.ci/analytics/gdpr-banner.html

+<div id="lap-cookies-banner" class="presentation-banner">
+    <div class="banner-intro">
+        <div class="close-button">
+            <a class="lap-refuse">
+                <i class="fa fa-times" aria-hidden="true"></i>
+            </a>
+        </div>
+        <div class="banner-img">
+            <img src="https://analytics.lcsb.uni.lu/lap/static/logos/r3-logo.svg" type="image/svg+xml"/>
+        </div>
+        <div class="banner-title">This website needs some cookies and similar means to function.</div>
+        <div class="banner-text">If you permit us, we will use those means to collect data on your visits for aggregated
+            statistics to improve our service.
+        </div>
+    </div>
+
+    <div class="banner-buttons">
+        <a class="btn lap-accept">Accept cookies for aggregated statistics</a>
+        <a class="btn lap-refuse">No thanks, only technically necessary cookies</a>
+        <a class="btn lap-cookies-more" href="https://courses.lcsb.uni.lu/privacy-policy">More information</a>
+    </div>
+</div>
\ No newline at end of file

.ci/analytics/head.html

+<script>
+    const settings = {
+        expires: "180",
+        matomoURL: "https://analytics.lcsb.uni.lu/hub/",
+        siteID: "8", //you get this siteID by sending an email to lcsb-r3@uni.lu
+        accept_all_text: "Aggregate statistics cookies accepted",
+        only_necessary_text: "Only necessary cookies accepted",
+        doNotTrack_text: "Do Not Track is enabled",
+        cookieName: "lap",
+        bots: /bot|crawler|spider|crawling/i,
+        timeout_hidebanner: "500",
+        cookieDomain: "courses.lcsb.uni.lu"
+    };
+</script>
+<script src="https://analytics.lcsb.uni.lu/lap/static/js/jquery.min.js"></script>
+<script src="https://analytics.lcsb.uni.lu/lap/static/js/lap.js"></script>
+
+<link rel="stylesheet" type="text/css" href="https://analytics.lcsb.uni.lu/lap/static/css/lap.css" />

.ci/analytics/policy.html

+<div class="bottomPrivacy">
+    <a href="https://courses.lcsb.uni.lu/privacy-policy">Privacy Policy</a>
+    (<span id="doNotTrack-text"><span id="gdpr-result-text"></span> - <a href="javascript: showBanner();">change</a></span>)
+</div>
\ No newline at end of file

.ci/deploy.sh

 #!/bin/bash
 
-PAGEURL="https://r3.pages.uni.lu/outreach/presentations"
+PAGEURL="https://courses.lcsb.uni.lu"
 
 rootDir=$(pwd)
 echo $rootDir
 
 # clean previous builds
 rm -rf $rootDir/public
+rm -rf $rootDir/theme
 mkdir $rootDir/public
 
+if [[ $CI_COMMIT_REF_NAME == "develop" ]]; then
+    version="latest";
+elif [[ $CI_COMMIT_REF_NAME == "master" ]]; then
+    version="stable";
+else
+    version="unstable";
+fi
+
+# build the unstable version - can be optimized
+git submodule update --init --recursive
+
+# add matomo
+sed -i "/matomohead/r./.ci/analytics/head.html" theme/templates/_index.html
+sed -i "/matomopolicy/r./.ci/analytics/policy.html" theme/templates/_index.html
+sed -i "/matomobanner/r./.ci/analytics/gdpr-banner.html" theme/templates/_index.html
+
+echo " > LAP included"
+
 # loop through all the presentations
 nBlades=0
 for d in $(find . -maxdepth 1 -type d)
 do
     if [[ "${d}" == *20* ]]; then
-        cd "${d}"
+        pushd "${d}"
         echo "changed to ${d}"
         for d1 in $(find . -maxdepth 1 -type d)
         do
             if [[ ${#d1} -ge 2 ]]; then
                 let "nBlades+=1"
-                #blades[$nBlades]="$tutorial"
                 BLADE=${d1:2}
                 echo " > -----------------------------------------------------"
                 echo "Building ... ${d1}"
 
                 # create the required folders in public
-                mkdir $rootDir/public/$BLADE
-                mkdir $rootDir/public/$BLADE/unstable
-                mkdir $rootDir/public/$BLADE/latest
-                mkdir $rootDir/public/$BLADE/stable
+                mkdir -p $rootDir/public/$BLADE/$version
 
-                # change to the blade directory to be built
-                cd $BLADE
+                echo "going to $BLADE..."
+                pushd $BLADE
+
+                # run contribute
+                cp -v ../../template/Gruntfile.coffee .
+                ln -sv ../../theme/package.json package.json
+                ln -sv ../../theme theme
 
