Upgrade build (#126)

* Try this * Setup * Some fixes * More URL fixes * More URL fixes * More fixes * Skip check --------- Co-authored-by: Aaron Meyer <[email protected]>
meyer-lab · Jan 1, 2024 · b6e6c8b · b6e6c8b
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -3,38 +3,37 @@ name: Build website
 on:
   push
 
-jobs:
-  build:
-    runs-on: ubuntu-latest
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
 
+jobs:
+  jekyll:
+    runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-    - uses: actions/cache@v3
-      with:
-        path: vendor/bundle
-        key: bundle-use-ruby-ubuntu-latest-3.2-${{ hashFiles('**/Gemfile.lock') }}
-        restore-keys: bundle-use-ruby-ubuntu-latest-3.2-
-    - name: Set up Ruby
-      uses: ruby/setup-ruby@v1
-      with:
-        ruby-version: 3.2
+      - name: Install ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.2'
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
 
-    - name: Install dependencies
-      run: |
-        bundle config deployment true
-        bundle config path vendor/bundle
-        bundle install --jobs 4
+      - name: Build jekyll
+        run: bundle exec jekyll build
 
-    - name: Jekyll build
-      run: bundle exec jekyll build
+      - name: Proof HTML
+        if: false
+        run: cd _site && bundle exec htmlproofer --ignore_status_codes "999, 400, 403"
 
-    - name: Proof HTML
-      run: echo Skip htmlproofer # bundle exec htmlproofer --check-html --url-ignore "/amgenscholars.com/" --http-status-ignore "412, 400" --assume-extension ./_site
-
-    - name: Deploy 🚀
-      if: github.ref == 'refs/heads/master'
-      uses: JamesIves/github-pages-deploy-action@releases/v4
-      with:
-        folder: _site # The folder the action should deploy.
-        single-commit: true
+      - name: Upload artifact
+        if: github.ref == 'refs/heads/master'
+        uses: actions/upload-pages-artifact@v2
+        with:
+          path: '_site'
+      - name: Deploy to GitHub Pages
+        if: github.ref == 'refs/heads/master'
+        id: deployment
+        uses: actions/deploy-pages@v2
diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,4 @@ vendor
 .jekyll-cache
 .bundle
 _site
+.ruby-version
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -2,7 +2,7 @@ GEM
   remote: https://rubygems.org/
   specs:
     Ascii85 (1.1.0)
-    addressable (2.8.5)
+    addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     afm (0.2.2)
     async (2.6.5)
@@ -19,7 +19,7 @@ GEM
       csl (~> 1.6)
     colorator (1.1.0)
     concurrent-ruby (1.2.2)
-    console (1.23.2)
+    console (1.23.3)
       fiber-annotation
       fiber-local
     csl (1.6.0)
@@ -37,7 +37,7 @@ GEM
     fiber-annotation (0.2.0)
     fiber-local (1.0.0)
     forwardable-extended (2.6.0)
-    google-protobuf (3.24.4)
+    google-protobuf (3.25.1)
     hashery (2.1.2)
     html-proofer (5.0.8)
       addressable (~> 2.3)
@@ -51,8 +51,8 @@ GEM
     http_parser.rb (0.8.0)
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
-    io-event (1.3.3)
-    jekyll (4.3.2)
+    io-event (1.4.0)
+    jekyll (4.3.3)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
@@ -93,19 +93,19 @@ GEM
     mercenary (0.4.0)
     mini_portile2 (2.8.5)
     namae (1.1.1)
-    nokogiri (1.15.4)
+    nokogiri (1.16.0)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    pdf-reader (2.11.0)
+    pdf-reader (2.12.0)
       Ascii85 (~> 1.0)
       afm (~> 0.2.1)
       hashery (~> 2.0)
       ruby-rc4
       ttfunk
-    public_suffix (5.0.3)
-    racc (1.7.2)
+    public_suffix (5.0.4)
+    racc (1.7.3)
     rainbow (3.1.1)
     rake (13.1.0)
     rb-fsevent (0.11.2)
@@ -115,14 +115,14 @@ GEM
     rouge (4.2.0)
     ruby-rc4 (0.1.5)
     safe_yaml (1.0.5)
-    sass-embedded (1.69.5)
-      google-protobuf (~> 3.23)
+    sass-embedded (1.69.6)
+      google-protobuf (~> 3.25)
       rake (>= 13.0.0)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
     timers (4.3.5)
     ttfunk (1.7.0)
-    typhoeus (1.4.0)
+    typhoeus (1.4.1)
       ethon (>= 0.9.0)
     unicode-display_width (2.5.0)
     webrick (1.8.1)

