restructure pythonizations and add further goodies

- fixed G.nodes(.byid)
- add node/edge/adjEntry to string
- fix BUILD_DIR ending with a slash
- enable doxygen URLs
- add jupyter cell magics

Author: N-Coder

docs/examples/cpp-interaction.ipynb

@@ -2,7 +2,7 @@
 import warnings
 
 import cppyy.ll
-from cppyy import include as cppinclude, cppdef, nullptr
+from cppyy import include as cppinclude, cppdef, cppexec, nullptr
 
 cppyy.ll.set_signals_as_exception(True)
 cppyy.add_include_path(os.path.dirname(os.path.realpath(__file__)))
@@ -14,7 +14,7 @@
 elif "OGDF_BUILD_DIR" in os.environ:
     BUILD_DIR = os.path.expanduser(os.getenv("OGDF_BUILD_DIR"))
     cppyy.add_include_path(os.path.join(BUILD_DIR, "include"))
-    cppyy.add_include_path(os.path.join(os.path.dirname(BUILD_DIR), "include"))
+    cppyy.add_include_path(os.path.join(BUILD_DIR, "..", "include"))
     cppyy.add_library_path(BUILD_DIR)
 else:
     warnings.warn("ogdf-python couldn't find OGDF. "
@@ -30,10 +30,12 @@
 
 import ogdf_python.doxygen
 import ogdf_python.pythonize
+import ogdf_python.jupyter
 from cppyy.gbl import ogdf
 
-__all__ = ["ogdf", "cppinclude", "cppdef", "nullptr"]
+__all__ = ["ogdf", "cppinclude", "cppdef", "cppexec", "nullptr"]
 __keep_imports = [cppyy,
                   ogdf_python.doxygen,
                   ogdf_python.pythonize,
-                  ogdf, cppinclude, cppdef, nullptr]
+                  ogdf_python.jupyter,
+                  ogdf, cppinclude, cppdef, cppexec, nullptr]

src/ogdf_python/__init__.py

@@ -59,25 +59,26 @@ def find_all_includes():
 # doc strings / help messages##########################################################################################
 
 def pythonize_docstrings(klass, name):
-    data = DOXYGEN_DATA["class"][klass.__cpp_name__]  # TODO do the same for namespace members
+    data = DOXYGEN_DATA["class"][klass.__cpp_name__.partition("<")[0]]  # TODO do the same for namespace members
     url = DOXYGEN_URL % (data["refid"], "")
     try:
         if klass.__doc__:
             klass.__doc__ = "%s\n%s" % (klass.__doc__, url)
         else:
             klass.__doc__ = url
     except AttributeError as e:
-        print(klass.__cpp_name__, e)  # TODO remove once we can overwrite the __doc__ of CPPOverload etc.
+        pass
+        # print(klass.__cpp_name__, e)  # TODO remove once we can overwrite the __doc__ of CPPOverload etc.
 
     for mem, val in klass.__dict__.items():
         if mem not in data["members"]:
-            print(klass.__cpp_name__, "has no member", mem)
+            # print(klass.__cpp_name__, "has no member", mem)
             continue
         try:
             for override in data["members"][mem].values():
                 val.__doc__ += "\n" + DOXYGEN_URL % (data["refid"], override["refid"][len(data["refid"]) + 2:])
         except AttributeError as e:
-            print(klass.__cpp_name__, e)  # TODO remove once we can overwrite the __doc__ of CPPOverload etc.
+            # print(klass.__cpp_name__, e)  # TODO remove once we can overwrite the __doc__ of CPPOverload etc.
             # import traceback
             # traceback.print_exc()
             # print(val.__doc__)
@@ -178,12 +179,4 @@ def helpful_getattribute(ns, name):
         with importlib_resources.files("ogdf_python").joinpath("doxygen.json").open("rt") as f:
             DOXYGEN_DATA = json.load(f)
 
