.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/school/courses"
+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
-
-                # change to the blade directory to be built
-                cd $BLADE
+                mkdir -p $rootDir/public/$BLADE/$version
 
-                # build the unstable version - can be optimized
-                git config submodule.theme.url https://$CI_DEPLOY_USER:$CI_DEPLOY_PASSWORD@git-r3lab.uni.lu/R3-core/outreach/theme.git
-                git submodule update --recursive --init
+                echo "going to $BLADE..."
+                pushd $BLADE
 
                 # run contribute
-                cp ../../template/Gruntfile.coffee .
-                ln -s ../../theme/package.json package.json
-                ln -s ../../theme theme
+                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
-                yarn global add grunt-cli generator-reveal
+                echo "installing deps"
+                yarn add grunt-cli generator-reveal grunt
                 yarn install
 
-                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 stash
-                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 stash
-                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 "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
@@ -85,9 +78,10 @@ do
                 echo "autoredirect file set"
 
                 # move back out
-                cd ..
+                popd
                 echo " > -----------------------------------------------------"
             fi
         done
+        popd
     fi
 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("..")

.gitignore

+*.ai
+site/
+courses.lcsb.uni.lu
 index.html
 package-lock.json
 dist/
@@ -20,3 +23,4 @@ package.json
 ./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 week
+    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"]
 	path = theme
-	url = https://git-r3lab.uni.lu/R3/outreach/theme.git
+	url = https://gitlab.lcsb.uni.lu/R3/outreach/theme.git
 
 

2019/2019-06-11_basicGitTraining/slides/thanks.md

@@ -38,5 +38,5 @@
 
 Contact us if you need help:
 
-r3lab.core@uni.lu
+lcsb-r3@uni.lu
 

2019/2019-08-22_IT101-DM/slides/howtos.md

@@ -2,5 +2,5 @@
 <br>
 https://howto.lcsb.uni.lu/
 <center>
-  <iframe data-src="https://howto.lcsb.uni.lu/" height="600px" width="1200px"></iframe>
+  <img src="slides/img/howtocard.png" width="50%" style="border: 1px solid #555;">
 </center>

2019/2019-08-22_IT101-DM/slides/thanks.md

@@ -7,5 +7,5 @@
 <center>
 Contact us if you need help:
 
-<a href="mailto:r3lab.core@uni.lu">r3lab.core@uni.lu</a>
+<a href="mailto:lcsb-r3@uni.lu">lcsb-r3@uni.lu</a>
 </center>

2019/2019-09-24_advancedGitTraining/slides/thanks.md

@@ -4,5 +4,5 @@
 
 Contact us if you need help:
 
-<a href="mailto:r3lab.core@uni.lu">r3lab.core@uni.lu</a>
+<a href="mailto:lcsb-r3@uni.lu">lcsb-r3@uni.lu</a>
 

2019/2019-10-03_basicGitTraining-SIU/slides/thanks.md

@@ -38,5 +38,5 @@
 
 Contact us if you need help:
 
-r3lab.core@uni.lu
+lcsb-r3@uni.lu
 

2019/2019-10-10_advancedGitTraining-SIU/slides/thanks.md

@@ -4,5 +4,5 @@
 
 Contact us if you need help:
 
-<a href="mailto:r3lab.core@uni.lu">r3lab.core@uni.lu</a>
+<a href="mailto:lcsb-r3@uni.lu">lcsb-r3@uni.lu</a>
 

2019/2019-10-15_gnuLinuxCourse/slides/outline.md

-#+TITLE: Entry Level GNU/Linux Course at LCSB
-
-
-* Outline
-** Before the shell
-   - SSH
-   - SSH Clients
-   - Client installation Win (Mac?)
-   - RSA key generation
-   - Logging into a *nix server
-
-** University's identity credentials management system : LUMS
-   - Submitting keys
-   - Other things one can do
-
-** Effective shell usage
-    Overview of the capabilities and possibilities.
-*** Basics
-**** Filesystem
-     - ls/cd/mv/rm/cp
-     - scp (rsync?)
-     - what goes where (home,dev,proc,etc,usr)
-**** Documentation systems
-     - info
-     - man
-    
-**** Permissions
-     - (Super)users and groups
-     - read, write, execute
-     - chmod, chgrp, chown
-
-**** Environment
-     - environment variables
-     - PATH, HOME
-     - .profile and friends
-     - source (.)
-     
-*** Effective use
-**** SSH agent on remote server
-     - adapt the (bash)_profile
-**** History commands
-     - !, !!, !-N, ^...^, ....
-     
-**** find
-
-**** grep
-
-**** sed
-
-   
-
-

