diff --git a/.Rprofile b/.Rprofile
new file mode 100644
index 0000000000000000000000000000000000000000..81b960f5c6a8ee40840badd620f8af9743787730
--- /dev/null
+++ b/.Rprofile
@@ -0,0 +1 @@
+source("renv/activate.R")
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a58bc532478825cbbafbb3a56ae4d02396504185..9c5b63dc35831f79e71ce1230fd5ed990ff3b40b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,12 +1,31 @@
+image: rocker/verse:4.0.0
+
+variables:
+ RENV_CONFIG_REPOS_OVERRIDE: "http://cran.r-project.org"
+ RENV_PATHS_CACHE: ${CI_PROJECT_DIR}/cache
+ RENV_PATHS_LIBRARY: ${CI_PROJECT_DIR}/renv/library
+
+cache:
+ key: ${CI_JOB_NAME}
+ paths:
+ - ${RENV_PATHS_CACHE}
+ - ${RENV_PATHS_LIBRARY}
+
+before_script:
+ - Rscript -e "if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv')"
+ - Rscript -e "install.packages('showtext')"
+ - Rscript -e "renv::restore()"
+
pages:
stage: deploy
script:
+ - Rscript -e "rmarkdown::render('presentation.Rmd', output_file = 'index.html')"
- mkdir public
- - cp presentation.html public/index.html
- - cp xaringan-themer.css mycss.css public/
- - cp -r images/ libs/ public/
+ - cp index.html xaringan-themer.css mycss.css public/
+ - cp -r images/ public/
artifacts:
paths:
- public
only:
- - main
+ - test_CICD
+ interruptible: true
diff --git a/presentation.html b/presentation.html
deleted file mode 100644
index 7dc94a018faf98f4eeea7d6ebec897a5b577825c..0000000000000000000000000000000000000000
--- a/presentation.html
+++ /dev/null
@@ -1,559 +0,0 @@
-<!DOCTYPE html>
-<html lang="" xml:lang="">
- <head>
- <title>L’écosystème Git</title>
- <meta charset="utf-8" />
- <meta name="author" content="Elise Maigné" />
- <meta name="date" content="2021-11-22" />
- <script src="libs/header-attrs/header-attrs.js"></script>
- <script src="libs/htmlwidgets/htmlwidgets.js"></script>
- <script src="libs/viz/viz.js"></script>
- <link href="libs/DiagrammeR-styles/styles.css" rel="stylesheet" />
- <script src="libs/grViz-binding/grViz.js"></script>
- <script src="libs/pymjs/pym.v1.min.js"></script>
- <link rel="stylesheet" href="xaringan-themer.css" type="text/css" />
- <link rel="stylesheet" href="mycss.css" type="text/css" />
- </head>
- <body>
- <textarea id="source">
-class: center, middle, inverse, title-slide
-
-# L’écosystème Git
-## Git : fonctionnement, outils, possibilités
-### Elise Maigné
-### 2021-11-22
-
----
-
-
-
-
-
-class: center, middle
-
-# git c'est quoi ?
-<img src="images/logo_git.png", width="300" height="300">
-
----
-# Git
-
-Un système de gestion de version (voir [Différence avec SVN](#bonus)).
-
---
-
-Qui permet :
-
-- De sauvegarder ses codes (si serveur distant)
-- De conserver l'historique des fichiers (qui a fait quoi ?)
-- Visualiser les changements au cours du temps
-- Travailler à plusieurs sur le même code
-- Revenir en arrière, changer d'avis, tester une solution dans une branche séparée
-
---
-
-.center[]
-.center[]
-
----
-# Pourquoi je m'y suis pas mise avant ?
-
-- 1ers mails sur git remontent à 2013 dans mon équipe et 2014 groupe RR.
-- J'avais vraiment du mal à comprendre comment ça marchait et ce que je pouvais faire.
-- J'étais perdue au milieu de tous les termes "git/push/github/tortoise".
