Standardize docs (#525)

* Standardized first half of tutorials * updating repo to match upstream * Suppressing graph messages up to latent_position_test * finished standardizing tutorials * standardize simulations * second standardize of simulations * standardize models * standardize embed * standardize cluster * standardize inference * standardize plot * standardize datasets * standardize utility * standardize pipeline * standardize matching * standardize subgraph * standardize align * blackened repo * fixing the version.txt file * responding to feedback * Correcting version to 3.7.0 * Changing to _ = to suppress graph summary output * Blackened repo * Final check of netlify build * correcting minor typos * correcting one last typo Co-authored-by: Benjamin Pedigo <benjamindpedigo@gmail.com>
graspologic-org · Nov 6, 2020 · 8d7d29f · 8d7d29f
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diff --git a/docs/tutorials/embedding/AdjacencySpectralEmbed.ipynb b/docs/tutorials/embedding/AdjacencySpectralEmbed.ipynb
@@ -46,14 +46,14 @@
     "undirected_sbm = sbm(2 * [n_verts], P)\n",
     "heatmap(undirected_sbm, title='2-block SBM (undirected)', inner_hier_labels=labels_sbm)\n",
     "directed_sbm = sbm(2 * [n_verts], P, directed=True)\n",
-    "heatmap(directed_sbm, title='2-block SBM (directed)', inner_hier_labels=labels_sbm)"
+    "_ = heatmap(directed_sbm, title='2-block SBM (directed)', inner_hier_labels=labels_sbm)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can use the AdjacencySpectralEmbed class to embed the adjacency matrix as follows. If no parameters are given to the AdjacencySpectralEmbed class, it will automatically choose the number of dimensions to embed into."
+    "We can use the ``AdjacencySpectralEmbed`` class to embed the adjacency matrix as follows. If no parameters are given to the ``AdjacencySpectralEmbed`` class, it will automatically choose the number of dimensions to embed into."
    ]
   },
   {
@@ -64,7 +64,7 @@
    "source": [
     "ase = AdjacencySpectralEmbed()\n",
     "Xhat = ase.fit_transform(undirected_sbm)\n",
-    "pairplot(Xhat, title='SBM adjacency spectral embedding')"
+    "_ = pairplot(Xhat, title='SBM adjacency spectral embedding')"
    ]
   },
   {
@@ -83,7 +83,7 @@
     "ase = AdjacencySpectralEmbed()\n",
     "Xhat, Yhat = ase.fit_transform(directed_sbm)\n",
     "pairplot(Xhat, title='SBM adjacency spectral embedding \"out\"')\n",
-    "pairplot(Yhat, title='SBM adjacency spectral embedding \"in\"')"
+    "_ = pairplot(Yhat, title='SBM adjacency spectral embedding \"in\"')"
    ]
   },
   {
@@ -101,7 +101,7 @@
    "source": [
     "ase = AdjacencySpectralEmbed(n_components=2, algorithm='truncated')\n",
     "Xhat = ase.fit_transform(undirected_sbm)\n",
-    "pairplot(Xhat, title='2-component embedding', height=4)"
+    "_ = pairplot(Xhat, title='2-component embedding', height=4)"
    ]
   },
   {

diff --git a/docs/tutorials/embedding/Omnibus.ipynb b/docs/tutorials/embedding/Omnibus.ipynb
@@ -32,11 +32,11 @@
     "\n",
     "\\begin{align*}\n",
     "P_1 = \n",
-    "\\begin{bmatrix}0.2 & 0.1\\\\\n",
+    "\\begin{bmatrix}0.3 & 0.1\\\\\n",
     "0.1 & 0.7\n",
     "\\end{bmatrix},~\n",
-    "P_2 = \\begin{bmatrix}0.2 & 0.1\\\\\n",
-    "0.1 & 0.2\n",
+    "P_2 = \\begin{bmatrix}0.3 & 0.1\\\\\n",
+    "0.1 & 0.3\n",
     "\\end{bmatrix}\n",
     "\\end{align*}\n",
     "\n",
@@ -82,7 +82,7 @@
     "from graspologic.plot import heatmap\n",
     "\n",
     "heatmap(G1, figsize=(7, 7), title='Visualization of Graph 1')\n",
-    "heatmap(G2, figsize=(7, 7), title='Visualization of Graph 2')"
+    "_ = heatmap(G2, figsize=(7, 7), title='Visualization of Graph 2')"
    ]
   },
   {
@@ -152,7 +152,7 @@
     "for i in range(50):\n",
     "    ax.plot([Xhat1[i, 0], Xhat2[i, 0]], [Xhat1[i, 1], Xhat2[i, 1]], 'black', alpha = 0.15)\n",
     "    \n",
-    "ax.set_title('Latent Positions from Omnibus Embedding', fontsize=20)"
+    "_ = ax.set_title('Latent Positions from Omnibus Embedding', fontsize=20)"
    ]
   }
  ],