diff --git a/_bibliography/pubs.bib b/_bibliography/pubs.bib
@@ -11,7 +11,7 @@ @Article{	  Mashayekhi:2009
   pages		= {1613--1623},
   doi		= {10.1002/bit.22188},
   issn		= {1097-0290},
-  url		= {http://dx.doi.org/10.1002/bit.22188},
+  url		= {https://dx.doi.org/10.1002/bit.22188},
   abstract	= { The concentration of biomarkers, such as DNA, prior to a subsequent detection step may
 		  facilitate the early detection of cancer, which could significantly increase chances for
 		  survival. In this study, the partitioning behavior of mammalian genomic DNA fragments in a
@@ -74,7 +74,7 @@ @InCollection{	  Tsao
   pages		= {27--32},
   doi		= {10.1007/978-90-481-3892-0_5},
   isbn		= {978-90-481-3891-3},
-  url		= {http://dx.doi.org/10.1007/978-90-481-3892-0_5}
+  url		= {https://dx.doi.org/10.1007/978-90-481-3892-0_5}
 }
 
 @Article{	  Kim10082011,
@@ -89,7 +89,7 @@ @Article{	  Kim10082011
   number	= 11,
   pages		= {1--12},
   doi		= {10.1074/mcp.M111.008433},
-  url		= {http://www.mcponline.org/content/10/11/M111.008433},
+  url		= {https://www.mcponline.org/content/10/11/M111.008433},
   abstract	= { Epithelial-mesenchymal transition (EMT), whether in developmental morphogenesis or
 		  malignant transformation, prominently involves modified cell motility behavior. While major
 		  advances have transpired in understanding the molecular pathways regulating the process of
@@ -107,7 +107,7 @@ @Article{	  Kim10082011
 		  behavior globally, modulation of the network interactions underlying the altered pathway
 		  activities was identified by ascertaining differences in quantitative topological influences
 		  among the nodes between the two conditions. },
-  file		= {http://www.mcponline.org/content/10/11/M111.008433.full.pdf}
+  file		= {https://www.mcponline.org/content/10/11/M111.008433.full.pdf}
 }
 
