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module2/ressources/jupyter.md
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...@@ -7,22 +7,22 @@ Date: Tue Feb 19 15:42:13 2019 ...@@ -7,22 +7,22 @@ Date: Tue Feb 19 15:42:13 2019
Table of Contents<span class="tag" data-tag-name="TOC"></span> Table of Contents<span class="tag" data-tag-name="TOC"></span>
============================================================== ==============================================================
- [1. Jupyter tips and tricks](#1-jupyter-tips-and-tricks) - [1 Jupyter tips and tricks](#1-jupyter-tips-and-tricks)
- [Creating or importing a notebook](#creating-or-importing-a-notebook) - [1.1 Creating or importing a notebook](#11-creating-or-importing-a-notebook)
- [Running R and Python in the same notebook](#running-r-and-python-in-the-same-notebook) - [1.2 Running R and Python in the same notebook](#12-running-r-and-python-in-the-same-notebook)
- [Other languages](#other-languages) - [1.3 Other languages](#13-other-languages)
- [2. Installing and configuring Jupyter on your computer](#2-installing-and-configuring-jupyter-on-your-computer) - [2 Installing and configuring Jupyter on your computer](#2-installing-and-configuring-jupyter-on-your-computer)
- [2.1 Installing Jupyter](#21-installing-jupyter) - [2.1 Installing Jupyter](#21-installing-jupyter)
- [2.2 Making sure Jupyter allows you to use R](#22-making-sure-jupyter-allows-you-to-use-r) - [2.2 Making sure Jupyter allows you to use R](#22-making-sure-jupyter-allows-you-to-use-r)
- [2.3 Additional tips](#23-additional-tips) - [2.3 Additional tips](#23-additional-tips)
1. Jupyter tips and tricks 1 Jupyter tips and tricks
========================== =========================
The following [webpage](https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/) lists several Jupyter tricks (in particular, it illustrates many `IPython magic` commands) that should improve your efficiency (note that this blog post is about two years old so some of the tricks may have been integrated in the default behavior of Jupyter now). The following [webpage](https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/) lists several Jupyter tricks (in particular, it illustrates many `IPython magic` commands) that should improve your efficiency (note that this blog post is about two years old so some of the tricks may have been integrated in the default behavior of Jupyter now).
Creating or importing a notebook 1.1 Creating or importing a notebook
-------------------------------- ------------------------------------
Using the Jupyter environment we deployed for this MOOC will allow to easily access any file from your default GitLab project. There are situations however where you may want to play with other notebooks. Using the Jupyter environment we deployed for this MOOC will allow to easily access any file from your default GitLab project. There are situations however where you may want to play with other notebooks.
...@@ -45,8 +45,8 @@ If your notebook is already in your GitLab project, then simply synchronize by u ...@@ -45,8 +45,8 @@ If your notebook is already in your GitLab project, then simply synchronize by u
3. Then from the top right button, `Upload` the previously downloaded notebook and confirm the upload. 3. Then from the top right button, `Upload` the previously downloaded notebook and confirm the upload.
4. Open the freshly uploaded notebook through the Jupyter file manager. 4. Open the freshly uploaded notebook through the Jupyter file manager.
Running R and Python in the same notebook 1.2 Running R and Python in the same notebook
----------------------------------------- ---------------------------------------------
`rpy2` package allows to use both languages in the same notebook by: `rpy2` package allows to use both languages in the same notebook by:
...@@ -72,8 +72,8 @@ Running R and Python in the same notebook ...@@ -72,8 +72,8 @@ Running R and Python in the same notebook
Note that this `%%R` notation indicates that R should be used for the whole cell but an other possibility is to use `%R` to have a single line of R within a python cell. Note that this `%%R` notation indicates that R should be used for the whole cell but an other possibility is to use `%R` to have a single line of R within a python cell.
Other languages 1.3 Other languages
--------------- -------------------
Jupyter is not limited to Pytyhon and R. Many other languages are available: [<https://github.com/jupyter/jupyter/wiki/Jupyter-kernels>](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels), including non-free languages like SAS, Mathematica, Matlab... Note that the maturity of these kernels differs widely. Jupyter is not limited to Pytyhon and R. Many other languages are available: [<https://github.com/jupyter/jupyter/wiki/Jupyter-kernels>](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels), including non-free languages like SAS, Mathematica, Matlab... Note that the maturity of these kernels differs widely.