-- Différence de langages entre info/stat
-
---
-
-</br></br>
-
-.center[
-*"Elise j'ai mis en place un SVN, c'est facile tu synchronyse avec tortoise et tu push tes modifs"*
-
-]
-
-
----
-class: center, middle
-
-# Git et son écosystème
-<img src="images/logo_git.png", width="300" height="300">
-
----
-# Etape 1
-#### un projet (de code) que l'on veut versionner
-<center>
-<img src="images/vocab1.png", width="90%">
-</center>
-
----
-# Etape 2 (facultatif sur linux et mac)
-#### un logiciel plus sympa que la ligne de commande
-<center>
-<img src="images/vocab2.png", width="90%">
-</center>
----
-# Etape 3 (facultative)
-#### choisir un endroit pour déposer son code
-<center>
-<img src="images/vocab3.png", width="90%">
-</center>
-
----
-class: center, middle
-
-# Git fonctionnement
-## Quelques commandes de base
-
----
-# Initialisation
-
-### Sur sa machine
-1. Depuis un projet (dossier) :
-
-
-```bash
-git init
-```
-
---
-
-### Sur un serveur distant (gitlab par exemple)
-1. Création d'un projet sur une forge
-2. Clone de ce projet sur sa machine en local avec `git clone`
-
-
-```bash
-git clone git@forgemia.inra.fr:elise.maigne/2021_git.git
-```
-
---
-
-<center>
-<div id="htmlwidget-e90ffe28e8b51a154c0d" style="width:504px;height:108px;" class="grViz html-widget"></div>
-<script>HTMLWidgets.pymChild = new pym.Child();HTMLWidgets.addPostRenderHandler(function(){
- setTimeout(function(){HTMLWidgets.pymChild.sendHeight();},100);
- });</script>
-<script type="application/json" data-for="htmlwidget-e90ffe28e8b51a154c0d">{"x":{"diagram":"\n digraph {\n rankdir = LR;\n bgcolor = \"#EAEAEA\";\n edge [minlen = 3]\n node [fontsize=40 shape=cylinder style=filled color=\"#822744\" fillcolor=\"#c98399\" fontcolor=\"#822744\" width=2 height=1.5]\n local [label=local penwidth=4]\n remote [label=remote penwidth=4]\n node [fontcolor=\"#b0b0b0\" color=\"#b0b0b0\" fillcolor = \"#ededed\"]\n stage [label=stage]\n head [label=HEAD]\n local -> stage -> head -> remote\n }\n","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
-</center>
-
----
-# Un commit = un changement
-
-#### 1. On indique à git qu'il doit suivre ces fichiers et on intègre les modifications au prochain commit `git add`
-.pull-left[
-
-```bash
-git add *
-```
-]
-
-.pull-right[
-
-```bash
-git add nomFichier.R
-```
-]
-
---
-
-#### 2. On fait un commit avec `git commit`
-
-```r
-git commit -m "Ma belle modification"
-```
-
---
-
-<center>
-<div id="htmlwidget-644c432baf33e19b867a" style="width:504px;height:108px;" class="grViz html-widget"></div>
-<script>HTMLWidgets.pymChild = new pym.Child();HTMLWidgets.addPostRenderHandler(function(){
- setTimeout(function(){HTMLWidgets.pymChild.sendHeight();},100);
- });</script>
-<script type="application/json" data-for="htmlwidget-644c432baf33e19b867a">{"x":{"diagram":"\n digraph {\n rankdir = TB;\n bgcolor = \"#EAEAEA\";\n edge [minlen = 3]\n node [fontsize=40 shape=cylinder style=filled color=\"#822744\" fillcolor=\"#c98399\" fontcolor=\"#822744\" width=2 height=1.5]\n local [label=local penwidth=4]\n stage [label=stage]\n head [label=HEAD]\n node [fontcolor=\"#b0b0b0\" color=\"#b0b0b0\" fillcolor = \"#ededed\"]\n remote [label=remote penwidth=4]\n local -> stage [label = add fontsize=30 penwidth=4]\n stage -> head [label=commit fontsize=30 penwidth=4]\n head -> remote\n {rank = same; local; stage; head; remote;}; \n }","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
-</center>
-
---
-
-En pratique (chez moi - sur RStudio) :
-
-
-```bash
-git add *
-git commit -m "Ce que j'ai fait comme modif"
-```
-
----
-# Envoi des modifications au remote
-
-#### Envoi des commits en attente sur le HEAD
-
-```bash
-git push
-```
-
-<center>
-<div id="htmlwidget-b09f7c264842b595133e" style="width:504px;height:108px;" class="grViz html-widget"></div>
-<script>HTMLWidgets.pymChild = new pym.Child();HTMLWidgets.addPostRenderHandler(function(){
- setTimeout(function(){HTMLWidgets.pymChild.sendHeight();},100);
- });</script>
-<script type="application/json" data-for="htmlwidget-b09f7c264842b595133e">{"x":{"diagram":"\n digraph {\n rankdir = TB;\n bgcolor = \"#EAEAEA\";\n edge [minlen = 3]\n node [fontsize=40 shape=cylinder style=filled color=\"#822744\" fillcolor=\"#c98399\" fontcolor=\"#822744\" width=2 height=1.5]\n head [label=HEAD]\n remote [label=remote penwidth=4]\n node [fontcolor=\"#b0b0b0\" color=\"#b0b0b0\" fillcolor = \"#ededed\"]\n local [label=local penwidth=4]\n stage [label=stage]\n local -> stage -> head\n head -> remote [label = push fontsize=30 penwidth=4]\n {rank = same; local; stage; head; remote;}; \n }","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