-if "OGDF_DOC_URL" in os.environ:
-    DOXYGEN_URL = os.environ["OGDF_DOC_URL"]
-else:
-    DOXYGEN_URL = "https://ogdf.github.io/doc/ogdf/%s.html#%s"
-
-import cppyy
-
-# cppyy.py.add_pythonization(pythonize_docstrings, "ogdf") # TODO needs to be added *before* any classes are loaded
-wrap_getattribute(cppyy.gbl.ogdf)
+DOXYGEN_URL = os.environ.get("OGDF_DOC_URL", "https://ogdf.github.io/doc/ogdf/%s.html#%s")

src/ogdf_python/doxygen.py

@@ -0,0 +1,77 @@
+import sys
+
+import cppyy
+
+try:
+    from IPython.core.magic import register_cell_magic
+except ImportError:
+    pass
+else:
+    cppyy.cppdef("""
+#include <sstream>
+#include <streambuf>
+#include <iostream>
+
+namespace ogdf_pythonization {
+std::ostringstream gCapturedStdout;
+std::streambuf* gOldStdoutBuffer = nullptr;
+
+static void BeginCaptureStdout() {
+    gOldStdoutBuffer = std::cout.rdbuf();
+    std::cout.rdbuf(gCapturedStdout.rdbuf());
+}
+
+static std::string EndCaptureStdout() {
+    std::cout.rdbuf(gOldStdoutBuffer);
+    gOldStdoutBuffer = nullptr;
+
+    std::string capturedStdout = std::move(gCapturedStdout).str();
+
+    gCapturedStdout.str("");
+    gCapturedStdout.clear();
+
+    return capturedStdout;
+}
+
+std::ostringstream gCapturedStderr;
+std::streambuf* gOldStderrBuffer = nullptr;
+
+static void BeginCaptureStderr() {
+    gOldStderrBuffer = std::cerr.rdbuf();
+    std::cerr.rdbuf(gCapturedStderr.rdbuf());
+}
+
+static std::string EndCaptureStderr() {
+    std::cerr.rdbuf(gOldStderrBuffer);
+    gOldStderrBuffer = nullptr;
+
+    std::string capturedStderr = std::move(gCapturedStderr).str();
+
+    gCapturedStderr.str("");
+    gCapturedStderr.clear();
+
+    return capturedStderr;
+}
+}
+""")
+
+
+    @register_cell_magic
+    def cpp(line, cell):
+        """
+        might yield "function definition is not allowed here" for some multi-part definitions
+        use `cppdef` instead if required
+        https://github.com/jupyter-xeus/xeus-cling/issues/40
+        """
+        cppyy.gbl.ogdf_pythonization.BeginCaptureStdout()
+        cppyy.gbl.ogdf_pythonization.BeginCaptureStderr()
+        try:
+            cppyy.cppexec(cell)
+        finally:
+            print(cppyy.gbl.ogdf_pythonization.EndCaptureStdout(), end="")
+            print(cppyy.gbl.ogdf_pythonization.EndCaptureStderr(), file=sys.stderr, end="")
+
+
+    @register_cell_magic
+    def cppdef(line, cell):
+        cppyy.cppdef(cell)

