gen_rst.py

# Author: Óscar Nájera
# License: 3-clause BSD
"""reST file generator.

Generate the rst files for the examples by iterating over the python
example files.

Files that generate images should start with 'plot'.
"""

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
from pathlib import Path
import re
import stat
from textwrap import indent
import warnings
from shutil import copyfile
import subprocess
import sys
import traceback
import codeop

from sphinx.errors import ExtensionError
import sphinx.util

from .scrapers import save_figures, ImagePathIterator, clean_modules, _find_image_ext
from .utils import (
    scale_image,
    get_md5sum,
    _replace_md5,
    optipng,
    status_iterator,
)
from . import glr_path_static
from .backreferences import (
    _write_backreferences,
    _thumbnail_div,
    identify_names,
    _make_ref_regex,
    THUMBNAIL_PARENT_DIV,
    THUMBNAIL_PARENT_DIV_CLOSE,
)
from . import py_source_parser
from .block_parser import BlockParser

from .notebook import jupyter_notebook, save_notebook
from .interactive_example import gen_binder_rst
from .interactive_example import gen_jupyterlite_rst


logger = sphinx.util.logging.getLogger("sphinx-gallery")


###############################################################################


class _LoggingTee:
    """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()

        # For TextIO compatibility
        self.closed = False
        self.encoding = "utf-8"

    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 = ""

    # For TextIO compatibility
    def close(self):
        pass

    def fileno(self):
        return self.output.fileno()

    def isatty(self):
        return self.output.isatty()

    def readable(self):
        return False

    def seekable(self):
        return False

    def tell(self):
        return self.output.tell()

    def writable(self):
        return True

    @property
    def errors(self):
        return self.output.errors

    @property
    def newlines(self):
        return self.output.newlines

    # 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
"""

CODE_OUTPUT = """.. rst-class:: sphx-glr-script-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

    <div class="output_subarea output_html rendered_html output_result">
{0}
    </div>
    <br />
    <br />"""

DOWNLOAD_LINKS_HEADER = """
.. _sphx_glr_download_{0}:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example
"""

CODE_DOWNLOAD = """
    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download {1} source code: {0} <{0}>`
"""

NOTEBOOK_DOWNLOAD = """
    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: {0} <{0}>`
"""

RECOMMENDATIONS_INCLUDE = """\n
.. include:: {0}.recommendations
"""


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 = f"   :lineno-start: {lineno + blank_lines}\n"
    else:
        lineno = ""
    # If the whole block is indented, prevent Sphinx from removing too much whitespace
    dedent = "   :dedent: 1\n"
    for line in codestr.splitlines():
        if line and not line.startswith((" ", "\t")):
            dedent = ""
            break
    code_directive = f".. code-block:: {lang}\n{dedent}{lineno}\n"
    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)

    # **string** --> string
    string = re.sub(r"\*\*([^\*]*)\*\*", r"\1", string)
    # *string* --> string
    string = re.sub(r"\*([^\*]*)\*", r"\1", string)
    # `link text <url>`_ --> link text
    string = re.sub(r"`([^`<>]+) <[^`<>]+>`\_\_?", r"\1", string)

    # :anchor:`the term` --> the term
    string = re.sub(r":[a-z]+:`([^`<>]+)( <[^`<>]+>)?`", r"\1", string)

    # r'\\dfrac' --> r'\dfrac'
    string = string.replace("\\\\", "\\")

    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(
            f"Could not find a title in first paragraph:\n{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] + "..."

