#!/usr/bin/env python # -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """ :mod:`nipype.sphinxext.plot_workflow` -- Workflow plotting extension ==================================================================== A directive for including a nipype workflow graph in a Sphinx document. This code is forked from the plot_figure sphinx extension of matplotlib. By default, in HTML output, `workflow` will include a .png file with a link to a high-res .png. In LaTeX output, it will include a .pdf. The source code for the workflow may be included as **inline content** to the directive `workflow`:: .. workflow :: :graph2use: flat :simple_form: no from niflow.nipype1.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline wf = create_connectivity_pipeline() For example, the following graph has been generated inserting the previous code block in this documentation: .. workflow :: :graph2use: flat :simple_form: no from niflow.nipype1.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline wf = create_connectivity_pipeline() Options ------- The ``workflow`` directive supports the following options: graph2use : {'hierarchical', 'colored', 'flat', 'orig', 'exec'} Specify the type of graph to be generated. simple_form: bool Whether the graph will be in detailed or simple form. 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 `workflow_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. Additionally, this directive supports all of the options of the `image` directive, except for `target` (since workflow will add its own target). These include `alt`, `height`, `width`, `scale`, `align` and `class`. Configuration options --------------------- The workflow directive has the following configuration options: graph2use Select a graph type to use simple_form determines if the node name shown in the visualization is either of the form nodename (package) when set to True or nodename.Class.package when set to False. wf_include_source Default value for the include-source option wf_html_show_source_link Whether to show a link to the source in HTML. wf_pre_code Code that should be executed before each workflow. wf_basedir Base directory, to which ``workflow::`` file names are relative to. (If None or empty, file names are relative to the directory where the file containing the directive is.) wf_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, .... wf_html_show_formats Whether to show links to the files in HTML. wf_rcparams A dictionary containing any non-standard rcParams that should be applied before each workflow. wf_apply_rcparams By default, rcParams are applied when `context` option is not used in a workflow directive. This configuration option overrides this behavior and applies rcParams before each workflow. wf_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. wf_template Provide a customized template for preparing restructured text. """ import sys import os import shutil import io import re import textwrap from os.path import relpath from errno import EEXIST import traceback missing_imports = [] try: from docutils.parsers.rst import directives, Directive from docutils.parsers.rst.directives.images import Image align = Image.align except ImportError as e: missing_imports = [str(e)] try: # Sphinx depends on either Jinja or Jinja2 import jinja2 def format_template(template, **kw): return jinja2.Template(template).render(**kw) except ImportError as e: missing_imports.append(str(e)) try: import jinja def format_template(template, **kw): return jinja.from_string(template, **kw) missing_imports.pop() except ImportError as e: missing_imports.append(str(e)) 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_graph2use(arg): return directives.choice(arg, ("hierarchical", "colored", "flat", "orig", "exec")) 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_wf_labels(app, document): """ To make graphs referenceable, we need to move the reference from the "htmlonly" (or "latexonly") node to the actual figure node itself. """ for name, explicit in list(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 WorkflowDirective(Directive): 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, "graph2use": _option_graph2use, "simple_form": _option_boolean, } def run(self): if missing_imports: raise ImportError("\n".join(missing_imports)) document = self.state_machine.document config = document.settings.env.config nofigs = "nofigs" in self.options formats = get_wf_formats(config) default_fmt = formats[0][0] graph2use = self.options.get("graph2use", "hierarchical") simple_form = self.options.get("simple_form", True) self.options.setdefault("include-source", config.wf_include_source) keep_context = "context" in self.options context_opt = None if not keep_context else self.options["context"] rst_file = document.attributes["source"] rst_dir = os.path.dirname(rst_file) if len(self.arguments): if not config.wf_basedir: source_file_name = os.path.join( setup.app.builder.srcdir, directives.uri(self.arguments[0]) ) else: source_file_name = os.path.join( setup.confdir, config.wf_basedir, directives.uri(self.arguments[0]) ) # If there is content, it will be passed as a caption. caption = "\n".join(self.content) # If the optional function name is provided, use it if len(self.arguments) == 2: function_name = self.arguments[1] else: function_name = None with io.open(source_file_name, "r", encoding="utf-8") as fd: code = fd.read() output_base = os.path.basename(source_file_name) else: source_file_name = rst_file code = textwrap.dedent("\n".join([str(c) for c in self.content])) counter = document.attributes.get("_wf_counter", 0) + 1 document.attributes["_wf_counter"] = counter base, _ = 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 self.options: if self.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), "wf_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, graph2use, simple_form, context_reset=context_opt == "reset", close_figs=context_opt == "close-figs", ) errors = [] except GraphError as err: reporter = self.state.memo.reporter sm = reporter.system_message( 2, "Exception occurred in plotting %s\n from %s:\n%s" % (output_base, source_file_name, err), line=self.