.ci/deploy.sh

@@ -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
-                cp -rL 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 = ["2022", "2021", "2020", "2019"]
+cardDirs = ["2023", "2022", "2021", "2020", "2019"]
 index=''
 
 # determine first the directories

.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
@@ -83,6 +84,5 @@ upload:
     - if: $CI_COMMIT_BRANCH == "develop"
     - if: $CI_COMMIT_BRANCH == "master"
   script:
-    - ssh -p $SSHPORT $SSHCONNECT "rm -rf ~/web/latest/*"
-    - 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
 
 

2022/2022-05-31_git-trilogy-part-1/slides/best_practices.md

+
+# Summary
+
+GitLab creates a convenient and efficient working environment
+  - merge requests
+  - issues
+  - assignments
+  - much much more...
+
+
+
+# Best practices
+
+* Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
+* Do **not commit** to `master`/`develop`, but **submit a merge request (MR)**
+* Get your code **reviewed** by your peers (submit a merge request!)
+* Submit a merge request **often**! (as soon as the feature is ready)
+* Make commits often (keeps increments small)
+
+

2022/2022-05-31_git-trilogy-part-1/slides/branches.md

+# New term:  <font color="color:red">branch</font>
+
+* A sequence of commits (changes) is referred to as *branch*.
+* A new branch can be created by *branching off* from a commit on another branch.
+* A *branch* can be understood as a named *version* of your repository.
+
+<div style="position:absolute;left:50%;top:1em">
+<img src="slides/img/branch_branch-off_detail.png" class="as-is" height="800px"/>
+</div>
+
+
+
+# Development scheme
+
+Generally, in a repository, there are guidelines for contributing.
+
+<br>
+
+A common development scheme is dual with a:
+
+- **development** version on `develop`
+  - things are still being changed and mistakes are being fixed
+- **stable** version on `master`
+  - actively used version in production environment
+
+
+<div class="fragment">
+<div style="position:absolute;left:60%;top:1em">
+<img src="slides/img/branch_master-develop.png" height="800px">
+</div>
+
+<font color="red">In the practice 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!
+
+
+
+# Create your own version
+
+Assume that you want to work on a new content.
+
+Best practice is to <font color="red">create a new **branch**!</font>
+
+<div class="fragment">
+<div style="position:absolute;left:60%;top:1em">
+<img src="slides/img/branch_my-branch.png" height="800em"/>
+</div>
+
+<br>
+
+Using branches ensures:
+* your changes are made separately from other (unrelated) changes
+* your version will not be affected by other contributors
+* all related changes are aggregated in one place
+* work can continue if the development of one feature gets stuck
+
+<br>
+Are you working on more features in parallel?
+
+<font color="red">Create a new **branch**!</font> for each of them!
+
+
+
+
+
+# Quick recap
+
+What is the difference between a *fork* and a *branch*?
+
+<div class="fragment">
+<br><br><br>
+<div align="center">
+<img src="slides/img/forking_detail-with-branches.png" height="500em"/>
+</div>
+
+
+
+
+# How to switch between branches?
+
+<div align="center">
+<img src="slides/img/branch_GUI_switch.png" height="500em"/>
+</div>
+
+
+![bulb](slides/img/bulb.png) Why is it best practice to branch off from `develop`?
\ No newline at end of file

2022/2022-05-31_git-trilogy-part-1/slides/commit.md

+# New term: <font color="color:red">commit</font>
+
+* Your repository (your file) is in a certain state.
+* Every change moves the repository to a new state.
+* Every change added to the sequence of changes is called **commit**.
+* Every commit has:
+  * content - what?
+  * a message - why?
+  * an author - who?
+  * a timestamp - when?
+  * unique identifier - tracking number
+
+<div style="position:absolute;left:60%;top:1em">
+<img src="slides/img/commit_history-diagram.png" class="as-is" height="800px"/>
+</div>
+
+<div class="fragment">
+Gitlab:
+<div style="position:absolute">
+<img src="slides/img/commit_GUI_1.png" class="as-is" height="350px"/>
+</div>
+</div>
+
+
+
+# New term: <font color="color:red">commit</font>
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+1. Notice last commits that modified files/folders
+<!-- .element: class="fragment" data-fragment-index="1" -->
+1. Review history of your repository
+<!-- .element: class="fragment" data-fragment-index="2" -->
+1. See changes in the last/second last/third last commit.
+<!-- .element: class="fragment" data-fragment-index="3" -->
+
+
+<div class="fragment fade-in-then-out" style="position:absolute;left:50%;top:1em" data-fragment-index="1">
+    <img src="slides/img/commit_GUI_main-last-commit.png" class="as-is" height="500px"/>
+</div>
+
+<div class="fragment fade-in-then-out" style="position:absolute;left:50%;top:1em" data-fragment-index="2">
+    <img src="slides/img/commit_GUI_main-history.png" class="as-is" height="500px"/>
+</div>
+
+<div class="fragment fade-in-then-out" style="position:absolute;left:50%;top:4em" data-fragment-index="3">
+<img src="slides/img/commit_GUI_click-on-commit.png" class="as-is" height="75px"/>
+</div>
+<div class="fragment fade-in-then-out" data-fragment-index="3">
+<img src="slides/img/commit_changes.png" class="as-is" width="90%"/>
+</div>