2020/2020-01-31_gitTrainingBioTech/slides/best_practices.md

+# Best practices
+
+* Fetch the upstream before creating a new branch.
+* Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
+* Get your code **reviewed** by your peers (submit a PR!)
+* Submit a PR **often**!
+* `Push` often - avoid conflicts
+
+Remember: **A `push` a day keeps conflicts away!**

2020/2020-01-31_gitTrainingBioTech/slides/branches.md

+# Development scheme
+
+
+Generally, in a repository, there are guidelines for contributing.
+
+<div class="fragment">
+
+A common development scheme is dual with a:
+
+- **development** version of the code on `develop`
+- **stable** version of the code on `master`
+
+
+A **version** of the code/text is referred to as a **branch**.
+
+<div class="fragment">
+
+<font color="red">In the `howto-cards-internal` repository, the development branch is called `develop`!</font>
+
+<div class="fragment">
+
+![bulb](slides/img/bulb.png) Use this dual development scheme for your own repositories!
+
+
+
+# Branches
+
+A **version** of the code (i.e., a **branch**) is made up of a sequence of code changes.
+
+<div class="fragment">
+
+These individual code changes are called **commits**.
+
+
+For instance, the `master` and `develop` branches can be represented as a timeline:
+<img src="slides/img/branch-master.png" class="branch-master" height="500em"/>
+
+
+
+# Switch between branches
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+
+# Create your own version
+
+Assume that you want to work on a file:
+
+<div class="fragment">
+
+<font color="red">Create a new **branch** and start editing!</font>
+
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+<img src="slides/img/branch-create.png" class="branch-create" height="500em"/>

2020/2020-01-31_gitTrainingBioTech/slides/configuration.md

+# How to configure `git`?
+
+```bash
+$ git config --global user.name "Firstname Lastname"
+$ git config --global user.email "first.last@uni.lu"
+```
+
+Test whether your username and email have been registered
+
+```bash
+$ git config --list
+```
+
+This should list the configuration with `user.name` and `user.email`.
+
+
+
+
+# What is an SSH key?
+
+An SSH key is a secure access credential.
+
+**Principle**: <br><br>
+Communicate **securely** with Github/Gitlab **without** entering the username/password.
+
+
+
+# How do I get and set my SSH key?
+
+Check if you already have an SSH key:
+
+```bash
+$ ls -al ~/.ssh
+```
+
+If there are 2 files named `id_rsa`, you have an SSH key.
+
+If you don’t have yet an SSH key, you have to generate one:
+```bash
+$ ssh-keygen -t rsa # -b 4096
+```
+
+Then, add the SSH key to your profile on git-r3lab.
+
+On Windows, please unmount `P:\` (your personal atlas folder) first.
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2020/2020-01-31_gitTrainingBioTech/slides/forks.md

+# What is a `fork`?
+
+<br><br>
+<center><img src="slides/img/fork.jpg" class="as-is" height="500em"/></center>
+<!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
+
+
+
+# Not really ...
+
+<br><br>
+<center><img src="slides/img/fork-crossed.png" class="as-is" height="500em"/></center>
+
+
+
+# What is a `fork`?
+
+- In general, when contributing to a repository, you only have **read** access.
+
+- In other words, you can only **pull** (unless it is your own repository or access has been granted).
+
+- In general, you **cannot write** changes. In other words, you do not have **push** access.
+
+- You have to work on your **own copy**.
+
+- In other words, you have to work on your own <font color="red">**fork**</font>.
+
+<br>
+<h2>How to get a fork?</h1>
+
+Browse to the original repository and click on the button `Fork`:
+
+![Fork the repo](https://help.github.com/assets/images/help/repository/fork_button.jpg)
+
+
+
+
+# How to update my fork?
+
+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!
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+**More on that during the demo!**
+
+
+
+
+# Time to practice!
+
+Fork the howto-cards (internal) repository: <br><br>
+https://git-r3lab.uni.lu/R3-core/howto-cards-internal/
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file