 @Article{	  BTPR:BTPR712,
@@ -122,7 +122,7 @@ @Article{	  BTPR:BTPR712
   pages		= {171--178},
   doi		= {10.1002/btpr.712},
   issn		= {1520-6033},
-  url		= {http://dx.doi.org/10.1002/btpr.712},
+  url		= {https://dx.doi.org/10.1002/btpr.712},
   abstract	= { In bioprocess development, the 96-well plate format has been widely used for
 		  high-throughput screening of production cell line or culture conditions. However, suspension
 		  cell cultures in conventional 96-well plates often fail to reach high cell density under
@@ -157,7 +157,7 @@ @Article{	  Meyer:2012fr
   number	= 6,
   pages		= {721--729},
   doi		= {10.1083/jcb.201201003},
-  url		= {http://jcb.rupress.org/content/197/6/721.abstract},
+  url		= {https://jcb.rupress.org/content/197/6/721.abstract},
   abstract	= { Growth factor--induced migration is a critical step in the dissemination and metastasis of
 		  solid tumors. Although differences in properties characterizing cell migration on
 		  two-dimensional (2D) substrata versus within three-dimensional (3D) matrices have been noted
@@ -256,7 +256,7 @@ @Article{	  Meyer:CellSys
   number	= 1,
   pages		= {25--36},
   doi		= {10.1016/j.cels.2015.06.002},
-  url		= {http://dx.doi.org/10.1016/j.cels.2015.06.002},
+  url		= {https://dx.doi.org/10.1016/j.cels.2015.06.002},
   abstract	= { The AXL receptor is a TAM (Tyro3, AXL, MerTK) receptor tyrosine kinase (RTK) important in
 		  physiological inflammatory processes such as blood clotting, viral infection, and innate
 		  immune-mediated cell clearance. Overexpression of the receptor in a number of solid tumors
@@ -310,7 +310,7 @@ @Article{	  Miller:2015aa
   journal	= {Scientific Reports},
   volume	= 5,
   pages		= {15150 Ep -},
-  url		= {http://www.nature.com/articles/srep15150},
+  url		= {https://www.nature.com/articles/srep15150},
   abstract	= { Dysregulation of ErbB-family signaling underlies numerous pathologies and has been
 		  therapeutically targeted through inhibiting ErbB-receptors themselves or their cognate
 		  ligands. For the latter, ``decoy'' antibodies have been developed to sequester ligands
@@ -341,7 +341,7 @@ @Article{	  Archer
   journal	= {Cancer Research},
   doi		= {10.1158/0008-5472.can-16-1580},
   issn		= {0008-5472},
-  url		= {http://cancerres.aacrjournals.org/content/early/2016/11/18/0008-5472.CAN-16-1580},
+  url		= {https://cancerres.aacrjournals.org/content/early/2016/11/18/0008-5472.CAN-16-1580},
   abstract	= { Cancer systems biology aims to understand cancer as an integrated system of genes,
 		  proteins, networks, and interactions rather than an entity of isolated molecular and
 		  cellular components. The inaugural Systems Approaches to Cancer Biology Conference,
@@ -353,7 +353,7 @@ @Article{	  Archer
 		  ensuring the reproducibility and impact of cancer systems biology studies will require
 		  widespread method and data sharing and, ultimately, the translation of important findings to
 		  the clinic. },
-  file		= {http://cancerres.aacrjournals.org/content/early/2016/11/18/0008-5472.CAN-16-1580.full.pdf}
+  file		= {https://cancerres.aacrjournals.org/content/early/2016/11/18/0008-5472.CAN-16-1580.full.pdf}
 }
 
 @Article{	  Miller16032016,
@@ -370,7 +370,7 @@ @Article{	  Miller16032016
   number	= 4,
   pages		= {331--333},
   doi		= {10.1158/2159-8290.cd-15-0933},
-  url		= {http://cancerdiscovery.aacrjournals.org/content/early/2016/03/15/2159-8290.CD-15-0933.abstract},
+  url		= {https://cancerdiscovery.aacrjournals.org/content/early/2016/03/15/2159-8290.CD-15-0933.abstract},
   abstract	= { Kinase inhibitor resistance often involves upregulation of poorly understood ``bypass''
 		  signaling pathways. Here, we show that extracellular proteomic adaptation is one path to
 		  bypass signaling and drug resistance. Proteolytic shedding of surface receptors, which can
@@ -398,7 +398,7 @@ @Article{	  filpodia
   number	= 2,
   pages		= {261--274},
   doi		= {10.1083/jcb.201509062},
-  url		= {http://jcb.rupress.org/content/213/2/261.long},
+  url		= {https://jcb.rupress.org/content/213/2/261.long},
   abstract	= { Axons navigate long distances through complex 3D environments to interconnect the nervous
 		  system during development. Although the precise spatiotemporal effects of most axon guidance
 		  cues remain poorly characterized, a prevailing model posits that attractive guidance cues
@@ -425,7 +425,7 @@ @Article{	  Manole5219
   pages		= {5219--5228},
   doi		= {10.1158/0008-5472.can-16-0123},
   issn		= {0008-5472},
-  url		= {http://cancerres.aacrjournals.org/content/76/18/5219},
+  url		= {https://cancerres.aacrjournals.org/content/76/18/5219},
   abstract	= { Resistance limits the effectiveness of receptor tyrosine kinase (RTK)-targeted therapies.
 		  Combination therapies targeting resistance mechanisms can considerably improve response, but
 		  will require an improved understanding of when particular combinations will be effective.
@@ -441,7 +441,7 @@ @Article{	  Manole5219
 		  bypass-mediated resistance and provide a basic understanding of this network-level change in
 		  kinase dependence that will inform the design of prognostic assays for identifying effective
 		  therapeutic combinations in individual patients. },
-  file		= {http://cancerres.aacrjournals.org/content/76/18/5219.full.pdf}
+  file		= {https://cancerres.aacrjournals.org/content/76/18/5219.full.pdf}
 }
 