    title = _sanitize_rst(title)

    return intro, title


def md5sum_is_current(src_file, mode="b"):
    """Checks whether src_file has the same md5 hash as the one on disk."""
    src_md5 = get_md5sum(src_file, mode)

    src_md5_file = str(src_file) + ".md5"
    if os.path.exists(src_md5_file):
        with open(src_md5_file) as file_checksum:
            ref_md5 = file_checksum.read()

        return src_md5 == ref_md5

    return False


def save_thumbnail(image_path_template, src_file, script_vars, 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
    script_vars : dict
        Configuration and run time variables
    file_conf : dict
        File-specific settings given in source file comments as:
        ``# sphinx_gallery_<name> = <value>``
    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, "
                f"got {thumbnail_number!r}"
            )
        # negative index means counting from the last one
        if thumbnail_number < 0:
            thumbnail_number += len(script_vars["image_path_iterator"]) + 1
        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, f"sphx_glr_{base_image_name}_thumb.{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
        default_thumb_path = gallery_conf["default_thumb_file"]
        if default_thumb_path is None:
            default_thumb_path = os.path.join(
                glr_path_static(),
                "no_image.png",
            )
        img, ext = _find_image_ext(default_thumb_path)
    else:
        return
    # update extension, since gallery_conf setting can be different
    # from file_conf
    # Here we have to do .new.ext so that optipng and PIL behave well
    thumb_file = f"{os.path.splitext(thumb_file)[0]}.new.{ext}"
    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"])
    fname_old = f"{os.path.splitext(thumb_file)[0][:-3]}{ext}"
    _replace_md5(thumb_file, fname_old=fname_old)


def _get_readme(dir_, gallery_conf, raise_error=True):
    # first check if there is an index.rst and that index.rst is in the
    # copyfile regexp:
    if re.match(gallery_conf["copyfile_regex"], "index.rst"):
        fpth = os.path.join(dir_, "index.rst")
        if os.path.isfile(fpth):
            return None
    # now look for README.txt, README.rst etc...
    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 {} does not have a README file with one "
            "of the expected file extensions {}. Please write one to "
            "introduce your gallery.".format(dir_, extensions)
        )
    return None


def generate_dir_rst(
    src_dir,
    target_dir,
    gallery_conf,
    seen_backrefs,
    include_toctree=True,
):
    """Generate the gallery reStructuredText for an example directory.

    Parameters
    ----------
    src_dir: str,
        Path to example directory containing python files
        and possibly sub categories
    target_dir: str,
        Path where parsed examples (rst, python files, etc)
        will be outputted
    gallery_conf : Dict[str, Any]
        Gallery configurations.
    seen_backrefs: set,
        Back references encountered when parsing this gallery
        will be stored in this set.
    include_toctree: bool
        Whether or not toctree should be included
        in generated rst file.
        Default = True.

    Returns
    -------
    index_path: str,
        Path to index rst file presenting the current example gallery
    index_content: str,
        Content which will be written to the index rst file
        presenting the current example gallery
    costs: List[Dict]
        List of dicts of costs for building each element of the gallery
         with keys "t", "mem", "src_file", and "target_dir".
    toctree_items: list,
        List of files included in toctree
        (independent of include_toctree's value)
    """
    head_ref = os.path.relpath(target_dir, gallery_conf["src_dir"])

    subsection_index_content = ""
    subsection_readme_fname = _get_readme(src_dir, gallery_conf)
    have_index_rst = False
    if subsection_readme_fname:
        with codecs.open(subsection_readme_fname, "r", encoding="utf-8") as fid:
            subsection_readme_content = fid.read()
            subsection_index_content += subsection_readme_content
    else:
        have_index_rst = True

    # Add empty lines to avoid bug in issue #165
    subsection_index_content += "\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 (s := Path(fname).suffix) and s in gallery_conf["example_extensions"]
    ]
    # 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)
    )

    # Add div containing all thumbnails;
    # this is helpful for controlling grid or flexbox behaviours
    subsection_index_content += THUMBNAIL_PARENT_DIV

    entries_text = []
    costs = []
    subsection_toctree_filenames = []
    build_target_dir = os.path.relpath(target_dir, gallery_conf["src_dir"])
    iterator = status_iterator(
        sorted_listdir,
        f"generating gallery for {build_target_dir}... ",
        length=len(sorted_listdir),
    )
    for fname in iterator:
        intro, title, (t, mem) = 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(dict(t=t, mem=mem, src_file=src_file, target_dir=target_dir))
        gallery_item_filename = (
            (Path(build_target_dir) / fname).with_suffix("").as_posix()
        )
        this_entry = _thumbnail_div(
            target_dir, gallery_conf["src_dir"], fname, intro, title
        )
        entries_text.append(this_entry)
        subsection_toctree_filenames.append("/" + gallery_item_filename)