src/ogdf_python/jupyter.py

@@ -0,0 +1,47 @@
+import re
+
+from ogdf_python.doxygen import pythonize_docstrings, wrap_getattribute
+from ogdf_python.pythonize.container import *
+from ogdf_python.pythonize.graph_attributes import *
+from ogdf_python.pythonize.render import *
+from ogdf_python.pythonize.str import *
+
+
+def pythonize_ogdf(klass, name):
+    # print(name, klass)
+    pythonize_docstrings(klass, name)
+
+    if name in ("Graph", "ClusterGraph"):
+        klass._repr_html_ = GraphAttributes_to_html
+    elif name in ("GraphAttributes", "ClusterGraphAttributes"):
+        replace_GraphAttributes(klass, name)
+        klass._repr_html_ = GraphAttributes_to_html
+
+    # TODO setitem?
+    # TODO array slicing
+    elif name.startswith("GraphObjectContainer"):
+        klass.byid = GraphObjectContainer_byindex
+        klass.__getitem__ = iterable_getitem
+    elif re.match("S?List(Pure)?", name):
+        klass.__getitem__ = iterable_getitem
+    elif re.match("List(Const)?(Reverse)?Iterator(Base)?(<.+>)?", name):
+        klass.__next__ = advance_iterator
+    elif re.match("(Node|Edge|AdjEntry|Cluster|Face)Array", name):
+        klass.__iter__ = cpp_iterator
+        # klass.__str__ = grapharray_str # TODO there is no generic way to get the key list (yet)
+
+    elif name == "NodeElement":
+        klass.__str__ = node_str
+        klass.__repr__ = node_repr
+    elif name == "EdgeElement":
+        klass.__str__ = edge_str
+        klass.__repr__ = edge_repr
+    elif name == "AdjElement":
+        klass.__str__ = adjEntry_str
+        klass.__repr__ = adjEntry_repr
+
+
+cppyy.py.add_pythonization(pythonize_ogdf, "ogdf")
+cppyy.py.add_pythonization(pythonize_ogdf, "ogdf::internal")
+generate_GA_setters()
+wrap_getattribute(cppyy.gbl.ogdf)

src/ogdf_python/pythonize/__init__.py

@@ -0,0 +1,45 @@
+def GraphObjectContainer_byindex(self, idx):
+    for e in self:
+        if e.index() == idx:
+            return e
+    raise IndexError("Container has no element with index %s." % idx)
+
+
+def advance_iterator(self):
+    if not self.valid():
+        raise StopIteration()
+    val = self.__deref__()
+    self.__preinc__()
+    return val
+
+
+def cpp_iterator(self):
+    it = self.begin()
+    while it != self.end():
+        yield it.__deref__()
+        it.__preinc__()
+
+
+def iterable_getitem(self, key):
+    if isinstance(key, slice):
+        indices = range(*key.indices(len(self)))
+        elems = []
+        try:
+            next_ind = next(indices)
+            for i, e in enumerate(self):
+                if i == next_ind:
+                    elems.append(e)
+                    next_ind = next(indices)
+        except StopIteration:
+            pass
+        return elems
+    elif isinstance(key, int):
+        if key < 0:
+            key += len(self)
+        if key < 0 or key >= len(self):
+            raise IndexError("The index (%d) is out of range." % key)
+        for i, e in enumerate(self):
+            if i == key:
+                return e
+    else:
+        raise TypeError("Invalid argument type %s." % type(key))

src/ogdf_python/pythonize/container.py

@@ -1,7 +1,3 @@
-import functools
-import re
-import tempfile
-
 import cppyy
 
 
@@ -17,8 +13,8 @@ def __setitem__(self, key, item):
     def __getitem__(self, key):
         return self.getter(self.GA, key)
 
-    def __call__(self, key):
-        return self.getter(self.GA, key)
+    def __call__(self, *args, **kwargs):
+        return self.getter(self.GA, *args, **kwargs)
 
 
 class GraphAttributesDescriptor(object):
@@ -96,98 +92,10 @@ def generate_GA_setters():
     cppyy.cppdef(DEFS + "};")
 
