Merge branch 'LCNS-SJTU:master' into master

Author: majingyang0119

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

@@ -0,0 +1,40 @@
+name: Docker Image CI (Upload Tag)
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Buildx
+      uses: docker/setup-buildx-action@v1
+
+    -
+      name: Docker meta
+      id: meta
+      uses: docker/metadata-action@v4
+      with:
+        images: amirpourmand/al-folio
+
+    - name: Login
+      uses: docker/login-action@v1
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Build and push
+      uses: docker/build-push-action@v3
+      with:
+        context: .
+        push: ${{ github.event_name != 'pull_request' }}
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}
+

.github/workflows/deploy-image.yml

@@ -0,0 +1,31 @@
+name: Docker Image CI
+
+on:
+  push:
+    branches: [ master ]
+
+jobs: 
+
+  build:
+
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'alshedivat'
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Buildx
+      uses: docker/setup-buildx-action@v1
+
+    - name: Login
+      uses: docker/login-action@v1
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+         
+    - name: Build and push
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        push: true
+        tags: amirpourmand/al-folio

.github/workflows/deploy.yml

@@ -1,4 +1,4 @@
-name: Deploy
+name: deploy
 
 on:
   push:
@@ -15,23 +15,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Setup Ruby
       uses: ruby/setup-ruby@v1
       with:
         ruby-version: '3.0.2'
-    - name: Enable bundler cache
-      uses: actions/cache@v2
-      with:
-        path: vendor/bundle
-        key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}
-        restore-keys: |
-          ${{ runner.os }}-gems-
+        bundler-cache: true
     - name: Install deps
       run: |
-        gem install bundler
-        bundle config path vendor/bundle
-        bundle install --jobs 4 --retry 3
         npm install -g mermaid.cli
     - name: Setup deploy options
       id: setup

.travis.yml

@@ -0,0 +1,13 @@
+FROM jekyll/jekyll
+Label MAINTAINER Amir Pourmand
+#install imagemagick tool for convert command
+RUN apk add --no-cache --virtual .build-deps \
+        libxml2-dev \
+        shadow \
+        autoconf \
+        g++ \
+        make \
+    && apk add --no-cache imagemagick-dev imagemagick
+WORKDIR /srv/jekyll
+ADD Gemfile /srv/jekyll/
+RUN bundle install

Dockerfile

@@ -5,16 +5,19 @@ group :jekyll_plugins do
     gem 'jekyll-diagrams'
     gem 'jekyll-email-protect'
     gem 'jekyll-feed'
-    gem 'jekyll-github-metadata'
     gem 'jekyll-imagemagick'
+    gem 'jekyll-minifier'
     gem 'jekyll-paginate-v2'
     gem 'jekyll-scholar'
     gem 'jekyll-sitemap'
     gem 'jekyll-target-blank'
     gem 'jekyll-twitter-plugin'
     gem 'jemoji'
+    gem 'mini_racer'
     gem 'unicode_utils'
     gem 'webrick'
-    gem 'htmlcompressor'
-    gem 'htmlbeautifier'
+end
+group :other_plugins do
+    gem 'httparty'
+    gem 'feedjira'
 end

Gemfile

@@ -9,12 +9,65 @@ Website is powered by [Jekyll](https://jekyllrb.com/) with [al-folio](https://gi
 
 ## Getting started
 
-For more about how to use Jekyll, check out [this tutorial](https://www.taniarascia.com/make-a-static-website-with-jekyll/).
+### Local setup
+Want to learn more about Jekyll? Check out [this tutorial](https://www.taniarascia.com/make-a-static-website-with-jekyll/).
+Why Jekyll? Read [Andrej Karpathy's blog post](https://karpathy.github.io/2014/07/01/switching-to-jekyll/)!
+
 
