Merge pull request #6 from agahkarakuzu/main

Resolve compatibility issues and improve the template

.github/workflows/draft-paper.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: neurolibre/neurolibre-draft-action@master
+        with:
+          journal: neurolibre
+          # This should be the path to the paper within your repo.
+          paper-path: paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

README.md

@@ -1,8 +1,8 @@
 ## Preprint template
 
-Template repository for NeuroLibre preprint submissions.
+Template repository for NeuroLibre reproducibe preprint submissions.
 
-### Step 1: Click `Use this template button` and give a name to your new repository
+### Step 1: Click `Use this template button` and name your new repository
 
 ### Step 2: Do the following changes in [_config.yml](content/_config.yml)
 

binder/data_requirement.json

@@ -1,3 +1,3 @@
 { "src": "from nilearn import datasets; datasets.fetch_development_fmri(data_dir=_dst, n_subjects=1);",
   "dataLayout": "neurolibre",
-  "projectName": "neurolibre_template"}
+  "projectName": "agah_template"}

binder/requirements.txt

@@ -1,5 +1,4 @@
-numpy==1.18.4
-scipy==1.5.4
-plotly==4.14.0
-nilearn==0.7.1
+plotly==5.14.1
+plotly-express==0.4.1
 repo2data>=2.6.0
+jupyter-book==0.14.0

binder/runtime.txt

@@ -0,0 +1 @@
+Python-3.8

content/00-simple_markdown.md

@@ -1,4 +1,4 @@
-## How to organize the preprint content? 
+# How to organize the preprint content? 
 
 NeuroLibre expects all the preprint content (except for `paper.md` and `preprint.md`) under 
 the `content` folder. You can add subfolders to organize your content as you see fit.
@@ -7,4 +7,4 @@ The `_toc.yml` file determines the structure of your Book. Please visit the [off
 
 ## How to configure Book settings?
 
-The `_config.yml` defines the majority Book configurations. Please visit the [official documentation]9https://jupyterbook.org/customize/config.html?highlight=_config%20yml) for details.
+The `_config.yml` defines the majority Book configurations. Please visit the [official documentation]https://jupyterbook.org/customize/config.html?highlight=_config%20yml) for details.

content/01-simple_notebook.ipynb

@@ -1,10 +1,11 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## How to make a code cell collapsible in the Jupyter Book? \n",
+    "# How to make a code cell collapsible in the Jupyter Book? \n",
     "\n",
     "1. In the title bar above: `View` --> `Cell Toolbar` --> `Edit Metadata`\n",
     "\n",
@@ -53,6 +54,7 @@
    "source": [
     "import plotly.express as px\n",
     "from plotly.offline import plot\n",
+    "from IPython.core.display import HTML\n",
     "\n",
     "# Example dataset \n",
     "df = px.data.gapminder()\n",
@@ -71,7 +73,7 @@
  "metadata": {
   "celltoolbar": "Edit Metadata",
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -85,7 +87,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.16"
   }
  },
  "nbformat": 4,

content/02-simple-myst.md

@@ -1,15 +1,18 @@
 ---
 jupytext:
+  formats: md:myst
   text_representation:
+    extension: .md
     format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.11.5
 kernelspec:
   display_name: Python 3
+  language: python
   name: python3
-repository:
-  url: https://github.com/neurolibre/template
 ---
 
-## What is MyST Markdown? 
+# What is MyST Markdown? 
 
 In addition to Jupyter Notebooks, Jupyter Book also supports a special flavour of Markdown called MyST (or Markedly Structured Text). It is designed to make it easier to create publishable computational documents written with Markdown notation.
 
@@ -44,6 +47,7 @@ The code cell below uses `Plotly` to generate a simple interactive figure. When
 
 import plotly.express as px
 from plotly.offline import plot
+from IPython.core.display import HTML
 
 # Example dataset 
 df = px.data.gapminder()
@@ -57,4 +61,4 @@ fig = px.scatter(df.query("year==2007"), x="gdpPercap", y="lifeExp", size="pop",
 plot(fig, filename = 'example_figure.html')
 display(HTML('example_figure.html'))
 
-```
+```

content/_config.yml

@@ -8,7 +8,7 @@
 title                       : "NeuroLibre preprint template"  # The title of the book. Will be placed in the left navbar.
 author                      : Robo Neuro  # The author of the book
 copyright                   : "2021"  # Copyright year to be placed in the footer
-logo                        : "../images/neurolibre-logo.png"  # A path to the book logo
+logo                        : "neurolibre-logo.png"  # A path to the book logo
 exclude_patterns            : []  # Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb")
 
 #######################################################################################
@@ -35,12 +35,18 @@ html:
 # Launch button settings
 launch_buttons:
   notebook_interface        : classic  # The interface interactive links will activate ["classic", "jupyterlab"]
-  binderhub_url             : https://binder.conp.cloud  # The URL of the Neurolibre BinderHub
+  binderhub_url             : https://test.conp.cloud  # The URL of the Neurolibre BinderHub
   thebe                     : false  # Add a thebe button to pages (requires the repository to run on Binder)
 
 repository:
-  url                       : https://github.com/neurolibre/template  # The URL to your book's repository
+  url                       : https://github.com/agahkarakuzu/template  # The URL to your book's repository
   path_to_book              : "content"  # A path to your book's folder, relative to the repository root.
   branch                    : main  # Which branch of the repository should be used when creating links
 
+
+html_theme_options:
+  logo:
+    image_light: "neurolibre-logo.png"
+    image_dark: "neurolibre-logo.png"
+
 #######################################################################################

content/_toc.yml

@@ -1,3 +1,9 @@
-- file: 00-simple_markdown
-- file: 01-simple_notebook
-- file: 02-simple_myst
+format: jb-book
+root: 00-simple_markdown
+parts:
+  - caption: Ipynb
+    chapters:
+    - file: 01-simple_notebook
+  - caption: MyST
+    chapters:
+    - file: 02-simple-myst