From 99511e7f0a1eca30d29ef2ab70bd29db7cbe9d34 Mon Sep 17 00:00:00 2001 From: Jonathan Peake Date: Fri, 1 Nov 2024 13:30:32 -0700 Subject: [PATCH 1/2] Insert content for first tutorial --- content/02-jupyterhub-setup-r.qmd | 19 ++++++++++--------- tutorials/tutorial-1.qmd | 25 +++++++++++++++---------- tutorials/tutorial-2.qmd | 21 ++++----------------- tutorials/tutorial-3.qmd | 21 ++++----------------- tutorials/tutorial-4.qmd | 21 +++------------------ tutorials/tutorial-5.qmd | 7 +++++++ 6 files changed, 43 insertions(+), 71 deletions(-) create mode 100644 tutorials/tutorial-5.qmd diff --git a/content/02-jupyterhub-setup-r.qmd b/content/02-jupyterhub-setup-r.qmd index f50118d..c914d5c 100644 --- a/content/02-jupyterhub-setup-r.qmd +++ b/content/02-jupyterhub-setup-r.qmd @@ -4,9 +4,9 @@ title: R/RStudio on JupyterHub Everything you need is installed for you. Note, before you can log in, we will need to add you to the access group. -* -* Click Start Server and accept defaults -* Click the RStudio button. If you don't see it, click the blue button in the top left to open a new 'Launcher' window. +- +- Click Start Server and accept defaults +- Click the RStudio button. If you don't see it, click the blue button in the top left to open a new 'Launcher' window. ![](content/img/jhub-launcher.png) @@ -14,9 +14,9 @@ Everything you need is installed for you. Note, before you can log in, we will n ### GitHub username -* Create a GitHub account (if you don’t already have one) at . Advice for choosing a GitHub username: this is a professional username that you will use in work settings. GitHub accounts are not anonymous; this is for sharing work. Using your real name is common. -* Write down your username and password; you will need to log in during the course! -* Here is [a video](https://www.youtube.com/watch?v=nHXw4mGoqiE) showing the whole process +- Create a GitHub account (if you don’t already have one) at . Advice for choosing a GitHub username: this is a professional username that you will use in work settings. GitHub accounts are not anonymous; this is for sharing work. Using your real name is common. +- Write down your username and password; you will need to log in during the course! +- Here is [a video](https://www.youtube.com/watch?v=nHXw4mGoqiE) showing the whole process ### Get on JupyterHub @@ -24,7 +24,8 @@ Once you have submitted your GitHub username and have been accepted as a member -* **Choose the default Py-R base geospatial image**. [Watch a video](https://youtu.be/o99jZWHqKi8) of the login process and basic JupyterHub orientation. +- **Choose the default Py-R base geospatial image**. [Watch a video](https://youtu.be/o99jZWHqKi8) of the login process and basic JupyterHub orientation. -* home directory is yours and no one else can see it. -* To share files, you can connect to a GitHub repository or use the `shared` directory. Everyone can read and write to this directory. Please don't delete content that is not your own. +- home directory is yours and no one else can see it. + +- To share files, you can connect to a GitHub repository or use the `shared` directory. Everyone can read and write to this directory. Please don't delete content that is not your own. \ No newline at end of file diff --git a/tutorials/tutorial-1.qmd b/tutorials/tutorial-1.qmd index 4ca5fb5..2281336 100644 --- a/tutorials/tutorial-1.qmd +++ b/tutorials/tutorial-1.qmd @@ -1,22 +1,27 @@ --- -title: Intro to Quarto +title: Introduction to RStudio and Quarto --- ::: {.callout-note title="Learning Objectives"} - -1. objective 1 -2. objective 2 -3. objective 3 +1. Understand what Quarto is and why we use it +2. Get familiar with RStudio +3. Create a Quarto file and understand its structure +4. Understand how Quarto projects differ from Quarto files ::: -## Summary - +## Logging onto JupyterHub -## Terminology +For this workshop, we'll be using the [NOAA NMFS JupyterHub](https://nmfs-openscapes.2i2c.cloud). You're welcome to use your own version of RStudio on your desktop, just make sure R and RStudio are updated to the latest versions. +## Using the Carpentries Tutorials -## Prerequisites +Instead of re-inventing the wheel, we will be leveraging open science principles by using the Carpentries Incubator [**Introduction to Reproducible Publications