From 45f28a19480b9c2bfde1b88c1cbce254382ded1c Mon Sep 17 00:00:00 2001 From: Tiago de Paula Peixoto Date: Fri, 15 Nov 2013 18:07:36 +0100 Subject: [PATCH] Update docstrings --- src/graph_tool/__init__.py | 2 +- src/graph_tool/centrality/__init__.py | 2 +- src/graph_tool/clustering/__init__.py | 4 +- src/graph_tool/community/blockmodel.py | 4 +- src/graph_tool/community/nested_blockmodel.py | 2 +- src/graph_tool/correlations/__init__.py | 6 +-- src/graph_tool/generation/__init__.py | 18 ++++----- src/graph_tool/topology/__init__.py | 37 +++++++++---------- 8 files changed, 37 insertions(+), 38 deletions(-) diff --git a/src/graph_tool/__init__.py b/src/graph_tool/__init__.py index 4fd7ee51..597d265e 100644 --- a/src/graph_tool/__init__.py +++ b/src/graph_tool/__init__.py @@ -1485,8 +1485,8 @@ class Graph(object): >>> g.graph_properties["gnat"] = g.new_graph_property("string", "hi there!") >>> g.list_properties() gnat (graph) (type: string, val: hi there!) - foo (vertex) (type: double) bar (vertex) (type: python::object) + foo (vertex) (type: double) foo (edge) (type: vector) """ diff --git a/src/graph_tool/centrality/__init__.py b/src/graph_tool/centrality/__init__.py index 9e18c136..94f137cf 100644 --- a/src/graph_tool/centrality/__init__.py +++ b/src/graph_tool/centrality/__init__.py @@ -695,7 +695,7 @@ def katz(g, alpha=0.01, beta=None, weight=None, vprop=None, epsilon=1e-6, >>> g = gt.collection.data["polblogs"] >>> g = gt.GraphView(g, vfilt=gt.label_largest_component(g)) >>> w = g.new_edge_property("double") - >>> w.a = np.random.random(len(w.a)) * 42 + >>> w.a = np.random.random(len(w.a)) >>> x = gt.katz(g, weight=w) >>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=x, ... vertex_size=gt.prop_to_size(x, mi=5, ma=15), diff --git a/src/graph_tool/clustering/__init__.py b/src/graph_tool/clustering/__init__.py index aa65807d..4e089298 100644 --- a/src/graph_tool/clustering/__init__.py +++ b/src/graph_tool/clustering/__init__.py @@ -121,7 +121,7 @@ def local_clustering(g, prop=None, undirected=True): >>> g = gt.random_graph(1000, lambda: (5,5)) >>> clust = gt.local_clustering(g) >>> print(gt.vertex_average(g, clust)) - (0.0072, 0.00039746045691969764) + (0.007177777777777778, 0.0003966968553716155) References ---------- @@ -182,7 +182,7 @@ def global_clustering(g): >>> g = gt.random_graph(1000, lambda: (5,5)) >>> print(gt.global_clustering(g)) - (0.007182172103638073, 0.0003970213508956326) + (0.007177777777777778, 0.0003970939493209407) References ---------- diff --git a/src/graph_tool/community/blockmodel.py b/src/graph_tool/community/blockmodel.py index cc351494..49c047de 100644 --- a/src/graph_tool/community/blockmodel.py +++ b/src/graph_tool/community/blockmodel.py @@ -1870,7 +1870,7 @@ def collect_edge_marginals(state, p=None): ... ds, nmoves = gt.mcmc_sweep(state) ... pe = gt.collect_edge_marginals(state, pe) >>> gt.bethe_entropy(state, pe)[0] - 16.31947774487215 + 17.443089842818125 """ if p is None: @@ -1922,7 +1922,7 @@ def collect_vertex_marginals(state, p=None): ... ds, nmoves = gt.mcmc_sweep(state) ... pv = gt.collect_vertex_marginals(state, pv) >>> gt.mf_entropy(state, pv) - 18.348761352514927 + 19.94955528942717 >>> gt.graph_draw(g, pos=g.vp["pos"], vertex_shape="pie", vertex_pie_fractions=pv, output="polbooks_blocks_soft_B4.pdf") <...