-</center>
-
-#### Récupération de l'état du remote
-
-```bash
-git pull
-```
-
-<center>
-<div id="htmlwidget-f8325999d4dcb613a7d4" style="width:504px;height:108px;" class="grViz html-widget"></div>
-<script>HTMLWidgets.pymChild = new pym.Child();HTMLWidgets.addPostRenderHandler(function(){
- setTimeout(function(){HTMLWidgets.pymChild.sendHeight();},100);
- });</script>
-<script type="application/json" data-for="htmlwidget-f8325999d4dcb613a7d4">{"x":{"diagram":"\n digraph {\n rankdir = TB;\n bgcolor = \"#EAEAEA\";\n edge [minlen = 3]\n node [fontsize=40 shape=cylinder style=filled color=\"#822744\" fillcolor=\"#c98399\" fontcolor=\"#822744\" width=2 height=1.5]\n local [label=local penwidth=4]\n remote [label=remote penwidth=4]\n node [fontcolor=\"#b0b0b0\" color=\"#b0b0b0\" fillcolor = \"#ededed\"]\n head [label=HEAD]\n stage [label=stage]\n local -> stage -> head -> remote\n remote -> local [label = pull fontsize=30 constraint=false penwidth=4]\n {rank = same; local; stage; head; remote;}; \n }","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
-</center>
-
----
-# Processus "classique" de travail avec git
-
-#### 1. Un projet versionné sur un serveur distant
-#### 2. Je travaille comme d'habitude sur mes fichiers
-#### 3. De temps en temps = une modification en particulier :
-
-```bash
-git add *
-git commit -m "Ce que j'ai fait"
-git push
-```
-#### 4. Si on travaille à plusieurs : on récupère les modifications des autres (avant de me remettre à travailler)
-
-```bash
-git pull
-```
-
----
-# Visualiser l'historique = les commits
-
-[Exemple :](https://forgemia.inra.fr/elise.maigne/2021_package_renv/-/commits/master/)
-
-
-
----
-# Regarder les différences entre le local et un autre état
-
-
-```bash
-git diff
-git diff --staged
-git diff HEAD
-```
-
-
----
-# Les fichiers git
-
-
-
-- Un dossier `.git` : contient tous les fichiers de gestion de version (on ne va jamais dedans).
-
---
-
-- Un fichier `.gitignore` : permet d'exclure certains fichiers ou dossiers des commits.
-
---
-
-Exemple de contenu d'un `.gitignore`:
-
-
-```bash
-.Rproj.user
-.Rhistory
-.RData
-.Ruserdata
-/data
-```
-
-En particulier on ne commite pas les données.
-
----
-# Les branches
-
-La branche par défaut est **main** (feu **master**).
-
-Il est possible de créer de nouvelles branches, pour tester une autre direction, ajouter une fonctionalité.
-
---
-
-.pull-left[
-Projet d'application à plusieurs, 1 branche = 1 fonctionalité, plusieurs fonctionalités en même temps.
-<div id="htmlwidget-5f853ca1817e5cd22643" style="width:504px;height:288px;" class="grViz html-widget"></div>
-<script>HTMLWidgets.pymChild = new pym.Child();HTMLWidgets.addPostRenderHandler(function(){
- setTimeout(function(){HTMLWidgets.pymChild.sendHeight();},100);
- });</script>
-<script type="application/json" data-for="htmlwidget-5f853ca1817e5cd22643">{"x":{"diagram":"\ndigraph {\n\trankdir=\"LR\";\n\tbgcolor=\"transparent\";\n\tnode[width=0.15, height=0.15, shape=point, color=\"#822744\"];\n\tedge[weight=2, arrowhead=none, color=\"#822744\"];\n\tnode[group=master];\n\t1 -> 2 -> 3 -> 4 -> 5;\n\tnode[group=branch];\n\t2 -> 6 -> 7 -> 4;\n\tnode[group=branch];\n\t2 -> 8 -> 9 -> 10;\n\tnode[group=branch];\n\t2 -> 11 -> 12 -> 13 -> 14 -> 15;\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
-]
-
---
-
-.pull-right[
-Développement d'un package R : une branche correspond à une modification majeure du code. La branche main est toujours supposée tourner.
-<div id="htmlwidget-f73e94314218f55a901c" style="width:504px;height:288px;" class="grViz html-widget"></div>
-<script>HTMLWidgets.pymChild = new pym.Child();HTMLWidgets.addPostRenderHandler(function(){
- setTimeout(function(){HTMLWidgets.pymChild.sendHeight();},100);
- });</script>
-<script type="application/json" data-for="htmlwidget-f73e94314218f55a901c">{"x":{"diagram":"\ndigraph {\n\trankdir=\"LR\";\n\tbgcolor=\"transparent\";\n\tnode[width=0.15, height=0.15, shape=point, color=\"#822744\"];\n\tedge[weight=2, arrowhead=none, color=\"#822744\"];\n\tnode[group=master];\n\t1 -> 2 -> 3 -> 4 -> 5 -> 6 -> 7 -> 8;\n\tnode[group=branch];\n\t2 -> 9 -> 10 -> 11 -> 3;\n\tnode[group=branch];\n\t5 -> 12 -> 13 -> 14 -> 6;\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
-]
-
----
-# Les branches
-
-#### Création d'une branche
-
-
-```bash
-git branch mabranche
-```
-
-#### Changer de branche
-
-
-```bash
-git checkout mabranche
-git checkout monautrebranche
-```
-
-On ne peut changer de branche uniquement si toutes les modifications (des fichiers suivis) sont commitées.
