diff --git a/src/graph_tool/centrality/__init__.py b/src/graph_tool/centrality/__init__.py index cc78cff0a3174e3cc84dcca672031094d6a1e459..62a41a90b0e59e69eff6a29e36171042d2b28e55 100644 --- a/src/graph_tool/centrality/__init__.py +++ b/src/graph_tool/centrality/__init__.py @@ -43,7 +43,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_centrality") -from .. core import _prop, ungroup_vector_property +from .. import _prop, ungroup_vector_property import sys import numpy diff --git a/src/graph_tool/clustering/__init__.py b/src/graph_tool/clustering/__init__.py index dc034fcbdb9635d9a0f45ddc863c70fa87724f90..1fa0ded65875ea8fdbb138dfa2219cb321375989 100644 --- a/src/graph_tool/clustering/__init__.py +++ b/src/graph_tool/clustering/__init__.py @@ -44,7 +44,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_clustering as _gt") -from .. core import _degree, _prop, Graph +from .. import _degree, _prop, Graph from .. topology import isomorphism from .. generation import random_rewire from .. stats import vertex_hist @@ -463,7 +463,7 @@ def motif_significance(g, k, n_shuffles=100, p=1.0, motif_list=None, shuffled networks. shuffle_strategy : string (optional, default: "uncorrelated") Shuffle strategy to use. Can be either "correlated" or "uncorrelated". - See random_rewire() for details. + See :func:`~graph_tool.generation.random_rewire` for details. Returns ------- diff --git a/src/graph_tool/community/__init__.py b/src/graph_tool/community/__init__.py index adeb27c67a9a114bcb0dfb59d33297e62e623135..bcfb2d4be0b1c621865770e23d6b5aced4ee83b6 100644 --- a/src/graph_tool/community/__init__.py +++ b/src/graph_tool/community/__init__.py @@ -42,7 +42,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_community") -from .. core import _degree, _prop, Graph, libcore +from .. import _degree, _prop, Graph, libcore import random import sys diff --git a/src/graph_tool/correlations/__init__.py b/src/graph_tool/correlations/__init__.py index 1e7a80e1e10716041d9e6b0de2aaf9f4169e2184..f3ba86b377782c567f20bd908efb05ca22a91d91 100644 --- a/src/graph_tool/correlations/__init__.py +++ b/src/graph_tool/correlations/__init__.py @@ -43,7 +43,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_correlations") -from .. core import _degree, _prop +from .. import _degree, _prop from numpy import * __all__ = ["assortativity", "scalar_assortativity", "corr_hist", diff --git a/src/graph_tool/draw/__init__.py b/src/graph_tool/draw/__init__.py index a749356cd59b27fe6d26aa23e591732343420a00..c0c107fe1a14035c9ef0d40cb432fc714b7d5068 100644 --- a/src/graph_tool/draw/__init__.py +++ b/src/graph_tool/draw/__init__.py @@ -37,7 +37,7 @@ Contents """ import sys, os, os.path, time, warnings, tempfile -from .. core import _degree, _prop, PropertyMap, _check_prop_vector,\ +from .. import _degree, _prop, PropertyMap, _check_prop_vector,\ _check_prop_scalar, _check_prop_writable, group_vector_property,\ ungroup_vector_property from .. decorators import _limit_args diff --git a/src/graph_tool/flow/__init__.py b/src/graph_tool/flow/__init__.py index 01e505797f2681614268c7eaeaa8b3e45fe82eb5..fb46ca8d7a4a21ddd77608a6905077e9e2296106 100644 --- a/src/graph_tool/flow/__init__.py +++ b/src/graph_tool/flow/__init__.py @@ -73,7 +73,7 @@ The following network will be used as an example throughout the documentation. from .. dl_import import dl_import dl_import("import libgraph_tool_flow") -from .. core import _prop, _check_prop_scalar, _check_prop_writable +from .. import _prop, _check_prop_scalar, _check_prop_writable __all__ = ["edmonds_karp_max_flow", "push_relabel_max_flow", "boykov_kolmogorov_max_flow", "max_cardinality_matching"] diff --git a/src/graph_tool/generation/__init__.py