update upstream

.github/ISSUE_TEMPLATE/1_bug_report.yml

@@ -81,7 +81,8 @@ body:
       description: select all environments where you have experienced this issue
       multiple: true
       options:
-        - "Running locally with Docker"
+        - "Running locally with Docker (docker compose)"
+        - "Running locally with Docker (devcontainer)"
         - "Running locally without Docker"
         - "Deployed site"
     validations:

.github/workflows/broken-links.yml

@@ -49,4 +49,4 @@ jobs:
         with:
           fail: true
           # removed md files that include liquid tags
-          args: --user-agent 'curl/7.54' --exclude-path README.md --exclude-path _pages/404.md --exclude-path _pages/blog.md --exclude-path _posts/2018-12-22-distill.md --verbose --no-progress './**/*.md' './**/*.html'
+          args: --user-agent 'curl/7.54' --exclude-path README.md --exclude-path _pages/404.md --exclude-path _pages/blog.md --exclude-path _posts/2018-12-22-distill.md --exclude-path _posts/2023-04-24-videos.md --verbose --no-progress './**/*.md' './**/*.html'

.github/workflows/deploy-docker-tag.yml

@@ -5,6 +5,8 @@ on:
     tags:
       - "v*"
     paths:
+      - ".github/workflows/deploy-docker-tag.yml"
+      - ".github/workflows/deploy-image.yml"
       - "bin/entry_point.sh"
       - "Dockerfile"
       - "Gemfile"

.github/workflows/deploy-image.yml

@@ -6,6 +6,7 @@ on:
       - master
       - main
     paths:
+      - ".github/workflows/deploy-image.yml"
       - "bin/entry_point.sh"
       - "Dockerfile"
       - "Gemfile"

.github/workflows/deploy.yml

@@ -7,6 +7,7 @@ on:
       - main
     paths:
       - "assets/**"
+      - "**.bib"
       - "**.html"
       - "**.js"
       - "**.liquid"
@@ -33,6 +34,7 @@ on:
       - main
     paths:
       - "assets/**"
+      - "**.bib"
       - "**.html"
       - "**.js"
       - "**.liquid"

.github/workflows/docker-slim.yml

@@ -2,6 +2,12 @@ name: Docker Slim
 
 #Only trigger, when the build workflow succeeded
 on:
+  push:
+    branches:
+      - master
+      - main
+    paths:
+      - ".github/workflows/docker-slim.yml"
   workflow_run:
     workflows: ["Docker Image CI"]
     types:
@@ -15,7 +21,7 @@ on:
 jobs:
   build:
     # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#running-a-workflow-based-on-the-conclusion-of-another-workflow
-    if: ${{ github.event.workflow_run.conclusion == 'success' }} and github.repository_owner == 'alshedivat'
+    if: ${{ github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'alshedivat' }}
     runs-on: ubuntu-latest
     defaults:
       run:

.github/workflows/lighthouse-badger.yml

@@ -12,10 +12,9 @@ name: "Lighthouse Badger"
 # DEFINE YOUR INPUTS AND TRIGGERS IN THE FOLLOWING
 ########################################################################
 
-# INPUTS as environmental variables (env) for not manually triggered workflows
+# INPUTS as Secrets (env) for not manually triggered workflows
 env:
   URLS: https://alshedivat.github.io/al-folio/
-  TOKEN_NAME: LIGHTHOUSE_BADGER_TOKEN
   # If any of the following env is blank, a default value is used instead
   REPO_BRANCH: "${{ github.repository }} master" # target repository & branch e.g. 'dummy/mytargetrepo main'
   MOBILE_LIGHTHOUSE_PARAMS: "--only-categories=performance,accessibility,best-practices,seo --throttling.cpuSlowdownMultiplier=2"
@@ -50,7 +49,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           repository: ${{ env.REPOSITORY }}
-          token: ${{ secrets[github.event.inputs.token_name] || secrets[env.TOKEN_NAME] }}
+          token: ${{ secrets.LIGHTHOUSE_BADGER_TOKEN }}
           ref: ${{ env.BRANCH }}
       - uses: actions/checkout@v4
         with:

.github/workflows/prettier-html.yml

@@ -0,0 +1,36 @@
+name: Prettify gh-pages
+
+on:
+  workflow_dispatch:
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+
+      - name: Find and Remove </source> Tags
+        run: find . -type f -name "*.html" -exec sed -i 's/<\/source>//g' {} +
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Check for Prettier
+        run: npx prettier --version || echo "Prettier not found"
+
+      - name: Run Prettier on HTML files
+        run: npx prettier --write '**/*.html'
+
+      - name: Commit and push changes
+        run: |
+          git config user.name "github-actions"
+          git config user.email "actions@github.com"
+          git add .
+          git commit -m "Formatted HTML files" || echo "No changes to commit"
+          git push