...@@ -83,8 +83,8 @@ Since the question was asked several times, if you really need to stay with SAS, ...@@ -83,8 +83,8 @@ Since the question was asked several times, if you really need to stay with SAS,
Since proprietary software such as SAS cannot easily be inspected, we discourage its use as it hinders reproducibility by essence. But perfection does not exist anyway and using Jupyter literate programming approach allied with systematic control version and environment control will certainly help anyway. Since proprietary software such as SAS cannot easily be inspected, we discourage its use as it hinders reproducibility by essence. But perfection does not exist anyway and using Jupyter literate programming approach allied with systematic control version and environment control will certainly help anyway.
2. Installing and configuring Jupyter on your computer 2 Installing and configuring Jupyter on your computer
====================================================== =====================================================
In this section, we explain how to set up a Jupyter environment on your own computer similar to the one deployed for this MOOC. In this section, we explain how to set up a Jupyter environment on your own computer similar to the one deployed for this MOOC.
......
module2/ressources/jupyter.org
View file @ f06dbd72
...@@ -7,22 +7,22 @@ ...@@ -7,22 +7,22 @@
#+PROPERTY: header-args :eval never-export #+PROPERTY: header-args :eval never-export
* Table of Contents :TOC: * Table of Contents :TOC:
- [[#1-jupyter-tips-and-tricks][1. Jupyter tips and tricks]] - [[#1-jupyter-tips-and-tricks][1 Jupyter tips and tricks]]
- [[#creating-or-importing-a-notebook][Creating or importing a notebook]] - [[#11-creating-or-importing-a-notebook][1.1 Creating or importing a notebook]]
- [[#running-r-and-python-in-the-same-notebook][Running R and Python in the same notebook]] - [[#12-running-r-and-python-in-the-same-notebook][1.2 Running R and Python in the same notebook]]
- [[#other-languages][Other languages]] - [[#13-other-languages][1.3 Other languages]]
- [[#2-installing-and-configuring-jupyter-on-your-computer][2. Installing and configuring Jupyter on your computer]] - [[#2-installing-and-configuring-jupyter-on-your-computer][2 Installing and configuring Jupyter on your computer]]
- [[#21-installing-jupyter][2.1 Installing Jupyter]] - [[#21-installing-jupyter][2.1 Installing Jupyter]]
- [[#22-making-sure-jupyter-allows-you-to-use-r][2.2 Making sure Jupyter allows you to use R]] - [[#22-making-sure-jupyter-allows-you-to-use-r][2.2 Making sure Jupyter allows you to use R]]
- [[#23-additional-tips][2.3 Additional tips]] - [[#23-additional-tips][2.3 Additional tips]]
* 1. Jupyter tips and tricks * 1 Jupyter tips and tricks
The following [[https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/][webpage]] lists several Jupyter tricks (in particular, it The following [[https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/][webpage]] lists several Jupyter tricks (in particular, it
illustrates many =IPython magic= commands) that should improve your illustrates many =IPython magic= commands) that should improve your
efficiency (note that this blog post is about two years old so some of efficiency (note that this blog post is about two years old so some of
the tricks may have been integrated in the default behavior of Jupyter the tricks may have been integrated in the default behavior of Jupyter
now). now).
** Creating or importing a notebook ** 1.1 Creating or importing a notebook
Using the Jupyter environment we deployed for this MOOC will allow to Using the Jupyter environment we deployed for this MOOC will allow to
easily access any file from your default GitLab project. There are easily access any file from your default GitLab project. There are
situations however where you may want to play with other notebooks. situations however where you may want to play with other notebooks.
...@@ -54,7 +54,7 @@ situations however where you may want to play with other notebooks. ...@@ -54,7 +54,7 @@ situations however where you may want to play with other notebooks.
notebook and confirm the upload. notebook and confirm the upload.
4. Open the freshly uploaded notebook through the Jupyter file 4. Open the freshly uploaded notebook through the Jupyter file
manager. manager.
