Skip to content
This repository was archived by the owner on Dec 12, 2025. It is now read-only.

Commit

Permalink
Add Gitea instructions
Browse files Browse the repository at this point in the history
  • Loading branch information
@tmiddelkoop
tmiddelkoop committed May 29, 2024
1 parent c9bf881 commit a878ea9
Show file tree
Hide file tree
Showing 2 changed files with 114 additions and 62 deletions.
138 changes: 100 additions & 38 deletions Notes.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,77 +2,120 @@

## 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"
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

Expand All @@ -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
38 changes: 14 additions & 24 deletions ReadMe.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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)

0 comments on commit a878ea9

Please sign in to comment.