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Source code for matplotlib.sphinxext.plot_directive

"""
A directive for including a matplotlib plot in a Sphinx document.

By default, in HTML output, `plot` will include a .png file with a
link to a high-res .png and .pdf.  In LaTeX output, it will include a
.pdf.

The source code for the plot may be included in one of three ways:

  1. **A path to a source file** as the argument to the directive::

       .. plot:: path/to/plot.py

     When a path to a source file is given, the content of the
     directive may optionally contain a caption for the plot::

       .. plot:: path/to/plot.py

          This is the caption for the plot

     Additionally, one may specify the name of a function to call (with
     no arguments) immediately after importing the module::

       .. plot:: path/to/plot.py plot_function1

  2. Included as **inline content** to the directive::

       .. plot::

          import matplotlib.pyplot as plt
          import matplotlib.image as mpimg
          import numpy as np
          img = mpimg.imread('_static/stinkbug.png')
          imgplot = plt.imshow(img)

  3. Using **doctest** syntax::

       .. plot::
          A plotting example:
          >>> import matplotlib.pyplot as plt
          >>> plt.plot([1,2,3], [4,5,6])

Options
-------

The ``plot`` directive supports the following options:

    format : {'python', 'doctest'}
        Specify the format of the input

    include-source : bool
        Whether to display the source code. The default can be changed
        using the `plot_include_source` variable in conf.py

    encoding : str
        If this source file is in a non-UTF8 or non-ASCII encoding,
        the encoding must be specified using the `:encoding:` option.
        The encoding will not be inferred using the ``-*- coding -*-``
        metacomment.

    context : bool or str
        If provided, the code will be run in the context of all
        previous plot directives for which the `:context:` option was
        specified.  This only applies to inline code plot directives,
        not those run from files. If the ``:context: reset`` option is
        specified, the context is reset for this and future plots, and
        previous figures are closed prior to running the code.
        ``:context:close-figs`` keeps the context but closes previous figures
        before running the code.

    nofigs : bool
        If specified, the code block will be run, but no figures will
        be inserted.  This is usually useful with the ``:context:``
        option.

Additionally, this directive supports all of the options of the
`image` directive, except for `target` (since plot will add its own
target).  These include `alt`, `height`, `width`, `scale`, `align` and
`class`.

Configuration options
---------------------

The plot directive has the following configuration options:

    plot_include_source
        Default value for the include-source option

    plot_html_show_source_link
        Whether to show a link to the source in HTML.

    plot_pre_code
        Code that should be executed before each plot. If not specified or None
        it will default to a string containing::

            import numpy as np
            from matplotlib import pyplot as plt

    plot_basedir
        Base directory, to which ``plot::`` file names are relative
        to.  (If None or empty, file names are relative to the
        directory where the file containing the directive is.)

    plot_formats
        File formats to generate. List of tuples or strings::

            [(suffix, dpi), suffix, ...]

        that determine the file format and the DPI. For entries whose
        DPI was omitted, sensible defaults are chosen. When passing from
        the command line through sphinx_build the list should be passed as
        suffix:dpi,suffix:dpi, ....

    plot_html_show_formats
        Whether to show links to the files in HTML.

    plot_rcparams
        A dictionary containing any non-standard rcParams that should
        be applied before each plot.

    plot_apply_rcparams
        By default, rcParams are applied when `context` option is not used in
        a plot directive.  This configuration option overrides this behavior
        and applies rcParams before each plot.

    plot_working_directory
        By default, the working directory will be changed to the directory of
        the example, so the code can get at its data files, if any.  Also its
        path will be added to `sys.path` so it can import any helper modules
        sitting beside it.  This configuration option can be used to specify
        a central directory (also added to `sys.path`) where data files and
        helper modules for all code are located.

    plot_template
        Provide a customized template for preparing restructured text.
"""

import contextlib
from io import StringIO
import itertools
import os
from os.path import relpath
from pathlib import Path
import re
import shutil
import sys
import textwrap
import traceback
import warnings

from docutils.parsers.rst import directives, Directive
from docutils.parsers.rst.directives.images import Image
import jinja2  # Sphinx dependency.