    for entry_text in entries_text:
        subsection_index_content += entry_text

    # Close thumbnail parent div
    subsection_index_content += THUMBNAIL_PARENT_DIV_CLOSE

    # Write subsection index file
    # only if nested_sections is True
    subsection_index_path = None
    if gallery_conf["nested_sections"] is True and not have_index_rst:
        subsection_index_path = os.path.join(target_dir, "index.rst.new")
        with codecs.open(subsection_index_path, "w", encoding="utf-8") as (findex):
            findex.write(
                "\n\n.. _sphx_glr_{}:\n\n".format(head_ref.replace(os.path.sep, "_"))
            )
            findex.write(subsection_index_content)

            # Create toctree for index file
            # with all gallery items which belong to current subsection
            # and add it to generated index rst file if need be.
            # Toctree cannot be empty
            # and won't be added if include_toctree is false
            # (this is useful when generating the example gallery's main
            # index rst file, which should contain only one toctree)
            if len(subsection_toctree_filenames) > 0 and include_toctree:
                subsection_index_toctree = """
.. toctree::
   :hidden:

   {}\n
""".format(
                    "\n   ".join(subsection_toctree_filenames)
                )
                findex.write(subsection_index_toctree)

    if have_index_rst:
        # the user has supplied index.rst, so blank out the content
        subsection_index_content = None

    # Copy over any other files.
    copyregex = gallery_conf["copyfile_regex"]
    if copyregex:
        listdir = [fname for fname in os.listdir(src_dir) if re.match(copyregex, fname)]
        readme = _get_readme(src_dir, gallery_conf, raise_error=False)
        # don't copy over the readme
        if readme:
            listdir = [fname for fname in listdir if fname != os.path.basename(readme)]
        for fname in listdir:
            src_file = os.path.normpath(os.path.join(src_dir, fname))
            target_file = os.path.join(target_dir, fname)
            _replace_md5(src_file, fname_old=target_file, method="copy")

    return (
        subsection_index_path,
        subsection_index_content,
        costs,
        subsection_toctree_filenames,
    )


def handle_exception(exc_info, src_file, script_vars, gallery_conf):
    """Trim and format exception, maybe raise error, etc."""
    from .gen_gallery import _expected_failing_examples

    etype, exc, tb = exc_info
    stack = traceback.extract_tb(tb)
    # The full traceback will look something like:
    #
    #   File "/home/larsoner/python/sphinx-gallery/sphinx_gallery/gen_rst.py...
    #     mem_max, _ = gallery_conf['call_memory'](
    #   File "/home/larsoner/python/sphinx-gallery/sphinx_gallery/gen_galler...
    #     mem, out = memory_usage(func, max_usage=True, retval=True,
    #   File "/home/larsoner/.local/lib/python3.8/site-packages/memory_profi...
    #     returned = f(*args, **kw)
    #   File "/home/larsoner/python/sphinx-gallery/sphinx_gallery/gen_rst.py...
    #     exec(self.code, self.fake_main.__dict__)
    #   File "/home/larsoner/python/sphinx-gallery/sphinx_gallery/tests/tiny...
    #     raise RuntimeError('some error')
    # RuntimeError: some error
    #
    # But we should trim these to just the relevant trace at the user level,
    # so we inspect the traceback to find the start and stop points.
    start = 0
    stop = len(stack)
    root = os.path.dirname(__file__) + os.sep
    for ii, s in enumerate(stack, 1):
        # Trim our internal stack
        if s.filename.startswith(root + "gen_gallery.py") and s.name == "call_memory":
            start = max(ii, start)
        elif s.filename.startswith(root + "gen_rst.py"):
            # SyntaxError
            if s.name == "execute_code_block" and (
                "compile(" in s.line or "save_figures" in s.line
            ):
                start = max(ii, start)
            # Any other error
            elif s.name == "__call__":
                start = max(ii, start)
            # Our internal input() check
            elif s.name == "_check_input" and ii == len(stack):
                stop = ii - 1
    stack = stack[start:stop]