> diff --git a/src/graph_tool/community/nested_blockmodel.py b/src/graph_tool/community/nested_blockmodel.py index 667cc4f3..9c5e091d 100644 --- a/src/graph_tool/community/nested_blockmodel.py +++ b/src/graph_tool/community/nested_blockmodel.py @@ -328,7 +328,7 @@ def nested_mcmc_sweep(state, beta=1., random_move=False, c=1., sequential=True, >>> state = gt.NestedBlockState(g, Bs=[10, 5, 3, 2, 1], deg_corr=True) >>> ret = gt.nested_mcmc_sweep(state) >>> print(ret) - [(-0.23943486013787463, 57), (-0.017558577944127587, 2), (0.0, 0), (-0.0012759602078996138, 1), (0.0, 0)] + [(-0.11881394061738723, 58), (-1.2855474804244876e-05, 1), (0.0, 0), (-0.003488958656098635, 1), (0.0, 0)] References ---------- diff --git a/src/graph_tool/correlations/__init__.py b/src/graph_tool/correlations/__init__.py index f5d090cd..83843cb7 100644 --- a/src/graph_tool/correlations/__init__.py +++ b/src/graph_tool/correlations/__init__.py @@ -115,7 +115,7 @@ def assortativity(g, deg): ... vertex_corr=lambda i,k: 1.0 / (1 + abs(i - k)), directed=False, ... n_iter=100) >>> gt.assortativity(g, "out") - (0.13903518011375607, 0.005051876804786422) + (0.1419534824769149, 0.005098622437085927) References ---------- @@ -191,13 +191,13 @@ def scalar_assortativity(g, deg): ... vertex_corr=lambda i,k: abs(i-k), ... directed=False, n_iter=100) >>> gt.scalar_assortativity(g, "out") - (-0.44070158356400696, 0.010592022444678632) + (-0.45182410730944034, 0.010288182870044639) >>> g = gt.random_graph(1000, lambda: sample_k(40), model="probabilistic", ... vertex_corr=lambda i, k: 1.0 / (1 + abs(i - k)), ... directed=False, n_iter=100) >>> gt.scalar_assortativity(g, "out") - (0.6007430887839058, 0.011569809783643956) + (0.6421210898147616, 0.010632143985746339) References ---------- diff --git a/src/graph_tool/generation/__init__.py b/src/graph_tool/generation/__init__.py index 840fe366..9b4217b5 100644 --- a/src/graph_tool/generation/__init__.py +++ b/src/graph_tool/generation/__init__.py @@ -189,7 +189,7 @@ def random_graph(N, deg_sampler, directed=True, ... vertex_corr=lambda i, k: 1.0 / (1 + abs(i - k)), directed=False, ... n_iter=100) >>> gt.scalar_assortativity(g, "out") - (0.6285094791115295, 0.010745128857935755) + (0.6197157767573332, 0.010781011616659146) The following samples an in,out-degree pair from the joint distribution: @@ -584,7 +584,7 @@ def random_rewire(g, model="uncorrelated", n_iter=1, edge_sweep=True, gt.graph_draw(g, pos=pos, output="rewire_orig.png", output_size=(300, 300)) >>> gt.random_rewire(g, "correlated") - 189 + 212 >>> pos = gt.arf_layout(g) >>> gt.graph_draw(g, pos=pos, output="rewire_corr.pdf", output_size=(300, 300)) <...> @@ -595,7 +595,7 @@ def random_rewire(g, model="uncorrelated", n_iter=1, edge_sweep=True, gt.graph_draw(g, pos=pos, output="rewire_corr.png", output_size=(300, 300)) >>> gt.random_rewire(g) - 197 + 207 >>> pos = gt.arf_layout(g) >>> gt.graph_draw(g, pos=pos, output="rewire_uncorr.pdf", output_size=(300, 300)) <...> @@ -606,7 +606,7 @@ def random_rewire(g, model="uncorrelated", n_iter=1, edge_sweep=True, gt.graph_draw(g, pos=pos, output="rewire_uncorr.png", output_size=(300, 300)) >>> gt.random_rewire(g, "erdos") - 26 + 21 >>> pos = gt.arf_layout(g) >>> gt.graph_draw(g, pos=pos, output="rewire_erdos.pdf", output_size=(300, 300)) <...> @@ -637,17 +637,17 @@ def random_rewire(g, model="uncorrelated", n_iter=1, edge_sweep=True, >>> errorbar(corr[2][:-1], corr[0], yerr=corr[1], fmt="o-", label="Original") <...> >>> gt.random_rewire(g, "correlated") - 206 + 212 >>> corr = gt.avg_neighbour_corr(g, "out", "out") >>> errorbar(corr[2][:-1], corr[0], yerr=corr[1], fmt="*", label="Correlated") <...> >>> gt.random_rewire(g) - 109 + 120 >>> corr = gt.avg_neighbour_corr(g, "out", "out") >>> errorbar(corr[2][:-1], corr[0], yerr=corr[1], fmt="o-", label="Uncorrelated") <...> >>> gt.random_rewire(g, "erdos") - 13 + 20 >>> corr = gt.avg_neighbour_corr(g, "out", "out") >>> errorbar(corr[2][:-1], corr[0], yerr=corr[1], fmt="o-", label=r"Erd\H{o}s") <...> @@ -693,7 +693,7 @@ def random_rewire(g, model="uncorrelated", n_iter=1, edge_sweep=True, ... label=r"$\left<\text{i}\right>$ vs o") <...> >>> gt.random_rewire(g, "correlated") - 4323 + 4130 >>> corr = gt.avg_neighbour_corr(g, "in", "out") >>> errorbar(corr[2][:-1], corr[0], yerr=corr[1], fmt="o-", ... label=r"$\left<\text{o}\right>$ vs i, corr.") @@ -703,7 +703,7 @@ def random_rewire(g, model="uncorrelated", n_iter=1, edge_sweep=True, ... label=r"$\left<\text{i}\right>$ vs o, corr.") <...