Compare revisions

31cee192 · fa814cb6 · bec9edd1 · 88f28e32 · af5bd282 · 1d578c3b
--- a/.ci/.autoRedirect
+++ b/.ci/.autoRedirect
-<html>
-<head>
-<meta http-equiv="refresh" content="0; url=https://r3.pages.uni.lu/school/theme/stable"/>
-</head>
-
-<body>
-</bod>
-</html>
--- a/.ci/analytics/gdpr-banner.html
+++ b/.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
--- a/.ci/analytics/head.html
+++ b/.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" />
--- a/.ci/analytics/policy.html
+++ b/.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
--- a/.ci/deploy.sh
+++ b/.ci/deploy.sh
 #!/bin/bash

-# install npm
-npm install -g npm@latest grunt-cli generator-reveal
-npm install
-
-# build the master version into stable
-git fetch --tags
-latestTag=$(git describe --tags `git rev-list --tags --max-count=1`)
-git checkout $latestTag
-git submodule update --init
-grunt dist
-mkdir stable
-mv public/* stable/.
-
-# build the develop version into latest
-git checkout -f develop
-git fetch origin develop
-git reset --hard origin/develop
-git submodule update --init
-grunt dist
-mkdir latest
-mv public/* latest/.
-
-# deploy the stable and latest directories
-mv stable public/.
-mv latest public/.
-
-# auto redirect file
-cp .ci/.autoRedirect public/index.html
+PAGEURL="https://courses.lcsb.uni.lu"
+
+rootDir=$(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
+        pushd "${d}"
+        echo "changed to ${d}"
+        for d1 in $(find . -maxdepth 1 -type d)
+        do
+            if [[ ${#d1} -ge 2 ]]; then
+                let "nBlades+=1"
+                BLADE=${d1:2}
+                echo " > -----------------------------------------------------"
+                echo "Building ... ${d1}"
+
+                # create the required folders in public
+                mkdir -p $rootDir/public/$BLADE/$version
+
+                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
+                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 ${BLADE}"
+
+                # auto redirect file to the stable version
+                echo '<html>\n
+                    <head>\n
+                    <meta http-equiv="refresh" content="0; url='$PAGEURL'/'$BLADE'/stable"/>\n
+                    </head>\n
+                    <body>\n
+                    </bod>\n
+                    </html>\n' > $rootDir/public/$BLADE/index.html
+
+                echo "autoredirect file set"
+
+                # move back out
+                popd
+                echo " > -----------------------------------------------------"
+            fi
+        done
+        popd
+    fi
+done
--- a/.ci/generateIndex.py
+++ b/.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("..")
--- a/.gitattributes
+++ b/.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
--- a/.gitignore
+++ b/.gitignore
+*.ai
+site/
+courses.lcsb.uni.lu
 index.html
 package-lock.json
 dist/
@@ -8,4 +11,16 @@ dist
 .sass-cache
 .grunt
 .DS_Store
-yarn.lock
\ No newline at end of file
+yarn.lock
+stable/
+latest/
+Gruntfile.coffee
+!template/Gruntfile.coffee
+package.json
+!template/package.json
+20*/*/theme
+!./theme
+./theme/package.json
+__pycache__/
+contribute.egg-info/
+.*.swp
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
-image: digitallyseamless/nodejs-bower-grunt
+stages:
+  - retrieve
+  - generate
+  - build
+  - deploy

-pages:
-  stage: deploy
-  only:
-    - develop
-    - master
+retrieve:repo:
+  image:
+    name: alpine/git:latest
+    entrypoint: [""]
+  stage: retrieve
  script:
-    # install npm
-    - 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
--- a/.gitmodules
+++ b/.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
+
+
--- a/2019/2019-06-11_basicGitTraining/slides/best_practices.md
+++ b/2019/2019-06-11_basicGitTraining/slides/best_practices.md
+# 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
+
+Remember: **A `push` a day keeps conflicts away!**
--- a/2019/2019-06-11_basicGitTraining/slides/branches.md
+++ b/2019/2019-06-11_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">
--- a/2019/2019-06-11_basicGitTraining/slides/cloneRepo.md
+++ b/2019/2019-06-11_basicGitTraining/slides/cloneRepo.md
+# How do I start working on a repository?
+
+You have to `clone` it first:
+
+```bash
+$ git clone git@github.com:userName/myRepo.git myRepo
+```
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://github.com/userName/myRepo.git myRepo
+```
+
+You will be prompted to enter your credentials.
--- a/2019/2019-06-11_basicGitTraining/slides/configuration.md
+++ b/2019/2019-06-11_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
+```
+
+Then, add the SSH key to Github/Gitlab.
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file
--- a/2019/2019-06-11_basicGitTraining/slides/essential_commands.md
+++ b/2019/2019-06-11_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 `template.md` in the folder `_attendees` and rename it with your firstname:
+
+```bash
+$ cd _attendees
+$ cp template.md myName.md
+```
+
+Then, make your changes with your favorite editor!
+
+
+
+# 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`
+
+
+
+# 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
--- a/2019/2019-06-11_basicGitTraining/slides/forks.md
+++ b/2019/2019-06-11_basicGitTraining/slides/forks.md
+# 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 ...
+
+<img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
+
+
+
+# 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
+
+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
+```
+
+
+
+# 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>
+
+**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!
+
+**More on that later!**
+
--- a/2019/2019-06-11_basicGitTraining/slides/github_gitlab.md
+++ b/2019/2019-06-11_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)
\ No newline at end of file
--- a/2019/2019-06-11_basicGitTraining/slides/img/Git-Logo-Black.png
+++ b/2019/2019-06-11_basicGitTraining/slides/img/Git-Logo-Black.png
--- a/2019/2019-06-11_basicGitTraining/slides/img/arianeLaunch.mov
+++ b/2019/2019-06-11_basicGitTraining/slides/img/arianeLaunch.mov
--- a/2019/2019-06-11_basicGitTraining/slides/img/branch-create.png
+++ b/2019/2019-06-11_basicGitTraining/slides/img/branch-create.png
No results found