^" * len(title) + "\n\n" if ( "_sg_api_entries" not in gallery_conf or gallery_conf["backreferences_dir"] is None ): source[0] += "No API entries found, not computed.\n\n" return backreferences_dir = os.path.join( gallery_conf["src_dir"], gallery_conf["backreferences_dir"] ) example_files = set.union( *[ gallery_conf["_sg_api_entries"][obj_type] for obj_type in ("class", "method", "function") if obj_type in gallery_conf["_sg_api_entries"] ] ) if len(example_files) == 0: source[0] += "No examples run, not computed.\n\n" return def get_entry_type(entry): if entry in gallery_conf["_sg_api_entries"].get("class", []): return "class" elif entry in gallery_conf["_sg_api_entries"].get("method", []): return "meth" else: assert entry in gallery_conf["_sg_api_entries"]["function"] return "func" # find used and unused API entries unused_api_entries = list() used_api_entries = dict() for entry in example_files: # don't include built-in methods etc. if re.match(gallery_conf["api_usage_ignore"], entry) is not None: continue # check if backreferences empty example_fname = os.path.join(backreferences_dir, f"{entry}.examples.new") if not os.path.isfile(example_fname): # use without new example_fname = os.path.splitext(example_fname)[0] assert os.path.isfile(example_fname) if os.path.getsize(example_fname) == 0: unused_api_entries.append(entry) else: used_api_entries[entry] = list() with open(example_fname, encoding="utf-8") as fid2: for line in fid2: if line.startswith(" :ref:"): example_name = line.split("`")[1] used_api_entries[entry].append(example_name) for entry in sorted(unused_api_entries): source[0] += f"- :{get_entry_type(entry)}:`{entry}`\n" source[0] += "\n\n" has_graphviz = _has_graphviz() if has_graphviz and unused_api_entries: source[0] += ( ".. graphviz:: ./sg_api_unused.dot\n" " :alt: API unused entries graph\n" " :layout: neato\n\n" ) used_count = len(used_api_entries) total_count = used_count + len(unused_api_entries) used_percentage = used_count / max(total_count, 1) # avoid div by zero source[0] += ( "\nAPI entries used: " f"{round(used_percentage * 100, 2)}% " f"({used_count}/{total_count})\n\n" ) if has_graphviz and unused_api_entries: _make_graph( os.path.join(app.builder.srcdir, "sg_api_unused.dot"), unused_api_entries, gallery_conf, ) if gallery_conf["show_api_usage"] is True and used_api_entries: title = "Used API Entries" source[0] += title + "\n" + "^" * len(title) + "\n\n" for entry in sorted(used_api_entries): source[0] += f"- :{get_entry_type(entry)}:`{entry}`\n\n" for ref in used_api_entries[entry]: source[0] += f" - :ref:`{ref}`\n" source[0] += "\n\n" if has_graphviz: used_modules = {entry.split(".")[0] for entry in used_api_entries} for module in sorted(used_modules): source[0] += ( f"{module}\n" + "^" * len(module) + "\n\n" f".. graphviz:: ./{module}_sg_api_used.dot\n" f" :alt: {module} usage graph\n" " :layout: neato\n\n" ) for module in used_modules: logger.info("Making API usage graph for %s", module) # select and format entries for this module entries = dict() for entry, ref in used_api_entries.items(): if entry.split(".")[0] == module: entry = entry.replace("sphx_glr_", "") # remove prefix for target_dir in gallery_conf["gallery_dirs"]: if entry.startswith(target_dir): entry = entry[len(target_dir) + 1 :] _make_graph( os.path.join(app.builder.srcdir, f"{module}_sg_api_used.dot"), entries, gallery_conf, )
[docs] def clean_api_usage_files(app, exception): """Remove api usage .dot files. To connect to 'build-finished' event. """ if os.path.isfile(os.path.join(app.builder.srcdir, "sg_api_usage.rst")): os.remove(os.path.join(app.builder.srcdir, "sg_api_usage.rst")) if os.path.isfile(os.path.join(app.builder.srcdir, "sg_api_unused.dot")): os.remove(os.path.join(app.builder.srcdir, "sg_api_unused.dot")) for file in os.listdir(app.builder.srcdir): if "sg_api_used.dot" in file: os.remove(os.path.join(app.builder.srcdir, file))
