""" A directive for including a Matplotlib plot in a Sphinx document ================================================================ This is a Sphinx extension providing a reStructuredText directive ``.. plot::`` for including a plot in a Sphinx document. 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 plot content may be defined 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 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 plt.plot([1, 2, 3], [4, 5, 6]) plt.title("A plotting exammple") 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. If unset, the format is auto-detected. ``:include-source:`` : bool Whether to display the source code. The default can be changed using the ``plot_include_source`` variable in :file:`conf.py` (which itself defaults to False). ``:show-source-link:`` : bool Whether to show a link to the source in HTML. The default can be changed using the ``plot_html_show_source_link`` variable in :file:`conf.py` (which itself defaults to True). ``: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. ``:caption:`` : str If specified, the option's argument will be used as a caption for the figure. This overwrites the caption given in the content, when the plot is generated from a file. Additionally, this directive supports all 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 (default: False). plot_html_show_source_link Whether to show a link to the source in HTML (default: True). plot_pre_code Code that should be executed before each plot. If None (the default), 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 (the default), file names are relative to the directory where the file containing the directive is. plot_formats File formats to generate (default: ['png', 'hires.png', 'pdf']). 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 (default: True). plot_rcparams A dictionary containing any non-standard rcParams that should be applied before each plot (default: {}). plot_apply_rcparams By default, rcParams are applied when ``:context:`` option is not used in a plot directive. If set, 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. plot_srcset Allow the srcset image option for responsive image resolutions. List of strings with the multiplicative factors followed by an "x". e.g. ["2.0x", "1.5x"]. "2.0x" will create a png with the default "png" resolution from plot_formats, multiplied by 2. If plot_srcset is specified, the plot directive uses the :doc:`/api/sphinxext_figmpl_directive_api` (instead of the usual figure directive) in the intermediary rst file that is generated. The plot_srcset option is incompatible with *singlehtml* builds, and an error will be raised. Notes on how it works --------------------- The plot directive runs the code it is given, either in the source file or the code under the directive. The figure created (if any) is saved in the sphinx build directory under a subdirectory named ``plot_directive``. It then creates an intermediate rst file that calls a ``.. figure:`` directive (or ``.. figmpl::`` directive if ``plot_srcset`` is being used) and has links to the ``*.png`` files in the ``plot_directive`` directory. These translations can be customized by changing the *plot_template*. See the source of :doc:`/api/sphinxext_plot_directive_api` for the templates defined in *TEMPLATE* and *TEMPLATE_SRCSET*. """ import contextlib import doctest 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. from sphinx.errors import ExtensionError import matplotlib from matplotlib.backend_bases import FigureManagerBase import matplotlib.pyplot as plt from matplotlib import _pylab_helpers, cbook matplotlib.use("agg") __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(f'{arg!r} unknown boolean') 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 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': Image.align, 'class': directives.class_option, 'include-source': _option_boolean, 'show-source-link': _option_boolean, 'format': _option_format, 'context': _option_context, 'nofigs': directives.flag, 'caption': directives.unchanged, } def run(self): """Run the plot directive.""" try: return run(self.arguments, self.content, self.options, self.state_machine, self.state, self.lineno) except Exception as e: raise self.error(str(e)) def _copy_css_file(app, exc): if exc is None and app.builder.format == 'html': src = cbook._get_data_path('plot_directive/plot_directive.css') dst = app.outdir / Path('_static') dst.mkdir(exist_ok=True) # Use copyfile because we do not want to copy src's permissions. shutil.copyfile(src, dst / Path('plot_directive.css')) def setup(app): 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.add_config_value('plot_srcset', [], True) app.connect('doctree-read', mark_plot_labels) app.add_css_file('plot_directive.css') app.connect('build-finished', _copy_css_file) 