b/src/graph_tool/generation/__init__.py index 8911e08442b6accd110a63d29c64f738d86661c0..d3c41cae4f9a8960d6b42e2193152f3f292872be 100644 --- a/src/graph_tool/generation/__init__.py +++ b/src/graph_tool/generation/__init__.py @@ -45,7 +45,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_generation") -from .. core import Graph, _check_prop_scalar, _prop, _limit_args +from .. import Graph, _check_prop_scalar, _prop, _limit_args from .. stats import label_parallel_edges, label_self_loops import sys, numpy, numpy.random diff --git a/src/graph_tool/run_action/inline.py b/src/graph_tool/run_action/inline.py index 90d6a94ab0160e1fe303f626eecb9e9e2be5a80d..d6e53353a3122475ad129f87733e5a09678213fb 100644 --- a/src/graph_tool/run_action/inline.py +++ b/src/graph_tool/run_action/inline.py @@ -18,7 +18,7 @@ # along with this program. If not, see . import sys, string, hashlib, os.path, re, glob -from .. import core +from .. import * from .. import libgraph_tool_core import numpy import DLFCN @@ -66,7 +66,7 @@ def clean_prop_type(t): replace("__", "_") for d in ["vertex", "edge", "graph"]: - for t in core.value_types(): + for t in value_types(): props += "typedef %s_prop_t::as<%s >::type %sprop_%s_t;\n" % \ (d, t.replace("bool", "uint8_t"), d[0], clean_prop_type(t)) @@ -158,7 +158,7 @@ def inline(code, arg_names=None, local_dict=None, arg_val = local_dict[arg] else: arg_val = global_dict[arg] - if issubclass(type(arg_val), core.Graph): + if issubclass(type(arg_val), Graph): alias = "__gt__" + arg gi = "__gt__" + arg + "__gi" graph_type = get_graph_type(arg_val) @@ -170,7 +170,7 @@ def inline(code, arg_names=None, local_dict=None, (arg, arg, graph_type, gi, gi) arg_alias.append(alias) alias_dict[alias] = gi_val - elif type(arg_val) == core.PropertyMap: + elif type(arg_val) == PropertyMap: alias = "__gt__" + arg if arg_val == arg_val.get_graph().vertex_index: prop_name = "GraphInterface::vertex_index_map_t" @@ -222,8 +222,8 @@ def inline(code, arg_names=None, local_dict=None, else: arg_val = global_dict[arg] if arg not in mask_ret and \ - type(arg_val) not in [numpy.ndarray, core.PropertyMap] and \ - not issubclass(type(arg_val), core.Graph): + type(arg_val) not in [numpy.ndarray, PropertyMap] and \ + not issubclass(type(arg_val), Graph): return_vals += 'return_vals["%s"] = %s;\n' % (arg, arg) support_code += globals()["support_template"] @@ -241,7 +241,7 @@ def inline(code, arg_names=None, local_dict=None, extra_compile_args +\ extra_objects + \ extra_link_args) + \ - headers_hash + core.__version__).hexdigest() + headers_hash + __version__).hexdigest() code += "\n// support code hash: " + support_hash inline_code = string.Template(globals()["code_template"]).\ substitute(var_defs=arg_def, var_extract=arg_conv, diff --git a/src/graph_tool/search/__init__.py b/src/graph_tool/search/__init__.py index dffc7d69ffe55dd524a53686eea294826d2d104a..e2ea1092911785ec588bb9d0823a2b0745fa8fa2 100644 --- a/src/graph_tool/search/__init__.py +++ b/src/graph_tool/search/__init__.py @@ -78,7 +78,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_search") -from .. core import _prop +from .. import _prop from .. decorators import _wraps import sys import weakref @@ -191,8 +191,7 @@ class BFSVisitor(object): @_perm_wrap(["initialize_vertex", "examine_vertex", "finish_vertex"], ["initialize_vertex"]) def bfs_search(g, source, visitor=BFSVisitor()): - r"""This function performs a breadth-first traversal of the vertices in a - directed or undirected graph. + r"""Breadth-first traversal of a directed or undirected graph. Parameters ---------- @@ -401,8 +400,7 @@ class DFSVisitor(object): @_perm_wrap(["initialize_vertex", "discover_vertex", "finish_vertex", "start_vertex"], ["initialize_vertex"]) def dfs_search(g, source, visitor=DFSVisitor()): - r"""This function performs a depth-first traversal of the vertices in a - directed or undirected graph. + r"""Depth-first traversal of a directed or undirected graph. Parameters ---------- @@ -631,7 +629,7 @@ class DijkstraVisitor(object): def dijkstra_search(g, source, weight, visitor=DijkstraVisitor(), dist_map=None, pred_map=None, combine=lambda a, b: a + b, compare=lambda a, b: a < b, zero=0, infinity=float('inf')): - r"""This function performs a Dijsktra traversal of the vertices in a directed or undirected graph, with non-negative weights. + r"""Dijsktra traversal of a directed or undirected graph, with non-negative weights. Parameters ---------- @@ -898,7 +896,7 @@ def bellman_ford_search(g, source, weight, visitor=BellmanFordVisitor(), combine=lambda a, b: a + b, compare=lambda a, b: a < b, zero=0, infinity=float('inf')): - r"""This function performs a Bellman-Ford traversal of the vertices in a directed or undirected graph, with negative weights. + r"""Bellman-Ford traversal of a directed or undirected graph, with negative weights. Parameters ---------- @@ -1171,7 +1169,7 @@ def astar_search(g, source, weight, visitor=AStarVisitor(), compare=lambda a, b: a < b, zero=0, infinity=float('inf'), implicit=False): r""" - This algorithm implements a heuristic :math:`A^*` search on a weighted, directed or undirected graph for the case where all edge weights are non-negative. + Heuristic :math:`A^*` search on a weighted, directed or undirected graph for the case where all edge weights are non-negative. Parameters ---------- diff --git a/src/graph_tool/spectral/__init__.py b/src/graph_tool/spectral/__init__.py index a40ddbb49f9ebd4e18a56cc78207d921d7c1eb6f..a3060181083658422f42b0e75e2fb05ce0c28b5e 100644 --- a/src/graph_tool/spectral/__init__.py +++ b/src/graph_tool/spectral/__init__.py @@ -36,7 +36,7 @@ Contents ++++++++ """ -from .. core import _degree, _prop, Graph, _limit_args +from .. import _degree, _prop, Graph, _limit_args from numpy import * import scipy.sparse diff --git a/src/graph_tool/stats/__init__.py b/src/graph_tool/stats/__init__.py index 13ab4792ea383999ac0ba62660145a7f3e210047..30019d3559c3122c3904b28b3351df47888a3cf7 100644 --- a/src/graph_tool/stats/__init__.py +++ b/src/graph_tool/stats/__init__.py @@ -47,7 +47,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_stats") -from .. core import _degree, _prop +from .. import _degree, _prop from numpy import * import numpy import sys diff --git a/src/graph_tool/topology/__init__.py b/src/graph_tool/topology/__init__.py index b40c3fc1b0bf5ad3415e4986cfc7adaa627fb095..3211e0cc9c9cefe83de12451f95910a3fe9b03dd 100644 --- a/src/graph_tool/topology/__init__.py +++ b/src/graph_tool/topology/__init__.py @@ -49,7 +49,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_topology") -from .. core import _prop, Vector_int32_t, _check_prop_writable, \ +from .. import _prop, Vector_int32_t, _check_prop_writable, \ _check_prop_scalar, _check_prop_vector, Graph, PropertyMap import random, sys, numpy, weakref __all__ = ["isomorphism", "subgraph_isomorphism", "mark_subgraph", diff --git a/src/graph_tool/util/__init__.py b/src/graph_tool/util/__init__.py index 2c2b6750b48a82ab86636d3b4241a2efb3452150..a4bf4323af54390bfbb6b796466de54ca5d62da5 100644 --- a/src/graph_tool/util/__init__.py +++ b/src/graph_tool/util/__init__.py @@ -41,7 +41,7 @@ Contents from .. dl_import import dl_import dl_import("import libgraph_tool_util") -from .. core import _degree, _prop +from .. import _degree, _prop import weakref __all__ = ["find_vertex", "find_vertex_range", "find_edge", "find_edge_range"]