Rstudio and Git setup instructions

Notes.Rmd

@@ -1,28 +1,116 @@
 ---
-title: "Show Notes"
 output: html_document
 editor_options:
   chunk_output_type: console
 ---
+# Show Notes
 
-# Navigate R Studio and Setup Project
+## Setup Repository in Gitea
+
+* Navigate to Gitea https://gitea-i2-cere-cloud.nrp-nautilus.io/
+  * This is a teaching environment and will be destroyed.
+
+## Navigate R Studio and Setup Project
 
   * Open RStudio
-  * Create a new "New Project" in `~/work`
-    * If you use Git (you should) use "New Project" -> "Version Control" -> "Git".
-    * "File" -> "New Project" -> "New Directory" -> "New Project" -> "work/skc-workshop". Projects and data must be saved in `~/work` otherwise they will be lost.  Use a good name such as "skc-workshop"
-  * Turn off saving `.RData` in workspace
-    * "Tools" -> "Global Options" -> "General" (already selected) -> "Basic" (already selected) -> Under "Workspace" turn off "Restore `.RData` …" and set "Save workspace to `.RData` …" to "Never"
-  * Create a new "R Markdown" File
-    * "File" -> "New File" -> "R Markdown" -> "Create Empty Document" (bottom left button).
-    * Save file (cmd-s for Mac, ctrl-s for Windows/Linux) and use a good name such as "R-Ecology-Workshop" (it will add the `.Rmd` extension)
+  * Create a new "New Project" in `~/work` with "Git"
+    * Projects and data must be saved in `~/work` otherwise they will be lost.  
+    * Use a good name such as "$USER-workshop"
+    * If you use Git (you are) use "New Project" -> "Version Control" -> "Git"
+      * Repository URL: your "https" repository value
+      * Project directory name: leave blank
+      * Create project as a subdirectory of: ~/work (click "Browse" to change)
+      * Click "Create Project"
+  * Turn off saving `.RData` in project (not workspace)
+    * It is not good to save data, especially in git.
+    * "Tools" -> "Project Options" 
+      * Under "Workspace" 
+        * Set "Restore .RData into workspace at startup" to "No"
+        * Set "Save workspace to .RData on exit" to "No"
+        * Set "Always save histroy" to "No"
+        * Click "Ok"
+  * Setup Git
+    * This needs to be done only once when you create a "new project".
+    * Click on the "Terminal"
+      * Verify that you are in your project folder `~/work/...`
+      * Run (note the quotes!) the following in the terminal:
+```{bash eval=FALSE}
+git config credential.helper cache
+git config user.name "First Last"
+git config user.email "first_last@skc.edu"
+git config --local --list
+```
+  * Create a new "R Markdown" file
+    * "File" -> "New File" -> "R Markdown" -> Click "Create Empty Document" (bottom left button).
+    * Save file ("R-Ecology"): Click the "disk" or press `cmd-s` for Mac, `ctrl-s` for Windows/Linux.
+      * Enter a good file name such as "R-Ecology" (it will add the `.Rmd` extension)
   * Write, Setup, and View RMarkdown
-    * Write title `# RStudio` 
+    * Write title `# RStudio Workshop` 
+    * Write some text (your name)
     * "Settings (gear)" -> "Preview in Viewer Pane"
     * "Settings (gear)" -> "Chunk Output in Console"
     * Save file
     * Knit (Knit to HTML)
     * Optionally set "Knit on Save" - (runs entire notebook)
+    * Verify output
+
+## Save your work (with Git)
+
+  * Access *Git menu* via "Tools" -> "Version Control"; or the "GIT" dropdown on the toolbar.
+  * Diff: Check what you have done with (under the Git Menu)
+    * "Diff ..." (you may need to click it twice?!)
+    * Ignore html files:
+      * right click `R-Ecology.html` and select ignore - change to `*.html`
+    * Add files:
+      * Verify changes
+      * Click the "Staged" box to add them
+    * Commit message
+      * Title (no period) and less than 50 characters
+      * Be descriptive on what you did - not "update"
+      * Should be "one" thing.
+      * Blank line then a description, wrapped at 72 characters (optional).
+      * Blank line followed by a list (optional)
+      * List starts with a '-' character (no space)
+    * Press "Commit" and "Close"
+    * Push
+      * Enter the username and password for the Git repo (not your account)
+    * Pull:
+      * Make sure that you get "Already up to date."
+      * Should not ask for password again.
+
+## Visual Setup
+
+  * Move Terminal and Console pane to the right
+    * "View" -> Panes -> Console on Right
+
+## Quit Envrionment
+
+  * Git Commit: (see above)
+  * Shutdown RStudio: "File" -> "Quit Session"
+  * Shutdown Jupyter: "File" -> "Hub Control Panel" -> "Stop My Server"
+  * Close all Jupyter and RStudio windows
+
+## Start Envrionment after setup
+
+  * Navigate to https://ci.skc.edu/ and click "Login to OSG Jupyter Notebook"
+  * Start Jupyter: Select "Data Science with RStudio" and click "Start"
+  * Start RStudio: 
+    * In the Launcher (should be open, otherwise open with "File" -> "New Launcher") 
+    * Click "RStudio" (under "Notebook" section)
+  * Open Project: "File" -> "Open Project" -> navigate to `work/project-name/project-name.Rproj` and click open
+  * Git Pull: "Tools" -> "Version Control" -> "Pull Branches"
+    * Enter git user and password
+
+## References and Resources
+
+Configure username, email address, and enable password saving for your new project. Run in terminal once after the project has been created. Note the use of double quotes.
+
+```{bash eval=FALSE}
+git config credential.helper cache
+git config user.name "First Last"
+git config user.email "first_last@skc.edu"
+git config --local --list
+```
 
 Resources:
 

ReadMe.md

@@ -14,9 +14,21 @@ Lessons (Day 2):
   * https://datacarpentry.org/R-ecology-lesson-alternative/working-with-data.html
   * https://datacarpentry.org/R-ecology-lesson/05-r-and-databases.html
 
-
 ## Hints
 
+Commands to setup Git with RStudio. Note the quotes and be sure to
+replace them with the correct values.
+
+```bash
+git config credential.helper cache
+git config user.name "First Last"
+git config user.email "first_last@skc.edu"
+git config --local --list
+```
+
+Don't forget to disable `.RData` restore and save in your project settings 
+("Tools" -> "Project Settings" and set to "No")
+
 RStudio keyboard:
 
   * cmd-r/ctrl-r - Run a line and move to the next

prep/Jupyter.ipynb

@@ -0,0 +1,37 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "16ae758a-5fb7-4037-bdf3-601b689440d7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Jupyter\n",
+    "\n",
+    "\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

prep/Instructor.Rmd → prep/RStudio.Rmd

@@ -32,7 +32,7 @@ Project should use a "R Project". Load by clicking on the `.RProj` file.
 
 Setup Git
 
-```{bash}
+```{bash eval=FALSE}
 git config color.ui auto
 git config pull.ff only
 git config push.default simple