    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:
    """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 0.0
    # 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", f"import time, sys; time.sleep({sleep}); sys.exit(0)"],
        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] + [0.0]
    memory_base = max(memories)
    return memory_base


def _ast_module():
    """Get ast.Module function, dealing with: https://bugs.python.org/issue35894."""
    if sys.version_info >= (3, 8):
        ast_Module = partial(ast.Module, type_ignores=[])
    else:
        ast_Module = ast.Module
    return ast_Module


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 _exec_and_get_memory(compiler, ast_Module, code_ast, gallery_conf, script_vars):
    """Execute ast, capturing output if last line expression and get max mem usage.

    Parameters
    ----------
    compiler : codeop.Compile
        Compiler to compile AST of code block.
    ast_Module : Callable
        ast.Module function.
    code_ast : ast.Module
        AST parsed code to execute.
    gallery_conf : Dict[str, Any]
        Gallery configurations.
    script_vars : Dict[str, Any]
        Configuration and runtime variables.

    Returns
    -------
    is_last_expr : bool
        Whether the last expression in `code_ast` is an ast.Expr.
    mem_max : float
        Max memory used during execution.
    """
    src_file = script_vars["src_file"]
    # 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"]
            )
        )
        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"])
        )
    return is_last_expr, mem_max


def _get_last_repr(capture_repr, ___):
    """Get repr of last expression, using first method in 'capture_repr' available."""
    for meth in 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:
            last_repr = None
            repr_meth = None
        else:
            if isinstance(last_repr, str):
                break
    return last_repr, repr_meth


def _get_code_output(
    is_last_expr, example_globals, gallery_conf, logging_tee, images_rst, file_conf
):
    """Obtain standard output and html output in reST.

    Parameters
    ----------
    is_last_expr : bool
        Whether the last expression in executed code is an ast.Expr.
    example_globals: Dict[str, Any]
        Global variables for examples.
    logging_tee : _LoggingTee
        Logging tee.
    images_rst : str
        rst code to embed the images in the document.
    gallery_conf : Dict[str, Any]
        Gallery configurations.
    file_conf : Dict[str, Any]
        File-specific settings given in source file comments as:
        ``# sphinx_gallery_<name> = <value>``.

    Returns
    -------
    code_output : str
        reST of output of executed code block, including images and captured output.
    """
    last_repr = None
    repr_meth = None
    if is_last_expr:
        # capture the last repr variable
        ___ = example_globals["___"]
        ignore_repr = False
        if gallery_conf["ignore_repr_types"]:
            ignore_repr = re.search(gallery_conf["ignore_repr_types"], str(type(___)))
        capture_repr = file_conf.get("capture_repr", gallery_conf["capture_repr"])
        if capture_repr != () and not ignore_repr:
            last_repr, repr_meth = _get_last_repr(capture_repr, ___)

    captured_std = logging_tee.output.getvalue().expandtabs()
    # normal string output
    if repr_meth in ["__repr__", "__str__"] and last_repr:
        captured_std = f"{captured_std}\n{last_repr}"
    if captured_std and not captured_std.isspace():
        captured_std = CODE_OUTPUT.format(indent(captured_std, " " * 4))
    else:
        captured_std = ""

    # Sanitize ANSI escape characters for reST output
    ansi_escape = re.compile(r"\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])")
    captured_std = ansi_escape.sub("", captured_std)

    # give html output its own header
    if repr_meth == "_repr_html_":
        captured_html = HTML_HEADER.format(indent(last_repr, " " * 4))
    else:
        captured_html = ""

    code_output = f"\n{images_rst}\n\n{captured_std}\n{captured_html}\n\n"
    return code_output


def _reset_cwd_syspath(cwd, sys_path):
    """Reset cwd and sys.path."""
    os.chdir(cwd)
    sys.path = sys_path


def execute_code_block(
    compiler, block, example_globals, script_vars, gallery_conf, file_conf
):
    """Execute the code block of the example file.