 
-SVGConf = None
-
-
-def GraphAttributes_to_html(self):
-    global SVGConf
-    if SVGConf == None:
-        SVGConf = cppyy.gbl.ogdf.GraphIO.SVGSettings()
-        SVGConf.margin(50)
-        SVGConf.bezierInterpolation(True)
-        SVGConf.curviness(0.3)
-    with tempfile.NamedTemporaryFile("w+t", suffix=".svg", prefix="ogdf-python-") as f:
-        # os = cppyy.gbl.std.ofstream(f.name)
-        # cppyy.bind_object(cppyy.addressof(os), "std::basic_ostream<char>")
-        cppyy.gbl.ogdf.GraphIO.drawSVG(self, f.name, SVGConf)
-        # os.close()
-        return f.read()
-
-
 def replace_GraphAttributes(klass, name):
-    if not name.endswith("GraphAttributes"): return
     klass.directed = property(klass.directed, cppyy.gbl.ogdf_pythonization.GraphAttributes_set_directed)
     for field in (CGA_FIELD_NAMES if name.startswith("Cluster") else GA_FIELD_NAMES):
         setattr(klass, field, GraphAttributesDescriptor(
             getattr(klass, field),
             getattr(cppyy.gbl.ogdf_pythonization, "GraphAttributes_set_%s" % field)
-        ))
-    klass._repr_html_ = GraphAttributes_to_html
-
-
-generate_GA_setters()
-# TODO use pythonization for this so that classes are loaded lazily
-replace_GraphAttributes(cppyy.gbl.ogdf.GraphAttributes, "GraphAttributes")
-replace_GraphAttributes(cppyy.gbl.ogdf.ClusterGraphAttributes, "ClusterGraphAttributes")
-cppyy.gbl.ogdf.Graph._repr_html_ = GraphAttributes_to_html  # TODO layout
-cppyy.gbl.ogdf.ClusterGraph._repr_html_ = GraphAttributes_to_html
-
-
-def GraphObjectContainer_getitem(self, idx):
-    for e in self:
-        if e.index() == idx:
-            return e
-    raise IndexError()
-
-
-def pythonize_ogdf_internal(klass, name):
-    if name.startswith("GraphObjectContainer"):
-        klass.__getitem__ = GraphObjectContainer_getitem
-
-
-cppyy.py.add_pythonization(pythonize_ogdf_internal, "ogdf::internal")
-
-
-class StreamToStr(object):
-    def __init__(self, klass):
-        self.klass = klass
-        self.old_str = klass.__str__
-
-    def __get__(self, obj, type=None):
-        @functools.wraps(self.old_str)
-        def to_str():
-            try:
-                return cppyy.gbl.ogdf_pythonization.to_string(obj)
-            except TypeError as e:
-                print(e)
-                return self.old_str(obj)
-
-        return to_str
-
-
-def generic_getitem(self, idx):
-    # TODO more efficient implementation for random-access, reverse iteration
-    for i, e in enumerate(self):
-        if i == idx:
-            return e
-    raise IndexError()
-
-
-def pythonize_ogdf(klass, name):
-    if not isinstance(klass.__str__, StreamToStr):
-        klass.__str__ = StreamToStr(klass)
-    if re.match("List(Const)?(Reverse)?Iterator(Base)?(<.+>)?", name):
-        def advance(self):
-            if not self.valid():
-                raise StopIteration()
-            val = self.__deref__()
-            self.__preinc__()
-            return val
-
-        klass.__next__ = advance
-    if re.match("S?List(Pure)?", name):
-        klass.__getitem__ = generic_getitem
-        # TODO setitem?
-
-
-cppyy.py.add_pythonization(pythonize_ogdf, "ogdf")
+        ))

src/ogdf_python/pythonize.py …gdf_python/pythonize/graph_attributes.pysrc/ogdf_python/pythonize.py renamed to src/ogdf_python/pythonize/graph_attributes.py src/ogdf_python/pythonize.py renamed to src/ogdf_python/pythonize/graph_attributes.py

@@ -0,0 +1,20 @@
+import tempfile
+
+import cppyy
+
+SVGConf = None
+
+
+def GraphAttributes_to_html(self):
+    global SVGConf
+    if SVGConf is None:
+        SVGConf = cppyy.gbl.ogdf.GraphIO.SVGSettings()
+        SVGConf.margin(50)
+        SVGConf.bezierInterpolation(True)
+        SVGConf.curviness(0.3)
+    with tempfile.NamedTemporaryFile("w+t", suffix=".svg", prefix="ogdf-python-") as f:
+        # os = cppyy.gbl.std.ofstream(f.name)
+        # cppyy.bind_object(cppyy.addressof(os), "std::basic_ostream<char>")
+        cppyy.gbl.ogdf.GraphIO.drawSVG(self, f.name, SVGConf)
+        # os.close()
+        return f.read()