                 # install npm
-                npm install -g npm@latest yo grunt-cli generator-reveal
-                npm install
-
-                # build the unstable version - can be optimized
-                git submodule update --init
-                grunt dist
-                mv public/* $rootDir/public/$BLADE/unstable/.
-                echo " > unstable built for file set ${BLADE}"
-
-                # build the master version into stable
-                git fetch --tags
-                latestTag=$(git describe --tags `git rev-list --tags --max-count=1`)
-                git checkout $latestTag
-                git submodule update --init
-                grunt dist
-                mv public/* $rootDir/public/$BLADE/stable/.
-                echo " > stable built for file set ${BLADE}"
-
-                # build the develop version into latest
-                git checkout -f develop
-                git fetch origin develop
-                git reset --hard origin/develop
-                git submodule update --init
-                grunt dist
-                mv public/* $rootDir/public/$BLADE/latest/.
+                echo "installing deps"
+                yarn add grunt-cli generator-reveal grunt
+                yarn install
+
+                echo "running dist"
+                yarn exec grunt dist
+                echo "copying to common public dir"
+                cp -rLv public/* $rootDir/public/$BLADE/$version/.
+
                 echo " > latest built for file set ${BLADE}"
 
                 # auto redirect file to the stable version
@@ -72,8 +76,12 @@ do
                     </html>\n' > $rootDir/public/$BLADE/index.html
 
                 echo "autoredirect file set"
+
+                # move back out
+                popd
                 echo " > -----------------------------------------------------"
             fi
         done
+        popd
     fi
-done
\ No newline at end of file
+done

.ci/generateIndex.py

+import os, re
+from os import path
+
+def build_link(title, href):
+    return f'- <a href="{href}">{title}</a>\n'
+
+def build_section_start(title):
+    return f'\n' #<h3>{title}</h3>\n
+
+def build_section_end():
+    return "" #\t\t</ul>\n\t</div>
+
+def camel_to_snake(name):
+  name = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
+  return re.sub('([a-z0-9])([A-Z])', r'\1_\2', name).lower()
+
+# loop through the entire internal tree
+localroot = os.getcwd()
+
+
+# generate the index properly speaking
+cardDirs = ["2023", "2022", "2021", "2020", "2019"]
+index=''
+
+# determine first the directories
+for direct in cardDirs:
+    if path.isdir(direct):
+        dirs = os.listdir(direct)
+        dirs.sort(reverse=True);
+        index += "\n# " + direct + "\n\n"
+        for d in dirs:
+            if d[0] != ".":
+                href = 'https://courses.lcsb.uni.lu/'+d
+                linkText = camel_to_snake(d)
+                linkText = linkText.replace("_", " ")
+                linkText = linkText.title()
+
+                # special rules
+                linkText = linkText.replace("Dm", "Data Management")
+                linkText = linkText.replace("It", "IT")
+                linkText = linkText.replace("Siu", "SIU")
+
+                index += build_link(linkText, href)
+
+# output the index
+print(index)
+
+
+# Read in the file
+repoName = "courses.lcsb.uni.lu"
+os.chdir(repoName)
+indexFile = "index.md"
+filedata = ""
+with open(indexFile, 'r') as file :
+    for line in file:
+        filedata += line
+
+        # stop reading once the index place holder has been reached
+        if re.search("<!-- index -->", line):
+            filedata += "[[ index ]]"
+            break
+
+# Replace the target string
+filedata = filedata.replace('[[ index ]]', index)
+
+# Write the file out again
+with open(indexFile, 'w') as file:
+  file.write(filedata)
+
+print("\n > New index generated and saved in " + indexFile)
+os.chdir("..")

.gitattributes

+*.psd filter=lfs diff=lfs merge=lfs -text
+*.mov filter=lfs diff=lfs merge=lfs -text
+*.mp4 filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text

.gitignore

+*.ai
+site/
+courses.lcsb.uni.lu
 index.html
 package-lock.json
 dist/
@@ -10,4 +13,14 @@ dist
 .DS_Store
 yarn.lock
 stable/
-latest/
\ No newline at end of file
+latest/
+Gruntfile.coffee
+!template/Gruntfile.coffee
+package.json
+!template/package.json
+20*/*/theme
+!./theme
+./theme/package.json
+__pycache__/
+contribute.egg-info/
+.*.swp

.gitlab-ci.yml

-image: digitallyseamless/nodejs-bower-grunt
+stages:
+  - retrieve
+  - generate
+  - build
+  - deploy
 