[docs] def write_junit_xml(gallery_conf, target_dir, costs): """Write JUnit XML file of example run times, successes, and failures. Parameters ---------- gallery_conf : Dict[str, Any] Sphinx-Gallery configuration dictionary. target_dir : Union[str, pathlib.Path] Build directory. costs: List[Tuple[Tuple[float], str]] List of dicts of computation costs and paths, see gen_rst.py for details. """ 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 = 0.0 src_dir = gallery_conf["src_dir"] output = "" for cost in costs: t, fname = cost["t"], cost["src_file"] 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 += ( '<testcase classname={!s} file={!s} line="1" ' 'name={!s} time="{!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 += '<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 += "<failure message={!s}>{!s}</failure>".format( quoteattr(traceback.splitlines()[-1].strip()), escape(traceback) ) output += "</testcase>" n_tests += 1 elapsed += t output += "</testsuite>" output = ( '<?xml version="1.0" encoding="utf-8"?>' '<testsuite errors="0" failures="{}" name="sphinx-gallery" ' 'skipped="{}" tests="{}" time="{}">'.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"], f"{name}.examples", ) if not os.path.exists(examples_path): # touch file open(examples_path, "w").close()
def _expected_failing_examples(gallery_conf): return { 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["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 ) idt = " " if failing_as_expected: logger.info(bold("Examples failing as expected:"), color="blue") for fail_example in failing_as_expected: path = os.path.relpath(fail_example, gallery_conf["src_dir"]) logger.info( f"{bold(blue(path))} failed leaving traceback:\n\n" f"{indent(gallery_conf['failing_examples'][fail_example], idt)}" ) fail_msgs = [] if failing_unexpectedly: fail_msgs.append(bold(red("Unexpected failing examples:\n"))) for fail_example in failing_unexpectedly: path = os.path.relpath(fail_example, gallery_conf["src_dir"]) fail_msgs.append( f" {bold(red(path))} failed leaving traceback:\n\n" f"{indent(gallery_conf['failing_examples'][fail_example], idt)}" ) if passing_unexpectedly: paths = [ os.path.relpath(p, gallery_conf["src_dir"]) for p in passing_unexpectedly ] fail_msgs.append( bold(red("Examples expected to fail, but not failing:\n\n")) + red("\n".join(indent(p, idt) for p in paths)) + "\n\nPlease remove these examples from " + "sphinx_gallery_conf['expected_failing_examples'] " + "in your conf.py file." ) # 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: fail_message = bold( purple( "Here is a summary of the problems encountered " "when running the examples:\n\n" + "\n".join(fail_msgs) + "\n" + "-" * 79 ) ) if gallery_conf["only_warn_on_example_error"]: logger.warning(fail_message) else: raise ExtensionError(fail_message)
[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 example file name(s) found. Having duplicate file " "names will break some links. " "List of files: %s", sorted(dup_names), )
[docs] def check_spaces_in_filenames(files): """Check for spaces in filenames across example directories.""" regex = re.compile(r"[\s]") files_with_space = list(filter(regex.search, files)) if files_with_space: logger.warning( "Example file name(s) with space(s) found. Having space(s) in " "file names will break some links. " "List of files: %s", sorted(files_with_space), )
[docs] def get_default_config_value(key): """Get default configuration function.""" 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.""" 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") # Early filling of sphinx_gallery_conf defaults at config-inited app.connect("config-inited", fill_gallery_conf_defaults, priority=10) # set small priority value, so that pre_configure_jupyterlite_sphinx is # called before jupyterlite_sphinx config-inited app.connect("config-inited", pre_configure_jupyterlite_sphinx, priority=100) # set high priority value, so that post_configure_jupyterlite_sphinx is # called after jupyterlite_sphinx config-inited app.connect("config-inited", post_configure_jupyterlite_sphinx, priority=900) if "sphinx.ext.autodoc" in app.extensions: app.connect("autodoc-process-docstring", touch_empty_backreferences) app.connect("autodoc-process-docstring", write_api_entries) app.connect("source-read", write_api_entry_usage) # Add the custom directive app.add_directive("minigallery", MiniGallery) app.add_directive("image-sg", ImageSg) imagesg_addnode(app) # Early update of sphinx_gallery_conf at builder-inited app.connect("builder-inited", update_gallery_conf_builder_inited, priority=10) app.connect("builder-inited", generate_gallery_rst) app.connect("build-finished", copy_binder_files) app.connect("build-finished", create_jupyterlite_contents) app.connect("build-finished", summarize_failing_examples) app.connect("build-finished", embed_code_links) app.connect("build-finished", clean_api_usage_files) metadata = { "parallel_read_safe": True, "parallel_write_safe": True, "version": _sg_version, } return metadata
[docs] def setup_module(): """Hack to stop nosetests running setup() above.""" pass