** Running R and Python in the same notebook ** 1.2 Running R and Python in the same notebook
=rpy2= package allows to use both languages in the same notebook by: =rpy2= package allows to use both languages in the same notebook by:
1. Loading =rpy2=: 1. Loading =rpy2=:
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
...@@ -74,7 +74,7 @@ situations however where you may want to play with other notebooks. ...@@ -74,7 +74,7 @@ situations however where you may want to play with other notebooks.
Note that this =%%R= notation indicates that R should be used for the whole cell but Note that this =%%R= notation indicates that R should be used for the whole cell but
an other possibility is to use =%R= to have a single line of R within a an other possibility is to use =%R= to have a single line of R within a
python cell. python cell.
** Other languages ** 1.3 Other languages
Jupyter is not limited to Pytyhon and R. Many other languages are available: Jupyter is not limited to Pytyhon and R. Many other languages are available:
[[https://github.com/jupyter/jupyter/wiki/Jupyter-kernels][https://github.com/jupyter/jupyter/wiki/Jupyter-kernels]], including [[https://github.com/jupyter/jupyter/wiki/Jupyter-kernels][https://github.com/jupyter/jupyter/wiki/Jupyter-kernels]], including
non-free languages like SAS, Mathematica, Matlab... Note that the maturity of these kernels differs widely. non-free languages like SAS, Mathematica, Matlab... Note that the maturity of these kernels differs widely.
...@@ -93,7 +93,7 @@ essence. But perfection does not exist anyway and using Jupyter ...@@ -93,7 +93,7 @@ essence. But perfection does not exist anyway and using Jupyter
literate programming approach allied with systematic control version literate programming approach allied with systematic control version
and environment control will certainly help anyway. and environment control will certainly help anyway.
* 2. Installing and configuring Jupyter on your computer * 2 Installing and configuring Jupyter on your computer
In this section, we explain how to set up a Jupyter environment on In this section, we explain how to set up a Jupyter environment on
your own computer similar to the one deployed for this MOOC. your own computer similar to the one deployed for this MOOC.
......
module2/ressources/jupyter_fr.md
View file @ f06dbd72
...@@ -7,22 +7,22 @@ Date: Tue Feb 19 17:43:42 2019 ...@@ -7,22 +7,22 @@ Date: Tue Feb 19 17:43:42 2019
Table of Contents<span class="tag" data-tag-name="TOC"></span> Table of Contents<span class="tag" data-tag-name="TOC"></span>
============================================================== ==============================================================
- [1. Jupyter tips and tricks](#1-jupyter-tips-and-tricks) - [1 Jupyter tips and tricks](#1-jupyter-tips-and-tricks)
- [Creating or importing a notebook](#creating-or-importing-a-notebook) - [1.1 Creating or importing a notebook](#11-creating-or-importing-a-notebook)
- [Running R and Python in the same notebook](#running-r-and-python-in-the-same-notebook) - [1.2 Running R and Python in the same notebook](#12-running-r-and-python-in-the-same-notebook)
- [Other languages](#other-languages) - [1.3 Other languages](#13-other-languages)
- [2. Installing and configuring Jupyter on your computer](#2-installing-and-configuring-jupyter-on-your-computer) - [2 Installing and configuring Jupyter on your computer](#2-installing-and-configuring-jupyter-on-your-computer)
- [2.1 Installing Jupyter](#21-installing-jupyter) - [2.1 Installing Jupyter](#21-installing-jupyter)
- [2.2 Making sure Jupyter allows you to use R](#22-making-sure-jupyter-allows-you-to-use-r) - [2.2 Making sure Jupyter allows you to use R](#22-making-sure-jupyter-allows-you-to-use-r)
- [2.3 Additional tips](#23-additional-tips) - [2.3 Additional tips](#23-additional-tips)
1. Jupyter tips and tricks 1 Jupyter tips and tricks
========================== =========================
The following [webpage](https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/) lists several Jupyter tricks (in particular, it illustrates many `IPython magic` commands) that should improve your efficiency (note that this blog post is about two years old so some of the tricks may have been integrated in the default behavior of Jupyter now). The following [webpage](https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/) lists several Jupyter tricks (in particular, it illustrates many `IPython magic` commands) that should improve your efficiency (note that this blog post is about two years old so some of the tricks may have been integrated in the default behavior of Jupyter now).
Creating or importing a notebook 1.1 Creating or importing a notebook
-------------------------------- ------------------------------------
Using the Jupyter environment we deployed for this MOOC will allow to easily access any file from your default GitLab project. There are situations however where you may want to play with other notebooks. Using the Jupyter environment we deployed for this MOOC will allow to easily access any file from your default GitLab project. There are situations however where you may want to play with other notebooks.
...@@ -45,8 +45,8 @@ If your notebook is already in your GitLab project, then simply synchronize by u ...@@ -45,8 +45,8 @@ If your notebook is already in your GitLab project, then simply synchronize by u
3. Then from the top right button, `Upload` the previously downloaded notebook and confirm the upload. 3. Then from the top right button, `Upload` the previously downloaded notebook and confirm the upload.
4. Open the freshly uploaded notebook through the Jupyter file manager. 4. Open the freshly uploaded notebook through the Jupyter file manager.
Running R and Python in the same notebook 1.2 Running R and Python in the same notebook
----------------------------------------- ---------------------------------------------
`rpy2` package allows to use both languages in the same notebook by: `rpy2` package allows to use both languages in the same notebook by:
...@@ -72,8 +72,8 @@ Running R and Python in the same notebook ...@@ -72,8 +72,8 @@ Running R and Python in the same notebook
Note that this `%%R` notation indicates that R should be used for the whole cell but an other possibility is to use `%R` to have a single line of R within a python cell. Note that this `%%R` notation indicates that R should be used for the whole cell but an other possibility is to use `%R` to have a single line of R within a python cell.
Other languages 1.3 Other languages
--------------- -------------------
Jupyter is not limited to Pytyhon and R. Many other languages are available: [<https://github.com/jupyter/jupyter/wiki/Jupyter-kernels>](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels), including non-free languages like SAS, Mathematica, Matlab... Note that the maturity of these kernels differs widely. Jupyter is not limited to Pytyhon and R. Many other languages are available: [<https://github.com/jupyter/jupyter/wiki/Jupyter-kernels>](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels), including non-free languages like SAS, Mathematica, Matlab... Note that the maturity of these kernels differs widely.
...@@ -83,8 +83,8 @@ Since the question was asked several times, if you really need to stay with SAS, ...@@ -83,8 +83,8 @@ Since the question was asked several times, if you really need to stay with SAS,
Since proprietary software such as SAS cannot easily be inspected, we discourage its use as it hinders reproducibility by essence. But perfection does not exist anyway and using Jupyter literate programming approach allied with systematic control version and environment control will certainly help anyway. Since proprietary software such as SAS cannot easily be inspected, we discourage its use as it hinders reproducibility by essence. But perfection does not exist anyway and using Jupyter literate programming approach allied with systematic control version and environment control will certainly help anyway.
2. Installing and configuring Jupyter on your computer 2 Installing and configuring Jupyter on your computer
====================================================== =====================================================
In this section, we explain how to set up a Jupyter environment on your own computer similar to the one deployed for this MOOC. In this section, we explain how to set up a Jupyter environment on your own computer similar to the one deployed for this MOOC.
......
module2/ressources/jupyter_fr.org
View file @ f06dbd72
...@@ -7,22 +7,22 @@ ...@@ -7,22 +7,22 @@
#+PROPERTY: header-args :eval never-export #+PROPERTY: header-args :eval never-export
* Table of Contents :TOC: * Table of Contents :TOC:
- [[#1-jupyter-tips-and-tricks][1. Jupyter tips and tricks]] - [[#1-jupyter-tips-and-tricks][1 Jupyter tips and tricks]]
- [[#creating-or-importing-a-notebook][Creating or importing a notebook]] - [[#11-creating-or-importing-a-notebook][1.1 Creating or importing a notebook]]
- [[#running-r-and-python-in-the-same-notebook][Running R and Python in the same notebook]] - [[#12-running-r-and-python-in-the-same-notebook][1.2 Running R and Python in the same notebook]]
- [[#other-languages][Other languages]] - [[#13-other-languages][1.3 Other languages]]
- [[#2-installing-and-configuring-jupyter-on-your-computer][2. Installing and configuring Jupyter on your computer]] - [[#2-installing-and-configuring-jupyter-on-your-computer][2 Installing and configuring Jupyter on your computer]]
- [[#21-installing-jupyter][2.1 Installing Jupyter]] - [[#21-installing-jupyter][2.1 Installing Jupyter]]
- [[#22-making-sure-jupyter-allows-you-to-use-r][2.2 Making sure Jupyter allows you to use R]] - [[#22-making-sure-jupyter-allows-you-to-use-r][2.2 Making sure Jupyter allows you to use R]]
- [[#23-additional-tips][2.3 Additional tips]] - [[#23-additional-tips][2.3 Additional tips]]
* 1. Jupyter tips and tricks * 1 Jupyter tips and tricks
The following [[https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/][webpage]] lists several Jupyter tricks (in particular, it The following [[https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/][webpage]] lists several Jupyter tricks (in particular, it
illustrates many =IPython magic= commands) that should improve your illustrates many =IPython magic= commands) that should improve your
efficiency (note that this blog post is about two years old so some of efficiency (note that this blog post is about two years old so some of
the tricks may have been integrated in the default behavior of Jupyter the tricks may have been integrated in the default behavior of Jupyter
now). now).
** Creating or importing a notebook ** 1.1 Creating or importing a notebook
Using the Jupyter environment we deployed for this MOOC will allow to Using the Jupyter environment we deployed for this MOOC will allow to
easily access any file from your default GitLab project. There are easily access any file from your default GitLab project. There are
situations however where you may want to play with other notebooks. situations however where you may want to play with other notebooks.
...@@ -54,7 +54,7 @@ situations however where you may want to play with other notebooks. ...@@ -54,7 +54,7 @@ situations however where you may want to play with other notebooks.
notebook and confirm the upload. notebook and confirm the upload.
4. Open the freshly uploaded notebook through the Jupyter file 4. Open the freshly uploaded notebook through the Jupyter file
manager. manager.
** Running R and Python in the same notebook ** 1.2 Running R and Python in the same notebook
=rpy2= package allows to use both languages in the same notebook by: =rpy2= package allows to use both languages in the same notebook by:
1. Loading =rpy2=: 1. Loading =rpy2=:
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
...@@ -74,7 +74,7 @@ situations however where you may want to play with other notebooks. ...@@ -74,7 +74,7 @@ situations however where you may want to play with other notebooks.
Note that this =%%R= notation indicates that R should be used for the whole cell but Note that this =%%R= notation indicates that R should be used for the whole cell but
an other possibility is to use =%R= to have a single line of R within a an other possibility is to use =%R= to have a single line of R within a
python cell. python cell.
** Other languages ** 1.3 Other languages
Jupyter is not limited to Pytyhon and R. Many other languages are available: Jupyter is not limited to Pytyhon and R. Many other languages are available:
[[https://github.com/jupyter/jupyter/wiki/Jupyter-kernels][https://github.com/jupyter/jupyter/wiki/Jupyter-kernels]], including [[https://github.com/jupyter/jupyter/wiki/Jupyter-kernels][https://github.com/jupyter/jupyter/wiki/Jupyter-kernels]], including
non-free languages like SAS, Mathematica, Matlab... Note that the maturity of these kernels differs widely. non-free languages like SAS, Mathematica, Matlab... Note that the maturity of these kernels differs widely.
...@@ -93,7 +93,7 @@ essence. But perfection does not exist anyway and using Jupyter ...@@ -93,7 +93,7 @@ essence. But perfection does not exist anyway and using Jupyter
literate programming approach allied with systematic control version literate programming approach allied with systematic control version
and environment control will certainly help anyway. and environment control will certainly help anyway.
* 2. Installing and configuring Jupyter on your computer * 2 Installing and configuring Jupyter on your computer
In this section, we explain how to set up a Jupyter environment on In this section, we explain how to set up a Jupyter environment on
your own computer similar to the one deployed for this MOOC. your own computer similar to the one deployed for this MOOC.
......
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