-pages:
-  stage: deploy
+retrieve:repo:
+  image:
+    name: alpine/git:latest
+    entrypoint: [""]
+  stage: retrieve
   script:
-    - bash .ci/deploy.sh
+    - git clone https://$CI_DEPLOY_TOKEN:$CI_DEPLOY_PASSWORD@git-r3lab.uni.lu/R3/school/courses.lcsb.uni.lu.git
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - courses.lcsb.uni.lu
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
 
+generate:index:
+  image: python
+  stage: generate
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+  script:
+    - python .ci/generateIndex.py
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - courses.lcsb.uni.lu
+
+build:website:
+  image: git-r3lab.uni.lu:4567/r3/docker/jekyll-lcsb
+  stage: build
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+  before_script:
+    - cd courses.lcsb.uni.lu
+    - gem install bundler -v2.0.2
+    - bundle install && bundle update jekyll-theme-lcsb-default && bundle update jekyll-theme-lcsb-frozen-components
+    - cd ..
+  script:
+    - cd courses.lcsb.uni.lu
+    - bundle exec jekyll build -d site --config "_config.yml"
+    - mv site ../.
+    - cd ..
   artifacts:
+    expire_in: 1 day
+    paths:
+      - site
+  variables:
+    JEKYLL_ENV: production
+
+build:courses:
+  image: node:19-bullseye
+  stage: build
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+  script:
+    - bash .ci/deploy.sh
+  artifacts:
+    expire_in: 1 day
     paths:
       - public
+
+upload:
+  stage: deploy
+  image: alpine
+  before_script:
+    - apk add rsync
+    - 'which ssh-agent || ( apk add --update openssh )'
+    - eval $(ssh-agent -s)
+    - echo "$B64SSHPRIVKEY" | base64 -d | tr -d '\r' | ssh-add - > /dev/null
+    - mkdir -p ~/.ssh && chmod 700 ~/.ssh
+    - 'echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config'
+    - echo "$KNOWNHOSTS" > ~/.ssh/known_hosts
+    - chmod 644 ~/.ssh/known_hosts
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+  script:
+    - rsync -ravu --info=progress2 -e "ssh -p $SSHPORT" site/* $SSHCONNECT:~/web/latest
+    - rsync -ravu --info=progress2 -e "ssh -p $SSHPORT" public/* $SSHCONNECT:~/web/latest

.gitmodules

-[submodule "theme/reveal.js"]
-	path = theme/reveal.js
-	url = https://github.com/hakimel/reveal.js.git
+[submodule "theme"]
+	path = theme
+	url = https://gitlab.lcsb.uni.lu/R3/outreach/theme.git
+
+

2019/2019-06-11_gitTraining/slides/best_practices.md → 2019/2019-06-11_basicGitTraining/slides/best_practices.md

-## Best practices
+# Best practices
 
 * `pull` before `push`
-
 * Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
-
 * Do **not push** to `master`, but **submit a PR**
-
 * Get your code **reviewed** by your peers (submit a PR!)
-
 * Submit a PR **often**!
-
 * `clone` a repository, do not download the `.zip` file.
-
-
 * Do **not** combine `git` commands
    ```bash
    $ git commit -am "myMessage" # do not do this
    ```
-
 * Stage only 1 file at once using
-
    ```bash
    $ git add myFile.md
    ```
-
 * Commit **only a few files** at once (after multiple separate `git add` commands)
-
 * `Push` often - avoid conflicts
 
-<br><br>
 Remember: **A `push` a day keeps conflicts away!**

2019/2019-06-11_gitTraining/slides/branches.md → 2019/2019-06-11_basicGitTraining/slides/branches.md

-## Development scheme
+# Development scheme
 
 
 Generally, in a repository, there are guidelines for contributing.
@@ -26,7 +26,7 @@ A **version** of the code is referred to as a **branch**.
 
 
 
-## Branches
+# Branches
 
 A **version** of the code (i.e., a **branch**) is made up of a sequence of code changes.
 
@@ -40,7 +40,7 @@ For instance, the `master` and `develop` branches can be represented as a timeli
 
 
 
-## Switch between branches
+# Switch between branches
 
 List all branches of the repository with
 ```bash
@@ -53,7 +53,7 @@ Exit by typing `q`. The branch with the * is the current branch.
 
 Checkout another branch
 ```bash
-$ git checkout branchName
+$ git checkout <branchName>
 ```
 
 <div class="fragment">
@@ -62,6 +62,7 @@ You can switch to the `develop` branch with
 ```bash
 $ git checkout develop
 ```
+If the local branch does not exist but the remote does, it is created automatically.
 
 <div class="fragment">
 
@@ -69,9 +70,9 @@ $ git checkout develop
 
 
 
-## Create your own version
+# Create your own version
 
-Assume that you want to work on a function for adding 2 numbers.
+Assume that you want to work on a file:
 
 <div class="fragment">
 

2019/2019-06-11_gitTraining/slides/cloneRepo.md → 2019/2019-06-11_basicGitTraining/slides/cloneRepo.md

-## How do I start working on a repository?
+# How do I start working on a repository?
 