> >>> gt.random_rewire(g, "uncorrelated") - 153 + 194 >>> corr = gt.avg_neighbour_corr(g, "in", "out") >>> errorbar(corr[2][:-1], corr[0], yerr=corr[1], fmt="o-", ... label=r"$\left<\text{o}\right>$ vs i, uncorr.") diff --git a/src/graph_tool/topology/__init__.py b/src/graph_tool/topology/__init__.py index 4e39955d..0d1c95f6 100644 --- a/src/graph_tool/topology/__init__.py +++ b/src/graph_tool/topology/__init__.py @@ -797,12 +797,12 @@ def label_largest_component(g, directed=None): >>> g = gt.random_graph(100, lambda: poisson(1), directed=False) >>> l = gt.label_largest_component(g) >>> print(l.a) - [1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 - 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 - 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1] + [0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 1 0 0 0 0 0 0 0 + 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 + 0 0 1 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 1 1 1 0] >>> u = gt.GraphView(g, vfilt=l) # extract the largest component as a graph >>> print(u.num_vertices()) - 16 + 18 """ label = g.new_vertex_property("bool") @@ -848,18 +848,18 @@ def label_out_component(g, root): >>> g = gt.random_graph(100, lambda: poisson(2.2), directed=False) >>> l = gt.label_out_component(g, g.vertex(2)) >>> print(l.a) - [1 1 1 1 0 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 0 1 1 1 0 - 1 1 0 0 1 1 0 1 1 0 0 1 1 1 1 0 1 0 0 1 1 1 1 1 1 1 1 1 0 0 1 0 1 1 1 1 1 - 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 0 0] + [1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 0 + 1 1 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 1 0 1 1 1 1 1 + 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 0 1 1 1 0] The in-component can be obtained by reversing the graph. >>> l = gt.label_out_component(gt.GraphView(g, reversed=True, directed=True), ... g.vertex(1)) >>> print(l.a) - [1 1 1 0 0 1 1 0 1 0 0 0 0 1 0 0 0 1 0 0 1 1 0 0 1 0 1 0 0 0 0 0 0 1 1 0 0 - 0 1 0 0 0 1 0 1 1 0 0 0 0 1 1 0 0 0 0 1 0 0 0 1 1 0 1 0 0 0 1 0 0 1 1 0 1 - 1 0 0 0 0 1 1 0 1 1 0 1 1 1 0 0 1 0 0 0 0 0 1 0 0 0] + [0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 + 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 1 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0] """ label = g.new_vertex_property("bool") @@ -931,18 +931,17 @@ def label_biconnected_components(g, eprop=None, vprop=None): >>> g = gt.random_graph(100, lambda: poisson(2), directed=False) >>> comp, art, hist = gt.label_biconnected_components(g) >>> print(comp.a) - [51 51 51 51 51 51 11 52 51 51 44 42 41 45 49 23 19 51 51 32 38 51 24 37 51 - 51 51 10 8 51 20 43 51 51 51 51 51 47 46 51 51 13 14 51 51 51 51 33 30 51 - 1 21 51 51 51 35 36 6 51 26 27 7 12 4 3 29 28 51 51 51 31 51 51 0 39 - 51 51 51 34 40 51 51 9 17 51 51 18 15 22 2 16 50 5 48 51 51 53 51 51 25] + [35 23 35 35 32 32 35 35 1 37 32 28 32 35 32 2 32 29 35 35 13 14 34 12 17 + 35 35 35 35 35 3 35 35 35 35 35 35 28 28 35 33 35 19 35 35 35 35 6 35 35 + 24 39 35 31 35 10 9 22 32 35 4 25 26 35 35 7 35 35 35 35 35 35 36 35 35 + 35 32 35 0 35 35 35 32 35 28 32 35 20 30 27 18 38 16 5 15 11 28 35 8 21] >>> print(art.a) - [1 0 1 0 0 1 0 0 1 1 0 0 1 1 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0 1 0 0 0 1 1 0 - 0 1 0 0 1 1 0 1 1 0 0 0 1 1 0 1 1 0 0 0 1 0 0 1 0 1 0 0 1 1 0 0 0 0 0 1 1 - 1 0 1 1 0 1 0 1 1 0 0 0 0 1 0 1 0 0 0 1 0 0 0 1 0 0] + [1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 1 0 0 1 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 + 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 0 1 0 0 1 1 0 0 0 0 0 1 0 + 1 0 1 1 0 0 0 0 1 0 0 1 0 1 1 1 0 0 0 0 0 0 0 1 0 0] >>> print(hist) [ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1 47 1 1] + 1 1 1 5 1 1 1 10 1 1 48 1 1 1 1] """ if vprop is None: -- GitLab