.github/workflows/schedule-posts.txt

@@ -0,0 +1,39 @@
+name: Publish posts scheduled for today
+
+on:
+  schedule:
+    # Run every day at 23:30 UTC or manually run
+    - cron: "30 23 * * *"
+  workflow_dispatch:
+
+jobs:
+  publish_scheduled:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main branch
+        uses: actions/checkout@v4
+        with:
+          ref: master
+
+      - name: Get the date for today
+        id: date
+        run: echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+
+      - name: Check for scheduled posts and move to posts
+        run: |
+          echo "Today is $TODAY"
+          shopt -s nullglob
+          for file in _scheduled/${TODAY}-*.md; do
+            echo "Found scheduled: $file"
+            mv "$file" "_posts/"
+            echo "Moved $file to _posts/"
+          done
+
+      - name: Commit and push changes
+        run: |
+          git config user.name "github-actions"
+          git config user.email "actions@github.com"
+          git add _posts/
+          git add _scheduled/
+          git commit -m "Posted Scheduled Drafts on $TODAY" || echo "No changes to commit"
+          git push

.gitignore

@@ -9,4 +9,5 @@ _site
 Gemfile.lock
 assets/libs/
 node_modules/
-vendor
+vendor
+.idea

.prettierignore

@@ -8,3 +8,4 @@ assets/js/search/*.js
 assets/plotly/demo.html
 lighthouse_results/**
 _posts/2015-10-20-math.md
+_sass/font-awesome/*.scss

CUSTOMIZE.md

@@ -80,7 +80,7 @@ You can easily create your own collections, apps, short stories, courses, or wha
 
 To add publications create a new entry in the [\_bibliography/papers.bib](_bibliography/papers.bib) file. You can find the BibTeX entry of a publication in Google Scholar by clicking on the quotation marks below the publication title, then clicking on "BibTeX", or also in the conference page itself. By default, the publications will be sorted by year and the most recent will be displayed first. You can change this behavior and more in the `Jekyll Scholar` section in [\_config.yml](_config.yml) file.
 
-You can add extra information to a publication, like a PDF file in the `assets/pdfs/` directory and add the path to the PDF file in the BibTeX entry with the `pdf` field. Some of the supported fields are: `abstract`, `altmetric`, `arxiv`, `bibtex_show`, `blog`, `code`, `dimensions`, `doi`, `eprint`, `html`, `isbn`, `pdf`, `pmid`, `poster`, `slides`, `supp`, `video`, and `website`.
+You can add extra information to a publication, like a PDF file in the `assets/pdfs/` directory and add the path to the PDF file in the BibTeX entry with the `pdf` field. Some of the supported fields are: `abstract`, `altmetric`, `annotation`, `arxiv`, `bibtex_show`, `blog`, `code`, `dimensions`, `doi`, `eprint`, `html`, `isbn`, `pdf`, `pmid`, `poster`, `slides`, `supp`, `video`, and `website`.
 
 ### Author annotation
 
@@ -92,7 +92,7 @@ scholar:
   first_name: [Albert, A.]
 ```
 
-If the entry matches one form of the last names and the first names, it will be underlined. Keep meta-information about your co-authors in [\_data/coauthors.yml](_data/coauthors.yml) and Jekyll will insert links to their webpages automatically. The co-author data format is as follows,
+If the entry matches one form of the last names and the first names, it will be underlined. Keep meta-information about your co-authors in [\_data/coauthors.yml](_data/coauthors.yml) and Jekyll will insert links to their webpages automatically. The co-author data format is as follows, with the last names lower cased and without accents as the key:
 
