mirror of
https://github.com/triqs/dft_tools
synced 2024-08-16 17:28:29 +02:00
![Alexander Hampel](/assets/img/avatar_default.png)
* moved the plovasp C++ code to c++/triqs_dft_tools/converters/vasp * added global header triqs_dft_tools/triqs_dft_tools.hpp * python dir based on single cmakelist file * registered C++ tests for plovasp * corrected imports for py3 tests for plovasp * corrected block order in sigma_from_file and srvo3_Gloc * exchanged ref files for sigma_from_file, srvo3_Gloc, SrVO3.ref.h5 * moved vasp converter bash scripts from dir shells to bin dir
408 lines
13 KiB
Python
408 lines
13 KiB
Python
"""
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Defines a docutils directive for inserting inheritance diagrams.
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Provide the directive with one or more classes or modules (separated
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by whitespace). For modules, all of the classes in that module will
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be used.
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Example::
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Given the following classes:
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class A: pass
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class B(A): pass
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class C(A): pass
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class D(B, C): pass
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class E(B): pass
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.. inheritance-diagram: D E
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Produces a graph like the following:
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A
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/ \
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B C
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/ \ /
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E D
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The graph is inserted as a PNG+image map into HTML and a PDF in
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LaTeX.
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"""
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import inspect
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import os
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import re
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import subprocess
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try:
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from hashlib import md5
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except ImportError:
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from md5 import md5
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from docutils.nodes import Body, Element
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from docutils.parsers.rst import directives
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from sphinx.roles import xfileref_role
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def my_import(name):
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"""Module importer - taken from the python documentation.
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This function allows importing names with dots in them."""
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mod = __import__(name)
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components = name.split('.')
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for comp in components[1:]:
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mod = getattr(mod, comp)
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return mod
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class DotException(Exception):
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pass
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class InheritanceGraph:
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"""
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Given a list of classes, determines the set of classes that
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they inherit from all the way to the root "object", and then
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is able to generate a graphviz dot graph from them.
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"""
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def __init__(self, class_names, show_builtins=False):
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"""
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*class_names* is a list of child classes to show bases from.
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If *show_builtins* is True, then Python builtins will be shown
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in the graph.
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"""
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self.class_names = class_names
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self.classes = self._import_classes(class_names)
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self.all_classes = self._all_classes(self.classes)
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if len(self.all_classes) == 0:
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raise ValueError("No classes found for inheritance diagram")
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self.show_builtins = show_builtins
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py_sig_re = re.compile(r'''^([\w.]*\.)? # class names
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(\w+) \s* $ # optionally arguments
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''', re.VERBOSE)
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def _import_class_or_module(self, name):
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"""
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Import a class using its fully-qualified *name*.
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"""
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try:
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path, base = self.py_sig_re.match(name).groups()
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except:
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raise ValueError(
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"Invalid class or module '%s' specified for inheritance diagram" % name)
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fullname = (path or '') + base
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path = (path and path.rstrip('.'))
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if not path:
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path = base
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try:
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module = __import__(path, None, None, [])
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# We must do an import of the fully qualified name. Otherwise if a
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# subpackage 'a.b' is requested where 'import a' does NOT provide
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# 'a.b' automatically, then 'a.b' will not be found below. This
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# second call will force the equivalent of 'import a.b' to happen
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# after the top-level import above.
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my_import(fullname)
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except ImportError:
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raise ValueError(
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"Could not import class or module '%s' specified for inheritance diagram" % name)
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try:
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todoc = module
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for comp in fullname.split('.')[1:]:
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todoc = getattr(todoc, comp)
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except AttributeError:
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raise ValueError(
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"Could not find class or module '%s' specified for inheritance diagram" % name)
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# If a class, just return it
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if inspect.isclass(todoc):
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return [todoc]
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elif inspect.ismodule(todoc):
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classes = []
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for cls in list(todoc.__dict__.values()):
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if inspect.isclass(cls) and cls.__module__ == todoc.__name__:
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classes.append(cls)
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return classes
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raise ValueError(
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"'%s' does not resolve to a class or module" % name)
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def _import_classes(self, class_names):
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"""
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Import a list of classes.