with RStudio**](https://carpentries-incubator.github.io/reproducible-publications-quarto/index.html)tutorial. The tutorial consists of a series of "episodes" that we will be walking through with you. Several of the episodes go a bit further in-depth than we will cover in the workshop, but feel free to explore further on your own time. +For today's session, we will be going through the following episodes: -## Load Required Packages +1. [Scientific reproducibility: What is it for?](https://carpentries-incubator.github.io/reproducible-publications-quarto/01-repro-project-org/01-introduction/index.html) +2. [Navigating RStudio and Quarto Documents](https://carpentries-incubator.github.io/reproducible-publications-quarto/02-quarto/01-basic-rstudio/index.html) +3. [Working with projects in RStudio](https://carpentries-incubator.github.io/reproducible-publications-quarto/02-quarto/02-projects-rstudio/index.html) +4. [Quarto Files vs Quarto Projects (Section in Working with projects in RStudio)](https://carpentries-incubator.github.io/reproducible-publications-quarto/01-repro-project-org/02-reproducibility/index.html#quarto-projects) +Follow along on your own computer as we walk through the tutorials. \ No newline at end of file diff --git a/tutorials/tutorial-2.qmd b/tutorials/tutorial-2.qmd index 4ca5fb5..12cc4bc 100644 --- a/tutorials/tutorial-2.qmd +++ b/tutorials/tutorial-2.qmd @@ -1,22 +1,9 @@ --- -title: Intro to Quarto +title: Working with Quarto files and the Markdown language --- ::: {.callout-note title="Learning Objectives"} +1. Coming Soon! -1. objective 1 -2. objective 2 -3. objective 3 -::: - -## Summary - - -## Terminology - - -## Prerequisites - - -## Load Required Packages - +## +::: \ No newline at end of file diff --git a/tutorials/tutorial-3.qmd b/tutorials/tutorial-3.qmd index 4ca5fb5..7920bb8 100644 --- a/tutorials/tutorial-3.qmd +++ b/tutorials/tutorial-3.qmd @@ -1,22 +1,9 @@ --- -title: Intro to Quarto +title: Dynamic output in Quarto files: Code, Tables, and Figures --- ::: {.callout-note title="Learning Objectives"} +1. Coming Soon! -1. objective 1 -2. objective 2 -3. objective 3 -::: - -## Summary - - -## Terminology - - -## Prerequisites - - -## Load Required Packages - +## +::: \ No newline at end of file diff --git a/tutorials/tutorial-4.qmd b/tutorials/tutorial-4.qmd index 4ca5fb5..797c8dd 100644 --- a/tutorials/tutorial-4.qmd +++ b/tutorials/tutorial-4.qmd @@ -1,22 +1,7 @@ --- -title: Intro to Quarto +title: Cross-references, bibliography and citations in Quarto files --- ::: {.callout-note title="Learning Objectives"} - -1. objective 1 -2. objective 2 -3. objective 3 -::: - -## Summary - - -## Terminology - - -## Prerequisites - - -## Load Required Packages - +1. Coming Soon! +::: \ No newline at end of file diff --git a/tutorials/tutorial-5.qmd b/tutorials/tutorial-5.qmd new file mode 100644 index 0000000..d30ec98 --- /dev/null +++ b/tutorials/tutorial-5.qmd @@ -0,0 +1,7 @@ +--- +title: Introduction to Quarto Projects +--- + +::: {.callout-note title="Learning Objectives"} +1. Coming Soon! +::: \ No newline at end of file From 47824a3c674ce4ce9fbcb8de146f6f052953213c Mon Sep 17 00:00:00 2001 From: Jonathan Peake Date: Fri, 1 Nov 2024 13:36:09 -0700 Subject: [PATCH 2/2] Change to correct link for JupyterHub; link to the setting up JupyterHub page of the website --- tutorials/tutorial-1.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/tutorial-1.qmd b/tutorials/tutorial-1.qmd index 2281336..357c33a 100644 --- a/tutorials/tutorial-1.qmd +++ b/tutorials/tutorial-1.qmd @@ -11,7 +11,7 @@ title: Introduction to RStudio and Quarto ## Logging onto JupyterHub -For this workshop, we'll be using the [NOAA NMFS JupyterHub](https://nmfs-openscapes.2i2c.cloud). You're welcome to use your own version of RStudio on your desktop, just make sure R and RStudio are updated to the latest versions. +For this workshop, we'll be using the [NOAA NMFS JupyterHub](https://dhub.opensci.live/). You're welcome to use your own version of RStudio on your desktop, just make sure R and RStudio are updated to the latest versions. Follow the instructions to set up your JupyterHub access here: [Intro to JupyterHubs](https://nmfs-opensci.github.io/Quarto-Workshop-2024/content/01-intro-to-jupyterhub.html) ## Using the Carpentries Tutorials