    Parameters
    ----------
    compiler : codeop.Compile
        Compiler to compile AST of code block.
    block : List[Tuple[str, str, int]]
        List of Tuples, each Tuple contains label ('text' or 'code'),
        the corresponding content string of block and the leading line number.
    example_globals: Dict[str, Any]
        Global variables for examples.
    script_vars : Dict[str, Any]
        Configuration and runtime variables.
    gallery_conf : Dict[str, Any]
        Gallery configurations.
    file_conf : Dict[str, Any]
        File-specific settings given in source file comments as:
        ``# sphinx_gallery_<name> = <value>``.

    Returns
    -------
    code_output : str
        Output of executing code in reST.
    """
    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
    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())

    # Save figures unless there is a `sphinx_gallery_defer_figures` flag
    match = re.search(
        r"^[\ \t]*#\s*sphinx_gallery_defer_figures[\ \t]*\n?", bcontent, re.MULTILINE
    )
    need_save_figures = match is None

    try:
        ast_Module = _ast_module()
        code_ast = ast_Module([bcontent])
        flags = ast.PyCF_ONLY_AST | compiler.flags
        code_ast = compile(bcontent, src_file, "exec", flags, dont_inherit=1)
        ast.increment_lineno(code_ast, lineno - 1)

        is_last_expr, mem_max = _exec_and_get_memory(
            compiler, ast_Module, code_ast, gallery_conf, script_vars
        )
        script_vars["memory_delta"].append(mem_max)
        # This should be inside the try block, e.g., in case of a savefig error
        logging_tee.restore_std()
        if need_save_figures:
            need_save_figures = False
            images_rst = save_figures(block, script_vars, gallery_conf)
        else:
            images_rst = ""
    except Exception:
        logging_tee.restore_std()
        except_rst = handle_exception(
            sys.exc_info(), src_file, script_vars, gallery_conf
        )
        code_output = f"\n{except_rst}\n\n\n\n"
        # still call this even though we won't use the images so that
        # figures are closed
        if need_save_figures:
            save_figures(block, script_vars, gallery_conf)
    else:
        _reset_cwd_syspath(cwd, sys_path)

        code_output = _get_code_output(
            is_last_expr,
            example_globals,
            gallery_conf,
            logging_tee,
            images_rst,
            file_conf,
        )
    finally:
        _reset_cwd_syspath(cwd, sys_path)
        logging_tee.restore_std()

    return code_output


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["filename_pattern"]
    execute = re.search(filename_pattern, src_file) and gallery_conf["plot_gallery"]
    return execute


def _check_input(prompt=None):
    raise ExtensionError(
        "Cannot use input() builtin function in Sphinx-Gallery examples"
    )


def execute_script(script_blocks, script_vars, gallery_conf, file_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
    file_conf : dict
        File-specific settings given in source file comments as:
        ``# sphinx_gallery_<name> = <value>``

    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
            # Don't let them use input()
            "input": _check_input,
        }
    )
    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:] = gallery_conf["reset_argv"](gallery_conf, script_vars)
        gc.collect()
        memory_start, _ = gallery_conf["call_memory"](lambda: None)
    else:
        memory_start = 0.0

    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,
                    file_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"], "t"))
        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_elapsed, memory_used)`` 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 = Path(target_dir) / fname
    _replace_md5(src_file, target_file, "copy", mode="t")

    if fname.endswith(".py"):
        parser = py_source_parser
        language = "Python"
    else:
        parser = BlockParser(fname, gallery_conf)
        language = parser.language

    file_conf, script_blocks, node = parser.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, mode="t"):
        do_return = True
        if executable:
            if gallery_conf["run_stale_examples"]:
                do_return = False
            else:
                gallery_conf["stale_examples"].append(str(target_file))
        if do_return:
            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": str(target_file),
    }

    if executable and gallery_conf["reset_modules_order"] in ["before", "both"]:
        clean_modules(gallery_conf, fname, "before")
    output_blocks, time_elapsed = execute_script(
        script_blocks, script_vars, gallery_conf, file_conf
    )

    logger.debug("%s ran in : %.2g seconds\n", src_file, time_elapsed)

