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- """
- 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
- The plot's caption.
- 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'}
- 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 :file:`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
- 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
- import matplotlib.pyplot as plt
- from matplotlib import _pylab_helpers, cbook
- matplotlib.use("agg")
- align = Image.align
- __version__ = 2
- # -----------------------------------------------------------------------------
- # Registration hook
- # -----------------------------------------------------------------------------
- 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"))
- 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
- class PlotDirective(Directive):
- """The ``.. plot::`` directive, as documented in the module's docstring."""
- 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,
- }
- 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)
- 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
- 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
- # -----------------------------------------------------------------------------
- # 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:: not html
- {% for img in images %}
- .. figure:: {{ build_dir }}/{{ img.basename }}.*
- {% for option in options -%}
- {{ option }}
- {% endfor %}
- {{ caption }}
- {% 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:
- 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]
- 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))
- class PlotError(RuntimeError):
- pass
- 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') from err
- except TypeError as err:
- raise TypeError(str(err) + '\n`plot_working_directory` option in '
- 'Sphinx configuration file must be a string or '
- 'None') from err
- 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()) from err
- 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
- 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 fmt, dpi in formats:
- if out_of_date(code_path, img.filename(fmt)):
- all_exists = False
- break
- img.formats.append(fmt)
- # 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 fmt, dpi in formats:
- try:
- figman.canvas.figure.savefig(img.filename(fmt), dpi=dpi)
- except Exception as err:
- raise PlotError(traceback.format_exc()) from err
- img.formats.append(fmt)
- 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')]
- # 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,
- 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
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