diff --git a/docs/tutorials/inference/latent_distribution_test.ipynb b/docs/tutorials/inference/latent_distribution_test.ipynb
@@ -50,7 +50,7 @@
     "A1 = sbm(csize, P)\n",
     "X1 = AdjacencySpectralEmbed(n_components=n_components).fit_transform(A1)\n",
     "heatmap(A1, title='2-block SBM adjacency matrix')\n",
-    "pairplot(X1, title='2-block adjacency spectral embedding', height=4.5)"
+    "_ = pairplot(X1, title='2-block adjacency spectral embedding', height=4.5)"
    ]
   },
   {
@@ -72,7 +72,7 @@
     "A1 = sbm(csize, P)\n",
     "X1 = AdjacencySpectralEmbed(n_components=n_components).fit_transform(A1)\n",
     "heatmap(A2, title='2-block SBM adjacency matrix')\n",
-    "pairplot(X2, title='2-block adjacency spectral embedding', height=4.5)"
+    "_ = pairplot(X2, title='2-block adjacency spectral embedding', height=4.5)"
    ]
   },
   {
@@ -144,7 +144,7 @@
     "ax[1].hist(ldt_mgc.null_distribution_, 50)\n",
     "ax[1].axvline(ldt_mgc.sample_T_statistic_, color='r')\n",
     "ax[1].set_title(\"MGC: P-value = {}\".format(ldt_mgc.p_value_), fontsize=20)\n",
-    "plt.show();"
+    "_ = plt.show()"
    ]
   },
   {
@@ -175,7 +175,7 @@
     "A3 = sbm(csize, P2)\n",
     "heatmap(A3, title='2-block SBM adjacency matrix A3')\n",
     "X3 = AdjacencySpectralEmbed(n_components=n_components).fit_transform(A3)\n",
-    "pairplot(X3, title='2-block adjacency spectral embedding A3', height=4.5)"
+    "_ = pairplot(X3, title='2-block adjacency spectral embedding A3', height=4.5)"
    ]
   },
   {
@@ -231,7 +231,7 @@
     "ax[1].hist(ldt_mgc.null_distribution_, 50)\n",
     "ax[1].axvline(ldt_mgc.sample_T_statistic_, color='r')\n",
     "ax[1].set_title(\"MGC: P-value = {}\".format(ldt_mgc.p_value_), fontsize=20)\n",
-    "plt.show();"
+    "_ = plt.show()"
    ]
   }
  ],

