.ci/deploy.sh

@@ -10,9 +10,9 @@ rm -rf $rootDir/public
 rm -rf $rootDir/theme
 mkdir $rootDir/public
 
-if [[ $CI_COMMIT_BRANCH == "develop" ]]; then
+if [[ $CI_COMMIT_REF_NAME == "develop" ]]; then
     version="latest";
-elif [[ $CI_COMMIT_BRANCH == "master" ]]; then
+elif [[ $CI_COMMIT_REF_NAME == "master" ]]; then
     version="stable";
 else
     version="unstable";
@@ -33,7 +33,7 @@ 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
@@ -46,20 +46,23 @@ do
                 # create the required folders in public
                 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 ../../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
-                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/$version/.
+                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}"
 
@@ -75,10 +78,10 @@ do
                 echo "autoredirect file set"
 
                 # move back out
-                cd ..
+                popd
                 echo " > -----------------------------------------------------"
             fi
         done
-        cd "${rootDir}"
+        popd
     fi
 done

.ci/generateIndex.py

@@ -19,7 +19,7 @@ localroot = os.getcwd()
 
 
 # generate the index properly speaking
-cardDirs = ["2020", "2019"]
+cardDirs = ["2023", "2022", "2021", "2020", "2019"]
 index=''
 
 # determine first the directories
@@ -68,4 +68,4 @@ with open(indexFile, 'w') as file:
   file.write(filedata)
 
 print("\n > New index generated and saved in " + indexFile)
-os.chdir("..")
\ No newline at end of file
+os.chdir("..")

.gitignore

+*.ai
 site/
 courses.lcsb.uni.lu
 index.html
@@ -22,3 +23,4 @@ package.json
 ./theme/package.json
 __pycache__/
 contribute.egg-info/
+.*.swp

.gitlab-ci.yml

@@ -56,7 +56,7 @@ build:website:
     JEKYLL_ENV: production
 
 build:courses:
-  image: git-r3lab.uni.lu:4567/r3/docker/nodejs-yarn-grunt
+  image: node:19-bullseye
   stage: build
   rules:
     - if: $CI_COMMIT_BRANCH == "develop"
@@ -72,6 +72,7 @@ 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
@@ -83,5 +84,5 @@ upload:
     - if: $CI_COMMIT_BRANCH == "develop"
     - if: $CI_COMMIT_BRANCH == "master"
   script:
-    - scp -P $SSHPORT -r site/* $SSHCONNECT:~/web/latest
-    - scp -P $SSHPORT -r public/* $SSHCONNECT:~/web/latest
+    - 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
 
 

2020/2020-05-12_IT101-DM/slides/rudi_balling.jpg

-../../2020-03-12_IT101-DM/slides/img/rudi_balling.jpg
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures

-../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/alexey_kolodkin.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/alexey_kolodkin.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/christophe_trefois.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/christophe_trefois.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/laurent_heirendt.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/laurent_heirendt.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/maharshi_vyas.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/maharshi_vyas.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/noua_toukourou.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/noua_toukourou.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/pinar_alper.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/pinar_alper.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/reinhard_schneider.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/reinhard_schneider.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/sarah_peter.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/sarah_peter.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/venkata_satagopam.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/venkata_satagopam.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/vilem_ded.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/vilem_ded.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/wei_gu.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/wei_gu.png
\ No newline at end of file

2020/2020-06-09_IT101-DM/slides/img/R3_profile_pictures/yohan_yarosz.png

+../../../../2020-03-12_IT101-DM/slides/img/R3_profile_pictures/yohan_yarosz.png
\ No newline at end of file

2021/2021-03-09_IT101-DM/slides/code_versioning.md

+# Code versioning
+<div style="position:absolute; width:40%">
+
+**git**
+
+  * Current standard for code versioning
+  * Maintain versions of your code as it develops
+  * Local system, which does not require an online repository
+  * Repositories allow distributed development
+
+<img  align="middle" height="300px" src="slides/img/Git-logo.png">
+</div>
+
+<div class="fragment" style="position:absolute; left:50%; width:40%"">
+
+**git@lcsb** 
+* Recommended, supported repository
+* Allows tracking of issues
+* Ready for continous integration - code checked on commits to the repository.
+* [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
+
+
+  **Use at LCSB** 
+
+   * All analyses code should be in a repository
+      * Minimally at submission of a manuscript
+      * Better daily
+      * Even better "analyses chunkwise"
+</div>
+
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
+<a href="https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-07" style="color:grey; font-size:0.8em;">LCSB-POL-BIC-07 Source Code Management Policy</a>
+</div>