Update doc to new repo name (#317)

* changed URL
ICB-DCM · Aug 20, 2024 · 030255f · 030255f
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diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -63,7 +63,7 @@ jobs:
         run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
         env:
           JEKYLL_ENV: production
-          PAGES_REPO_NWO: leaseep/OmicShiny
+          PAGES_REPO_NWO: leaseep/cOmicsArt
 
       - name: Upload artifact
         # Automatically uploads an artifact from the './_site' directory by default

diff --git a/README.md b/README.md
@@ -1,13 +1,13 @@
 # Data Input Notes:
 ## Status Quo
 General Test:
-![example workflow](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg)
+![example workflow](https://github.com/LeaSeep/cOmicsArt/actions/workflows/run-tests.yaml/badge.svg)
 
 Develop-Version Test-Status:
-![develop status](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg?branch=develop)
+![develop status](https://github.com/LeaSeep/cOmicsArt/actions/workflows/run-tests.yaml/badge.svg?branch=develop)
 
 Main-Version Test-Status:
-![main status](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg?branch=main)
+![main status](https://github.com/LeaSeep/cOmicsArt/actions/workflows/run-tests.yaml/badge.svg?branch=main)
 
 3 tables are needed:
 1. data-table (e.g. counts or intensitites)

diff --git a/docs/_config.yml b/docs/_config.yml
@@ -3,7 +3,7 @@
 title: cOmicsART Documentation
 logo: "/assets/images/Logo_cOmicsArt.svg"  # Update to the new image file path
 description: Here you find all the information you need to use cOmicsART
-baseurl: "/OmicShiny"
+baseurl: "/cOmicsART"
 url: "https://leaseep.github.io/"
 #theme: just-the-docs
 remote_theme: just-the-docs/just-the-docs

diff --git a/docs/code-and-data.md b/docs/code-and-data.md
@@ -6,5 +6,5 @@ nav_order: 3
 ---
 
 
-![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsPenguin.png)
+![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsPenguin.png)
 *Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
diff --git a/docs/faq.md b/docs/faq.md
@@ -6,7 +6,7 @@ nav_order: 7
 
 # Frequently Asked Questions (FAQ)
 
-![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsGiraffe.png)
+![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsGiraffe.png)
 *Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
 
 <style>

diff --git a/docs/index.md b/docs/index.md
@@ -7,10 +7,10 @@ nav_exclude: true
 # Welcome to   <span style="color:#EC0014"> c</span><span style="color:#FD8D33">O</span><span style="color:#3897F1">m</span><span style="color:#FFD335">i</span><span style="color:#A208BA">c</span><span style="color:#EF0089">s</span><span style="color:#EC0014">A</span><span style="color:#FD8D33">r</span><span style="color:#3897F1">t</span> Documentation 🎨
 
 
-![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsCat.png)
+![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsCat.png)
 *Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
 
-If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://shiny.iaas.uni-bonn.de/OmicShiny/)
+If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://shiny.iaas.uni-bonn.de/cOmicsArt/)
 
 Otherwise, you can navigate through the documentation using the sidebar on the left. If you’re searching for something specific, try using the search bar at the top. 🔍 It can search through the entire documentation and guide you to the relevant section.
 

diff --git a/docs/installation.md b/docs/installation.md
@@ -10,12 +10,12 @@ editor_options:
 # Introduction
 
 ![A comic about a cat finding
-cOmicsART](/OmicShiny/assets/images/cOmicsTurtle.png) *Image generated
+cOmicsART](/cOmicsArt/assets/images/cOmicsTurtle.png) *Image generated
 using DALL-E by OpenAI. Adjusted by Lea Seep*
 
 Why do you want to install cOmicsART locally? If you just want to use it
 make sure to checkout the website:
-[cOmicsART](https://shiny.iaas.uni-bonn.de/OmicShiny/). For this there
+[cOmicsART](https://shiny.iaas.uni-bonn.de/cOmicsArt/). For this there
 is no installation effort required. If you know you are right here,
 let's get started.
 
@@ -41,15 +41,15 @@ Open a terminal or command prompt and use the following command to clone
 the repository:
 
 ``` bash
-git clone https://github.com/leaseep/OmicShiny.git
+git clone https://github.com/leaseep/cOmicsArt.git
 ```
 
 ### 2. Navigate to the Project Directory
 
 Change the directory to the cloned repository:
 
 ``` bash
-cd OmicShiny
+cd cOmicsArt
 ```
 
 ## 3. Restore the R Environment

diff --git a/docs/interface-details.md b/docs/interface-details.md
@@ -6,7 +6,7 @@ nav_order: 2
 ---
 
 # Interface Details
-![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsOctopus.png)
+![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsOctopus.png)
 *Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
 