2022/2022-05-31_git-trilogy-part-1/slides/example.md

+# Complete example
+
+Task: add your name to the list of attendees in the practice repository.
+
+- Repository: [https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages](https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages)
+- Development Branch: `develop`
+- Website: [https://r3.pages.uni.lu/school/git/basic-practice-pages](https://r3.pages.uni.lu/school/git/basic-practice-pages)
+
+
+<img src="slides/img/icon-live-demo.png" height="100px">

2022/2022-05-31_git-trilogy-part-1/slides/forks.md

+# New term:  <font color="color:red">fork</font>
+## What is a `fork`?
+
+<center>
+<img src="slides/img/fork.jpg" class="as-is" height="500em"/>
+</center>
+
+
+
+# New term:  <font color="color:red">fork</font>
+## Not really ...
+
+<center>
+<img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
+</center>
+
+
+
+# New term:  <font color="color:red">fork</font>
+## What is a `fork`?
+
+- In general, by default, you can only **read** files in a repository. You **cannot write**.
+
+<div class="fragment">
+<div align="center">
+<img src="slides/img/forking.png" width="80%">
+</div>
+
+- You have to work on your **own copy** of the repository in order to make changes.
+- In other words, you have to work on your own <font color="red">**fork**</font>.
+
+
+
+
+# How to get a fork?
+
+Browse to the original repository and click on the button `Fork`:
+
+<div align="center">
+<img src="https://docs.gitlab.com/ee/user/project/repository/img/forking_workflow_fork_button_v13_10.png" height="150">
+</div>
+
+<br>
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+## Time to practice!
+
+1. Fork the training repository  [https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages](https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages)
+
+
+Congrats! Now you have your own **fork**!
+
+
+
+# How to update my fork?
+
+As you have your own copy (fork), it will not automatically be updated once the original repository is updated.
+
+![bulb](slides/img/bulb.png) You have to update it yourself!
+
+<br>
+
+**More on that later - time permitting**

2022/2022-05-31_git-trilogy-part-1/slides/gitlab.md

+# Git repository hosting platforms
+
+<div style="position:absolute; left:70%">
+<img src="https://gitlab.com/gitlab-com/gitlab-artwork/raw/master/logo/logo-extra-whitespace.png" alt="GitLab" style="width: 500px;"/>
+</div>
+
+Web-based platforms with **many** features facilitating storing, tracking and collaborating on `git` repositories.
+
+* cloud based - everything on remote server
+* authentication and authorization - who can see or access the repository and how
+* access to files via browser - manage, view, make changes, ...
+* collaboration supporting features - comment, create issues, documentation, ...
+
+**Gitlab** is both publicly available or can be deployed on-premise.
+
+- Public GitLab: [https://gitlab.com](https://gitlab.com)
+- **LCSB** specific: [https://gitlab.lcsb.uni.lu](https://gitlab.lcsb.uni.lu)
+
+Other popular platforms:
+- **GitHub**: [https://github.com](https://github.com)
+- **BitBucket**: [https://bitbucket.org](https://bitbucket.org)
+- **Gitea**: [https://gitea.io](https://gitea.io)
+
+
+
+# Login and report and issue
+
+1. Login to [https://gitlab.lcsb.uni.lu](https://gitlab.lcsb.uni.lu)
+   * use your LUMS credentials
+2. Browse the existing repositories
+   * Explore and Search
+   * Navigate to the training repository [https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages](https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages)
+3. Inspect project/repository folder structure
+4. Report an issue
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+