.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
 
 

2021/2021-03-18_basicGitTraining/slides/best_practices.md

+# Best practices
+
+* `pull` before `push` and, generally, before starting to work
+* 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 Pull Request (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
+
+Remember: **A `push` a day keeps conflicts away!**

2021/2021-03-18_basicGitTraining/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 is referred to as a **branch**.
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+<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!
+
+
+
+# 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
+
+List all branches of the repository with
+```bash
+$ git branch -a
+```
+
+Exit by typing `q`. The branch with the * is the current branch.
+
+<div class="fragment">
+
+Checkout another branch
+```bash
+$ git checkout <branchName>
+```
+
+<div class="fragment">
+
+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">
+
+<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**!</font>
+
+```bash
+$ git checkout -b myBranch
+```
+The `-b` flag creates the branch. Locally, you have your own version now:
+<img src="slides/img/branch-create.png" class="branch-create" height="500em"/>
+
+
+
+
+Push your version to your fork:
+```bash
+$ git push origin myBranch
+```
+
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px">

2021/2021-03-18_basicGitTraining/slides/cloneRepo.md

+# How do I start working on a repository?
+
+You have to `clone` it first:
+
+```bash
+$ git clone git@github.com:LCSB-BioCore/basic-git-practice.git
+```
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://github.com/LCSB-BioCore/basic-git-practice.git
+```
+
+You will be prompted to enter your credentials.

2021/2021-03-18_basicGitTraining/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`.
+
+Exit by typing `q`.
+
+
+
+# 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
+```
+
+If you set a password to your key (recommended), add it to the `ssh-agent`:
+```bash
+$ eval "$(ssh-agent -s)"
+$ ssh-add -K ~/.ssh/id_rsa
+```
+
+Then, add the SSH key to Github/Gitlab.
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2021/2021-03-18_basicGitTraining/slides/essential_commands.md

+# The 5 essential commands
+
+
+**Yes**, you only need 5 commands!
+
+`pull, status, add, commit, push`
+
+or in other words (remember these!):
+```bash
+$ git pull <remote> <branch>
+$ git status
+$ git add myFile.md # example
+$ git commit -m "myMessage" # example
+$ git push <remote> <branch>
+```
+
+
+
+
+# Pull the latest version of an existing branch
+
+Pull the latest revision on branch `myBranch`:
+```bash
+$ git pull origin myBranch
+# Already up to date
+```
+
+<div class="fragment">
+
+Verify its `status` with:
+```bash
+$ git status
+```
+
+
+
+# Modify a file
+
+Copy the file `firstnameLastname.md` in the folder `_attendees` and rename it with your firstname:
+
+```bash
+$ cd _attendees
+$ cp firstnameLastname.md myName.md
+```
+
+Then, make your changes with your favorite editor!
+
+<br><br>
+Reference for markdown: https://howto.lcsb.uni.lu/?contribute:markdown
+
+
+
+# Add your file to the stage
+
+First, check the repository status
+```bash
+$ git status
+# uncommitted changes (displayed in red)
+```
+
+
+<div class="fragment">
+
+Now, add the file (bring it on stage)
+```bash
+$ git add myName.md # replace myName
+$ 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`.
+
+<br>
+
+![bulb](slides/img/bulb.png)  If it is a long diff, you can display additional lines with space.
+
+
+
+# Add a commit message
+
+```bash
+$ git commit -m "Add the profile of <myName>"
+$ git status
+```
+
+
+
+# Push your file to your fork
+
+```bash
+$ git push origin myBranch
+```
+
+<div class="fragment">
+
+**ADVANCED**: see the log of all the commits (and your last one) in the terminal
+```bash
+$ git log
+```
+exit by typing `q`.
\ No newline at end of file

2021/2021-03-18_basicGitTraining/slides/forks.md

+# What is a `fork`?
+
+<center>
+<img src="slides/img/fork.jpg" class="as-is" height="500em"/>
+</center>
+<!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
+
+
+
+# Not really ...
+
+<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>.
+
+
+
+# How to get a fork?
+
+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)
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+
+# Time to practice!
+
+Fork the practice repository: <br><br>
+https://github.com/LCSB-BioCore/basic-git-practice<br><br>
+
+
+Then, clone your fork to your home directory!
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+```bash
+$ git clone git@github.com:<yourName>/basic-git-practice.git
+```
+
+Change to the practice directory with:
+```bash
+$ cd basic-git-practice
+```
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://github.com/<yourName>/basic-git-practice.git
+```
+
+
+
+# A note on shortcuts ...
+
+<font color="red">
+Any other rudimentary method such as
+
+*'I simply download the `.zip` and unzip it - works like a charm!'*
+
+shall **be avoided**!
+</font>
+
+<br>
+
+**Why?**
+
+
+
+# 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!
+
+<br>
+
+**More on that later!**

2021/2021-03-18_basicGitTraining/slides/github_gitlab.md

+# 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;"/>
+
+GitHub and GitLab are VCS systems.
+
+GitHub/Gitlab are both **publicly available**, but GitLab can be **on-premise**.
+
+Positive point: GitHub and GitLab are (almost) the same.
+
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+- **GitHub**: [https://github.com](https://github.com)
+- Public GitLab: [https://gitlab.com](https://gitlab.com)
+- LCSB specific: [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)

2021/2021-03-18_basicGitTraining/slides/img/Git-Logo-Black.png

+../../../../2020/2020-03-30_basicGitTraining/slides/img/Git-Logo-Black.png
\ No newline at end of file

2021/2021-03-18_basicGitTraining/slides/img/branch-create.png

+../../../../2020/2020-03-30_basicGitTraining/slides/img/branch-create.png
\ No newline at end of file

2021/2021-03-18_basicGitTraining/slides/img/branch-master.png

+../../../../2020/2020-03-30_basicGitTraining/slides/img/branch-master.png
\ No newline at end of file

2021/2021-03-18_basicGitTraining/slides/img/branch-merge.png

+../../../../2020/2020-03-30_basicGitTraining/slides/img/branch-merge.png
\ No newline at end of file

2021/2021-03-18_basicGitTraining/slides/img/bulb.png

+../../../../2020/2020-03-30_basicGitTraining/slides/img/bulb.png
\ No newline at end of file

2021/2021-03-18_basicGitTraining/slides/img/computerCode.png

+../../../../2020/2020-03-30_basicGitTraining/slides/img/computerCode.png
\ No newline at end of file

2021/2021-03-18_basicGitTraining/slides/img/favicon.ico

+../../../../2020/2020-03-30_basicGitTraining/slides/img/favicon.ico
\ No newline at end of file