 If you need tab-specific information, navigate to the respective documentation using the left sidebar.
@@ -52,6 +52,6 @@ To get more information on the tabs, navigate to the respective documentation us
     </ol>
   </div>
   <div style="float: right; width: 30%;">
-    <img src="/OmicShiny/assets/images/design_principleSidePanel.png" alt="The design of the side panel" style="width: 100%;">
+    <img src="/cOmicsArt/assets/images/design_principleSidePanel.png" alt="The design of the side panel" style="width: 100%;">
   </div>
 </div>
diff --git a/docs/interface-details/required-data-input.md b/docs/interface-details/required-data-input.md
@@ -21,7 +21,7 @@ Within cOmicsART, you have several options to do so:
 # General Remarks on Data Input 🏷️
 cOmicsART expects three data tables, which can be supplied in different ways, holding information about the measurement itself, information regarding the measured samples, and information regarding the measured entities, such as genes, metabolites, or lipids. We'll provide here the description of the minimal requirements, but please keep in mind that you are not limited to these. Adjusting the data input, especially annotation, is often part of the explorative phase. Check out [Showcase A](showcases/showcase-a.md) for examples.
 
-![Required Data input consists out of three tables](/OmicShiny/assets/images/DataInputShiny.png)
+![Required Data input consists out of three tables](/cOmicsArt/assets/images/DataInputShiny.png)
 
 ## Starting with a Single Table - Data Matrix 📝
 When you have only your omics data table (referred to as the Data Matrix), ensure that entities are organized in rows and samples in columns. There are no limitations on the number of rows and columns (e.g., genes and samples), but you should have more than two entities and samples for meaningful analysis. While cOmicsART is designed for omics analysis, you can upload any type of measurements arranged in a data matrix format. However, please note that some analyses, such as enrichment analysis, might not be meaningful with non-omics data. Also, some provided pre-processing options then might not be relevant - you have the option to select 'None' as pre-processing, giving you the option to perform pre-processing beforehand and upload and analyze the uploaded data.

diff --git a/docs/screen_recording.md b/docs/screen_recording.md
@@ -4,5 +4,5 @@ layout: default
 nav_order: 8
 ---
 
-![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsRabbit.png)
+![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsRabbit.png)
 *Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
diff --git a/docs/showcases.md b/docs/showcases.md
@@ -7,7 +7,7 @@ nav_order: 4
 
 # Showcases Overview
 
-![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsUnicorn.png)
+![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsUnicorn.png)
 *Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
 
 In this section, you will find two showcases, each utilizing different datasets to illustrate various features and functionalities of the App.

diff --git a/docs/welcome.md b/docs/welcome.md
@@ -6,7 +6,7 @@ nav_order: 1
 
 # Welcome to <span style="color:#EC0014"> c</span><span style="color:#FD8D33">O</span><span style="color:#3897F1">m</span><span style="color:#FFD335">i</span><span style="color:#A208BA">c</span><span style="color:#EF0089">s</span><span style="color:#EC0014">A</span><span style="color:#FD8D33">r</span><span style="color:#3897F1">t</span> Documentation 🎨
 
-![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsCat.png)
+![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsCat.png)
 *Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
 
 If you are looking for the web app, please visit: 🌐 [cOmicsART Web App](https://comicsart.org/)

diff --git a/program/shinyApp/R/util.R b/program/shinyApp/R/util.R
@@ -11,7 +11,7 @@ error_modal <- function(e, additional_text = NULL){
   additional_text <- paste0(
     additional_text,
     "<br><br>Otherwise, please contact the cOmicsArtist Lea and Paul via [email protected]",
-    "or open an issue on <a href='https://github.com/LeaSeep/OmicShiny'>github</a> ",
+    "or open an issue on <a href='https://github.com/LeaSeep/cOmicsArt'>github</a> ",
     "describing your problem."
   )
   showModal(modalDialog(

diff --git a/program/shinyApp/R/version.R b/program/shinyApp/R/version.R
@@ -1,3 +1,3 @@
 VERSION <<- "v0.1.0"
-DOCUMENTATION <<- "https://leaseep.github.io/OmicShiny/welcome.html"
-SERVER <<- "https://shiny.iaas.uni-bonn.de/OmicShiny/"
+DOCUMENTATION <<- "https://leaseep.github.io/cOmicsArt/welcome.html"
+SERVER <<- "https://shiny.iaas.uni-bonn.de/cOmicsArt/"
diff --git a/program/shinyApp/ui.R b/program/shinyApp/ui.R
@@ -209,7 +209,7 @@ ui <- shiny::fluidPage(
   ),
   splitLayout(
     cellWidths = c("75%", "10%", "15%"),
-    tags$a(href = "https://leaseep.github.io/OmicShiny/", "Go To Documentation", target = "_blank"),
+    tags$a(href = "https://leaseep.github.io/cOmicsArt/", "Go To Documentation", target = "_blank"),
     NULL
   ),