This section is illustrated in a <ahref="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Mise en place
This section is illustrated in a <ahref="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Mise en place
Emacs/Orgmode"</i> in French). Watching it before following the
Emacs/Orgmode"</i> in French). Watching it before following the
...
@@ -296,9 +305,9 @@ adding a few org-mode specific configurations.
...
@@ -296,9 +305,9 @@ adding a few org-mode specific configurations.
<h2id="org86b127a">A stub of replicable article</h2>
<h2id="orgb88bcaf">A stub of replicable article</h2>
<divclass="outline-text-2"id="text-org86b127a">
<divclass="outline-text-2"id="text-orgb88bcaf">
<p>
<p>
This section is illustrated in a <ahref="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Écrire un article
This section is illustrated in a <ahref="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Écrire un article
réplicable avec Emacs/Orgmode"</i> in French). Watching it before
réplicable avec Emacs/Orgmode"</i> in French). Watching it before
...
@@ -495,22 +504,22 @@ chunk of code when exporting.
...
@@ -495,22 +504,22 @@ chunk of code when exporting.
<listyle="margin-bottom:0;"><ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<listyle="margin-bottom:0;"><ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<listyle="margin-bottom:0;"><ahref="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</a></li>
<listyle="margin-bottom:0;"><ahref="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</a></li>
...
@@ -519,9 +528,9 @@ cheat-sheats. Here is a selection in case it helps:
...
@@ -519,9 +528,9 @@ cheat-sheats. Here is a selection in case it helps:
<listyle="margin-bottom:0;"><ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<listyle="margin-bottom:0;"><ahref="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<listyle="margin-bottom:0;"><ahref="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
<listyle="margin-bottom:0;"><ahref="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
...
@@ -530,22 +539,22 @@ cheat-sheats. Here is a selection in case it helps:
...
@@ -530,22 +539,22 @@ cheat-sheats. Here is a selection in case it helps:
<ahref="https://magit.vc/">Magit</a> is an emacs interface for Git. Its usage is briefly illustrated
<ahref="https://magit.vc/">Magit</a> is an emacs interface for Git. Its usage is briefly illustrated
in the context of this MOOC in a <ahref="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Utilisation
in the context of this MOOC in a <ahref="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Utilisation
...
@@ -574,9 +583,9 @@ invoke magit by using <code>C-x g</code>.
...
@@ -574,9 +583,9 @@ invoke magit by using <code>C-x g</code>.
<listyle="margin-bottom:0;"><ahref="https://github.com/dfeich/org-babel-examples">Many examples illustrating the use of different languages in org-mode</a></li>
<listyle="margin-bottom:0;"><ahref="https://github.com/dfeich/org-babel-examples">Many examples illustrating the use of different languages in org-mode</a></li>
<h3id="org0e8c2f3">Getting your default password on GitLab (and possibly changing it)</h3>
<h3id="org6a9f6ba">Getting your default password on GitLab (and possibly changing it)</h3>
<divclass="outline-text-3"id="text-org0e8c2f3">
<divclass="outline-text-3"id="text-org6a9f6ba">
<p>
<p>
<b>Warning (Jupyter users) :</b> changing your default Gitlab password will prevent you from committing in Jupyter. You will have to do the extra step of changing your Jupyter <code>~/.git-credentials</code>
<b>Warning (Jupyter users) :</b> changing your default Gitlab password will prevent you from committing in Jupyter. You will have to do the extra step of changing your Jupyter <code>~/.git-credentials</code>
</p>
</p>
...
@@ -224,8 +224,8 @@ button).
...
@@ -224,8 +224,8 @@ button).
</div>
</div>
</div></li>
</div></li>
<listyle="margin-bottom:0;"><p>
<listyle="margin-bottom:0;"><p>
If you wish to modify your password, you shoul go to <code>Account >
If you wish to modify your password, you shoul go to <code>Account > Settings > Password</code>
Settings > Password</code>and define your password using the default
and define your password using the default
password you just retrieved. Again, if you use the Jupyter
password you just retrieved. Again, if you use the Jupyter
notebooks we have deployed for the MOOC, remember that changing
notebooks we have deployed for the MOOC, remember that changing
your default Gitlab password will prevent you from committing in
your default Gitlab password will prevent you from committing in
The following <ahref="https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/">webpage</a> lists several Jupyter tricks (in particular, it
The following <ahref="https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/">webpage</a> lists several Jupyter tricks (in particular, it
illustrates many <code>Ipython magic</code> commands) that should improve your
illustrates many <code>Ipython magic</code> commands) that should improve your
...
@@ -43,28 +45,11 @@ the tricks may have been integrated in the default behavior of Jupyter
...
@@ -43,28 +45,11 @@ the tricks may have been integrated in the default behavior of Jupyter
<h2id="org745ca35">2. Installing and configuring Jupyter on your computer</h2>
<divclass="outline-text-2"id="text-org745ca35">
<p>
<p>
If you want to use a specific style, then the <code>nbconvert</code> exporter
In this Section, we provide information on how to set up on your own
should be customized. This is discussed and demoed <ahref="http://markus-beuckelmann.de/blog/customizing-nbconvert-pdf.html">here</a>. We encourage
computer a Jupyter environment similar to the one deployed for this
you to simply read the <ahref="https://nbconvert.readthedocs.io/en/latest/">doc of nbconvert</a>.
MOOC.
</p>
</p>
<p>
<p>
Instead of going directly through LaTeX and playing too much with the
Note that Jupyter notebooks are only a small part of the picture and
<code>nbconvert</code> exporter, an other option consists in exporting to Markdown
that Jupyter is now part of a bigger project: <ahref="https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906">JupyterLab</a>, which allows
and playing with <ahref="https://pandoc.org/">pandoc</a>. Both approaches work, it's rather a matter of
you to mix various components (including notebooks) in your
taste.
browser. In the context of this MOOC, our time frame was too short to
benefit from JupyterLab which was still under active development but
this is probably the best option now if you want to benefit from
<h3id="orgbafde52">Side note about Jupyter, JupyterLab, JupyterHub, …</h3>
<h3id="orgb5f2e75">2.2 Making sure Jupyter allows you to use R</h3>
<divclass="outline-text-3"id="text-orgbafde52">
<divclass="outline-text-3"id="text-orgb5f2e75">
<p>
<p>
Note that Jupyter notebooks are only a small part of the picture and
The previous environment should ship with R but if you proceeded
that Jupyter is now part of a bigger project: <ahref="https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906">JupyterLab</a>, which allows
otherwise and only have python available in Jupyter, you may want to
you to mix various components (including notebooks) in your
read the following section.
browser. In the context of this MOOC, our time frame was too short to
</p>
benefit from JupyterLab which was still under active development but
</div>
this is probably the best option now if you want to benefit from
IRkernel::installspec() <spanstyle="font-weight: bold; font-style: italic;"># </span><spanstyle="font-weight: bold; font-style: italic;">to register the kernel in the current R installation</span>
Obviously, you can convert to html or pdf using the using the <code>File > Download as > HTML</code> (or <code>PDF</code>) menu option. This can also be done from
the command line with the following command:
</p>
<divclass="org-src-container">
<prestyle="padding-left: 30px; background-color: #f6f8fa;"class="src src-sh">ipython3 nbconvert --to pdf Untitled.ipynb
</pre>
</div>
<p>
If you want to use a specific style, then the <code>nbconvert</code> exporter
should be customized. This is discussed and demoed <ahref="http://markus-beuckelmann.de/blog/customizing-nbconvert-pdf.html">here</a>. We encourage
you to simply read the <ahref="https://nbconvert.readthedocs.io/en/latest/">doc of nbconvert</a>.
</p>
<p>
Instead of going directly through LaTeX and playing too much with the
<code>nbconvert</code> exporter, an other option consists in exporting to Markdown
and playing with <ahref="https://pandoc.org/">pandoc</a>. Both approaches work, it's rather a matter of
taste.
</p>
<p>
<b>Windows</b>
</p>
<p>
Download and install MiKTeX from the <ahref="https://miktex.org/download">MiKTeX webpage</a>
by choosing the right operating system. You will be prompted to install some specific
<h4id="orgb3e3b0d">• Using other languages (e.g., SAS, Matlab, Mathematica, etc.)</h4>
<divclass="outline-text-4"id="text-orgb3e3b0d">
<p>
For any reason, you may be unsatisfied with the use of R or of
Python. Many other languages are available:
<ahref="https://github.com/jupyter/jupyter/wiki/Jupyter-kernels">https://github.com/jupyter/jupyter/wiki/Jupyter-kernels</a>, including
non-free languages like SAS, Mathematica, Matlab…
</p>
<p>
Since the question was asked several times, if you really need to stay
with SAS, you should know that SAS can be used within Jupyter using
either the <ahref="https://sassoftware.github.io/sas_kernel/">Python SASKernel</a> or the <ahref="https://sassoftware.github.io/saspy/">Python SASPy</a> package (step by step
explanations about this are given <ahref="https://app-learninglab.inria.fr/gitlab/85bc36e0a8096c618fbd5993d1cca191/mooc-rr/blob/master/documents/tuto_jupyter_windows/tuto_jupyter_windows.md">here</a>).
</p>
<p>
Since such software cannot easily be opened for inspection not widely
used, we discourage this approach 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.