    # Create dummy images
    if not executable:
        dummy_image = file_conf.get("dummy_images", None)
        if dummy_image is not None:
            if isinstance(dummy_image, bool) or not isinstance(dummy_image, int):
                raise ExtensionError(
                    "sphinx_gallery_dummy_images setting is not an integer, "
                    "got {dummy_image!r}"
                )

            image_path_iterator = script_vars["image_path_iterator"]
            stock_img = os.path.join(glr_path_static(), "no_image.png")
            for _, path in zip(range(dummy_image), image_path_iterator):
                if not os.path.isfile(path):
                    copyfile(stock_img, path)

    # Ignore blocks must be processed before the
    # remaining config comments are removed.
    script_blocks = [
        (label, parser.remove_ignore_blocks(content), line_number)
        for label, content, line_number in script_blocks
    ]

    if gallery_conf["remove_config_comments"]:
        script_blocks = [
            (label, parser.remove_config_comments(content), line_number)
            for label, content, line_number in script_blocks
        ]

    # Remove final empty block, which can occur after config comments
    # are removed
    if script_blocks[-1][1].isspace():
        script_blocks = script_blocks[:-1]
        output_blocks = output_blocks[:-1]

    example_rst = rst_blocks(
        script_blocks, output_blocks, file_conf, gallery_conf, language=language
    )
    memory_used = gallery_conf["memory_base"] + script_vars["memory_delta"]
    if not executable:
        time_elapsed = memory_used = 0.0  # don't let the output change
    save_rst_example(
        example_rst,
        target_file,
        time_elapsed,
        memory_used,
        gallery_conf,
        language=language,
    )

    save_thumbnail(image_path_template, src_file, script_vars, file_conf, gallery_conf)

    if target_file.suffix in gallery_conf["notebook_extensions"]:
        example_nb = jupyter_notebook(script_blocks, gallery_conf, target_dir)
        ipy_fname = target_file.with_suffix(".ipynb.new")
        save_notebook(example_nb, ipy_fname)
        _replace_md5(ipy_fname, mode="t")

    # Write names
    if gallery_conf["inspect_global_variables"]:
        global_variables = script_vars["example_globals"]
    else:
        global_variables = None
    ref_regex = _make_ref_regex(gallery_conf["app"].config)
    example_code_obj = identify_names(script_blocks, ref_regex, global_variables, node)
    if example_code_obj:
        codeobj_fname = target_file.with_name(target_file.stem + "_codeobj.pickle.new")
        with open(codeobj_fname, "wb") as fid:
            pickle.dump(example_code_obj, fid, pickle.HIGHEST_PROTOCOL)
        _replace_md5(codeobj_fname)
    exclude_regex = gallery_conf["exclude_implicit_doc_regex"]
    backrefs = {
        "{module_short}.{name}".format(**cobj)
        for cobjs in example_code_obj.values()
        for cobj in cobjs
        if cobj["module"].startswith(gallery_conf["doc_module"])
        and (
            cobj["is_explicit"]
            or (not exclude_regex)
            or (not exclude_regex.search("{module}.{name}".format(**cobj)))
        )
    }

    # Write backreferences
    _write_backreferences(
        backrefs, seen_backrefs, gallery_conf, target_dir, fname, intro, title
    )

    # This can help with garbage collection in some instances
    if global_variables is not None and "___" in global_variables:
        del global_variables["___"]
    del script_vars, global_variables  # don't keep these during reset
    if executable and gallery_conf["reset_modules_order"] in ["after", "both"]:
        clean_modules(gallery_conf, fname, "after")

    return intro, title, (time_elapsed, memory_used)


