Improvements Jelle (#30)

* Update for 2024

* Add workflow that forms the Quatro files

* Add the build workflow

* rename yaml myl

* Add the Quarto Build Workflow

* Output dir is set in _quarto.yml

* Add website publishing to workflow

* Revert "Add website publishing to workflow"

This reverts commit cf1aaed.

* Update build with publish command

* Add artifacts

* Commit new files

* stage only updated files

* Commit html files instead

* Don't recommit license

* Update Quarto files

* Move docs/images to images

* Update Quarto files

* Move images and automate the copying of images

* Add status badge for rendering the Academy

* Create image folder

* Update Quarto files

* change public to docs

* Update docs folder

* Change cmd to terminal

* Update step 1 image

* Update Quarto files

* `` to all quotes

* Update Quarto files

* Fix mistake with overzealous ``ing

* Update Quarto files

* Remove loose `

* Update Quarto files

* Change image sizes

* Update Quarto files

* Centeralign images

* Update Quarto files

* update simulation page

* Fix qmd file simulations

* Update author info

* Update Quarto files

* Add some more figures

* Update Quarto files

* Add cloud info

* Update Quarto files

* add cli image

* Update Quarto files

* add simulation page

* Update Quarto files

* Update some typos

* Update Quarto files

* Move to up to date files

* Update Quarto files

* Update Quarto files

---------

Co-authored-by: jteijema <j.j.teijema@uu.nl>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

Author: 3 people

ASReviewLAB.qmd

@@ -3,12 +3,10 @@ title: "Introductory exercise to ASReview LAB"
 author: "The ASReview Academy Team"
 ---
 
-**This exercise was made using ASReview LAB version 1.6. If you have a different version you can observe differences between your setup and the exercise.**
-
-## Introduction to the software ASReview LAB v1.6
+## Introduction to the software ASReview LAB
 
 The **goal** of this exercise is to get familiar with AI-aided screening
-by making use of ASReview LAB v1.6.
+by making use of ASReview LAB v1.x.
 
 You will learn how to install and set up the software, upload data,
 screen records, and export and interpret the results. The exercise will
@@ -31,41 +29,81 @@ Before you start, you might want to read a bit more on:
 -   The paper that was published in [Nature Machine
     Intelligence](https://www.nature.com/articles/s42256-020-00287-7){target="_blank"}
 
-## Prerequisites
+## The software
+
+### Step 1: Installing Python and ASReview LAB
+
+First, you need to install [Python](https://www.python.org/downloads/){target="_blank"}.
+
+Once you have Python installed, you can go through the easy 3-step
+[guide to installing (or upgrading)
+ASReview](https://asreview.nl/download/){target="_blank"} on the ASReview-website.
+
+More detailed installation information, troubleshooting, and
+installation on a server or via a Docker are available on
+[ReadTheDocs](https://asreview.readthedocs.io/en/latest/installation.html#install-asreview){target="_blank"}.  
+
+*Have you installed the latest version of ASReview? You can proceed to
+step 2!*
 
-### Installing ASReview LAB
+### Step 2: Starting ASReview LAB
 
-Before you start the tutorial ASReview LAB needs to be installed; see for instructions the [ASReview website](https://asreview.nl/download/){target="_blank"}.
+To open ASReview LAB in your browser, you need to start it in the terminal. You can 
+open your terminal by typing ‘`terminal`’ (`cmd` on Windows 10 or lower) in your 
+computer’s search bar (select ‘`Run as administrator`’ if you have this option).
 
-*Have you installed ASReview LAB? You can proceed to the exercise!*
+![](images/ASReviewLAB/step_1.png){width=85% fig-align="center"}
 
-## Exercise
+The terminal will open, in which you can type the following
+command and press enter:
 
-### Step 1: Starting ASReview LAB
+``` bash
+asreview lab
+```
+
+Note that you have to keep your command-line interpreter running while
+using ASReview LAB, even though the interface is in your browser!
+
+![](images/ASReviewLAB/step_2.png){width=85% fig-align="center"}
+
+It takes a few seconds for ELAS - your Electronic Learning Assistant -
+to start the software. It will appear in your (default) web browser. 
+
+But why do you need to start it up by running code in your command
+prompt? This ensures that ASReview LAB is run locally. More
+specifically, <u>your data is and stays your own</u>. Small price to pay
+for complete privacy, right?! Read more about the key principles in the
+[Zen of Elas](https://asreview.nl/blog/the-zen-of-elas/){target="_blank"}!
+
+You can also run the software via a server, but you need to take care of
+[hosting the server
+yourself](https://asreview.readthedocs.io/en/latest/installation.html#server-installation){target="_blank"}
+(or ask your IT-department).
 
-Open ASReview LAB in your browser. Note that if you do this via Command Prompt (Windows) or Terminal (MacOS) you have to keep your command-line interpreter running while using ASReview LAB, even though the interface is in your browser!
 
 *Have you opened ASReview LAB in your browser? If so, you can proceed to
-step 2!*
+step 3!*
 
-### Step 2: Creating a project
+### Step 3: Creating a project
 
-Now that you have opened ASReview LAB, you can create a
-new project. Below you will find a step-by-step guide. 
+Now that you have installed and opened ASReview LAB, you can create a
+new project. Below you will find a step-by-step guide. Note that the
+screenshots shown below are made in [dark
+mode](https://asreview.readthedocs.io/en/latest/screening.html#display){target="_blank"}.
 
 1.  *New project;*
 
 Hover your mouse over the ‘`create`’ button with the plus sign in the
 bottom right corner.
 
