From a878ea90860e62a2bc34aaa94545f5cd66dbcfce Mon Sep 17 00:00:00 2001 From: Timothy Middelkoop Date: Wed, 29 May 2024 21:15:30 +0000 Subject: [PATCH] Add Gitea instructions --- Notes.md | 138 +++++++++++++++++++++++++++++++++++++++--------------- ReadMe.md | 38 ++++++--------- 2 files changed, 114 insertions(+), 62 deletions(-) diff --git a/Notes.md b/Notes.md index 80fcc97..3978a6c 100644 --- a/Notes.md +++ b/Notes.md @@ -2,34 +2,61 @@ ## 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 to Gitea: + * https://gitea-i2-cere-cloud.nrp-nautilus.io/ + * This is a teaching environment and will be destroyed. + * Sign in: + * Click on Sign In + * Click on "Sign in with Google" + * Authorize Google Account + * Register New Account: + * Username: Enter username (your_name), which is the same as the first part of your your_name@skc.edu email address. + * Click on "Complete Account" (you may need to click on "Leave") + * Set a password: + * Click your avitar (colorful box in the top right) for a dropdown box + * Click "Settings" in the dropdown box + * Click on "Account" tab on the left + * **DO NOT USE YOUR SKC PASSWORD HERE!** + * Enter "New Password" and "Confirm New password" + * Click "Update Password" + * Create new repo: + * Click the"+" in the upper right and select "+ New Repository" + * Repository Name: skc-your_name + * Make repository private (Visiblity): check the checkbox + * Initialize Repository: check the checkbox + * Click "Create Repository" + * Navigate to your repo: + * Click the green teacup in the top right corner + * Click on your repository name in the list on the right under "Repositories" + * Copy your repository address to your clipboard: + * Navigate to your repository + * Select "HTTPS" (already selected) + * Click on the copy button (⧉) to the right of the repository address next to the "HTTPS" box (to the left of the 3 dots). ## Navigate R Studio and Setup Project * Open RStudio * 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 + * Note: Projects and data must be saved in `~/work` otherwise they will be lost. + * Select "Version Control" -> "Git" + * Repository URL: your "https" repository value (see instructions above) * 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" + * 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} + * Run (note the quotes and replace with your information) the following in the terminal: +``` git config credential.helper cache git config user.name "First Last" git config user.email "first_last@skc.edu" @@ -37,42 +64,58 @@ 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. + * 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, Configure, and View RMarkdown * Write title `# RStudio Workshop` * Write some text (your name) * Configure rendering - * "Settings (gear)" -> "Preview in Viewer Pane" - * "Settings (gear)" -> "Chunk Output in Console" + * "Settings (gear in file tab toolbar)" -> "Preview in Viewer Pane" + * "Settings (gear in file tab toolbar)" -> "Chunk Output in Console" * Save file * Knit (Knit to HTML) - * Optionally set "Knit on Save" - (runs entire notebook) + * 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 (optional): - * Right click `R-Ecology.html` and select ignore - change to `*.html` - * Add files: - * Verify changes + * **Make sure all files are saved!** + * Unsaved files will have a star at the end of the file name in the tab + * Access the *Git menu* + * Use "Tools" -> "Version Control"; + * or the "GIT" dropdown in the main RStudio toolbar. + * Select "Commit" in the *Git menu*: + * **Verify the work you have done** + * Click the name of each file and see the changes + * Check for unwanted files (secrets)! + * Ignore html files (optional): + * Right click `R-Ecology.html` and select ignore + * (optionally) change to `*.html` + * Click "Save" + * Add files (stage): * 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). + * Make sure a "check" not a square box + * Add a "Commit message": + * Note: Commits should be "one" thing. + * Title (no period) + * Be descriptive on what you did - not "update" + * less than 50 characters + * Example: "Create a new RStudio project" + * Blank line then a description, + * wrap at 72 characters (optional). * Blank line followed by a list (optional) - * List starts with a '-' character (no space) - * Press "Commit" and "Close" - * Push + * List starts with a '-' character (no space) + * Press "Commit" and "Close" + * "Push" to repository (top right of Git window): * 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. + * Make sure there is not an error + * Verify push + * Click "Push" again and make sure it says "Everyting up-to-date" + * Close + * Verify commit: + * Click "Commit" under the *Git menu* + * There should be no files in the "Staged" list on the left. ## Visual Setup @@ -96,18 +139,37 @@ git config --local --list * 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 + * Watch for errors + * Verify Pull: + * "Pull" again and it should say "Already up to date." ## References and Resources +RStudio keyboard shortcuts: + + * cmd-r/ctrl-r - Run a line and move to the next + * option-r/alt-r - Run a single line and stay on that line + +Git Configuration: + 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} +```bash git config credential.helper cache git config user.name "First Last" git config user.email "first_last@skc.edu" git config --local --list ``` - + +Git Status: + +Check the status of your project with the remote repository. In a terminal run: +```bash +git fetch +git status +``` + Resources: + * Git book: https://git-scm.com/book/en * https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html diff --git a/ReadMe.md b/ReadMe.md index 2ada371..0bb2e9c 100644 --- a/ReadMe.md +++ b/ReadMe.md @@ -4,32 +4,22 @@ Lessons (Day 1): - * https://datacarpentry.org/R-ecology-lesson-alternative/index.html - * https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html - * https://datacarpentry.org/R-ecology-lesson-alternative/visualizing-ggplot.html - * https://datacarpentry.org/R-ecology-lesson-alternative/how-r-thinks-about-data.html + * Welcome and overview + * Introduction to Jupyter Notebooks, RStudio, and Git + * RStudio (Data Analysis and Visualization in R for Ecologists) + * https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html + * https://datacarpentry.org/R-ecology-lesson-alternative/visualizing-ggplot.html + * https://datacarpentry.org/R-ecology-lesson-alternative/how-r-thinks-about-data.html + * https://datacarpentry.org/R-ecology-lesson-alternative/working-with-data.html 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 + * Welcome and overview + * Sharing & collaborating with code (Github introduction) + * https://datacarpentry.org/rr-version-control/ + * Technical overview of the infrastrcture. -## Hints +## Resources -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 - * option-r/alt-r - Run a single line and stay on that line + * Login to the environment (SKC-CARE): https://ci.skc.edu/ + * Instructor Notes: [Notes.md](Notes.md)