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, '', 'exec') return False except SyntaxError: pass r = re.compile(r'^\s*>>>', re.M) m = r.search(text) return bool(m) def _split_code_at_show(text, function_name): """Split code at plt.show().""" is_doctest = contains_doctest(text) if function_name is None: parts = [] part = [] for line in text.split("\n"): if ((not is_doctest and line.startswith('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)) else: parts = [text] return is_doctest, parts # ----------------------------------------------------------------------------- # Template # ----------------------------------------------------------------------------- _SOURCECODE = """ {{ source_code }} .. only:: html {% if src_name or (html_show_formats and not multi_image) %} ( {%- if src_name -%} :download:`Source code <{{ build_dir }}/{{ src_name }}>` {%- endif -%} {%- if html_show_formats and not multi_image -%} {%- for img in images -%} {%- for fmt in img.formats -%} {%- if src_name or not loop.first -%}, {% endif -%} :download:`{{ fmt }} <{{ build_dir }}/{{ img.basename }}.{{ fmt }}>` {%- endfor -%} {%- endfor -%} {%- endif -%} ) {% endif %} """ TEMPLATE_SRCSET = _SOURCECODE + """ {% for img in images %} .. figure-mpl:: {{ build_dir }}/{{ img.basename }}.{{ default_fmt }} {% for option in options -%} {{ option }} {% endfor %} {%- if caption -%} {{ caption }} {# appropriate leading whitespace added beforehand #} {% endif -%} {%- if srcset -%} :srcset: {{ build_dir }}/{{ img.basename }}.{{ default_fmt }} {%- for sr in srcset -%} , {{ build_dir }}/{{ img.basename }}.{{ sr }}.{{ default_fmt }} {{sr}} {%- endfor -%} {% endif %} {% if html_show_formats and multi_image %} ( {%- for fmt in img.formats -%} {%- if not loop.first -%}, {% endif -%} :download:`{{ fmt }} <{{ build_dir }}/{{ img.basename }}.{{ fmt }}>` {%- endfor -%} ) {% endif %} {% endfor %} .. only:: not html {% for img in images %} .. figure-mpl:: {{ build_dir }}/{{ img.basename }}.* {% for option in options -%} {{ option }} {% endfor -%} {{ caption }} {# appropriate leading whitespace added beforehand #} {% endfor %} """ TEMPLATE = _SOURCECODE + """ {% 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 -%} :download:`{{ fmt }} <{{ build_dir }}/{{ img.basename }}.{{ fmt }}>` {%- endfor -%} ) {%- endif -%} {{ caption }} {# appropriate leading whitespace added beforehand #} {% endfor %} .. only:: not html {% for img in images %} .. figure:: {{ build_dir }}/{{ img.basename }}.* {% for option in options -%} {{ option }} {% endfor -%} {{ caption }} {# appropriate leading whitespace added beforehand #} {% 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, f"{self.basename}.{format}") def filenames(self): return [self.filename(fmt) for fmt in self.formats] def out_of_date(original, derived, includes=None): """ Return whether *derived* is out-of-date relative to *original* or any of the RST files included in it using the RST include directive (*includes*). *derived* and *original* are full paths, and *includes* is optionally a list of full paths which may have been included in the *original*. """ if not os.path.exists(derived): return True if includes is None: includes = [] files_to_check = [original, *includes] def out_of_date_one(original, derived_mtime): return (os.path.exists(original) and derived_mtime < os.stat(original).st_mtime) derived_mtime = os.stat(derived).st_mtime return any(out_of_date_one(f, derived_mtime) for f in files_to_check) 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(f'{err}\n`plot_working_directory` option in ' f'Sphinx configuration file must be a valid ' f'directory path') from err except TypeError as err: raise TypeError(f'{err}\n`plot_working_directory` option in ' f'Sphinx configuration file must be a string or ' f'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: 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 _parse_srcset(entries): """ Parse srcset for multiples... """ srcset = {} for entry in entries: entry = entry.strip() if len(entry) >= 2: mult = entry[:-1] srcset[float(mult)] = entry else: raise ExtensionError(f'srcset argument {entry!r} is invalid.') return srcset def render_figures(code, code_path, output_dir, output_base, context, function_name, config, context_reset=False, close_figs=False, code_includes=None): """ Run a pyplot script and save the images in *output_dir*. Save the images under *output_dir* with file names derived from *output_base* """ if function_name is not None: output_base = f'{output_base}_{function_name}' formats = get_plot_formats(config) # Try to determine if all images already exist is_doctest, code_pieces = _split_code_at_show(code, function_name) # Look for single-figure output files first img = ImageFile(output_base, output_dir) for format, dpi in formats: if context or out_of_date(code_path, img.filename(format), includes=code_includes): all_exists = False break img.formats.append(format) else: all_exists = True if all_exists: return [(code, [img])] # Then look for multi-figure output files results = [] 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 context or out_of_date(code_path, img.filename(fmt), includes=code_includes): 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)) else: all_exists = True if all_exists: return results # We didn't find the files, so build them results = [] ns = plot_context if context else {} 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(doctest.script_from_examples(code_piece) if is_doctest else 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) if fmt == formats[0][0] and config.plot_srcset: # save a 2x, 3x etc version of the default... srcset = _parse_srcset(config.plot_srcset) for mult, suffix in srcset.items(): fm = f'{suffix}.{fmt}' img.formats.append(fm) figman.canvas.figure.savefig(img.filename(fm), dpi=int(dpi * mult)) 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 if config.plot_srcset and setup.app.builder.name == 'singlehtml': raise ExtensionError( 'plot_srcset option not compatible with single HTML writer') formats = get_plot_formats(config) default_fmt = formats[0][0] options.setdefault('include-source', config.plot_include_source) options.setdefault('show-source-link', config.plot_html_show_source_link) if 'class' in options: # classes are parsed into a list of string, and output by simply # printing the list, abusing the fact that RST guarantees to strip # non-conforming characters options['class'] = ['plot-directive'] + options['class'] else: options.setdefault('class', ['plot-directive']) 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) # Enforce unambiguous use of captions. if "caption" in options: if caption: raise ValueError( 'Caption specified in both content and options.' ' Please remove ambiguity.' ) # Use caption option caption = options["caption"] # 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 = options.get('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).lstrip(os.path.sep) # 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) os.makedirs(build_dir, exist_ok=True) # how to link to files from the RST file 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 # get list of included rst files so that the output is updated when any # plots in the included files change. These attributes are modified by the # include directive (see the docutils.parsers.rst.directives.misc module). try: source_file_includes = [os.path.join(os.getcwd(), t[0]) for t in state.document.include_log] except AttributeError: # the document.include_log attribute only exists in docutils >=0.17, # before that we need to inspect the state machine possible_sources = {os.path.join(setup.confdir, t[0]) for t in state_machine.input_lines.items} source_file_includes = [f for f in possible_sources if os.path.isfile(f)] # remove the source file itself from the includes try: source_file_includes.remove(source_file_name) except ValueError: pass # save script (if necessary) if options['show-source-link']: Path(build_dir, output_base + source_ext).write_text( doctest.script_from_examples(code) if source_file_name == rst_file and is_doctest else code, encoding='utf-8') # make figures try: results = render_figures(code=code, code_path=source_file_name, output_dir=build_dir, output_base=output_base, context=keep_context, function_name=function_name, config=config, context_reset=context_opt == 'reset', close_figs=context_opt == 'close-figs', code_includes=source_file_includes) 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 if caption and config.plot_srcset: caption = f':caption: {caption}' elif caption: caption = '\n' + '\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 = [ f':{key}: {val}' for key, val in options.items() if key in ('alt', 'height', 'width', 'scale', 'align', 'class')] # Not-None src_name signals the need for a source download in the # generated html if j == 0 and options['show-source-link']: src_name = output_base + source_ext else: src_name = None if config.plot_srcset: srcset = [*_parse_srcset(config.plot_srcset).values()] template = TEMPLATE_SRCSET else: srcset = None template = TEMPLATE result = jinja2.Template(config.plot_template or template).render( default_fmt=default_fmt, build_dir=build_dir_link, src_name=src_name, multi_image=len(images) > 1, options=opts, srcset=srcset, 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) return errors