Lychee and link updates (#177)

* Get lychee working again

* Fix a link

* Fix some other links

---------

Co-authored-by: Aaron Meyer <[email protected]>

Author: aarmey

.github/workflows/build.yml

@@ -1,7 +1,6 @@
 name: Build website
 
-on:
-  push
+on: push
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
@@ -13,12 +12,12 @@ jobs:
   jekyll:
     runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Install ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '3.4'
+          ruby-version: "3.4"
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
 
       - name: Install Typst
@@ -40,12 +39,12 @@ jobs:
         uses: lycheeverse/lychee-action@v2
         with:
           fail: false
-          args: "--base _site --accept '100..=103,200..=299,403' --cache --max-cache-age 14d _site"
+          args: --root-dir "$(pwd)/_site" --accept '100..=103,200..=299,403' --cache --max-cache-age 14d _site
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
         with:
-          path: '_site'
+          path: "_site"
       - name: Deploy to GitHub Pages
         if: github.ref == 'refs/heads/main'
         id: deployment

_bibliography/pubs.bib

@@ -1369,7 +1369,7 @@ @Article{	  Tan2024
 		  decomposition},
   keywords	= {tensors, reviews, computational-example, highlight},
   month		= {August},
-  preprint	= {http://arxiv.org/abs/2402.16638},
+  preprint	= {https://arxiv.org/abs/2402.16638},
   url		= {https://www.sciencedirect.com/science/article/abs/pii/S2405471224002035},
   doi		= {10.1016/j.cels.2024.07.004},
   pages		= {679--693},

_posts/news/2019-05-15-CSBC-west-coast.md

@@ -4,4 +4,4 @@ title:  CSBC West Coast Talk
 date:   2019-05-15 00:00:01
 categories: news
 ---
-Drs. Meyer and Bae will present at the [CSBC's Inaugural West Coast Symposium](https://csbconsortium.org/event/inaugural-cancer-systems-biology-consortium-west-coast-symposium/).
+Drs. Meyer and Bae will present at the CSBC's Inaugural West Coast Symposium.

_posts/news/2020-08-16-autoencoder-pilot.md

@@ -4,4 +4,4 @@ title:  New funding
 date:   2020-08-16 12:00:00
 categories: news
 ---
-The lab has been awarded a pilot grant from the NCI to combine mechanistic models and AI in the form of autoencoders to model patient-specific phosphoproteomic changes. This is in collaboration with [Emek Demir at OHSU](https://www.ohsu.edu/people/emek-demir), [Sara Gosline at PNNL](https://saragosline.wordpress.com), and [Fabian Fröhlich at Harvard](https://scholar.harvard.edu/fabianfroehlich/home).
+The lab has been awarded a pilot grant from the NCI to combine mechanistic models and AI in the form of autoencoders to model patient-specific phosphoproteomic changes. This is in collaboration with [Emek Demir at OHSU](https://www.ohsu.edu/people/emek-demir-phd), [Sara Gosline at PNNL](https://saragosline.wordpress.com), and [Fabian Fröhlich at Harvard](https://scholar.harvard.edu/fabianfroehlich/home).

_posts/news/2023-01-31-Andrew-EDI-award.md

@@ -4,4 +4,4 @@ title:  Andrew EDI Leadership Award
 date:   2023-01-31 12:00:00
 categories: news
 ---
-Congratulations to Andrew for [winning a UCLA EDI Student Leadership Award](https://equity.ucla.edu/ucla-edi-student-leadership-award/overview-and-application/)! This is a campus-wide award recognizing UCLA students who have exhibited exceptional leadership aligning with and contributing to UCLA's EDI mission and priorities.
+Congratulations to Andrew for winning a UCLA EDI Student Leadership Award! This is a campus-wide award recognizing UCLA students who have exhibited exceptional leadership aligning with and contributing to UCLA's EDI mission and priorities.

team/index.md

@@ -10,7 +10,7 @@ title: Team
 Ph. D., Biological Engineering, MIT    
 B.S., Bioengineering, University of California, Los Angeles       
 
-Aaron is an Associate Professor of [Bioengineering](https://www.bioeng.ucla.edu) and a member of the [Bioinformatics IDP](https://bioinformatics.ucla.edu), [Jonsson Comprehensive Cancer Center](https://cancer.ucla.edu), [Broad Stem Cell Research Center](https://stemcell.ucla.edu), and [Institute for Quantitative and Computational Biosciences](https://qcb.ucla.edu). He strives to learn how we can use computational models to control biological systems and treat disease. Outside of the lab, he can be found consuming anything that might be considered science fiction, reading about the philosophy/history of science, or cycling in the Santa Monica mountains.
+Aaron is an Associate Professor of [Bioengineering](https://www.bioeng.ucla.edu) and a member of the [Bioinformatics IDP](https://bioinformatics.ucla.edu), [Jonsson Comprehensive Cancer Center](https://www.uclahealth.org/cancer), [Broad Stem Cell Research Center](https://stemcell.ucla.edu), and [Institute for Quantitative and Computational Biosciences](https://qcb.ucla.edu). He strives to learn how we can use computational models to control biological systems and treat disease. Outside of the lab, he can be found consuming anything that might be considered science fiction, reading about the philosophy/history of science, or cycling in the Santa Monica mountains.
 
 <br />