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 self.options["include-source"]: if is_doctest: lines = [""] lines += [row.rstrip() for row in code_piece.split("\n")] else: lines = [".. code-block:: python", ""] lines += [" %s" % row.rstrip() for row in code_piece.split("\n")] source_code = "\n".join(lines) else: source_code = "" if nofigs: images = [] opts = [ ":%s: %s" % (key, val) for key, val in list(self.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.wf_html_show_source_link: src_link = source_link else: src_link = None result = format_template( config.wf_template or TEMPLATE, 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.wf_html_show_formats and len(images), caption=caption, ) total_lines.extend(result.split("\n")) total_lines.extend("\n") if total_lines: self.state_machine.insert_input(total_lines, source=source_file_name) # copy image files to builder's output directory, if necessary os.makedirs(dest_dir, 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) target_name = os.path.join(dest_dir, output_base + source_ext) with io.open(target_name, "w", encoding="utf-8") as f: if source_file_name == rst_file: code_escaped = unescape_doctest(code) else: code_escaped = code f.write(code_escaped) return errors def setup(app): setup.app = app setup.config = app.config setup.confdir = app.confdir app.add_directive("workflow", WorkflowDirective) app.add_config_value("graph2use", "hierarchical", "html") app.add_config_value("simple_form", True, "html") app.add_config_value("wf_pre_code", None, True) app.add_config_value("wf_include_source", False, True) app.add_config_value("wf_html_show_source_link", True, True) app.add_config_value("wf_formats", ["png", "svg", "pdf"], True) app.add_config_value("wf_basedir", None, True) app.add_config_value("wf_html_show_formats", True, True) app.add_config_value("wf_rcparams", {}, True) app.add_config_value("wf_apply_rcparams", False, True) app.add_config_value("wf_working_directory", None, True) app.add_config_value("wf_template", None, True) app.connect("doctree-read", mark_wf_labels) metadata = {"parallel_read_safe": True, "parallel_write_safe": True} 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 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*(>>>|\.\.\.) (.*)$", line) if m: code += m.group(2) + "\n" elif line.strip(): code += "# " + line.strip() + "\n" else: code += "\n" return code def remove_coding(text): """ Remove the coding comment, which exec doesn't like. """ sub_re = re.compile(r"^#\s*-\*-\s*coding:\s*.*-\*-$", flags=re.MULTILINE) return sub_re.sub("", text) # ------------------------------------------------------------------------------ # Template # ------------------------------------------------------------------------------ TEMPLATE = """ {{ source_code }} {{ only_html }} {% 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 %} {% 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 %} {{ 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 = """ .. htmlonly:: [`source code <%(linkdir)s/%(basename)s.py>`__] Exception occurred rendering plot. """ # the context of the plot for all directives specified with the # :context: option wf_context = dict() class ImageFile(object): def __init__(self, basename, dirname): self.basename = basename self.dirname = dirname self.formats = [] def filename(self, fmt): return os.path.join(self.dirname, "%s.%s" % (self.basename, fmt)) def filenames(self): return [self.filename(fmt) for fmt in self.formats] def out_of_date(original, derived): """ Returns True if derivative is out-of-date wrt 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 GraphError(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 = str(os.getcwd()) old_sys_path = list(sys.path) if setup.config.wf_working_directory is not None: try: os.chdir(setup.config.wf_working_directory) except OSError as err: raise OSError( str(err) + "\n`wf_working_directory` option in" "Sphinx configuration file must be a valid " "directory path" ) except TypeError as err: raise TypeError( str(err) + "\n`wf_working_directory` option in " "Sphinx configuration file must be a string or " "None" ) sys.path.insert(0, setup.config.wf_working_directory) elif code_path is not None: dirname = os.path.abspath(os.path.dirname(code_path)) os.chdir(dirname) sys.path.insert(0, dirname) # Reset sys.argv old_sys_argv = sys.argv sys.argv = [code_path] # Redirect stdout stdout = sys.stdout sys.stdout = io.StringIO() # Assign a do-nothing print function to the namespace. There # doesn't seem to be any other way to provide a way to (not) print # that works correctly across Python 2 and 3. def _dummy_print(*arg, **kwarg): pass try: try: code = unescape_doctest(code) if ns is None: ns = {} if not ns: if setup.config.wf_pre_code is not None: exec(str(setup.config.wf_pre_code), ns) ns["print"] = _dummy_print if "__main__" in code: exec("__name__ = '__main__'", ns) code = remove_coding(code) exec(code, ns) if function_name is not None: exec(function_name + "()", ns) except (Exception, SystemExit) as err: raise GraphError(traceback.format_exc()) finally: os.chdir(pwd) sys.argv = old_sys_argv sys.path[:] = old_sys_path sys.stdout = stdout return ns def get_wf_formats(config): default_dpi = {"png": 80, "hires.png": 200, "pdf": 200} formats = [] wf_formats = config.wf_formats if isinstance(wf_formats, (str, bytes)): # String Sphinx < 1.3, Split on , to mimic # Sphinx 1.3 and later. Sphinx 1.3 always # returns a list. wf_formats = wf_formats.split(",") for fmt in wf_formats: if isinstance(fmt, (str, bytes)): 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 GraphError('invalid image format "%r" in wf_formats' % fmt) return formats def render_figures( code, code_path, output_dir, output_base, context, function_name, config, graph2use, simple_form, context_reset=False, close_figs=False, ): """ Run a nipype workflow creation script and save the graph in *output_dir*. Save the images under *output_dir* with file names derived from *output_base* """ formats = get_wf_formats(config) ns = wf_context if context else {} if context_reset: wf_context.clear() run_code(code, code_path, ns, function_name) img = ImageFile(output_base, output_dir) for fmt, dpi in formats: try: img_path = img.filename(fmt) imgname, ext = os.path.splitext(os.path.basename(img_path)) ns["wf"].base_dir = output_dir src = ns["wf"].write_graph( imgname, format=ext[1:], graph2use=graph2use, simple_form=simple_form ) shutil.move(src, img_path) except Exception: raise GraphError(traceback.format_exc()) img.formats.append(fmt) return [(code, [img])]