 ```yaml
 "adams":
@@ -115,7 +115,7 @@ If the entry matches one form of the last names and the first names, it will be
     url: https://en.wikipedia.org/wiki/Carl_Philipp_Emanuel_Bach
 ```
 
-If the entry matches one of the combinations of the last names and the first names, it will be highlighted and linked to the url provided.
+If the entry matches one of the combinations of the last names and the first names, it will be highlighted and linked to the url provided. Note that the keys **MUST BE** lower cased and **MUST NOT** contain accents. This is because the keys are used to match the last names in the BibTeX entries, considering possible variations.
 
 ### Buttons (through custom bibtex keywords)
 
@@ -124,6 +124,7 @@ There are several custom bibtex keywords that you can use to affect how the entr
 - `abbr`: Adds an abbreviation to the left of the entry. You can add links to these by creating a venue.yaml-file in the \_data folder and adding entries that match.
 - `abstract`: Adds an "Abs" button that expands a hidden text field when clicked to show the abstract text
 - `altmetric`: Adds an [Altmetric](https://www.altmetric.com/) badge (Note: if DOI is provided just use `true`, otherwise only add the altmetric identifier here - the link is generated automatically)
+- `annotation`: Adds a popover info message to the end of the author list that can potentially be used to clarify superscripts. HTML is allowed.
 - `arxiv`: Adds a link to the Arxiv website (Note: only add the arxiv identifier here - the link is generated automatically)
 - `bibtex_show`: Adds a "Bib" button that expands a hidden text field with the full bibliography entry
 - `blog`: Adds a "Blog" button redirecting to the specified link
@@ -145,3 +146,54 @@ A variety of beautiful theme colors have been selected for you to choose from. T
 ## Adding social media information
 
 You can add your social media links by adding the specified information at the `Social integration` section in the [\_config.yml](_config.yml) file. This information will appear at the bottom of the `About` page.
+
+## Adding a newsletter
+
+You can add a newsletter subscription form by adding the specified information at the `newsletter` section in the [\_config.yml](_config.yml) file. To set up a newsletter, you can use a service like [Loops.so](https://loops.so/), which is the current supported solution. Once you have set up your newsletter, you can add the form [endpoint](https://loops.so/docs/forms/custom-form) to the `endpoint` field in the `newsletter` section of the [\_config.yml](_config.yml) file.
+
+Depending on your specified footer behavior, the sign up form either will appear at the bottom of the `About` page and at the bottom of blogposts if `related_posts` are enabled, or in the footer at the bottom of each page.
+
+## Adding Token for Lighthouse Badger
+
+To add secrets for [lighthouse-badger](https://github.com/alshedivat/al-folio/actions/workflows/lighthouse-badger.yml), create a [personal access token (PAT)](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-fine-grained-personal-access-token) and add it as a [secret](https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions#creating-encrypted-secrets-for-a-repository) named `LIGHTHOUSE_BADGER_TOKEN` to your repository. The [lighthouse-badger documentation](https://github.com/MyActionWay/lighthouse-badger-workflows#lighthouse-badger-easyyml) specifies using an environment variable, but using it as a secret is more secure and appropriate for a PAT.
+
+Also In case you face the error: "Input required and not supplied: token" in the Lighthouse Badger action, this solution resolves it.
+
+### Personal Access Token (fine-grained) Permissions for Lighthouse Badger:
+
+- **contents**: access: read and write
+- **metadata**: access: read-only
+
+Due to the necessary permissions (PAT and others mentioned above), it is recommended to use it as a secret rather than an environment variable.
+
+## Customizing fonts, spacing, and more
+
+You can customize the fonts, spacing, and more by editing [\_sass/\_base.scss](_sass/_base.scss). The easiest way to try in advance the changes is by using [chrome dev tools](https://developer.chrome.com/docs/devtools/css) or [firefox dev tools](https://firefox-source-docs.mozilla.org/devtools-user/). In there you can click in the element and find all the attributes that are set for that element and where are they. For more information on how to use this, check [chrome](https://developer.chrome.com/docs/devtools/css) and [firefox](https://firefox-source-docs.mozilla.org/devtools-user/page_inspector/how_to/examine_and_edit_css/index.html) how-tos, and [this tutorial](https://www.youtube.com/watch?v=l0sgiwJyEu4).
+
+## Scheduled Posts
+
+`al-folio` contains a workflow which automatically publishes all posts scheduled at a specific day, at the end of the day (23:30). By default the action is disabled, and to enable it you need to go to `.github/workflows/` and find the file called `schedule-posts.txt`. This is the workflow file. For GitHub to recognize it as one (or to enable the action), you need to rename it to `schedule-posts.yml`.
+
+In order to use this you need to save all of your "Completed" blog posts which are scheduled to be uploaded on a specific date, in a folder named `_scheduled/` in the root directory.
+
+> Incomplete posts should be saved in `_drafts/`
+
+### Name Format
+
+In this folder you need to store your file in the same format as you would in `_posts/`
+
+> Example file name: `2024-08-26-This file will be uploaded on 26 August.md`
+
+### Important Notes
+
+- The scheduler uploads posts everyday at 🕛 23:30 UTC
+- It will only upload posts at 23:30 UTC of their respective scheduled days, It's not uploaded in 23:59 in case there are a lot of files as the scheduler must finish before 00:00
+- It will only upload files which follow the pattern `yyyy-mm-dd-title.md`
+  - This means that only markdown files will be posted
+  - It means that any markdown which do not follow this pattern will not be posted
+- The scheduler works by moving posts from the `_scheduled/` directory to `_posts/`, it will not post to folders like `_projects/` or `_news/`
+- The date in the name of the file is the day that file will be uploaded on
+  - `2024-08-27-file1.md` will not be posted before or after 27-August-2024 (Scheduler only works for posts scheduled on the present day)
+  - `2025-08-27-file2.md` will be posted exactly on 27-August-2025
+  - `File3.md` will not be posted at all
+  - `2026-02-31-file4.md` is supposed to be posted on 31-February-2026, but there is no 31st in February hence this file will never be posted either

Dockerfile

@@ -8,9 +8,10 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \
     imagemagick \
     build-essential \
     zlib1g-dev \
-    jupyter-nbconvert \
+    python3-pip \
     inotify-tools procps && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* /var/cache/apt/archives/*
+    apt-get clean && rm -rf /var/lib/apt/lists/* /var/cache/apt/archives/* && \
+    pip install nbconvert --break-system-packages
 
 
 RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \