diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5e34c08c96cc5e40cb3531ebf34af6ba764d03ab..f7e6360d8eb7c15052c6dffc8eb5f5ef76ccfc44 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -11,9 +11,9 @@ before_script:
pages:
stage: deploy
- only:
- - develop
- - master
+ rules:
+ - if: $CI_COMMIT_BRANCH == "master"
+ - if: $CI_COMMIT_BRANCH == "develop"
script:
- bash .ci/deploy.sh
diff --git a/external/contribute/markdown/markdown.md b/external/contribute/markdown/markdown.md
index ae7abca9e99d8f23b1983c366c58b868b4175316..7c64eb2f8a59c8ebd998e7685e300165aabfabad 100644
--- a/external/contribute/markdown/markdown.md
+++ b/external/contribute/markdown/markdown.md
@@ -32,35 +32,24 @@ Markdown is a lightweight markup language with plain text formatting syntax whic
<img src="img/visual-code_img_10.png">
-- **tips to write in markdown:**
-
- <img src="img/visual-code_img_18.png">
-
-**insert pictures:**
- <img src="img/visual-code_img_19.png" width="1000">
-
-**create a table**
- <img src="img/visual-code_img_20.png">
-
-
-## Syntax
+## Tips to write in markdown:
<table>
<thead>
- <tr>
- <th>Markdown</th>
- <th>Rendered Output</th>
- </tr>
+ <tr>
+ <th>Markdown</th>
+ <th>Rendered Output</th>
+ </tr>
</thead>
<tbody>
<tr>
<td>
- <code>
+ <pre>
# Header 1<br>
## Header 2<br>
### Header 3 <br>
#### Header 4
- </code>
+ </pre>
</td>
<td>
<h1>Header 1</h1><br>
@@ -68,107 +57,194 @@ Markdown is a lightweight markup language with plain text formatting syntax whic
<h3>Header 3</h3><br>
<h4>Header 4</h4>
</td>
- </tr>
- <tr>
- <td>
- <code>
- To **bold** text, add **two asterisks** or __underscores__ before and after a word or phrase.</br>
- To make text **italic** text, add *one asterisks* or _underscores_.
- </code>
- </td>
- <td>
- To make phrase <strong>bold</strong> text, add <strong>two asterisks</strong> or <strong>underscores</strong> before and after a word or phrase.</br>
- To make text <i>italic</i>, add <i>one asterisks</i> or <i>underscores</i>.
- </td>
- </tr>
- <tr>
- <td>
- <code>
- Use numbers for ordered lists: <br />
- 1. First item<br />
- 2. Second item<br />
- 3. Third item<br />
- 1. Indented item<br />
- 2. Indented item<br />
- 4. Fourth item
- </code>
- </td>
- <td>
- <ol>
- <li>First item</li>
- <li>Second item</li>
- <li>Third item
- <ol>
- <li>Indented item</li>
- <li>Indented item</li>
- </ol>
- </li>
- <li>Fourth item</li>
- </ol>
- </td>
- </tr>
- <tr>
- <td>
- <code>
- For unordered lists
- * First item<br />
- * Second item<br />
- * Third item<br />
- * Fourth item
- </code>
- </td>
- <td>
- <ul>
- <li>First item</li>
- <li>Second item</li>
- <li>Third item</li>
- <li>Fourth item</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>
- <code>
- Include links referring to a web [page](https://www.markdownguide.org/)
- </code>
- </td>
- <td>
- Include links referring to a web <a href="https://www.markdownguide.org/">page</a>
- </td>
- </tr>
- <tr>
- <td>
- <code>
- Include local pictures: 
- </code>
- </td>
- <td>
- Include local pictures: <img src="img/img.png">
- </td>
- </tr>
- <tr>
- <td>
- <code>
- Include code blocks! </br>
- ```</br>
- myAwesomeFunction <- function(x) x+1;</br>
- # Apply function </br>
- myAwesomeFunction(2);</br>
- ```
- </code>
- </td>
- <td>
- Include code blocks! </br>
+ </tr>
+ <tr>
+ <td>
+ <pre>
+ To make a text **bold**, use **double asterisk** or __underscores__ before and after a word or phrase.
+ To make a text **italic**, use *one asterisk* or _underscore_.
+ </pre>
+ </td>
+ <td>
+ To make a text <strong>bold</strong>, use <strong>double asterisk</strong> or <strong>underscores</strong> before and after a word or phrase.<br>
+ To make text <i>italic</i>, use <i>one asterisk</i> or <i>underscore</i>.
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <pre>
+ Use numbers for ordered lists:
+ 1. First item
+ 2. Second item
+ 3. Third item
+ 1. Indented item
+ 1. Indented item
+ 4. Fourth item
+ </pre>
+ </td>
+ <td>
+ Use numbers for ordered lists:
+ <ol>
+ <li>First item</li>
+ <li>Second item</li>
+ <li>Third item
+ <ol>
+ <li>Indented item</li>
+ <li>Indented item</li>
+ </ol>
+ </li>
+ <li>Fourth item</li>
+ </ol>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <pre>
+ For unordered lists use asterisk, minus or plus
+ - First item
+ - Second item
+ * Third item
+ * Indented item
+ + Indented item
+ * Fourth item
+ </pre>
+ </td>
+ <td>
+ For unordered lists use asterisk, minus or plus
+ <ul>
+ <li>First item</li>
+ <li>Second item</li>
+ <li>Third item</li>
+ <ul>
+ <li>Indented item</li>
+ <li>Indented item</li>
+ </ul>
+ <li>Fourth item</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <pre>
+ Include links referring to a web [page](https://www.markdownguide.org/)
+ </pre>
+ </td>
+ <td>
+ Include links referring to a web <a href="https://www.markdownguide.org/">page</a>
+ </td>
+ </tr>
+ <tr>
+ <td>
+
+ <pre>
+ Include local pictures using markdown:
+
+ 
+ </pre><br>
+ <pre>
+ Or use HTML tag allowing you to alter the image properties (e.g. size):
+
+ <img src="img/r3_logo.png" width="40">
+ </pre>
+ </td>
+ <td>
+ Include local pictures using markdown: <br>
+ <img src="img/r3_logo.png"> <br>
+ Or use HTML tag allowing you to alter the image properties (e.g. size):<br>
+ <img src="img/r3_logo.png" width="40">
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <pre>
+ Include code blocks!