 You have to `clone` it first:
 

2019/2019-06-11_gitTraining/slides/configuration.md → 2019/2019-06-11_basicGitTraining/slides/configuration.md

-## How to configure `git`?
+# How to configure `git`?
 
 ```bash
 $ git config --global user.name "Firstname Lastname"
@@ -17,7 +17,7 @@ Exit by typing `q`.
 
 
 
-## What is an SSH key?
+# What is an SSH key?
 
 An SSH key is a secure access credential.
 
@@ -26,7 +26,7 @@ Communicate **securely** with Github/Gitlab **without** entering the username/pa
 
 
 
-## How do I get and set my SSH key?
+# How do I get and set my SSH key?
 
 Check if you already have an SSH key:
 

2019/2019-06-11_gitTraining/slides/essential_commands.md → 2019/2019-06-11_basicGitTraining/slides/essential_commands.md

-## The 5 essential commands
+# The 5 essential commands
 
 
 **Yes**, you only need 5 commands!
@@ -16,7 +16,7 @@ $ git push <remote> <branch>
 
 
 
-## Pull the latest version of an existing branch
+# Pull the latest version of an existing branch
 
 Pull the latest revision on branch `myBranch`:
 ```bash
@@ -33,7 +33,7 @@ $ git status
 
 
 
-## Modify a file
+# Modify a file
 
 Copy the file `template.md` in the folder `_attendees` and rename it with your firstname:
 
@@ -46,7 +46,7 @@ Then, make your changes with your favorite editor!
 
 
 
-## Add your file to the stage
+# Add your file to the stage
 
 First, check the repository status
 ```bash
@@ -54,13 +54,6 @@ $ git status
 # uncommitted changes (displayed in red)
 ```
 
-<div class="fragment">
-
-**ADVANCED**: see your changes in the terminal
-```bash
-$ git diff
-```
-exit with `q`
 
 <div class="fragment">
 
@@ -71,9 +64,17 @@ $ git status
 # returns the same as before, generally in green (means staged)
 ```
 
+<div class="fragment">
+
+**ADVANCED**: If there have been more changes after the file has been added, you can see your changes in the terminal
+```bash
+$ git diff
+```
+exit with `q`
+
 
 
-## Add a commit message
+# Add a commit message
 
 ```bash
 $ git commit -m "Add the profile of <myName>"
@@ -82,7 +83,7 @@ $ git status
 
 
 
-## Push your file to your fork
+# Push your file to your fork
 
 ```bash
 $ git push origin myBranch

2019/2019-06-11_gitTraining/slides/forks.md → 2019/2019-06-11_basicGitTraining/slides/forks.md

-
-## What is a `fork`?
+# What is a `fork`?
 
 <img src="slides/img/fork.jpg" class="as-is" height="500em"/>
 <!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
 
 
 
-## Not really ...
+# Not really ...
 
 <img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
 
 
 
-## What is a `fork`?
+# What is a `fork`?
 
 In general, when contributing to a repository, you only have **read** access.
 
@@ -26,7 +25,7 @@ In other words, you have to work on your own <font color="red">**fork**</font>.
 
 
 
-## How to get a fork?
+# How to get a fork?
 
 Browse to the original repository and click on the button `Fork`:
 
@@ -36,7 +35,7 @@ Browse to the original repository and click on the button `Fork`:
 
 
 
-## Time to practice!
+# Time to practice!
 
 Fork the practice repository: <br><br>
 https://github.com/LCSB-BioCore/basic-git-practice
@@ -56,7 +55,7 @@ $ cd basic-git-practice
 
 
 
-## A note on shortcuts ...
+# A note on shortcuts ...
 
 <font color="red">
 Any other rudimentary method such as
@@ -70,9 +69,9 @@ shall **be avoided**!
 
 
 
-## How to update my fork?
+# How to update my fork?
 
-As you have your own fork, it will not automatically update once the original repository is update.
+As you have your own fork, it will not automatically be updated once the original repository is updated.
 
 ![bulb](slides/img/bulb.png) You have to update it yourself!
 

2019/2019-06-11_gitTraining/slides/github_gitlab.md → 2019/2019-06-11_basicGitTraining/slides/github_gitlab.md

-## GitHub and GitLab
+# GitHub and GitLab
 
 <img src="https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png" alt="GitHub" style="width: 200px;"/>
 <img src="https://gitlab.com/gitlab-com/gitlab-artwork/raw/master/logo/logo-extra-whitespace.png" alt="GitLab" style="width: 200px;"/>