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"""
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classes = []
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for name in class_names:
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classes.extend(self._import_class_or_module(name))
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return classes
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def _all_classes(self, classes):
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"""
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Return a list of all classes that are ancestors of *classes*.
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"""
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all_classes = {}
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def recurse(cls):
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all_classes[cls] = None
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for c in cls.__bases__:
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if c not in all_classes:
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recurse(c)
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for cls in classes:
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recurse(cls)
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return list(all_classes.keys())
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def class_name(self, cls, parts=0):
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"""
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Given a class object, return a fully-qualified name. This
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works for things I've tested in matplotlib so far, but may not
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be completely general.
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"""
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module = cls.__module__
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if module == '__builtin__':
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fullname = cls.__name__
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else:
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fullname = "%s.%s" % (module, cls.__name__)
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if parts == 0:
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return fullname
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name_parts = fullname.split('.')
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return '.'.join(name_parts[-parts:])
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def get_all_class_names(self):
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"""
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Get all of the class names involved in the graph.
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"""
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return [self.class_name(x) for x in self.all_classes]
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# These are the default options for graphviz
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default_graph_options = {
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"rankdir": "LR",
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"size": '"8.0, 12.0"'
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}
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default_node_options = {
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"shape": "box",
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"fontsize": 10,
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"height": 0.25,
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"fontname": "Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",
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"style": '"setlinewidth(0.5)"'
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}
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default_edge_options = {
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"arrowsize": 0.5,
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"style": '"setlinewidth(0.5)"'
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}
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def _format_node_options(self, options):
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return ','.join(["%s=%s" % x for x in list(options.items())])
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def _format_graph_options(self, options):
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return ''.join(["%s=%s;\n" % x for x in list(options.items())])
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def generate_dot(self, fd, name, parts=0, urls={},
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graph_options={}, node_options={},
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edge_options={}):
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"""
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Generate a graphviz dot graph from the classes that
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were passed in to __init__.
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*fd* is a Python file-like object to write to.
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*name* is the name of the graph
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*urls* is a dictionary mapping class names to http urls
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*graph_options*, *node_options*, *edge_options* are
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dictionaries containing key/value pairs to pass on as graphviz
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properties.
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"""
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g_options = self.default_graph_options.copy()
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g_options.update(graph_options)
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n_options = self.default_node_options.copy()
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n_options.update(node_options)
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e_options = self.default_edge_options.copy()
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e_options.update(edge_options)
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fd.write('digraph %s {\n' % name)
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fd.write(self._format_graph_options(g_options))
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for cls in self.all_classes:
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if not self.show_builtins and cls in list(__builtins__.values()):
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continue
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name = self.class_name(cls, parts)
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# Write the node
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this_node_options = n_options.copy()
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url = urls.get(self.class_name(cls))
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if url is not None:
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this_node_options['URL'] = '"%s"' % url
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fd.write(' "%s" [%s];\n' %
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(name, self._format_node_options(this_node_options)))
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# Write the edges
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for base in cls.__bases__:
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if not self.show_builtins and base in list(__builtins__.values()):
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continue
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base_name = self.class_name(base, parts)
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fd.write(' "%s" -> "%s" [%s];\n' %
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(base_name, name,
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self._format_node_options(e_options)))
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fd.write('}\n')
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def run_dot(self, args, name, parts=0, urls={},
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graph_options={}, node_options={}, edge_options={}):
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"""
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Run graphviz 'dot' over this graph, returning whatever 'dot'
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writes to stdout.
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*args* will be passed along as commandline arguments.
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*name* is the name of the graph
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*urls* is a dictionary mapping class names to http urls
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Raises DotException for any of the many os and
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installation-related errors that may occur.
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"""
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try:
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dot = subprocess.Popen(['dot'] + list(args),
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stdin=subprocess.PIPE, stdout=subprocess.PIPE,
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close_fds=True)
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except OSError:
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raise DotException("Could not execute 'dot'. Are you sure you have 'graphviz' installed?")
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except ValueError:
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raise DotException("'dot' called with invalid arguments")
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except:
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raise DotException("Unexpected error calling 'dot'")
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self.generate_dot(dot.stdin, name, parts, urls, graph_options,
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node_options, edge_options)
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dot.stdin.close()
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result = dot.stdout.read()
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returncode = dot.wait()
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if returncode != 0:
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raise DotException("'dot' returned the errorcode %d" % returncode)
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return result
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class inheritance_diagram(Body, Element):
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"""
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A docutils node to use as a placeholder for the inheritance
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diagram.
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"""
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pass
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def inheritance_diagram_directive(name, arguments, options, content, lineno,
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content_offset, block_text, state,
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state_machine):
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"""
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Run when the inheritance_diagram directive is first encountered.
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"""
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node = inheritance_diagram()
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class_names = arguments
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# Create a graph starting with the list of classes
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graph = InheritanceGraph(class_names)
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# Create xref nodes for each target of the graph's image map and
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# add them to the doc tree so that Sphinx can resolve the
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# references to real URLs later. These nodes will eventually be
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# removed from the doctree after we're done with them.
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for name in graph.get_all_class_names():
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refnodes, x = xfileref_role(
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'class', ':class:`%s`' % name, name, 0, state)
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node.extend(refnodes)
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# Store the graph object so we can use it to generate the
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# dot file later
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node['graph'] = graph
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# Store the original content for use as a hash
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node['parts'] = options.get('parts', 0)
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node['content'] = " ".join(class_names)
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return [node]
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def get_graph_hash(node):
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return md5(node['content'] + str(node['parts'])).hexdigest()[-10:]
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def html_output_graph(self, node):
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"""
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Output the graph for HTML. This will insert a PNG with clickable
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image map.
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"""
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graph = node['graph']
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parts = node['parts']
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graph_hash = get_graph_hash(node)
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name = "inheritance%s" % graph_hash
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path = '_images'
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dest_path = os.path.join(setup.app.builder.outdir, path)
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if not os.path.exists(dest_path):
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os.makedirs(dest_path)
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png_path = os.path.join(dest_path, name + ".png")
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path = setup.app.builder.imgpath
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# Create a mapping from fully-qualified class names to URLs.
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urls = {}
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for child in node:
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if child.get('refuri') is not None:
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urls[child['reftitle']] = child.get('refuri')
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elif child.get('refid') is not None:
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urls[child['reftitle']] = '#' + child.get('refid')
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# These arguments to dot will save a PNG file to disk and write
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# an HTML image map to stdout.
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image_map = graph.run_dot(['-Tpng', '-o%s' % png_path, '-Tcmapx'],
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name, parts, urls)
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return ('<img src="%s/%s.png" usemap="#%s" class="inheritance"/>%s' %
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(path, name, name, image_map))
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def latex_output_graph(self, node):
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"""
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Output the graph for LaTeX. This will insert a PDF.
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"""
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graph = node['graph']
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parts = node['parts']
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graph_hash = get_graph_hash(node)
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name = "inheritance%s" % graph_hash
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dest_path = os.path.abspath(os.path.join(setup.app.builder.outdir, '_images'))
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if not os.path.exists(dest_path):
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os.makedirs(dest_path)
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pdf_path = os.path.abspath(os.path.join(dest_path, name + ".pdf"))
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graph.run_dot(['-Tpdf', '-o%s' % pdf_path],
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name, parts, graph_options={'size': '"6.0,6.0"'})
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return '\n\\includegraphics{%s}\n\n' % pdf_path
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def visit_inheritance_diagram(inner_func):
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"""
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This is just a wrapper around html/latex_output_graph to make it
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easier to handle errors and insert warnings.
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"""
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def visitor(self, node):
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try:
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content = inner_func(self, node)
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except DotException as e:
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# Insert the exception as a warning in the document
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warning = self.document.reporter.warning(str(e), line=node.line)
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warning.parent = node
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node.children = [warning]
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else:
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source = self.document.attributes['source']
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self.body.append(content)
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node.children = []
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return visitor
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def do_nothing(self, node):
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pass
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def setup(app):
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setup.app = app
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setup.confdir = app.confdir
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app.add_node(
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inheritance_diagram,
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latex=(visit_inheritance_diagram(latex_output_graph), do_nothing),
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html=(visit_inheritance_diagram(html_output_graph), do_nothing))
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app.add_directive(
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'inheritance-diagram', inheritance_diagram_directive,
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False, (1, 100, 0), parts = directives.nonnegative_int)
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