Small notebook fix (#148)

* Improved the plotting tutorial notebook * Formatted all notebooks with black and updated the developer requirements to match.
xgi-org · Aug 8, 2022 · 4069c0d · 4069c0d
1 parent 43ffb28
commit 4069c0d
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Showing 11 changed files with 262 additions and 158 deletions.
diff --git a/benchmarks/hypernetx.ipynb b/benchmarks/hypernetx.ipynb
@@ -46,7 +46,9 @@
     "start = time.time()\n",
     "H2 = hnx.Hypergraph(df, static=True)\n",
     "print(f\"HyperNetX construction time: {time.time() - start} sec\")\n",
-    "print(f\"The hypergraph has {H2.number_of_nodes()} nodes and {H2.number_of_edges()} edges.\")"
+    "print(\n",
+    "    f\"The hypergraph has {H2.number_of_nodes()} nodes and {H2.number_of_edges()} edges.\"\n",
+    ")"
    ]
   },
   {

diff --git a/benchmarks/networkx.ipynb b/benchmarks/networkx.ipynb
@@ -40,7 +40,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(f\"The NetworkX graph has {G1.number_of_nodes()} nodes and {G1.number_of_edges()} edges\")\n",
+    "print(\n",
+    "    f\"The NetworkX graph has {G1.number_of_nodes()} nodes and {G1.number_of_edges()} edges\"\n",
+    ")\n",
     "print(f\"The XGI graph has {G2.num_nodes} nodes and {G2.num_edges} edges\")"
    ]
   },

diff --git a/requirements/developer.txt b/requirements/developer.txt
@@ -1,4 +1,4 @@
-black==22.3.0
+black[jupyter]==22.3.0
 pre-commit>=2.12
 isort==5.10.1
 pylint>=2.10
diff --git a/tutorials/Tutorial 1 - Basic Hypergraph Functionality.ipynb b/tutorials/Tutorial 1 - Basic Hypergraph Functionality.ipynb
@@ -53,10 +53,16 @@
     "max_edge_size = 25\n",
     "\n",
     "# hyperedge list\n",
-    "hyperedge_list = [random.sample(range(n), random.choice(range(min_edge_size,max_edge_size+1))) for i in range(m)]\n",
+    "hyperedge_list = [\n",
+    "    random.sample(range(n), random.choice(range(min_edge_size, max_edge_size + 1)))\n",
+    "    for i in range(m)\n",
+    "]\n",
     "\n",
     "# hyperedge dict\n",
-    "hyperedge_dict = {i : random.sample(range(n), random.choice(range(min_edge_size,max_edge_size+1))) for i in range(m)}\n",
+    "hyperedge_dict = {\n",
+    "    i: random.sample(range(n), random.choice(range(min_edge_size, max_edge_size + 1)))\n",
+    "    for i in range(m)\n",
+    "}\n",
     "\n",
     "# pandas dataframe\n",
     "fname = \"../data/disGene.txt\"\n",
@@ -243,7 +249,10 @@
     "max_edge_size = 10\n",
     "\n",
     "# hyperedge list\n",
-    "hyperedge_list = [random.sample(range(n), random.choice(range(min_edge_size,max_edge_size+1))) for i in range(m)]\n",
+    "hyperedge_list = [\n",
+    "    random.sample(range(n), random.choice(range(min_edge_size, max_edge_size + 1)))\n",
+    "    for i in range(m)\n",
+    "]\n",
     "H = xgi.Hypergraph(hyperedge_list)"
    ]
   },
@@ -274,7 +283,9 @@
     "print([len(component) for component in xgi.connected_components(H)])\n",
     "\n",
     "node = np.random.choice(H.nodes)\n",
-    "print(f\"The size of the component containing node {node} is {len(xgi.node_connected_component(H, node))}\")"
+    "print(\n",
+    "    f\"The size of the component containing node {node} is {len(xgi.node_connected_component(H, node))}\"\n",
+    ")"
    ]
   },
   {
@@ -297,7 +308,9 @@
     "# A subhypergraph induced on edges\n",
     "edge_subhypergraph = xgi.subhypergraph(H, edges=list(range(100)))\n",
     "# A subhypergraph induced on both nodes and edges\n",
-    "arbitrary_subhypergraph = xgi.subhypergraph(H, nodes=list(range(100)), edges=list(range(100)))"
+    "arbitrary_subhypergraph = xgi.subhypergraph(\n",
+    "    H, nodes=list(range(100)), edges=list(range(100))\n",
+    ")"
    ]
   },
   {