+ ```
+ def myAwesomeFunction(x):
+ x+1
+ myAwesomeFunction(2)
+ ```
+ </pre>
+ </td>
+ <td>
+ Include code blocks! <br>
<code>
- myAwesomeFunction <- function(x) x+1;</br>
- # Apply function</br>
- myAwesomeFunction(2);
+ def myAwesomeFunction(x):<br>
+ x+1<br>
+ myAwesomeFunction(2)
</code>
- </td>
- </tr>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <pre>
+ Create table:
+ | Tables | Are | Cool |
+ |------------|:------:|:-----:|
+ | value one | blue | $1024 |
+ | value two | red | $256 |
+ | value three| green | $128 |
+ </pre>
+ </td>
+ <td>
+ Create table:
+ <div>
+ <table>
+ <thead>
+ <tr>
+ <th>
+ Tables
+ </th>
+ <th>
+ Are
+ </th>
+ <th>
+ Cool
+ </th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ value one
+ </td>
+ <td>
+ blue
+ </td>
+ <td>
+ $1024
+ </td>
+ </tr>
+ <tr>
+ <td>
+ value two
+ </td>
+ <td>
+ red
+ </td>
+ <td>
+ $256
+ </td>
+ </tr>
+ <tr>
+ <td>
+ value tree
+ </td>
+ <td>
+ green
+ </td>
+ <td>
+ $128
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </td>
+ </tr>
</tbody>
</table>
+
This is an overview of basic Markdown features. For more in-build features, please see various online [documentation](https://www.markdownguide.org/basic-syntax/).
### Advanced formatting
@@ -185,55 +261,53 @@ Another big advantage of Markdown is that it can contain HTML tags, which makes
* **Blogging and tutorials** - structured document with chunks of code, pictures and results of the analyses can be easily converted to HTML format and posted on personal/team websites.
* **Notes and meeting minutes** - you can use following template for simple and nicely structured meeting notes:
+
<table>
<thead>
<tr>
- <th>Markdown</th>
+ <th>Markdown template</th>
<th>Rendered Output</th>
</tr>
</thead>
<tbody>
- <tr>
- <td>
- <code>
- # DocTitle</br>
- ### Attendees:</br>
- ### Location:</br>
- ## Objective / Agenda</br>
- ## Meeting Notes</br>
- * first note </br>
- * second note </br>
- * ...</br>
- </br>
- ## Actions</br>
- - [ ] Josh, Alice and Cindy will do this.</br>
- - [x] Bob stops doing that.</br>
- - [ ] Will and Tom will take care of those
- </code>
- </td>
- <td>
- <code>
- <h1>DocTitle</h1></br>
- <h3> Attendees:<h3></br>
- <h3> Location:</h3></br>
- <h2> Objective / Agenda</h2></br>
- <h2> Meeting Notes</h2></br>
- <ul>
- <li> first note</li>
- <li>second note</li>
- <li>...</li>
- </ul>
- <h2> Actions</h2></br>
- <input type="checkbox" > Josh, Alice and Cindy will do this.</input></br>
- <input type="checkbox" checked="checked"> Bob stops doing that.</input></br>
- <input type="checkbox" > Vanessa and Tom will take care of those</input></br>
- </code>
- </td>
- </tr>
-</tbody>
+ <tr>
+ <td>
+ <pre>
+ # DocTitle
+ ### Attendees:
+ ### Location:
+ ## Objective / Agenda
+ ## Meeting Notes
+ * first note
+ * second note
+ * ...
+ ## Actions
+ - [ ] Josh, Alice and Cindy will do this.
+ - [x] Bob stops doing that.
+ - [ ] Will and Tom will take care of those
+ </pre>
+ </td>
+ <td>
+ <h1>DocTitle</h1><br>
+ <h3> Attendees:</h3><br>
+ <h3> Location:</h3><br>
+ <h2> Objective / Agenda</h2><br>
+ <h2> Meeting Notes</h2><br>
+ <ul>
+ <li> first note</li>
+ <li>second note</li>
+ <li>...</li>
+ </ul>
+ <h2> Actions</h2><br>
+ <input type="checkbox"> Josh, Alice and Cindy will do this.<br>
+ <input type="checkbox" checked="checked"> Bob stops doing that.<br>
+ <input type="checkbox"> Vanessa and Tom will take care of those<br>
+ </td>
+ </tr>
+ </tbody>
</table>
- * **Analyses,reports and papers** - embedding [R markdown](https://rmarkdown.rstudio.com/) in an R project allows you to include executable code and related text in the very same document. This brings unprecedented level of consistency, shareability and reproducibility into the workflows.
+ * **Analyses, reports and papers** - embedding [R markdown](https://rmarkdown.rstudio.com/) in an R project allows you to include executable code and related text in the very same document. This brings unprecedented level of consistency, shareability and reproducibility into the workflows.
* **Online discussion forums** - many scientific and non-scientific discussion forums and social networks support Markdown for formatting the content of messages (e.g. [StackOverflow](https://stackoverflow.com/editing-help), [GitHub](https://help.github.com/en/github/writing-on-github/basic-writing-and-formatting-syntax), Reddit or even Facebook)