EXAMPLE_HEADER = """
.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "{0}"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_{1}>`
        to download the full example code{2}

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_{1}:

"""
RST_BLOCK_HEADER = """\
.. GENERATED FROM PYTHON SOURCE LINES {0}-{1}

"""


def rst_blocks(
    script_blocks, output_blocks, file_conf, gallery_conf, *, language="python"
):
    """Generate 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>``
    language : str
        The language to be used for syntax highlighting in code blocks. Must be a name
        or alias recognized by Pygments.
    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 = ""
    for bi, ((blabel, bcontent, lineno), code_output) in enumerate(
        zip(script_blocks, output_blocks)
    ):
        # do not add comment to the title block, otherwise the linking does
        # not work properly
        if bi > 0:
            example_rst += RST_BLOCK_HEADER.format(
                lineno, lineno + bcontent.count("\n")
            )
        if blabel == "code":
            if not file_conf.get("line_numbers", gallery_conf["line_numbers"]):
                lineno = None

            code_rst = codestr2rst(bcontent, lang=language, 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,
    *,
    language="python",
):
    """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
    language : str
        Name of the programming language the example is in
    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
    """
    example_file = Path(example_file)
    example_fname = str(example_file.relative_to(gallery_conf["src_dir"]))
    ref_fname = example_fname.replace(os.path.sep, "_")

    binder_conf = gallery_conf["binder"]
    is_binder_enabled = len(binder_conf) > 0

    jupyterlite_conf = gallery_conf["jupyterlite"]
    is_jupyterlite_enabled = jupyterlite_conf is not None

    interactive_example_text = ""
    if is_binder_enabled or is_jupyterlite_enabled:
        interactive_example_text += " or to run this example in your browser via "

    if is_binder_enabled and is_jupyterlite_enabled:
        interactive_example_text += "JupyterLite or Binder"
    elif is_binder_enabled:
        interactive_example_text += "Binder"
    elif is_jupyterlite_enabled:
        interactive_example_text += "JupyterLite"

    example_rst = (
        EXAMPLE_HEADER.format(example_fname, ref_fname, interactive_example_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 += f"**Estimated memory usage:** {memory_used: .0f} MB\n\n"

    example_rst += DOWNLOAD_LINKS_HEADER.format(ref_fname)

    save_notebook = example_file.suffix in gallery_conf["notebook_extensions"]

    # Generate a binder URL if specified
    if is_binder_enabled and save_notebook:
        binder_badge_rst = gen_binder_rst(example_file, binder_conf, gallery_conf)
        binder_badge_rst = indent(binder_badge_rst, "  ")  # need an extra two
        example_rst += binder_badge_rst

    if is_jupyterlite_enabled and save_notebook:
        jupyterlite_rst = gen_jupyterlite_rst(example_file, gallery_conf)
        jupyterlite_rst = indent(jupyterlite_rst, "  ")  # need an extra two
        example_rst += jupyterlite_rst

    if save_notebook:
        example_rst += NOTEBOOK_DOWNLOAD.format(example_file.with_suffix(".ipynb").name)

    example_rst += CODE_DOWNLOAD.format(example_file.name, language)

    if gallery_conf["recommender"]["enable"]:
        # extract the filename without the extension
        recommend_fname = os.path.splitext(os.path.split(example_fname)[1])[0]
        example_rst += RECOMMENDATIONS_INCLUDE.format(recommend_fname)

    if gallery_conf["show_signature"]:
        example_rst += SPHX_GLR_SIG

    write_file_new = example_file.with_suffix(".rst.new")
    with codecs.open(write_file_new, "w", encoding="utf-8") as f:
        f.write(example_rst)
    # make it read-only so that people don't try to edit it
    mode = os.stat(write_file_new).st_mode
    ro_mask = 0x777 ^ (stat.S_IWRITE | stat.S_IWGRP | stat.S_IWOTH)
    os.chmod(write_file_new, mode & ro_mask)
    # in case it wasn't in our pattern, only replace the file if it's
    # still stale.
    _replace_md5(write_file_new, mode="t")