diff --git a/tutorials/Tutorial 2 - Read and Write.ipynb b/tutorials/Tutorial 2 - Read and Write.ipynb
@@ -44,7 +44,10 @@
     "max_edge_size = 10\n",
     "\n",
     "# hyperedge list\n",
-    "hyperedge_list = [random.sample(range(n), random.choice(range(min_edge_size,max_edge_size+1))) for i in range(m)]\n",
+    "hyperedge_list = [\n",
+    "    random.sample(range(n), random.choice(range(min_edge_size, max_edge_size + 1)))\n",
+    "    for i in range(m)\n",
+    "]\n",
     "H = xgi.Hypergraph(hyperedge_list)"
    ]
   },
@@ -64,7 +67,7 @@
    "outputs": [],
    "source": [
     "# Write the example hypergraph to a JSON file\n",
-    "xgi.write_json(H,\"hypergraph_json.json\")\n",
+    "xgi.write_json(H, \"hypergraph_json.json\")\n",
     "# Load the file just written and store it in a new hypergraph\n",
     "H_json = xgi.read_json(\"hypergraph_json.json\")"
    ]
@@ -108,7 +111,9 @@
     "# Write the hypergraph as a bipartite edge list\n",
     "xgi.write_bipartite_edgelist(H, \"bipartite_edge_list.csv\", delimiter=\",\")\n",
     "# Read the file just written as a new hypergraph\n",
-    "H_bel = xgi.read_bipartite_edgelist(\"bipartite_edge_list.csv\", delimiter=\",\", nodetype=int)"
+    "H_bel = xgi.read_bipartite_edgelist(\n",
+    "    \"bipartite_edge_list.csv\", delimiter=\",\", nodetype=int\n",
+    ")"
    ]
   }
  ],

diff --git a/tutorials/Tutorial 3 - Basic simplicial complex usage.ipynb b/tutorials/Tutorial 3 - Basic simplicial complex usage.ipynb
@@ -47,7 +47,7 @@
    "outputs": [],
    "source": [
     "SC = xgi.SimplicialComplex()\n",
-    "H  = xgi.Hypergraph()"
+    "H = xgi.Hypergraph()"
    ]
   },
   {
@@ -115,8 +115,8 @@
    },
    "outputs": [],
    "source": [
-    "SC.add_simplex([0,1,2])\n",
-    "H.add_edge([0,1,2])"
+    "SC.add_simplex([0, 1, 2])\n",
+    "H.add_edge([0, 1, 2])"
    ]
   },
   {
@@ -245,9 +245,9 @@
     }
    ],
    "source": [
-    "for dim in [0,1,2]:\n",
-    "    print('# edges in H at order', dim, H.edges.filterby(\"order\", dim))\n",
-    "    print('# edges in SC at order', dim, SC.edges.filterby(\"order\", dim), '\\n')"
+    "for dim in [0, 1, 2]:\n",
+    "    print(\"# edges in H at order\", dim, H.edges.filterby(\"order\", dim))\n",
+    "    print(\"# edges in SC at order\", dim, SC.edges.filterby(\"order\", dim), \"\\n\")"
    ]
   },
   {
@@ -281,9 +281,14 @@
     }
    ],
    "source": [
-    "for dim in [0,1,2]:\n",
+    "for dim in [0, 1, 2]:\n",
     "    edge_sel = list(SC.edges.filterby(\"order\", dim))\n",
-    "    print('Composition of simplices at order', dim, [SC.edges.members(x) for x in edge_sel], '\\n')"
+    "    print(\n",
+    "        \"Composition of simplices at order\",\n",
+    "        dim,\n",
+    "        [SC.edges.members(x) for x in edge_sel],\n",
+    "        \"\\n\",\n",
+    "    )"
    ]
   },
   {
@@ -317,9 +322,14 @@
     }
    ],
    "source": [
-    "for dim in [0,1,2]:\n",
+    "for dim in [0, 1, 2]:\n",
     "    edge_sel = list(H.edges.filterby(\"order\", dim))\n",
-    "    print('Composition of edges at order', dim, [H.edges.members(x) for x in edge_sel], '\\n')\n"
+    "    print(\n",
+    "        \"Composition of edges at order\",\n",
+    "        dim,\n",
+    "        [H.edges.members(x) for x in edge_sel],\n",
+    "        \"\\n\",\n",
+    "    )"
    ]
   },
   {
@@ -348,7 +358,7 @@
    },
    "outputs": [],
    "source": [
-    "facets = [[0,1,2], [0,1,3,4]]\n",
+    "facets = [[0, 1, 2], [0, 1, 3, 4]]\n",
     "SC1 = xgi.SimplicialComplex(facets)"
    ]
   },
@@ -418,7 +428,10 @@
     "min_edge_size = 2\n",
     "max_edge_size = 4\n",
     "\n",
-    "hyperedge_list = [random.sample(range(n), random.choice(range(min_edge_size,max_edge_size+1))) for i in range(m)]\n",
+    "hyperedge_list = [\n",
+    "    random.sample(range(n), random.choice(range(min_edge_size, max_edge_size + 1)))\n",
+    "    for i in range(m)\n",
+    "]\n",
     "SC_big = xgi.SimplicialComplex(hyperedge_list)\n",
     "str(SC_big)"
    ]

diff --git a/tutorials/Tutorial 4 - Generative_Models.ipynb b/tutorials/Tutorial 4 - Generative_Models.ipynb
@@ -112,8 +112,8 @@
    "outputs": [],
    "source": [
     "n = 1000\n",
-    "k1 = {i : random.randint(10, 30) for i in range(n)}\n",
-    "k2 = {i : sorted(k1.values())[i] for i in range(n)}\n",
+    "k1 = {i: random.randint(10, 30) for i in range(n)}\n",
+    "k2 = {i: sorted(k1.values())[i] for i in range(n)}\n",
     "H = xgi.chung_lu_hypergraph(k1, k2)"
    ]
   },
@@ -145,10 +145,10 @@
    ],
    "source": [
     "n = 1000\n",
-    "k1 = {i : random.randint(1, 100) for i in range(n)}\n",
-    "k2 = {i : sorted(k1.values())[i] for i in range(n)}\n",
-    "g1 = {i : random.choice([0, 1]) for i in range(n)}\n",
-    "g2 = {i : random.choice([0, 1]) for i in range(n)}\n",
+    "k1 = {i: random.randint(1, 100) for i in range(n)}\n",
+    "k2 = {i: sorted(k1.values())[i] for i in range(n)}\n",
+    "g1 = {i: random.choice([0, 1]) for i in range(n)}\n",
+    "g2 = {i: random.choice([0, 1]) for i in range(n)}\n",
     "omega = np.array([[100, 10], [10, 100]])\n",
     "H = xgi.dcsbm_hypergraph(k1, k2, g1, g2, omega)"
    ]
@@ -182,7 +182,7 @@
    },
    "outputs": [],
    "source": [
-    "n = 20;\n",
+    "n = 20\n",
     "ps = [0.1, 0.2, 0.1]\n",
     "SC = xgi.random_simplicial_complex(n, ps)"
    ]
@@ -270,7 +270,8 @@
    },
    "outputs": [],
    "source": [
-    "import networkx as nx \n",
+    "import networkx as nx\n",
+    "\n",
     "G = nx.karate_club_graph()\n",
     "\n",
     "SC_KC = xgi.flag_complex(G, max_order=3)"

diff --git a/tutorials/Tutorial 5 - Plotting.ipynb b/tutorials/Tutorial 5 - Plotting.ipynb
@@ -38,7 +38,9 @@
    "outputs": [],
    "source": [
     "H = xgi.Hypergraph()\n",
-    "H.add_edges_from([[1,2,3],[3,4,5],[3,6],[6,7,8,9],[1,4,10,11,12],[1,4]])"
+    "H.add_edges_from(\n",
+    "    [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]\n",
+    ")"
    ]
   },
   {
@@ -100,18 +102,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(10,4))\n",
+    "plt.figure(figsize=(10, 4))\n",
     "\n",
-    "#Sequential colormap\n",
+    "# Sequential colormap\n",
     "cmap = plt.cm.Paired\n",
     "\n",
-    "ax = plt.subplot(1,2,1)\n",
+    "ax = plt.subplot(1, 2, 1)\n",
     "xgi.draw(H, pos, ax=ax, edge_face_colormap=cmap)\n",
     "\n",
-    "#Qualitative colormap\n",
+    "# Qualitative colormap\n",
     "cmap = plt.cm.Purples\n",
     "\n",
-    "ax = plt.subplot(1,2,2)\n",
+    "ax = plt.subplot(1, 2, 2)\n",
     "xgi.draw(H, pos, ax=ax, edge_face_colormap=cmap)"
    ]
   },
@@ -131,15 +133,24 @@
    "outputs": [],
    "source": [
     "cmap = plt.cm.Reds\n",
-    "edge_lc = 'gray'\n",
+    "edge_lc = \"gray\"\n",
     "edge_lw = 4\n",
-    "node_fc = 'black'\n",
-    "node_ec = 'white'\n",
+    "node_fc = \"black\"\n",
+    "node_ec = \"white\"\n",
     "node_lw = 2\n",
     "node_size = 20\n",
     "\n",
-    "xgi.draw(H, pos, edge_lc=edge_lc, edge_lw=edge_lw,\n",
-    "         node_fc=node_fc, node_ec=node_ec, node_lw=node_lw, node_size=node_size, edge_face_colormap=cmap)"
+    "xgi.draw(\n",
+    "    H,\n",
+    "    pos,\n",
+    "    edge_lc=edge_lc,\n",
+    "    edge_lw=edge_lw,\n",
+    "    node_fc=node_fc,\n",
+    "    node_ec=node_ec,\n",
+    "    node_lw=node_lw,\n",
+    "    node_size=node_size,\n",
+    "    edge_face_colormap=cmap,\n",
+    ")"
    ]
   },
   {
@@ -172,7 +183,7 @@
    "outputs": [],
    "source": [
     "SC = xgi.SimplicialComplex()\n",
-    "SC.add_simplices_from([[3,4,5],[3,6],[6,7,8,9],[1,4,10,11,12],[1,4]])"
+    "SC.add_simplices_from([[3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]])"
    ]
   },
   {
@@ -212,7 +223,10 @@
    "outputs": [],
    "source": [
     "n = 100\n",
-    "H = xgi.random_hypergraph(100, [0.03, 0.0002, 0.00001])\n",
+    "is_connected = False\n",
+    "while not is_connected:\n",
+    "    H = xgi.random_hypergraph(n, [0.03, 0.0002, 0.00001])\n",
+    "    is_connected = xgi.is_connected(H)\n",
     "pos = xgi.barycenter_spring_layout(H)"
    ]
   },
@@ -231,17 +245,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(10,10))\n",
+    "plt.figure(figsize=(10, 10))\n",
     "ax = plt.subplot(111)\n",
-    "xgi.draw(H, pos, node_size = 10, ax=ax)"
+    "xgi.draw(H, pos, node_size=10, ax=ax)"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "39e2d438",
    "metadata": {},
    "source": [
-    "We can even size/color the nodes by their degree!"
+    "We can even size/color the nodes and edges by NodeStats or EdgeStats (e.g., degree, centrality, size, etc.)!"
    ]
   },
   {
@@ -251,9 +265,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(10,10))\n",
+    "plt.figure(figsize=(10, 10))\n",
     "ax = plt.subplot(111)\n",
-    "xgi.draw(H, pos, node_size = H.nodes.degree, node_lw = H.nodes.degree, node_fc=H.nodes.cec_centrality, edge_fc=H.edges.node_edge_centrality, ax=ax)"
+    "xgi.draw(\n",
+    "    H,\n",
+    "    pos,\n",
+    "    node_size=H.nodes.degree,\n",
+    "    node_lw=H.nodes.degree,\n",
+    "    node_fc=H.nodes.cec_centrality,\n",
+    "    edge_fc=H.edges.node_edge_centrality,\n",
+    "    ax=ax,\n",
+    ")"
    ]
   },
   {
@@ -274,13 +296,13 @@
    "source": [
     "centers, heights = xgi.degree_histogram(H)\n",
     "\n",
-    "plt.figure(figsize=(12,4))\n",
+    "plt.figure(figsize=(12, 4))\n",
     "ax = plt.subplot(111)\n",
     "\n",
     "ax.bar(centers, heights)\n",
-    "ax.set_ylabel('Count')\n",
-    "ax.set_xlabel('Degree')\n",
-    "ax.set_xticks(np.arange(1, max(centers)+1, step=1));"
+    "ax.set_ylabel(\"Count\")\n",
+    "ax.set_xlabel(\"Degree\")\n",
+    "ax.set_xticks(np.arange(1, max(centers) + 1, step=1));"
    ]
   }
  ],