-
----
-# Les branches
-#### Fusionner des branches
-
-```bash
-git checkout mabranche
-git merge main
-```
-
-#### Les conflits
-Si un fichier est modifié 2 fois au même endroit.
-
-```bash
-<<<<<<< HEAD:fichier.R
-J'avais mis ça avant dans ma (vieille) branche
-======
-Et maintenant j'ai ça, je ne suis qu'un logiciel je ne sais pas quoi faire
->>>>>>> iss53:fichier.R
-```
-
-Il faut choisir entre les 2 versions pour pouvoir finaliser le merge
-
----
-# Possibilités (pour des statisticiens)
-
-#### Publication/partage du code
-
---
-
-#### gitlab pages
-Faire des sites webs très facilement ! avec juste un fichier yml à la racine du dépôt
-
-Exemple : j'ai un projet qui crée un fichier html à l'aide de Rmarkdown. --> Si j'active gitlab pages je peux en faire un site web.
-(exemple : https://elise.maigne.pages.mia.inra.fr/2021_git/index.html)
-
---
-
-#### CI/CD (integration continue)
-Par exemple compiler ses Rmd automatiquement.
-Faire des tests automatiques.
-
---
-
-#### Enseignement
-Un projet "principal" forké (`git fork`) par les étudiants qui partent de la même copie et faire leurs propres modifications, indépendemment les un des autres.
-
----
-# Vocabulaire
-
-.pull-left[
-#### Au démarrage
-- `git clone`
-- `git fork`
-
-#### Faire des modifications
-- `git add` + `git commit -m "Message'`
-- `git push`
-- `git pull`
-
-#### Visualiser
-- `git diff`
-- `git blame`
-]
-
-.pull-right[
-#### Branches
-- `git branch`
-- `git checkout`
-- `git merge`
-- `git rebase`
-
-#### Revenir en arrière
-- `git revert`
-
-#### Savoir où on en est
-- `git status`
-...
-]
-
----
-# des questions ?
-
-Lien vers le dépôt de cette présentation :
-https://forgemia.inra.fr/elise.maigne/2021_git/
-
-#### Références
-
-Merci aux sites suivants :
-- https://perso.liris.cnrs.fr/pierre-antoine.champin/enseignement/intro-git/
-- http://rogerdudler.github.io/git-guide/index.fr.html
-- Doc de la forgemia : https://forgemia.inra.fr/adminforgemia/doc-public/-/wikis/GIT-sous-Windows
-- branches git en graphviz : https://correl.phoenixinquis.net/2015/07/12/git-graphs.html
-
----
-name: bonus
-# Bonus - Différence SVN/Git ()
-#### SVN
-
-SVN est un système de contrôle de version **centralisé**. Vous avez un serveur qui contient votre référentiel de code. Vous pouvez en extraire du code sur votre ordinateur local, y apporter des modifications locales, puis les renvoyer dans le référentiel central.
-
-Votre copie du code correspond généralement à ce que vous avez extrait et à la dernière version. De nombreuses opérations nécessiteront une connexion réseau au référentiel central.
-
-#### Git
-
-Git est un système de contrôle de version **décentralisé**. Chaque participant a un clone de l’ensemble du référentiel. Il est utilisé pour suivre les changements dans le code source.
-
-La plupart des opérations ne nécessitent pas de connexion réseau, car elles ne travaillent que sur votre clone du référentiel.