diff --git a/docs/tutorials/inference/latent_position_test.ipynb b/docs/tutorials/inference/latent_position_test.ipynb
@@ -50,18 +50,18 @@
     "A = sbm(csize, P)\n",
     "X = AdjacencySpectralEmbed(n_components=n_components).fit_transform(A)\n",
     "heatmap(A, title='4-block SBM adjacency matrix')\n",
-    "pairplot(X, title='4-block adjacency spectral embedding')"
+    "_ = pairplot(X, title='4-block adjacency spectral embedding')"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In the adjacency matrix above, there is a clearly defined block structrure corresponding to the 4 communities in the graph that we established. On the right, we see the **adjacency spectral embedding (ASE)** of this graph. ASE(A) recovers an estimate of the **latent positions** of $A $. Latent positions refer to the idea of a **random dot product graph (RDPG)** which can be modeled as follows:\n",
+    "In the adjacency matrix above, there is a clearly defined block structrure corresponding to the 4 communities in the graph that we established. On the right, we see the **adjacency spectral embedding (ASE)** of this graph. $\\text{ASE}(A)$ recovers an estimate of the **latent positions** of $A$. Latent positions refer to the idea of a **random dot product graph (RDPG)** which can be modeled as follows:\n",
     "\n",
-    "For an adjacency matrix $A \\in \\mathbb{R}^{n x n}$, the probability of an edge existing between node $i$ and node $j$ (aka whether or not $A_{ij}$ is a 1) is determined by the matrix $P \\in \\mathbb{R}^{n x n}$\n",
+    "For an adjacency matrix $A \\in \\mathbb{R}^{n \\times n}$, the probability of an edge existing between node $i$ and node $j$ (aka whether or not $A_{ij}$ is a 1) is determined by the matrix $P \\in \\mathbb{R}^{n \\times n}$\n",
     "\n",
-    "$P = XX^T$, where $X \\in \\mathbb{R}^{n x d} $ and is referred to as the latent positions of the graph. $X$ is referred to as the latent positions of the graph because each node $n_i$ is modeled as having a hidden, usually unobserved location in $\\mathbb{R}^d$ (we'll call it $x_i$). The probability of an edge existing between $n_i$ and $n_j$ is equal to the dot product $x_i \\cdot x_j$\n",
+    "$P = XX^T$, where $X \\in \\mathbb{R}^{n \\times d}$ and is referred to as the latent positions of the graph. $X$ is referred to as the latent positions of the graph because each node $n_i$ is modeled as having a hidden, usually unobserved location in $\\mathbb{R}^d$ (we'll call it $x_i$). The probability of an edge existing between $n_i$ and $n_j$ is equal to the dot product $x_i \\cdot x_j$\n",
     "\n",
     "ASE is one way to obtain an estimate of the latent positions of a graph, $\\hat{X}$\n",
     "\n",
@@ -73,7 +73,7 @@
    "metadata": {},
    "source": [
     "## Sample new RDPGs from this latent position\n",
-    "Given the estimate of X, we now sample two new RDPGs from the same latent position above"
+    "Given the estimate of $X$, we now sample two new RDPGs from the same latent position above"
    ]
   },
   {
@@ -97,7 +97,7 @@
     "heatmap(A1, title='Sampled RDPG 1 adjacency matrix')\n",
     "heatmap(A2, title='Sampled RDPG 2 adjacency matrix')\n",
     "pairplot(Xhat1, title='Sampled RDPG 1 adjacency spectral embedding')\n",
-    "pairplot(Xhat2, title='Sampled RDPG 2 adjacency spectral embedding')"
+    "_ = pairplot(Xhat2, title='Sampled RDPG 2 adjacency spectral embedding')"
    ]
   },
   {
@@ -120,7 +120,7 @@
     "\n",
     "Here, R is an orthogonal rotation matrix found from solving the [orthogonal procrustes problem](https://docs.scipy.org/doc/scipy-0.18.1/reference/generated/scipy.linalg.orthogonal_procrustes.html) (Note: this constraint can be relaxed for other versions of semipar)\n",
     "\n",
-    "Note that LatentPositionTest.fit() may take several minutes"
+    "Note that ``LatentPositionTest.fit()`` may take several minutes"
    ]
   },
   {
@@ -177,7 +177,7 @@
     "heatmap(A3, title='Sampled RDPG 3 adjacency matrix')\n",
     "heatmap(A4, title='Sampled RDPG 4 (distorted) adjacency matrix')\n",
     "pairplot(Xhat3, title='Sampled RDPG 3 adjacency spectral embedding')\n",
-    "pairplot(Xhat4, title='Sampled RDPG 4 (distorted) adjacency spectral embedding')"
+    "_ = pairplot(Xhat4, title='Sampled RDPG 4 (distorted) adjacency spectral embedding')"
    ]
   },
   {

