Add markdown and improve myst.yml

_toc.yml

@@ -2,4 +2,4 @@ format: jb-book
 root: paper.md
 chapters:
   - file: content/figure_1.ipynb
-  - file: content/figure_2.ipynb
+  - file: content/figure_2.md

content/figure_2.md

@@ -0,0 +1,114 @@
+---
+kernelspec:
+  name: python3
+  display_name: 'Python 3'
+---
+
+## Jupyter Notebooks are fun, but...
+
+> They not necessarily the best format for comparing changes across commits. 
+
+A more diff-friendly way to write your executable content is to use a markdown file with code blocks!
+
+:::{admonition} Kernel Specification
+As you can see at the top of the file, we have a kernel specification in the front matter of the file. This tells MyST builder to use the `python3` kernel for executing the code cells. Needless to say, the specified kernel must be available in your runtime environment (`binder` folder).
+:::
+
+The blow code cell importing libraries wil not be visible in the rendered MyST document, because we have specified the `remove-input` tag. You can find the full documentation on executable markdown files [here](https://mystmd.org/guide/notebooks-with-markdown#kernel-specification).
+
+```{code-cell} python
+:tags: remove-input
+import plotly.graph_objects as go
+import networkx as nx
+import plotly.io as pio
+pio.renderers.default = "plotly_mimetype"
+
+G = nx.random_geometric_graph(200, 0.125)
+```
+
+Now onto the next code cell, which will be visible in the rendered document.
+
+```{code-cell} python
+edge_x = []
+edge_y = []
+for edge in G.edges():
+    x0, y0 = G.nodes[edge[0]]['pos']
+    x1, y1 = G.nodes[edge[1]]['pos']
+    edge_x.append(x0)
+    edge_x.append(x1)
+    edge_x.append(None)
+    edge_y.append(y0)
+    edge_y.append(y1)
+    edge_y.append(None)
+
+edge_trace = go.Scatter(
+    x=edge_x, y=edge_y,
+    line=dict(width=0.5, color='#888'),
+    hoverinfo='none',
+    mode='lines')
+
+node_x = []
+node_y = []
+for node in G.nodes():
+    x, y = G.nodes[node]['pos']
+    node_x.append(x)
+    node_y.append(y)
+
+node_trace = go.Scatter(
+    x=node_x, y=node_y,
+    mode='markers',
+    hoverinfo='text',
+    marker=dict(
+        showscale=True,
+        # colorscale options
+        #'Greys' | 'YlGnBu' | 'Greens' | 'YlOrRd' | 'Bluered' | 'RdBu' |
+        #'Reds' | 'Blues' | 'Picnic' | 'Rainbow' | 'Portland' | 'Jet' |
+        #'Hot' | 'Blackbody' | 'Earth' | 'Electric' | 'Viridis' |
+        colorscale='YlGnBu',
+        reversescale=True,
+        color=[],
+        size=10,
+        colorbar=dict(
+            thickness=15,
+            title='Node Connections',
+            xanchor='left',
+            titleside='right'
+        ),
+        line_width=2))
+
+node_adjacencies = []
+node_text = []
+for node, adjacencies in enumerate(G.adjacency()):
+    node_adjacencies.append(len(adjacencies[1]))
+    node_text.append('# of connections: '+str(len(adjacencies[1])))
+
+node_trace.marker.color = node_adjacencies
+node_trace.text = node_text
+```
+
+The next code cell will be generating the output we are interested in! We will `label` it, so that we can embed its output in the body of our main MyST article. That being said, depending on the purpose of your document (e.g., if you'd like to use the `book-theme` for an interactive tutorial) you may not be interested in embedding the output of a code cell.
+
+```{code-cell} python
+#| label: fig2cell
+
+fig = go.Figure(data=[edge_trace, node_trace],
+             layout=go.Layout(
+                height = 600, 
+                title='<br>Network graph made with Python',
+                titlefont_size=16,
+                showlegend=False,
+                hovermode='closest',
+                margin=dict(b=20,l=5,r=5,t=40),
+                annotations=[ dict(
+                    text="Python code: <a href='https://plotly.com/python/network-graphs/'> https://plotly.com/python/network-graphs/</a>",
+                    showarrow=False,
+                    xref="paper", yref="paper",
+                    x=0.005, y=-0.002 ) ],
+                xaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
+                yaxis=dict(showgrid=False, zeroline=False, showticklabels=False))
+                )
+fig.show()
+```
+
+
+

myst.yml

@@ -5,41 +5,83 @@ project:
   subtitle: A template for reproducible preprints
   thebe:
     binder:
-      url: https://binder-preview.conp.cloud
-      repo: neurolibre/mystical-article
-      ref: HEAD
+      url: https://binder-preview.conp.cloud # NeuroLibre binder URL, production will override this.
+      repo: neurolibre/mystical-article # Production will override this.
+      ref: HEAD # Production will override this.
   authors:
     - name: Agah Karakuzu
       orcid: 0000-0001-7283-271X
-      affiliations:
-        - NeuroPoly, Polytechnique Montreal, Quebec, Canada
-        - Montreal Heart Institute, Montreal, Quebec, Canada
+      affiliations: polymtl; mhi
+      corresponding: true
+      email: agah.karakuzu@polymtl.ca
+      twitter: agahkarakuzu
+      equal_contributor: true
+      url: https://agah.dev
+      github: agahkarakuzu
+      roles:
+        - Conceptualization
+        - Software
+        - Writing – original draft
     - name: Robo Neuro
-      affiliations:
-        - NeuroLibre, Montreal, Quebec, Canada
+      affiliations: polymtl
+      equal_contributor: true
+      github: roboneurolibre
+      note: Roboneuro is a friendly publishing bot who fails the Turing test.
+      roles:
+        - Project administration
+        - Writing – review & editing
+  affiliations:
+    - id: polymtl
+      institution: NeuroPoly Lab, Polytechnique Montreal
+      ror: https://ror.org/05f8d4e86
+      isni: 0000 0004 0435 3292
+      department: Electrical Engineering
+      address: 2500 Chem. de Polytechnique
+      city: Montreal
+      region: Quebec
+      country: Canada
+      postal_code: H3T 1J4
+      phone: 1 (514) 340-4711
+    - id: mhi
+      institution: Montreal Heart Institute
+      ror: https://ror.org/03vs03g62
+      isni: 0000 0000 8995 9090
+      address: 5000 Rue Belanger
+      city: Montreal
+      region: Quebec
+      country: Canada
+      postal_code: H1T 1C8
   keywords:
     - reproducible publishing
     - mystmd
     - next-gen preprints
   github: https://github.com/neurolibre/mystical-article
   banner: static/banner.jpg
-  venue: Neurolibre
-  subject: Living Preprint
+  venue: Neurolibre #Production will override this.
+  subject: Living Preprint # Production will override this.
   numbering:
     headings: true
-  doi: 10.55458/neurolibre.xxxxx
+  doi: 10.55458/neurolibre.xxxxx # Production will override this.
   open_access: true
-  license: CC-BY-4.0
+  license:
+    - content: CC-BY-4.0
+    - code: MIT
   abbreviations:
     MyST: Markedly Structured Markdown
   bibliography:
     - paper.bib
   resources:
     - content/figure1.ipynb
-    - content/figure2.ipynb
+    - content/figure2.md
 site:
+  template: article-theme # Or book-theme
+  options:
+    favicon: static/favicon.ico # Production will override this for branding.
+    logo: static/logo.png # Production will override this for branding.
+    twitter: neurolibre
   template: article-theme
 
+# This section is under development
 neurolibre:
   rees:
     runtime: