Update notebooks to generate new plots for paper

Update plots for paper

Improve section about example

Add new version of figure

Update notebook for plots, but it will overwritten in the next commit

Generated new plots

Update figure

Edit paper.md
Edit figure caption in paper.md
Create github action to compile the paper

Reduce number of words

Add hyperlink, and fix table

Fix notebook

Improve table; add info about machine, correct notebook

Fix tutorial

Edit paper.bib - add reference real-world data
Edit paper.md
Update execution times

Update table

Correct table

Update pdf

Remove plots

Remove unnecessary files

Author: diegoabt

.github/workflows/draft-pdf.yml

@@ -0,0 +1,20 @@
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          paper-path: publication/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          path: publication/paper.pdf

docs/source/tutorials/JointCRep.ipynb

@@ -19,6 +19,7 @@ def plot_hard_membership(
     node_size: np.ndarray,
     colors: Dict,
     edge_color: str,
+    edgewidth: float = 0.5,
 ) -> plt.Figure:
     """
     Plot a graph with nodes colored by their hard memberships.
@@ -53,7 +54,7 @@ def plot_hard_membership(
             node_size=node_size,
             node_color=[colors[node] for node in communities[k]],
             with_labels=False,
-            width=0.5,
+            width=edgewidth,
             edge_color=edge_color,
             arrows=True,
             arrowsize=5,
@@ -103,6 +104,7 @@ def plot_soft_membership(
     node_size: np.ndarray,
     colors: Dict,
     edge_color: str,
+    edgewidth: float = 0.5,
 ) -> plt.Figure:
     """
     Plot a graph with nodes colored by their mixed (soft) memberships.
@@ -128,14 +130,14 @@ def plot_soft_membership(
           The matplotlib figure object.
     """
 
-    fig = plt.figure(figsize=(9, 4))
+    fig = plt.figure(figsize=(8, 3))
     for j, k in enumerate(thetas):
         plt.subplot(1, 2, j + 1)
         ax = plt.gca()
         nx.draw_networkx_edges(
             graph,
             pos,
-            width=0.5,
+            width=edgewidth,
             edge_color=edge_color,
             arrows=True,
             arrowsize=5,