diff --git a/module1/ressources/introduction_to_markdown.org b/module1/ressources/introduction_to_markdown.org index 8369e828762e1cad7fba1ac5bc318c7a9d0595f3..eac2f5decf116b2e8467a8169d11207a71e4201d 100644 --- a/module1/ressources/introduction_to_markdown.org +++ b/module1/ressources/introduction_to_markdown.org @@ -9,6 +9,24 @@ Voici un aperçu rapide de la syntaxe Markdown repris d'une [[https://guides.github.com/features/mastering-markdown/][présentation de Github]] ainsi que de celles d'[[http://csrgxtu.github.io/2015/03/20/Writing-Mathematic-Fomulars-in-Markdown/][Archer Reilly]]. +* Table des matières :TOC: +- [[#syntaxe][Syntaxe]] + - [[#headers][Headers]] + - [[#emphasis][Emphasis]] + - [[#lists][Lists]] + - [[#images][Images]] + - [[#links][Links]] + - [[#blockquotes][Blockquotes]] + - [[#inline-code][Inline code]] +- [[#écrire-des-maths][Écrire des Maths]] + - [[#lettres-grecques][Lettres grecques]] + - [[#fonctions-et-opérateurs][Fonctions et opérateurs]] + - [[#exposants-et-indices][Exposants et indices]] + - [[#fractions-coefficients-binomiaux-racines-][Fractions, coefficients binomiaux, racines, ...]] + - [[#sommes-et-intégrales][Sommes et intégrales]] + - [[#déguisements][Déguisements]] +- [[#autour-de-markdown][Autour de =markdown=]] + * Syntaxe ** Headers #+BEGIN_EXAMPLE diff --git a/module2/ressources/gitlab.org b/module2/ressources/gitlab.org index a280924300903015de5f099b28cc7cee7a477329..58e40625a78c5481e5a2969b858139bd15b9c18c 100644 --- a/module2/ressources/gitlab.org +++ b/module2/ressources/gitlab.org @@ -28,6 +28,17 @@ section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41 Please read all these instructions carefully, in particular the one on "Configuring your password on GitLab". +* Table of Contents :TOC: +- [[#installing-git][Installing Git]] + - [[#linux-debian-ubuntu][Linux (Debian, Ubuntu)]] + - [[#mac-osx-and-windows][Mac OSX and Windows]] +- [[#configuring-git][Configuring Git]] + - [[#telling-git-who-you-are-name-and-email][Telling Git who you are: Name and Email]] + - [[#dealing-with-proxies][Dealing with proxies]] + - [[#getting-your-default-password-on-gitlab-and-possibly-changing-it][Getting your default password on GitLab (and possibly changing it)]] + - [[#remembering-your-password-locally][Remembering your password locally]] + - [[#optional-authenticating-through-ssh][Optional: authenticating through SSH]] +- [[#using-git-through-the-command-line-to-synchronize-your-local-files-with-gitlab][Using Git through the command line to synchronize your local files with Gitlab]] * Installing Git ** Linux (Debian, Ubuntu) diff --git a/module2/ressources/gitlab_fr.org b/module2/ressources/gitlab_fr.org index 19d60c3451e3070a81fd909be44200573fcddd65..e3da55af94dc08173badb6a708e354a3211e28ef 100644 --- a/module2/ressources/gitlab_fr.org +++ b/module2/ressources/gitlab_fr.org @@ -30,6 +30,18 @@ français). Veuillez lire attentivement toutes ces instructions, en particulier celle sur la "Configuration de votre mot de passe sur GitLab". +* Table des matières :TOC: +- [[#installer-git][Installer Git]] + - [[#linux-debian-ubuntu][Linux (Debian, Ubuntu)]] + - [[#mac-osx-et-windows][Mac OSX et Windows]] +- [[#configurer-git][Configurer Git]] + - [[#dire-à-git-qui-vous-êtes-nom-et-email][Dire à Git qui vous êtes : nom et email]] + - [[#gérer-les-proxy][Gérer les proxy]] + - [[#récupérer-votre-mot-de-passe-par-défaut-sur-gitlab-et-le-changer-éventuellement][Récupérer votre mot de passe par défaut sur GitLab (et le changer éventuellement)]] + - [[#enregistrer-votre-mot-de-passe-localement][Enregistrer votre mot de passe localement]] + - [[#optionnel-authentification-par-ssh][Optionnel : authentification par SSH]] +- [[#utiliser-git-par-lignes-de-commandes-pour-synchroniser-vos-fichiers-locaux-avec-gitlab][Utiliser Git par lignes de commandes pour synchroniser vos fichiers locaux avec Gitlab]] + * Installer Git ** Linux (Debian, Ubuntu) Nous ne fournissons ici que des instructions pour les distributions diff --git a/module2/ressources/jupyter.org b/module2/ressources/jupyter.org index 1d1d53791ccd39dc8b4795e3b2475c52cf4e519f..875905f630e98bd05c61c0314eb3afb9cdc3ce89 100644 --- a/module2/ressources/jupyter.org +++ b/module2/ressources/jupyter.org @@ -6,6 +6,16 @@ #+OPTIONS: num:nil toc:t #+PROPERTY: header-args :eval never-export +* Table of Contents :TOC: +- [[#1-jupyter-tips-and-tricks][1. Jupyter tips and tricks]] + - [[#creating-or-importing-a-notebook][Creating or importing a notebook]] + - [[#running-r-and-python-in-the-same-notebook][Running R and Python in the same notebook]] + - [[#other-languages][Other languages]] +- [[#2-installing-and-configuring-jupyter-on-your-computer][2. Installing and configuring Jupyter on your computer]] + - [[#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]] + - [[#23-additional-tips][2.3 