Add watermark module

pierrepo · Sep 21, 2023 · 542eac9 · 542eac9
1 parent 77c0ad7
commit 542eac9
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Showing 3 changed files with 67 additions and 6 deletions.
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -18,5 +18,9 @@ dependencies:
     - r-irkernel
     - r-base>=4.0
     - r-tidyverse
+    # For DUO example with DESeq2
+    - bioconductor-deseq2
+    - bioconductor-parathyroidse
     - pip:
         - bash_kernel
+        - watermark
diff --git a/notebooks/intro_Python.ipynb b/notebooks/intro_Python.ipynb
@@ -223,6 +223,32 @@
     "<h1>Jupyter notebooks can render HTML</h1>"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "\n",
+    "## Bonne pratique\n",
+    "\n",
+    "Une bonne pratique pour améliorer la reproductibilité d'un notebook est d'afficher à la fin (ou au début) du notebook la liste des bibliothèques utilisées ainsi que la version de Python.\n",
+    "\n",
+    "Le module `watermark` permet de faire cela automatiquement."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "%load_ext watermark\n",
+    "%watermark --python --machine\n",
+    "%watermark --packages jupyterlab --iversions --watermark"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -257,7 +283,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/matplotlib.ipynb b/notebooks/matplotlib.ipynb
@@ -2,7 +2,9 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "source": [
     "# Introduction à la bibliothèque Matplotlib\n",
     "\n",
@@ -166,7 +168,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Diagramme en bâtons"
+    "## Diagramme en bâtons"
    ]
   },
   {
@@ -329,6 +331,28 @@
     "</details>"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Enregistrement des versions des bibliothèques utilisées\n",
+    "\n",
+    "Pour améliorer la reproductibilité du notebook, on liste les bibliothèques utilisées ainsi que la version de Python."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "%load_ext watermark\n",
+    "%watermark --python --machine\n",
+    "%watermark --packages jupyterlab --iversions --watermark"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -343,7 +367,7 @@
     "\n",
     "![](black-hole.png)\n",
     "\n",
-    "[NumFOCUS tools help create the first ever image of a black hole](https://numfocus.org/case-studies/first-photograph-black-hole)\n",
+    "Source : [NumFOCUS tools help create the first ever image of a black hole](https://numfocus.org/case-studies/first-photograph-black-hole)\n",
     "\n",
     "Voici quelques ressources supplémentaires si vous souhaitez approfondir ces possibilités :\n",
     "\n",
@@ -352,11 +376,18 @@
     "\n",
     "Enfin, d'autres modules comme [seaborn](https://seaborn.pydata.org/), [Bokeh](https://bokeh.pydata.org/en/latest/) ou [plotly](https://plot.ly/) permettent de générer des graphiques plus élégants ou interactifs."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -370,7 +401,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,