diff --git a/docs/tutorials/matching/faq.ipynb b/docs/tutorials/matching/faq.ipynb
@@ -26,7 +26,7 @@
     "\n",
     "\\begin{equation}\n",
     "\\begin{aligned}\n",
-    "\\min & {\\;-trace(APB^T P^T)}\\\\\n",
+    "\\min & {\\;-\\text{trace}(APB^T P^T)}\\\\\n",
     "\\text{s.t. } & {\\;P \\: \\epsilon \\: \\mathcal{P}} \\\\\n",
     "\\end{aligned}\n",
     "\\end{equation}\n",
@@ -44,7 +44,7 @@
     "\n",
     "\\begin{equation}\n",
     "\\begin{aligned}\n",
-    "\\min & {\\; trace(APB^T P^T)}\\\\\n",
+    "\\min & {\\; \\text{trace}(APB^T P^T)}\\\\\n",
     "\\text{s.t. } & {\\;P \\: \\epsilon \\: \\mathcal{P}} \\\\\n",
     "\\end{aligned}\n",
     "\\end{equation}\n",
@@ -110,7 +110,7 @@
    "source": [
     "from graspologic.plot import heatmap\n",
     "heatmap(G1, cbar=False, title = 'G1 [ER-NP(50, 0.3) Simulation]')\n",
-    "heatmap(G2, cbar=False, title = 'G2 [G1 Randomly Shuffled]')"
+    "_ = heatmap(G2, cbar=False, title = 'G2 [G1 Randomly Shuffled]')"
    ]
   },
   {
@@ -141,7 +141,7 @@
    "outputs": [],
    "source": [
     "heatmap(G1, cbar=False, title = 'G1[ER-NP(50, 0.3) Simulation]')\n",
-    "heatmap(G2, cbar=False, title = 'G2[ER-NP(50, 0.3) Randomly Shuffled] unshuffled')"
+    "_ = heatmap(G2, cbar=False, title = 'G2[ER-NP(50, 0.3) Randomly Shuffled] unshuffled')"
    ]
   }
  ],

diff --git a/docs/tutorials/matching/padded_gm.ipynb b/docs/tutorials/matching/padded_gm.ipynb
@@ -99,7 +99,7 @@
     "heatmap(G1p, ax=axs[0], cbar=False, title=\"G1'\")\n",
     "heatmap(G2, ax=axs[1], cbar=False, title=\"G2\")\n",
     "heatmap(c, ax=axs[2], cbar=False, title=\"G1\")\n",
-    "heatmap(topleft_G1, ax=axs[3], cbar=False, title=\"G1 (to top left corner)\")"
+    "_ = heatmap(topleft_G1, ax=axs[3], cbar=False, title=\"G1 (to top left corner)\")"
    ]
   },
   {
@@ -146,13 +146,6 @@
     "\n",
     "On the other hand, we see that adopted padding preserves the common block structure between $G_1$ and $G_2$."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -171,7 +164,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.7.0"
   }
  },
  "nbformat": 4,

diff --git a/docs/tutorials/matching/sgm.ipynb b/docs/tutorials/matching/sgm.ipynb
@@ -77,7 +77,7 @@
     "fig, axs = plt.subplots(1, 3, figsize=(10, 5))\n",
     "heatmap(A1, ax=axs[0], cbar=False, title=\"Graph 1\")\n",
     "heatmap(A2, ax=axs[1], cbar=False, title=\"Graph 2\")\n",
-    "heatmap(A1 - A2, ax=axs[2], cbar=False, title=\"Diff (G1 - G2)\")"
+    "_ = heatmap(A1 - A2, ax=axs[2], cbar=False, title=\"Diff (G1 - G2)\")"
    ]
   },
   {
@@ -116,7 +116,7 @@
     "fig, axs = plt.subplots(1, 3, figsize=(10, 5))\n",
     "heatmap(A1, ax=axs[0], cbar=False, title=\"Graph 1\")\n",
     "heatmap(A2_shuffle, ax=axs[1], cbar=False, title=\"Graph 2 shuffled\")\n",
-    "heatmap(A1 - A2_shuffle, ax=axs[2], cbar=False, title=\"Diff (G1 - G2 shuffled)\")\n"
+    "_ = heatmap(A1 - A2_shuffle, ax=axs[2], cbar=False, title=\"Diff (G1 - G2 shuffled)\")"
    ]
   },
   {
@@ -181,7 +181,7 @@
     "heatmap(A1 - A2_unshuffle, ax=axs[2], cbar=False, title=\"Diff (G1 - G2 unshuffled)\")\n",
     "\n",
     "match_ratio = 1-(np.count_nonzero(abs(sgm.perm_inds_-node_unshuffle_input))/n_verts)\n",
-    "print(\"Match Ratio with 10 seeds: \", match_ratio)\n"
+    "print(\"Match Ratio with 10 seeds: \", match_ratio)"
    ]
   },
   {

diff --git a/docs/tutorials/models/models.ipynb b/docs/tutorials/models/models.ipynb
@@ -47,11 +47,11 @@
     "\n",
     "adj, labels = load_drosophila_right(return_labels=True)\n",
     "adj = binarize(adj)\n",
-    "heatmap(adj,\n",
+    "_ = heatmap(adj,\n",
     "        inner_hier_labels=labels,\n",
     "        title='Drosophila right MB',\n",
     "        font_scale=1.5,\n",
-    "        sort_nodes=True);"
+    "        sort_nodes=True)"
    ]
   },
   {
@@ -115,11 +115,11 @@
     "        title=\"ER probability matrix\",\n",
     "        vmin=0, vmax=1, \n",
     "        sort_nodes=True)\n",
-    "heatmap(er.sample()[0],\n",
+    "_ = heatmap(er.sample()[0],\n",
     "        inner_hier_labels=labels,\n",
     "        font_scale=1.5,\n",
     "        title=\"ER sample\",\n",
-    "        sort_nodes=True);"
+    "        sort_nodes=True)"
    ]
   },
   {
@@ -154,11 +154,11 @@
     "        font_scale=1.5,\n",
     "        title=\"DCER probability matrix\", \n",
     "        sort_nodes=True);\n",
-    "heatmap(dcer.sample()[0],\n",
+    "_ = heatmap(dcer.sample()[0],\n",
     "        inner_hier_labels=labels,\n",
     "        font_scale=1.5,\n",
     "        title=\"DCER sample\", \n",
-    "        sort_nodes=True);"
+    "        sort_nodes=True)"
    ]
   },
   {
@@ -191,11 +191,11 @@
     "        font_scale=1.5,\n",
     "        title=\"SBM probability matrix\", \n",
     "        sort_nodes=True)\n",
-    "heatmap(sbme.sample()[0],\n",
+    "_ = heatmap(sbme.sample()[0],\n",
     "        inner_hier_labels=labels,\n",
     "        font_scale=1.5,\n",
     "        title=\"SBM sample\", \n",
-    "        sort_nodes=True);"
+    "        sort_nodes=True)"
    ]
   },
   {
@@ -230,11 +230,11 @@
     "        vmin=0,\n",
     "        vmax=1,\n",
     "        sort_nodes=True)\n",
-    "heatmap(dcsbme.sample()[0],\n",
+    "_ = heatmap(dcsbme.sample()[0],\n",
     "        inner_hier_labels=labels,\n",
     "        title=\"DCSBM sample\",\n",
     "        font_scale=1.5,\n",
-    "        sort_nodes=True);"
+    "        sort_nodes=True)"
    ]
   },
   {
@@ -271,11 +271,11 @@
     "        title=\"RDPG probability matrix\",\n",
     "        sort_nodes=True\n",
     "       )\n",
-    "heatmap(rdpge.sample()[0],\n",
+    "_ = heatmap(rdpge.sample()[0],\n",
     "        inner_hier_labels=labels,\n",
     "        font_scale=1.5,\n",
     "        title=\"RDPG sample\",\n",
-    "        sort_nodes=True);"
+    "        sort_nodes=True)"
    ]
   },
   {
@@ -336,7 +336,7 @@
     "# add colorbar\n",
     "sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)\n",
     "sm.set_array(dcsbme.p_mat_)\n",
-    "fig.colorbar(sm,\n",
+    "_ = fig.colorbar(sm,\n",
     "             ax=axs,\n",
     "             orientation=\"horizontal\",\n",
     "             pad=0.04,\n",

diff --git a/docs/tutorials/simulations/corr.ipynb b/docs/tutorials/simulations/corr.ipynb
@@ -82,7 +82,7 @@
    "source": [
     "from graspologic.plot import heatmap\n",
     "heatmap(G1, title = 'Correlated ER Simulation Graph 1')\n",
-    "heatmap(G2, title = 'Correlated ER Simulation Graph 2')"
+    "_ = heatmap(G2, title = 'Correlated ER Simulation Graph 2')"
    ]
   },
   {
@@ -147,15 +147,8 @@
    "outputs": [],
    "source": [
     "heatmap(G1, title = 'Correlated SBM Simulation Graph 1')\n",
-    "heatmap(G2, title = 'Correlated SBM Simulation Graph 2')"
+    "_ = heatmap(G2, title = 'Correlated SBM Simulation Graph 2')"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {