Merge branch 'issues/CSD-339-joss-first-draft' into develop

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

.gitignore

@@ -50,5 +50,12 @@ docs/source/tutorials/tutorial_outputs/
 outputs/
 
 doc/source/tutorials/.ipynb_checkpoints/
+
 /docs/source/tutorials/ACD_RD.ipynb
 /docs/source/tutorials/.ipynb_checkpoints/
+
+publication/template/--env
+
+publication/template/--user
+
+publication/template/--volume

docs/source/conf.py

@@ -48,7 +48,7 @@
     "myst_nb",  # add Jupyter notebooks
     "sphinx.ext.napoleon",  # 'sphinxcontrib.napoleon' is deprecated  # Google style docs
     "sphinxcontrib.bibtex",
-    "sphinx_copybutton",  # adds a copy button to code blocks
+    "sphinx_copybutton" # adds a copy button to code blocks
 ]
 autodoc_default_options = {
     "members": True,  # when set to True, Sphinx will automatically document all members
@@ -74,7 +74,7 @@
 nb_execution_timeout = 1000  # This is the timeout for executing a notebook cell
 
 # -- Options for  sphinxcontrib extension ---------------------------------------
-bibtex_bibfiles = ["references.bib"]
+bibtex_bibfiles = ['references.bib']
 
 # -- Options for HTML evaluation -------------------------------------------------
 

docs/source/tutorials/JointCRep.ipynb

@@ -10,6 +10,8 @@
 
 import numpy as np
 
+import numpy as np
+
 from .models.acd import AnomalyDetection
 from .models.base import ModelBaseParameters
 from .models.crep import CRep

probinet/main.py

@@ -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,