Additional tips]] + * 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 illustrates many =IPython magic= commands) that should improve your diff --git a/module2/ressources/maintaining_a_journal.org b/module2/ressources/maintaining_a_journal.org index 1a757046ab5f26dc7050cd3ff52d91c4728bebaf..5956c06a294b328450bf561d0bc646b0e6a74108 100644 --- a/module2/ressources/maintaining_a_journal.org +++ b/module2/ressources/maintaining_a_journal.org @@ -6,6 +6,13 @@ #+OPTIONS: num:nil toc:t #+PROPERTY: header-args :eval never-export +* Table of Contents :TOC: +- [[#some-examples-of-labbooks-provided-for-inspiration][Some examples of LabBooks provided for inspiration]] +- [[#how-to-report-efficiently-by-martin-quinson][How to report efficiently (by Martin Quinson)]] + - [[#reporting][Reporting]] + - [[#reporting-logistics][Reporting Logistics]] + - [[#reporting-document-organization][Reporting Document Organization]] + * Some examples of LabBooks provided for inspiration Since a few years, we systematically require any or our students to have a laboratory notebook in org-mode. Most of the time, they start diff --git a/module2/ressources/rstudio.org b/module2/ressources/rstudio.org index 25ea9cf6dd7bf0f19de4b34e237bb343fea39012..81f441169a3dd2583cc540cbc6e2b3cd84dd7edb 100644 --- a/module2/ressources/rstudio.org +++ b/module2/ressources/rstudio.org @@ -5,6 +5,15 @@ #+STARTUP: overview indent #+OPTIONS: num:nil toc:t +* Table of Contents :TOC: +- [[#installing-rstudio][Installing RStudio]] + - [[#linux-debian-ubuntu][Linux (debian, ubuntu)]] + - [[#mac-osx-and-windows][Mac OSX and Windows]] +- [[#rstudio-documentation][RStudio documentation]] +- [[#using-git-from-rstudio][Using Git from RStudio]] + - [[#cloning-a-repository][Cloning a repository]] + - [[#modifying-a-file][Modifying a file]] + * Installing RStudio ** Linux (debian, ubuntu) We provide here only instructions for Debian-based distributions. Feel diff --git a/module2/ressources/rstudio_fr.org b/module2/ressources/rstudio_fr.org index 2237c92961afe5bda4bbb4efc1cf58774de8caad..536a7868c6d3a324769c9781b937317b446c9f1f 100644 --- a/module2/ressources/rstudio_fr.org +++ b/module2/ressources/rstudio_fr.org @@ -5,6 +5,15 @@ #+STARTUP: overview indent #+OPTIONS: num:nil toc:t +* Table des matières :TOC: +- [[#installer-rstudio][Installer RStudio]] + - [[#linux-debian-ubuntu][Linux (debian, ubuntu)]] + - [[#mac-osx-and-windows][Mac OSX and Windows]] +- [[#documentation-rstudio][Documentation RStudio]] +- [[#utiliser-git-avec-rstudio][Utiliser Git avec RStudio]] + - [[#cloner-un-dépôt][Cloner un dépôt]] + - [[#modifier-un-fichier][Modifier un fichier]] + * Installer RStudio ** Linux (debian, ubuntu) Nous ne fournissons ici que des instructions pour les distributions diff --git a/module4/ressources/resources_refs.org b/module4/ressources/resources_refs.org index 6ecdb642688fd7db2d5018e16e1462815dc74fae..a038785a2a2c004cf2e1bd7cb89bb702800ca37a 100644 --- a/module4/ressources/resources_refs.org +++ b/module4/ressources/resources_refs.org @@ -6,6 +6,15 @@ #+OPTIONS: num:nil toc:t #+PROPERTY: header-args :eval never-export +* Table of Contents :TOC: +- [[#thoughts-on-languagesoftware-stability]["Thoughts" on language/software stability]] +- [[#controlling-your-software-environment][Controlling your software environment]] +- [[#preservationarchiving][Preservation/Archiving]] +- [[#workflows][Workflows]] +- [[#numerical-and-statistical-issues][Numerical and statistical issues]] +- [[#publication-practices][Publication practices]] +- [[#experimentation][Experimentation]] + * "Thoughts" on language/software stability As we explained, the programming language used in an analysis has a clear influence on the reproducibility of your analysis. It is not a diff --git a/module4/ressources/resources_refs_fr.org b/module4/ressources/resources_refs_fr.org index 591eb4396db11fd4e6dd51d699923c609b876f3c..2b4ada93cc794925a866c2519187abdbcf528666 100644 --- a/module4/ressources/resources_refs_fr.org +++ b/module4/ressources/resources_refs_fr.org @@ -6,6 +6,15 @@ #+OPTIONS: num:nil toc:t #+PROPERTY: header-args :eval never-export +* Table des matières :TOC: +- [[#réflexions-sur-la-stabilité-des-langages-de-programmation][Réflexions sur la stabilité des langages de programmation]] +- [[#contrôler-votre-environnement-logiciel][Contrôler votre environnement logiciel]] +- [[#préservationarchivage][Préservation/Archivage]] +- [[#workflows][Workflows]] +- [[#problèmes-numériques-et-statistiques][Problèmes numériques et statistiques]] +- [[#pratiques-de-publication][Pratiques de publication]] +- [[#expérimentation][Expérimentation]] + * Réflexions sur la stabilité des langages de programmation Comme nous l'avons expliqué, le langage de programmation utilisé dans une analyse a une influence évidente sur la reproductibilité de