-
-*Source : https://waytolearnx.com/2019/03/difference-entre-git-et-svn.html*
- </textarea>
-<style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
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diff --git a/renv.lock b/renv.lock
new file mode 100644
index 0000000000000000000000000000000000000000..7108b7dcd960ffac0a8a0f288208997f5765bf88
--- /dev/null
+++ b/renv.lock
@@ -0,0 +1,622 @@
+{
+ "R": {
+ "Version": "4.0.3",
+ "Repositories": [
+ {
+ "Name": "CRAN",
+ "URL": "https://cran.rstudio.com"
+ }
+ ]
+ },
+ "Packages": {
+ "BH": {
+ "Package": "BH",
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+ "Repository": "CRAN",
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+ "Repository": "CRAN",
+ "Hash": "abea3384649ef37f60ef51ce002f3547"
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+ "Repository": "CRAN",
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+ "Repository": "CRAN",
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+ "Repository": "CRAN",
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+ "Repository": "CRAN",
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+ "Repository": "CRAN",
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+ "Repository": "CRAN",
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+ "Repository": "CRAN",
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+ },
+ "highr": {
+ "Package": "highr",
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+ "Repository": "CRAN",
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+ },
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+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca"
+ },
+ "htmltools": {
+ "Package": "htmltools",
+ "Version": "0.5.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "526c484233f42522278ab06fb185cb26"
+ },
+ "htmlwidgets": {
+ "Package": "htmlwidgets",
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+ "Repository": "CRAN",
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+ "Repository": "CRAN",
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+ "Hash": "611f9a55ad32ccfa17ccbd77be7a2804"
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+ "Repository": "CRAN",
+ "Hash": "53647fb507373700028b2ce6cd30751a"
+ },
+ "jsonlite": {
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+ "Repository": "CRAN",
+ "Hash": "98138e0994d41508c7a6b84a0600cfcb"
+ },
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+ "Package": "knitr",
+ "Version": "1.30",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "eed7ee0d02eee88d53881cdc92457c62"
+ },
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+ "Repository": "CRAN",
+ "Hash": "3d5108641f47470611a32d0bdf357a72"
+ },
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+ "Version": "1.1.0.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "d0a62b247165aabf397fded504660d8a"
+ },
+ "lattice": {
+ "Package": "lattice",
+ "Version": "0.20-41",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "fbd9285028b0263d76d18c95ae51a53d"
+ },
+ "lifecycle": {
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+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "a6b6d352e3ed897373ab19d8395c98d0"
+ },
+ "magrittr": {
+ "Package": "magrittr",
+ "Version": "2.0.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "41287f1ac7d28a92f0a286ed507928d3"
+ },
+ "markdown": {
+ "Package": "markdown",
+ "Version": "1.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "61e4a10781dd00d7d81dd06ca9b94e95"
+ },
+ "mgcv": {
+ "Package": "mgcv",
+ "Version": "1.8-33",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "eb7b6439bc6d812eed2cddba5edc6be3"
+ },
+ "mime": {
+ "Package": "mime",
+ "Version": "0.9",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "e87a35ec73b157552814869f45a63aa3"
+ },
+ "munsell": {
+ "Package": "munsell",
+ "Version": "0.5.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "6dfe8bf774944bd5595785e3229d8771"
+ },
+ "nlme": {
+ "Package": "nlme",
+ "Version": "3.1-151",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "42c8ba2b6a32a6bf0874e93e3bd86a43"
+ },
+ "pillar": {
+ "Package": "pillar",
+ "Version": "1.6.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "3323bc1a0988d63b5c65771ba0d3935d"
+ },
+ "pkgconfig": {
+ "Package": "pkgconfig",
+ "Version": "2.0.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "01f28d4278f15c76cddbea05899c5d6f"
+ },
+ "pkgload": {
+ "Package": "pkgload",
+ "Version": "1.2.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "53139eedf68b98eecd5289664969c3f2"
+ },
+ "praise": {
+ "Package": "praise",
+ "Version": "1.0.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "a555924add98c99d2f411e37e7d25e9f"
+ },
+ "processx": {
+ "Package": "processx",
+ "Version": "3.5.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "0cbca2bc4d16525d009c4dbba156b37c"
+ },
+ "promises": {
+ "Package": "promises",
+ "Version": "1.1.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "a8730dcbdd19f9047774909f0ec214a4"
+ },
+ "ps": {
+ "Package": "ps",
+ "Version": "1.5.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "ebaed51a03411fd5cfc1e12d9079b353"
+ },
+ "purrr": {
+ "Package": "purrr",
+ "Version": "0.3.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "97def703420c8ab10d8f0e6c72101e02"
+ },