import matplotlib
from matplotlib.backend_bases import FigureManagerBase
try:
    with warnings.catch_warnings(record=True):
        warnings.simplefilter("error", UserWarning)
        matplotlib.use('Agg')
except UserWarning:
    import matplotlib.pyplot as plt
    plt.switch_backend("Agg")
else:
    import matplotlib.pyplot as plt
from matplotlib import _pylab_helpers, cbook
align = Image.align

__version__ = 2


# -----------------------------------------------------------------------------
# Registration hook
# -----------------------------------------------------------------------------


[docs]@cbook.deprecated("3.1", alternative="PlotDirective") def plot_directive(name, arguments, options, content, lineno, content_offset, block_text, state, state_machine): """Implementation of the ``.. plot::`` directive. See the module docstring for details. """ return run(arguments, content, options, state_machine, state, lineno)
def _option_boolean(arg): if not arg or not arg.strip(): # no argument given, assume used as a flag return True elif arg.strip().lower() in ('no', '0', 'false'): return False elif arg.strip().lower() in ('yes', '1', 'true'): return True else: raise ValueError('"%s" unknown boolean' % arg) def _option_context(arg): if arg in [None, 'reset', 'close-figs']: return arg raise ValueError("argument should be None or 'reset' or 'close-figs'") def _option_format(arg): return directives.choice(arg, ('python', 'doctest')) def _option_align(arg): return directives.choice(arg, ("top", "middle", "bottom", "left", "center", "right"))
[docs]def mark_plot_labels(app, document): """ To make plots referenceable, we need to move the reference from the "htmlonly" (or "latexonly") node to the actual figure node itself. """ for name, explicit in document.nametypes.items(): if not explicit: continue labelid = document.nameids[name] if labelid is None: continue node = document.ids[labelid] if node.tagname in ('html_only', 'latex_only'): for n in node: if n.tagname == 'figure': sectname = name for c in n: if c.tagname == 'caption': sectname = c.astext() break node['ids'].remove(labelid) node['names'].remove(name) n['ids'].append(labelid) n['names'].append(name) document.settings.env.labels[name] = \ document.settings.env.docname, labelid, sectname break
[docs]class PlotDirective(Directive): """Implementation of the ``.. plot::`` directive. See the module docstring for details. """ has_content = True required_arguments = 0 optional_arguments = 2 final_argument_whitespace = False option_spec = { 'alt': directives.unchanged, 'height': directives.length_or_unitless, 'width': directives.length_or_percentage_or_unitless, 'scale': directives.nonnegative_int, 'align': _option_align, 'class': directives.class_option, 'include-source': _option_boolean, 'format': _option_format, 'context': _option_context, 'nofigs': directives.flag, 'encoding': directives.encoding, }
[docs] def run(self): """Run the plot directive.""" return run(self.arguments, self.content, self.options, self.state_machine, self.state, self.lineno)
def setup(app): import matplotlib setup.app = app setup.config = app.config setup.confdir = app.confdir app.add_directive('plot', PlotDirective) app.add_config_value('plot_pre_code', None, True) app.add_config_value('plot_include_source', False, True) app.add_config_value('plot_html_show_source_link', True, True) app.add_config_value('plot_formats', ['png', 'hires.png', 'pdf'], True) app.add_config_value('plot_basedir', None, True) app.add_config_value('plot_html_show_formats', True, True) app.add_config_value('plot_rcparams', {}, True) app.add_config_value('plot_apply_rcparams', False, True) app.add_config_value('plot_working_directory', None, True) app.add_config_value('plot_template', None, True) app.connect('doctree-read', mark_plot_labels) metadata = {'parallel_read_safe': True, 'parallel_write_safe': True, 'version': matplotlib.__version__} return metadata # ----------------------------------------------------------------------------- # Doctest handling # ----------------------------------------------------------------------------- def contains_doctest(text): try: # check if it's valid Python as-is compile(text, '<string>', 'exec') return False except SyntaxError: pass r = re.compile(r'^\s*>>>', re.M) m = r.search(text) return bool(m)
[docs]def unescape_doctest(text): """ Extract code from a piece of text, which contains either Python code or doctests. """ if not contains_doctest(text): return text code = "" for line in text.split("\n"): m = re.match(r'^\s*(>>>|\.\.\.) (.*)$', line) if m: code += m.group(2) + "\n" elif line.strip(): code += "# " + line.strip() + "\n" else: code += "\n" return code
[docs]def split_code_at_show(text): """Split code at plt.show().""" parts = [] is_doctest = contains_doctest(text) part = [] for line in text.split("\n"): if (not is_doctest and line.strip() == 'plt.show()') or \ (is_doctest and line.strip() == '>>> plt.show()'): part.append(line) parts.append("\n".join(part)) part = [] else: part.append(line) if "\n".join(part).strip(): parts.append("\n".join(part)) return parts
[docs]def remove_coding(text): r"""Remove the coding comment, which six.exec\_ doesn't like.""" cbook.warn_deprecated('3.0', name='remove_coding', removal='3.1') sub_re = re.compile(r"^#\s*-\*-\s*coding:\s*.*-\*-$", flags=re.MULTILINE) return sub_re.sub("", text)
# ----------------------------------------------------------------------------- # Template # ----------------------------------------------------------------------------- TEMPLATE = """ {{ source_code }} {{ only_html }} {% if source_link or (html_show_formats and not multi_image) %} ( {%- if source_link -%} `Source code <{{ source_link }}>`__ {%- endif -%} {%- if html_show_formats and not multi_image -%} {%- for img in images -%} {%- for fmt in img.formats -%} {%- if source_link or not loop.first -%}, {% endif -%} `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__ {%- endfor -%} {%- endfor -%} {%- endif -%} ) {% endif %} {% for img in images %} .. figure:: {{ build_dir }}/{{ img.basename }}.{{ default_fmt }} {% for option in options -%} {{ option }} {% endfor %} {% if html_show_formats and multi_image -%} ( {%- for fmt in img.formats -%} {%- if not loop.first -%}, {% endif -%} `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__ {%- endfor -%} ) {%- endif -%} {{ caption }} {% endfor %} {{ only_latex }} {% for img in images %} {% if 'pdf' in img.formats -%} .. figure:: {{ build_dir }}/{{ img.basename }}.pdf {% for option in options -%} {{ option }} {% endfor %} {{ caption }} {% endif -%} {% endfor %} {{ only_texinfo }} {% for img in images %} .. image:: {{ build_dir }}/{{ img.basename }}.png {% for option in options -%} {{ option }} {% endfor %} {% endfor %} """ exception_template = """ .. only:: html [`source code <%(linkdir)s/%(basename)s.py>`__] Exception occurred rendering plot. """ # the context of the plot for all directives specified with the # :context: option plot_context = dict() class ImageFile(object): def __init__(self, basename, dirname): self.basename = basename self.dirname = dirname self.formats = [] def filename(self, format): return os.path.join(self.dirname, "%s.%s" % (self.basename, format)) def filenames(self): return [self.filename(fmt) for fmt in self.formats]
[docs]def out_of_date(original, derived): """ Return whether *derived* is out-of-date relative to *original*, both of which are full file paths. """ return (not os.path.exists(derived) or (os.path.exists(original) and os.stat(derived).st_mtime < os.stat(original).st_mtime))
[docs]class PlotError(RuntimeError): pass
[docs]def run_code(code, code_path, ns=None, function_name=None): """ Import a Python module from a path, and run the function given by name, if function_name is not None. """ # Change the working directory to the directory of the example, so # it can get at its data files, if any. Add its path to sys.path # so it can import any helper modules sitting beside it. pwd = os.getcwd() if setup.config.plot_working_directory is not None: try: os.chdir(setup.config.plot_working_directory) except OSError as err: raise OSError(str(err) + '\n`plot_working_directory` option in' 'Sphinx configuration file must be a valid ' 'directory path') except TypeError as err: raise TypeError(str(err) + '\n`plot_working_directory` option in ' 'Sphinx configuration file must be a string or ' 'None') elif code_path is not None: dirname = os.path.abspath(os.path.dirname(code_path)) os.chdir(dirname) with cbook._setattr_cm( sys, argv=[code_path], path=[os.getcwd(), *sys.path]), \ contextlib.redirect_stdout(StringIO()): try: code = unescape_doctest(code) if ns is None: ns = {} if not ns: if setup.config.plot_pre_code is None: exec('import numpy as np\n' 'from matplotlib import pyplot as plt\n', ns) else: exec(str(setup.config.plot_pre_code), ns) if "__main__" in code: ns['__name__'] = '__main__' # Patch out non-interactive show() to avoid triggering a warning. with cbook._setattr_cm(FigureManagerBase, show=lambda self: None): exec(code, ns) if function_name is not None: exec(function_name + "()", ns) except (Exception, SystemExit) as err: raise PlotError(traceback.format_exc()) finally: os.chdir(pwd) return ns