 ### Installation
 
-Please install Ruby, Bundler and Jekyll with the help of [link](https://jekyllrb.com/docs/installation/) here on your system.
-### Local setup
+For a hands-on walkthrough of al-folio installation, check out [this cool video tutorial](https://www.youtube.com/watch?v=g6AJ9qPPoyc) by one of the community members! 🎬 🍿
+
+---
+
+#### Local setup using Docker (Recommended on Windows)
+
+You need to take the following steps to get `al-folio` up and running in your local machine:
+
+- First, [install docker](https://docs.docker.com/get-docker/)
+- Then, clone this repository to your machine:
+
+```bash
+$ git clone git@github.com:<your-username>/<your-repo-name>.git
+$ cd <your-repo-name>
+```
+
+Finally, run the following command that will pull a pre-built image from DockerHub and will run your website.
+
+```bash
+$ ./bin/dockerhub_run.sh
+```
+
+Note that when you run it for the first time, it will download a docker image of size 300MB or so.
+
+Now, feel free to customize the theme however you like (don't forget to change the name!). After you are done, you can use the same command (`bin/dockerhub_run.sh`) to render the webpage with all you changes. Also, make sure to commit your final changes.
+
+<details><summary>(click to expand) <strong>Build your own docker image (more advanced):</strong></summary>
+
+> Note: this approach is only necessary if you would like to build an older or very custom version of al-folio.
+
+First, download the necessary modules and install them into a docker image called `al-folio:Dockerfile` (this command will build an image which is used to run your website afterwards. Note that you only need to do this step once. After you have the image, you no longer need to do this anymore):
+  
+
+```bash
+$ ./bin/docker_build_image.sh  
+```
+
+Run the website!
+
+```bash
+$ ./bin/docker_run.sh
+```
+
+> To change port number, you can edit `docker_run.sh` file.
+
+> If you want to update jekyll, install new ruby packages, etc., all you have to do is build the image again using `docker_build_image.sh`! It will download ruby and jekyll and install all ruby packages again from scratch.
+
+</details>
+
+---
+
+#### Local Setup (Standard)
 
 Assuming you have [Ruby](https://www.ruby-lang.org/en/downloads/) and [Bundler](https://bundler.io/) installed on your system (*hint: for ease of managing ruby gems, consider using [rbenv](https://github.com/rbenv/rbenv)*), first [fork](https://guides.github.com/activities/forking/) the repo from `github.com:LCNS-SJTU/lcns-sjtu.github.io` to `github.com:<your-username>/<your-repo-name>` and do the following:
 
@@ -45,11 +98,11 @@ Check [here](docs/people.md) for docs about adding new profiles of group members
 
 Check [here](docs/publications.md) for docs about adding new bib items.
 
-
 ---
+
 ## TODO
 
-- [ ] Add tutorial for openning a pull-request.
+- [x] Add tutorial for openning a pull-request.
+- [x] Add profile avatars for rest of group members.
 - [ ] Finish the resource page.
-- [ ] Add profile avatars for rest of group members.
 - [ ] Create project page.

README.md

@@ -3,6 +3,23 @@
 
 @string{aps = {American Physical Society,}}
 
+@article{Qian2022111111,
+title = {A striatal SOM-driven ChAT-iMSN loop generates beta oscillations and produces motor deficits},
+journal = {Cell Reports},
+volume = {40},
+number = {3},
+pages = {111111},
+year = {2022},
+issn = {2211-1247},
+doi = {https://doi.org/10.1016/j.celrep.2022.111111},
+html = {https://www.sciencedirect.com/science/article/pii/S2211124722009172},
+author = {Dandan Qian and Wei Li and Jinwen Xue and Yi Wu and Ziling Wang and Tao Shi and Songting Li and Jingxuan Yang and Shi Qiu and Shaoli Wang and Yousheng Shu and Liang Chen and Qiao Wang and Ti-Fei Yuan and Douglas Zhou and Wei Lu},
+keywords = {striatum, SNc, SOM cells, ChAT cells, beta oscillations},
+abstract = {Summary
+Enhanced beta oscillations within the cortico-basal ganglia-thalamic (CBT) network are correlated with motor deficits in Parkinson’s disease (PD), whose generation has been associated recently with amplified network dynamics in the striatum. However, how distinct striatal cell subtypes interact to orchestrate beta oscillations remains largely unknown. Here, we show that optogenetic suppression of dopaminergic control over the dorsal striatum (DS) elevates the power of local field potentials (LFPs) selectively at beta band (12–25 Hz), accompanied by impairments in locomotion. The amplified beta power originates from a striatal loop driven by somatostatin-expressing (SOM) interneurons and constituted by choline acetyltransferase (ChAT)-expressing interneurons and dopamine D2 receptor (D2R)-expressing medium spiny neurons (iMSNs). Moreover, closed-loop intervention selectively targeting striatal iMSNs or ChATs diminishes beta oscillations and restores motor function. Thus, we reveal a striatal microcircuit motif that underlies beta oscillation generation and accompanied motor deficits upon perturbation of dopaminergic control over the striatum.},
+bibtex_show = {true},
+}
+
 @article{Song2021,
   abbr = {Cereb. Cortex},
   bibtex_show={true},