+ "readr": {
+ "Package": "readr",
+ "Version": "1.4.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "2639976851f71f330264a9c9c3d43a61"
+ },
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+ "Package": "rematch2",
+ "Version": "2.1.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "76c9e04c712a05848ae7a23d2f170a40"
+ },
+ "renv": {
+ "Package": "renv",
+ "Version": "0.12.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "b5510c50c7f31d453c385c7b460af2b9"
+ },
+ "rlang": {
+ "Package": "rlang",
+ "Version": "0.4.11",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "515f341d3affe0de9e4a7f762efb0456"
+ },
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+ "Package": "rmarkdown",
+ "Version": "2.6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "bc4bac38960b446c183957bfd563e763"
+ },
+ "rprojroot": {
+ "Package": "rprojroot",
+ "Version": "2.0.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "249d8cd1e74a8f6a26194a91b47f21d1"
+ },
+ "rstudioapi": {
+ "Package": "rstudioapi",
+ "Version": "0.13",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "06c85365a03fdaf699966cc1d3cf53ea"
+ },
+ "scales": {
+ "Package": "scales",
+ "Version": "1.1.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "6f76f71042411426ec8df6c54f34e6dd"
+ },
+ "servr": {
+ "Package": "servr",
+ "Version": "0.21",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "48d1289a847c801b3f0e76fc619fa65d"
+ },
+ "stringi": {
+ "Package": "stringi",
+ "Version": "1.5.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "a063ebea753c92910a4cca7b18bc1f05"
+ },
+ "stringr": {
+ "Package": "stringr",
+ "Version": "1.4.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "0759e6b6c0957edb1311028a49a35e76"
+ },
+ "testthat": {
+ "Package": "testthat",
+ "Version": "3.1.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "89e55ebe4f5ddd7f43f0f2bc6d96c950"
+ },
+ "tibble": {
+ "Package": "tibble",
+ "Version": "3.1.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "36eb05ad4cfdfeaa56f5a9b2a1311efd"
+ },
+ "tidyr": {
+ "Package": "tidyr",
+ "Version": "1.1.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "c8fbdbd9fcac223d6c6fe8e406f368e1"
+ },
+ "tidyselect": {
+ "Package": "tidyselect",
+ "Version": "1.1.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "6ea435c354e8448819627cf686f66e0a"
+ },
+ "tinytex": {
+ "Package": "tinytex",
+ "Version": "0.28",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "ff73961a77fba606fbf944dc3468e5b9"
+ },
+ "utf8": {
+ "Package": "utf8",
+ "Version": "1.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7"
+ },
+ "vctrs": {
+ "Package": "vctrs",
+ "Version": "0.3.8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "ecf749a1b39ea72bd9b51b76292261f1"
+ },
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+ "Package": "viridis",
+ "Version": "0.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "6f6b49e5b3b5ee5a6d0c28bf1b4b9eb3"
+ },
+ "viridisLite": {
+ "Package": "viridisLite",
+ "Version": "0.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "ce4f6271baa94776db692f1cb2055bee"
+ },
+ "visNetwork": {
+ "Package": "visNetwork",
+ "Version": "2.0.9",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "12545f2acf49d1d346d075580122d89c"
+ },
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+ "Package": "waldo",
+ "Version": "0.3.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "ad8cfff5694ac5b3c354f8f2044bd976"
+ },
+ "whisker": {
+ "Package": "whisker",
+ "Version": "0.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "ca970b96d894e90397ed20637a0c1bbe"
+ },
+ "widgetframe": {
+ "Package": "widgetframe",
+ "Version": "0.3.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "0ee89e6cb58182d39b30a5b506e04808"
+ },
+ "withr": {
+ "Package": "withr",
+ "Version": "2.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "ad03909b44677f930fa156d47d7a3aeb"
+ },
+ "xaringan": {
+ "Package": "xaringan",
+ "Version": "0.19",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "0d0e49333c8a4841db419aea628ac16f"
+ },
+ "xaringanthemer": {
+ "Package": "xaringanthemer",
+ "Version": "0.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "402482b841f115baa6250a3fc49f802f"
+ },
+ "xfun": {
+ "Package": "xfun",
+ "Version": "0.24",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "88cdb9779a657ad80ad942245fffba31"
+ },
+ "yaml": {
+ "Package": "yaml",
+ "Version": "2.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "2826c5d9efb0a88f657c7a679c7106db"
+ }
+ }
+}
diff --git a/renv/.gitignore b/renv/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..62e60ad4a77df42753a26ab8412dfc91898bf4db
--- /dev/null
+++ b/renv/.gitignore
@@ -0,0 +1,4 @@
+library/
+lock/
+python/
+staging/
diff --git a/renv/activate.R b/renv/activate.R
new file mode 100644
index 0000000000000000000000000000000000000000..6841a967e3636f27ef4aa1b5d5612ba886a225d8
--- /dev/null
+++ b/renv/activate.R
@@ -0,0 +1,400 @@
+
+local({
+
+ # the requested version of renv
+ version <- "0.12.3"
+
+ # the project directory
+ project <- getwd()
+
+ # avoid recursion
+ if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA)))
+ return(invisible(TRUE))
+
+ # signal that we're loading renv during R startup
+ Sys.setenv("RENV_R_INITIALIZING" = "true")
+ on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE)
+
+ # signal that we've consented to use renv
+ options(renv.consent = TRUE)
+
+ # load the 'utils' package eagerly -- this ensures that renv shims, which
+ # mask 'utils' packages, will come first on the search path
+ library(utils, lib.loc = .Library)
+
+ # check to see if renv has already been loaded
+ if ("renv" %in% loadedNamespaces()) {
+
+ # if renv has already been loaded, and it's the requested version of renv,
+ # nothing to do
+ spec <- .getNamespaceInfo(.getNamespace("renv"), "spec")
+ if (identical(spec[["version"]], version))
+ return(invisible(TRUE))
+
+ # otherwise, unload and attempt to load the correct version of renv
+ unloadNamespace("renv")
+
+ }
+
+ # load bootstrap tools
+ bootstrap <- function(version, library) {
+
+ # read repos (respecting override if set)
+ repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+ if (is.na(repos))
+ repos <- getOption("repos")
+
+ # fix up repos
+ on.exit(options(repos = repos), add = TRUE)
+ repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
+ options(repos = repos)
+
+ # attempt to download renv
+ tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
+ if (inherits(tarball, "error"))
+ stop("failed to download renv ", version)
+
+ # now attempt to install
+ status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity)
+ if (inherits(status, "error"))
+ stop("failed to install renv ", version)
+
+ }
+
+ renv_bootstrap_download_impl <- function(url, destfile) {
+
+ mode <- "wb"
+
+ # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+ fixup <-
+ Sys.info()[["sysname"]] == "Windows" &&
+ substring(url, 1L, 5L) == "file:"
+
+ if (fixup)
+ mode <- "w+b"
+
+ download.file(
+ url = url,
+ destfile = destfile,
+ mode = mode,
+ quiet = TRUE
+ )
+
+ }
+
+ renv_bootstrap_download <- function(version) {
+
+ # if the renv version number has 4 components, assume it must
+ # be retrieved via github
+ nv <- numeric_version(version)
+ components <- unclass(nv)[[1]]
+
+ methods <- if (length(components) == 4L) {
+ list(renv_bootstrap_download_github)
+ } else {
+ list(
+ renv_bootstrap_download_cran_latest,
+ renv_bootstrap_download_cran_archive
+ )
+ }
+
+ for (method in methods) {
+ path <- tryCatch(method(version), error = identity)
+ if (is.character(path) && file.exists(path))
+ return(path)
+ }
+
+ stop("failed to download renv ", version)
+
+ }
+
+ renv_bootstrap_download_cran_latest <- function(version) {
+
+ repos <- renv_bootstrap_download_cran_latest_find(version)
+
+ message("* Downloading renv ", version, " from CRAN ... ", appendLF = FALSE)
+
+ info <- tryCatch(
+ download.packages("renv", repos = repos, destdir = tempdir(), quiet = TRUE),
+ condition = identity
+ )
+
+ if (inherits(info, "condition")) {
+ message("FAILED")
+ return(FALSE)
+ }
+
+ message("OK")
+ info[1, 2]
+
+ }
+
+ renv_bootstrap_download_cran_latest_find <- function(version) {
+
+ # check for renv on CRAN matching this version
+ all <- unique(c(
+ getOption("repos"),
+ getOption("renv.bootstrap.repos", default = "https://cloud.r-project.org")
+ ))
+
+ for (repos in all) {
+
+ db <- tryCatch(
+ as.data.frame(available.packages(repos = repos), stringsAsFactors = FALSE),
+ error = identity
+ )
+
+ if (inherits(db, "error"))
+ next
+
+ entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+ if (nrow(entry) == 0)
+ next
+
+ return(repos)
+
+ }
+
+ fmt <- "renv %s is not available from your declared package repositories"
+ stop(sprintf(fmt, version))
+
+ }
+
+ renv_bootstrap_download_cran_archive <- function(version) {
+
+ name <- sprintf("renv_%s.tar.gz", version)
+ repos <- getOption("repos")
+ urls <- file.path(repos, "src/contrib/Archive/renv", name)
+ destfile <- file.path(tempdir(), name)
+
+ message("* Downloading renv ", version, " from CRAN archive ... ", appendLF = FALSE)
+
+ for (url in urls) {
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (identical(status, 0L)) {
+ message("OK")
+ return(destfile)
+ }
+
+ }
+
+ message("FAILED")
+ return(FALSE)
+
+ }
+
+ renv_bootstrap_download_github <- function(version) {
+
+ enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
+ if (!identical(enabled, "TRUE"))
+ return(FALSE)
+
+ # prepare download options
+ pat <- Sys.getenv("GITHUB_PAT")
+ if (nzchar(Sys.which("curl")) && nzchar(pat)) {
+ fmt <- "--location --fail --header \"Authorization: token %s\""
+ extra <- sprintf(fmt, pat)
+ saved <- options("download.file.method", "download.file.extra")
+ options(download.file.method = "curl", download.file.extra = extra)
+ on.exit(do.call(base::options, saved), add = TRUE)
+ } else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
+ fmt <- "--header=\"Authorization: token %s\""
+ extra <- sprintf(fmt, pat)
+ saved <- options("download.file.method", "download.file.extra")
+ options(download.file.method = "wget", download.file.extra = extra)
+ on.exit(do.call(base::options, saved), add = TRUE)
+ }
+
+ message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE)
+
+ url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
+ name <- sprintf("renv_%s.tar.gz", version)
+ destfile <- file.path(tempdir(), name)
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (!identical(status, 0L)) {
+ message("FAILED")
+ return(FALSE)
+ }
+
+ message("Done!")
+ return(destfile)
+
+ }
+
+ renv_bootstrap_install <- function(version, tarball, library) {
+
+ # attempt to install it into project library
+ message("* Installing renv ", version, " ... ", appendLF = FALSE)
+ dir.create(library, showWarnings = FALSE, recursive = TRUE)
+
+ # invoke using system2 so we can capture and report output
+ bin <- R.home("bin")
+ exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
+ r <- file.path(bin, exe)
+ args <- c("--vanilla", "CMD", "INSTALL", "-l", shQuote(library), shQuote(tarball))
+ output <- system2(r, args, stdout = TRUE, stderr = TRUE)
+ message("Done!")
+
+ # check for successful install
+ status <- attr(output, "status")
+ if (is.numeric(status) && !identical(status, 0L)) {
+ header <- "Error installing renv:"
+ lines <- paste(rep.int("=", nchar(header)), collapse = "")
+ text <- c(header, lines, output)
+ writeLines(text, con = stderr())
+ }
+
+ status
+
+ }
+
+ renv_bootstrap_prefix <- function() {
+
+ # construct version prefix
+ version <- paste(R.version$major, R.version$minor, sep = ".")
+ prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
+
+ # include SVN revision for development versions of R
+ # (to avoid sharing platform-specific artefacts with released versions of R)
+ devel <-
+ identical(R.version[["status"]], "Under development (unstable)") ||
+ identical(R.version[["nickname"]], "Unsuffered Consequences")
+
+ if (devel)
+ prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
+
+ # build list of path components
+ components <- c(prefix, R.version$platform)
+
+ # include prefix if provided by user
+ prefix <- Sys.getenv("RENV_PATHS_PREFIX")
+ if (nzchar(prefix))
+ components <- c(prefix, components)
+
+ # build prefix
+ paste(components, collapse = "/")
+
+ }
+
+ renv_bootstrap_library_root <- function(project) {
+
+ path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+ if (!is.na(path))
+ return(path)
+
+ path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+ if (!is.na(path)) {
+ id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
+ name <- paste(basename(project), id, sep = "-")
+ return(file.path(path, name))
+ }
+
+ file.path(project, "renv/library")
+
+ }
+
+ renv_bootstrap_validate_version <- function(version) {
+
+ loadedversion <- utils::packageDescription("renv", fields = "Version")
+ if (version == loadedversion)
+ return(TRUE)
+
+ # assume four-component versions are from GitHub; three-component
+ # versions are from CRAN
+ components <- strsplit(loadedversion, "[.-]")[[1]]
+ remote <- if (length(components) == 4L)
+ paste("rstudio/renv", loadedversion, sep = "@")
+ else
+ paste("renv", loadedversion, sep = "@")
+
+ fmt <- paste(
+ "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
+ "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
+ "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
+ sep = "\n"
+ )
+
+ msg <- sprintf(fmt, loadedversion, version, remote)
+ warning(msg, call. = FALSE)
+
+ FALSE
+
+ }
+
+ renv_bootstrap_hash_text <- function(text) {
+
+ hashfile <- tempfile("renv-hash-")
+ on.exit(unlink(hashfile), add = TRUE)
+
+ writeLines(text, con = hashfile)
+ tools::md5sum(hashfile)
+
+ }
+
+ renv_bootstrap_load <- function(project, libpath, version) {
+
+ # try to load renv from the project library
+ if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
+ return(FALSE)
+
+ # warn if the version of renv loaded does not match
+ renv_bootstrap_validate_version(version)
+
+ # load the project
+ renv::load(project)
+
+ TRUE
+
+ }
+
+ # construct path to library root
+ root <- renv_bootstrap_library_root(project)
+
+ # construct library prefix for platform
+ prefix <- renv_bootstrap_prefix()
+
+ # construct full libpath
+ libpath <- file.path(root, prefix)
+
+ # attempt to load
+ if (renv_bootstrap_load(project, libpath, version))
+ return(TRUE)
+
+ # load failed; inform user we're about to bootstrap
+ prefix <- paste("# Bootstrapping renv", version)
+ postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "")
+ header <- paste(prefix, postfix)
+ message(header)
+
+ # perform bootstrap
+ bootstrap(version, libpath)
+
+ # exit early if we're just testing bootstrap
+ if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+ return(TRUE)
+
+ # try again to load
+ if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
+ message("* Successfully installed and loaded renv ", version, ".")
+ return(renv::load())
+ }
+
+ # failed to download or load renv; warn the user
+ msg <- c(
+ "Failed to find an renv installation: the project will not be loaded.",
+ "Use `renv::activate()` to re-initialize the project."
+ )
+
+ warning(paste(msg, collapse = "\n"), call. = FALSE)
+
+})
diff --git a/renv/settings.dcf b/renv/settings.dcf
new file mode 100644
index 0000000000000000000000000000000000000000..bf722e81883bdf3f109d8f4e8d1c0fcbda61815f
--- /dev/null
+++ b/renv/settings.dcf
@@ -0,0 +1,7 @@
+external.libraries:
+ignored.packages:
+package.dependency.fields: Imports, Depends, LinkingTo
+r.version:
+snapshot.type: implicit
+use.cache: TRUE
+vcs.ignore.library: TRUE