def clear_state(plot_rcparams, close=True): if close: plt.close('all') matplotlib.rc_file_defaults() matplotlib.rcParams.update(plot_rcparams) def get_plot_formats(config): default_dpi = {'png': 80, 'hires.png': 200, 'pdf': 200} formats = [] plot_formats = config.plot_formats for fmt in plot_formats: if isinstance(fmt, str): if ':' in fmt: suffix, dpi = fmt.split(':') formats.append((str(suffix), int(dpi))) else: formats.append((fmt, default_dpi.get(fmt, 80))) elif isinstance(fmt, (tuple, list)) and len(fmt) == 2: formats.append((str(fmt[0]), int(fmt[1]))) else: raise PlotError('invalid image format "%r" in plot_formats' % fmt) return formats
[docs]def render_figures(code, code_path, output_dir, output_base, context, function_name, config, context_reset=False, close_figs=False): """ Run a pyplot script and save the images in *output_dir*. Save the images under *output_dir* with file names derived from *output_base* """ formats = get_plot_formats(config) # -- Try to determine if all images already exist code_pieces = split_code_at_show(code) # Look for single-figure output files first all_exists = True img = ImageFile(output_base, output_dir) for format, dpi in formats: if out_of_date(code_path, img.filename(format)): all_exists = False break img.formats.append(format) if all_exists: return [(code, [img])] # Then look for multi-figure output files results = [] all_exists = True for i, code_piece in enumerate(code_pieces): images = [] for j in itertools.count(): if len(code_pieces) > 1: img = ImageFile('%s_%02d_%02d' % (output_base, i, j), output_dir) else: img = ImageFile('%s_%02d' % (output_base, j), output_dir) for format, dpi in formats: if out_of_date(code_path, img.filename(format)): all_exists = False break img.formats.append(format) # assume that if we have one, we have them all if not all_exists: all_exists = (j > 0) break images.append(img) if not all_exists: break results.append((code_piece, images)) if all_exists: return results # We didn't find the files, so build them results = [] if context: ns = plot_context else: ns = {} if context_reset: clear_state(config.plot_rcparams) plot_context.clear() close_figs = not context or close_figs for i, code_piece in enumerate(code_pieces): if not context or config.plot_apply_rcparams: clear_state(config.plot_rcparams, close_figs) elif close_figs: plt.close('all') run_code(code_piece, code_path, ns, function_name) images = [] fig_managers = _pylab_helpers.Gcf.get_all_fig_managers() for j, figman in enumerate(fig_managers): if len(fig_managers) == 1 and len(code_pieces) == 1: img = ImageFile(output_base, output_dir) elif len(code_pieces) == 1: img = ImageFile("%s_%02d" % (output_base, j), output_dir) else: img = ImageFile("%s_%02d_%02d" % (output_base, i, j), output_dir) images.append(img) for format, dpi in formats: try: figman.canvas.figure.savefig(img.filename(format), dpi=dpi) except Exception as err: raise PlotError(traceback.format_exc()) img.formats.append(format) results.append((code_piece, images)) if not context or config.plot_apply_rcparams: clear_state(config.plot_rcparams, close=not context) return results
def run(arguments, content, options, state_machine, state, lineno): document = state_machine.document config = document.settings.env.config nofigs = 'nofigs' in options formats = get_plot_formats(config) default_fmt = formats[0][0] options.setdefault('include-source', config.plot_include_source) keep_context = 'context' in options context_opt = None if not keep_context else options['context'] rst_file = document.attributes['source'] rst_dir = os.path.dirname(rst_file) if len(arguments): if not config.plot_basedir: source_file_name = os.path.join(setup.app.builder.srcdir, directives.uri(arguments[0])) else: source_file_name = os.path.join(setup.confdir, config.plot_basedir, directives.uri(arguments[0])) # If there is content, it will be passed as a caption. caption = '\n'.join(content) # If the optional function name is provided, use it if len(arguments) == 2: function_name = arguments[1] else: function_name = None code = Path(source_file_name).read_text(encoding='utf-8') output_base = os.path.basename(source_file_name) else: source_file_name = rst_file code = textwrap.dedent("\n".join(map(str, content))) counter = document.attributes.get('_plot_counter', 0) + 1 document.attributes['_plot_counter'] = counter base, ext = os.path.splitext(os.path.basename(source_file_name)) output_base = '%s-%d.py' % (base, counter) function_name = None caption = '' base, source_ext = os.path.splitext(output_base) if source_ext in ('.py', '.rst', '.txt'): output_base = base else: source_ext = '' # ensure that LaTeX includegraphics doesn't choke in foo.bar.pdf filenames output_base = output_base.replace('.', '-') # is it in doctest format? is_doctest = contains_doctest(code) if 'format' in options: if options['format'] == 'python': is_doctest = False else: is_doctest = True # determine output directory name fragment source_rel_name = relpath(source_file_name, setup.confdir) source_rel_dir = os.path.dirname(source_rel_name) while source_rel_dir.startswith(os.path.sep): source_rel_dir = source_rel_dir[1:] # build_dir: where to place output files (temporarily) build_dir = os.path.join(os.path.dirname(setup.app.doctreedir), 'plot_directive', source_rel_dir) # get rid of .. in paths, also changes pathsep # see note in Python docs for warning about symbolic links on Windows. # need to compare source and dest paths at end build_dir = os.path.normpath(build_dir) if not os.path.exists(build_dir): os.makedirs(build_dir) # output_dir: final location in the builder's directory dest_dir = os.path.abspath(os.path.join(setup.app.builder.outdir, source_rel_dir)) if not os.path.exists(dest_dir): os.makedirs(dest_dir) # no problem here for me, but just use built-ins # how to link to files from the RST file dest_dir_link = os.path.join(relpath(setup.confdir, rst_dir), source_rel_dir).replace(os.path.sep, '/') try: build_dir_link = relpath(build_dir, rst_dir).replace(os.path.sep, '/') except ValueError: # on Windows, relpath raises ValueError when path and start are on # different mounts/drives build_dir_link = build_dir source_link = dest_dir_link + '/' + output_base + source_ext # make figures try: results = render_figures(code, source_file_name, build_dir, output_base, keep_context, function_name, config, context_reset=context_opt == 'reset', close_figs=context_opt == 'close-figs') errors = [] except PlotError as err: reporter = state.memo.reporter sm = reporter.system_message( 2, "Exception occurred in plotting {}\n from {}:\n{}".format( output_base, source_file_name, err), line=lineno) results = [(code, [])] errors = [sm] # Properly indent the caption caption = '\n'.join(' ' + line.strip() for line in caption.split('\n')) # generate output restructuredtext total_lines = [] for j, (code_piece, images) in enumerate(results): if options['include-source']: if is_doctest: lines = ['', *code_piece.splitlines()] else: lines = ['.. code-block:: python', '', *textwrap.indent(code_piece, ' ').splitlines()] source_code = "\n".join(lines) else: source_code = "" if nofigs: images = [] opts = [ ':%s: %s' % (key, val) for key, val in options.items() if key in ('alt', 'height', 'width', 'scale', 'align', 'class')] only_html = ".. only:: html" only_latex = ".. only:: latex" only_texinfo = ".. only:: texinfo" # Not-None src_link signals the need for a source link in the generated # html if j == 0 and config.plot_html_show_source_link: src_link = source_link else: src_link = None result = jinja2.Template(config.plot_template or TEMPLATE).render( default_fmt=default_fmt, dest_dir=dest_dir_link, build_dir=build_dir_link, source_link=src_link, multi_image=len(images) > 1, only_html=only_html, only_latex=only_latex, only_texinfo=only_texinfo, options=opts, images=images, source_code=source_code, html_show_formats=config.plot_html_show_formats and len(images), caption=caption) total_lines.extend(result.split("\n")) total_lines.extend("\n") if total_lines: state_machine.insert_input(total_lines, source=source_file_name) # copy image files to builder's output directory, if necessary Path(dest_dir).mkdir(parents=True, exist_ok=True) for code_piece, images in results: for img in images: for fn in img.filenames(): destimg = os.path.join(dest_dir, os.path.basename(fn)) if fn != destimg: shutil.copyfile(fn, destimg) # copy script (if necessary) Path(dest_dir, output_base + source_ext).write_text( unescape_doctest(code) if source_file_name == rst_file else code, encoding='utf-8') return errors