-![](images/ASReviewLAB/step_2a_V1_6.png){width=85% fig-align="center"}
+![](images/ASReviewLAB/step_3.png){width=85% fig-align="center"}
 
 2.  *Project name;*
 
 Select Validation Mode, fill out a project name and press ‘`NEXT`’. Note
 that you can fill out your name and a description as well.
 
-![](images/ASReviewLAB/step_2b_V1_6.png){width=85% fig-align="center"}
+![](images/ASReviewLAB/step_3b.png){width=85% fig-align="center"}
 
 For this exercise we are screening in the so-called ‘`Validation Mode`’
 of ASReview. By screening in the [Validation
@@ -83,11 +121,11 @@ More detailed information about setting up a project can be found on
 
 
 *Have you started creating a new project? If so, you can proceed to step
-3!*
+4!*
 
 ## Project setup
 
-### Step 3: The dataset
+### Step 4: The dataset
 
 Now that you have created your ASReview project (woohoo!), you need to set it
 up. Without data, we have nothing to screen. So, you need to tell ELAS
@@ -102,14 +140,14 @@ Go to the ‘`Benchmark datasets`’ button, open the first dataset (i.e. the
 Van de Schoot (2017) dataset about PTSD trajectories) and click on
 ‘`ADD`’. After you select the dataset, click on ‘`SAVE`’.
 
-![](images/ASReviewLAB/step_3_V1_6.png){width=85% fig-align="center"}
+![](images/ASReviewLAB/step_4.png){width=85% fig-align="center"}
 
 
 
 *Have you successfully selected/uploaded the dataset? If so, you can
-proceed to step 4!*
+proceed to step 5!*
 
-### Step 4: Prior knowledge
+### Step 5: Prior knowledge
 
 Before you can start screening the records, you need to tell ELAS what
 kind of records you <u>are</u> and what kind of records you <u>are
@@ -148,7 +186,7 @@ To add the relevant records, you click on ‘`Search`’, copy and paste the tit
 of these relevant records one by one in the search bar and add them as
 relevant.
 
-![](images/ASReviewLAB/step_4_V1_6.png){width=85% fig-align="center"}
+![](images/ASReviewLAB/step_5.png){width=85% fig-align="center"}
 
 
 After adding all five relevant records, you can add some irrelevant ones
@@ -157,9 +195,9 @@ to be able to select this button) and by changing ‘`relevant`’ to
 ‘`irrelevant`’. Select five irrelevant records and click on ‘`CLOSE`’.
 
 *Have you selected five relevant and five irrelevant records? If so, you
-can proceed to step 5!*
+can proceed to step 6!*
 
-### Step 5: Active learning model
+### Step 6: Active learning model
 
 The last step to complete the setup is to select the active learning
 model you want to use. The default settings (i.e. Naïve Bayes, Max and
@@ -179,15 +217,15 @@ Learning?](https://asreview.nl/blog/active-learning-explained/){target="_blank"}
 
 After the project is successfully initialized, you can start reviewing.
 
-![](images/ASReviewLAB/step_5a_V1_6.png){width=85% fig-align="center"}
+![](images/ASReviewLAB/step_6.png){width=85% fig-align="center"}
 
-*Have you finished the setup? If so, you can proceed to step 6!*
+*Have you finished the setup? If so, you can proceed to step 7!*
 
-![](images/ASReviewLAB/step_5b_V1_6.png){width=85% fig-align="center"}
+![](images/ASReviewLAB/step_7.png){width=85% fig-align="center"}
 
 ## Screening phase
 
-### Step 6: Screening the records
+### Step 7: Screening the records
 
 Everything is set up and ready to screen, well done!
 
@@ -239,7 +277,7 @@ Rule. Read more about Stopping Rules and how to decide on a good
 strategy for your data on the [discussion
 platform](https://github.com/asreview/asreview/discussions){target="_blank"}. 
 
-### Step 7: Extracting and inspecting the data
+### Step 8: Extracting and inspecting the data
 
 Now that you found all or most relevant records, you can export your
 data using [these
@@ -303,10 +341,10 @@ Some suggestions:
     code](https://github.com/asreview/asreview/tree/master/asreview){target="_blank"} on
     Github… +1 for open-science!)
 
-![](images/ASReviewLAB/game_V1_6.png){width=85% fig-align="center"}
 
+![](https://raw.githubusercontent.com/asreview/asreview/main/docs/images/game.png){width=85% fig-align="center"}
 
 [^1]: Wang Z, Nayfeh T, Tetzlaff J, O’Blenis P, Murad MH (2020) Error
     rates of human reviewers during abstract screening in systematic
     reviews. PLOS ONE 15(1): e0227742.
-    <[https://doi.org/10.1371/journal.pone.0227742](https://doi.org/10.1371/journal.pone.0227742){target="_blank"}>
+    <[https://doi.org/10.1371/journal.pone.0227742](https://doi.org/10.1371/journal.pone.0227742){target="_blank"}>

README.md

@@ -12,6 +12,11 @@ This repository contains a website with open teaching materials for using ASRevi
 
 The work is published under the CC BY 4.0 license.
 
+## Development
+[![Render and Publish Quarto Site](https://github.com/jteijema/asreview-academy/actions/workflows/build.yml/badge.svg)](https://github.com/jteijema/asreview-academy/actions/workflows/build.yml)
+
+All files in the `docs` folder are generated by the GitHub Action workflow. Do not place or adjust files in the `docs` folder.
+
 ## Contact
 
 This repository is part of the ASReview project ([asreview.ai](https://asreview.ai)). It is maintained by the

_quarto.yml

@@ -31,13 +31,9 @@ website:
            text: Datatools
          - href: simulation.qmd
            text: Simulation Mode
-          
 
 format:
   html:
     theme: cosmo
     css: styles.css
     toc: true
-
-
-