delete html, add workflows, fix list wrappers

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+  - package-ecosystem: bundler
+    directory: /
+    schedule:
+      interval: daily
+    allow:
+      - dependency-type: direct

.github/workflows/ci.yml

@@ -0,0 +1,22 @@
+name: CI
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 0 # Increment this number if you need to re-download cached gems
+      - name: Build with Jekyll
+        run: bundle exec jekyll build

.github/workflows/pages.yml

@@ -0,0 +1,62 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll site to Pages
+
+on:
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 0 # Increment this number if you need to re-download cached gems
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v3
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - name: Upload artifact
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v1
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.gitignore

@@ -13,11 +13,11 @@ _site/
 __pycache__/
 _build/
 venv/
-slides/reveal.js/
-slides/theme/
-slides/filter/
-slides/convert.sh
-slides/*.html
+_slides/reveal.js/
+_slides/theme/
+_slides/filter/
+_slides/convert.sh
+_slides/*.html
 *.lock
 
 # Ignore folders generated by Bundler

part-1/allas/allas-backup.md

@@ -21,14 +21,14 @@ permalink: /hands-on/allas/tutorial_allas-file-backup.html
 csc-workspaces
 ```
 
-{:start="3"}
+{:style="counter-reset:step-counter 2"}
 3. Switch to the `/scratch` directory of your project
 
 ```bash
 cd /scratch/<project>    # replace <project> with your CSC project, e.g. project_2001234
 ```
 
-{:start="4"}
+{:style="counter-reset:step-counter 3"}
 4. Create your own subdirectory named as your username (tip! your username is automatically stored in the environment variable `$USER`):
 
 ```bash
@@ -47,22 +47,22 @@ allas-conf
 
 💡 It might take a while to run `module load allas`.
 
-{:start="2"}
+{:style="counter-reset:step-counter 1"}
 2. If you have several projects with the Allas service available, select the one where you want to perform the backup.
 3. Check how the `allas-backup` tool works with the command:
 
 ```bash
 allas-backup -h
 ```
 
-{:start="4"}
+{:style="counter-reset:step-counter 3"}
 4. Create a backup snapshot with the command:
 
 ```bash
 allas-backup <filename>    # replace <filename> with the name of the file that you want to backup
 ```
 
-{:start="5"}
+{:style="counter-reset:step-counter 4"}
 5. Check what snapshots the backup contains:
 
 ```bash
@@ -72,21 +72,21 @@ allas-backup list | grep $USER
 
 - Make note of the snapshot `ID` in the first column!
 
-{:start="6"}
+{:style="counter-reset:step-counter 5"}
 6. Check what files your backup contains:
 
 ```bash
 allas-backup files <snapshot_id>      # replace the <snapshot_id>
 ```
 
-{:start="7"}
+{:style="counter-reset:step-counter 6"}
 7. Restore the files from your backup to Puhti:
 
 ```bash
 allas-backup restore <snapshot_id>      # replace the <snapshot_id>
 ```
 
-{:start="8"}
+{:style="counter-reset:step-counter 7"}
 8. If you want to delete your backup, use command:
 
 ```bash

part-1/allas/allas-batch-jobs.md

@@ -30,7 +30,7 @@ allas-conf -k
 
 ☝🏻 Note that if you mistype your password when using the `-k` option, you must use the command `unset OS_PASSWORD` before you can try again.
 
-{:start="2"}
+{:style="counter-reset:step-counter 1"}
 2. Refresh the connection with the command:
 
 ```bash
@@ -39,21 +39,21 @@ allas-conf -k <project>    # replace <project> with your CSC project, e.g. proje
 
 ☝🏻 When `$OS_PASSWORD` is set, the `a-commands` (`a-put`, `a-get`, `a-list`, `a-delete`) automatically refresh the Allas connection when the commands are executed in a batch job.
 
-{:start="3"}
+{:style="counter-reset:step-counter 2"}
 3. Choose a file from Allas. The file should have text in it.
 
 ```bash
 a-list <project number>_$USER   # replace <project number> with your CSC project number, e.g. 2001234, to match the bucket you created earlier
 ```
 
-{:start="4"}
+{:style="counter-reset:step-counter 3"}
 4. Create a new batch job script. First open a new text file with the command:
 
 ```bash
 nano allas_<myjobname>.sh    # replace <myjobname> with a custom name for your job
 ```
 
-{:start="5"}
+{:style="counter-reset:step-counter 4"}
 5. Copy the batch job script below to the text file you are editing:
 
 - Option 1: `a-commands`
@@ -76,7 +76,7 @@ wc -l $filename > $filename.num_rows   # file name
 a-put -b $bucketname $filename.num_rows
 ```
 
-{:start="6"}
+{:style="counter-reset:step-counter 5"}
 6. In the script, replace `<project number>_$USER` to match your bucket name and `<filename>` to the name of the file you have in Allas. Remember to also define your billing project (`--account`).
 
 - Option 2: `rclone`  
@@ -107,15 +107,15 @@ source /appl/opt/csc-cli-utils/allas-cli-utils/allas_conf -f -k $OS_PROJECT_NAME
 rclone copy $filename.num_rows allas:$bucketname
 ```
 
-{:start="6"}
+{:style="counter-reset:step-counter 5"}
 6. Replace `<project number>_$USER` to match your bucket name and `<filename>` to the name of the file you have in Allas. Remember to also define your billing project (`--account`).
 7. Submit the batch job with the command:
 
 ```bash
 sbatch allas_<myjobname>.sh
 ```
 
-{:start="8"}
+{:style="counter-reset:step-counter 7"}
 8. Monitor the progress of your batch job:
 
 ```bash