 @Article{	  ZweemerLauf,
@@ -452,7 +452,7 @@ @Article{	  ZweemerLauf
   journal	= {Molecular Cancer Research},
   doi		= {10.1158/1541-7786.mcr-17-0012},
   issn		= {1541-7786},
-  url		= {http://mcr.aacrjournals.org/content/early/2017/09/16/1541-7786.MCR-17-0012},
+  url		= {https://mcr.aacrjournals.org/content/early/2017/09/16/1541-7786.MCR-17-0012},
   abstract	= { Metastases are a major cause of cancer mortality. AXL, a receptor tyrosine kinase (RTK)
 		  aberrantly expressed in many tumors, is a potent oncogenic driver of metastatic cell
 		  motility and has been identified as broadly relevant in cancer drug resistance. Despite its
@@ -470,7 +470,7 @@ @Article{	  ZweemerLauf
 		  Gas6-bearing apoptotic bodies generated from tumor treatment with therapeutics that produce
 		  killing of a portion of the tumor cells present but not all, hence generating potentially
 		  problematic invasive and metastatic behavior of the surviving tumor cells. },
-  file		= {http://mcr.aacrjournals.org/content/early/2017/09/16/1541-7786.MCR-17-0012.full.pdf}
+  file		= {https://mcr.aacrjournals.org/content/early/2017/09/16/1541-7786.MCR-17-0012.full.pdf}
 }
 
 @Article{	  BarneyPeyton,
@@ -481,7 +481,7 @@ @Article{	  BarneyPeyton
 		  Resistance},
   journal	= {Integrative Biology},
   doi		= {10.1039/c7ib00128b},
-  url		= {http://pubs.rsc.org/en/content/articlelanding/2017/ib/c7ib00128b},
+  url		= {https://pubs.rsc.org/en/content/articlelanding/2017/ib/c7ib00128b},
   abstract	= { Traditional drug screening methods lack features of the tumor microenvironment that can
 		  contribute to resistance. There remains a gap in whether extracellular signals, such as
 		  stiffness, dimensionality, and cell-cell contacts act independently, or are integrated
@@ -513,7 +513,7 @@ @Article{	  Muffat142497
   journal	= {Proceedings of the National Academy of Sciences},
   doi		= {10.1073/pnas.1719266115},
   issn		= {0027-8424},
-  url		= {http://www.pnas.org/content/early/2018/06/15/1719266115/},
+  url		= {https://www.pnas.org/content/early/2018/06/15/1719266115/},
   abstract	= { Maternal Zika virus (ZIKV) infection during pregnancy is recognized as the cause of an
 		  epidemic of microcephaly and other neurological anomalies in human fetuses. It remains
 		  unclear how ZIKV accesses the highly vulnerable population of neural progenitors of the
@@ -533,7 +533,7 @@ @Article{	  Muffat142497
 		  pregnancy, before angiogenesis in the brain rudiments. Our data are also consistent with
 		  ZIKV and DENV affecting the integrity of the blood–brain barrier, thus allowing infection
 		  of the brain later in life. },
-  file		= {http://www.pnas.org/content/early/2018/06/15/1719266115.full.pdf}
+  file		= {https://www.pnas.org/content/early/2018/06/15/1719266115.full.pdf}
 }
 
 @Article{	  FcgR,
@@ -568,7 +568,7 @@ @Article{	  SITU2018170
   pages		= {170--181},
   doi		= {https://doi.org/10.1016/j.virol.2018.09.017},
   issn		= {0042-6822},
-  url		= {http://www.sciencedirect.com/science/article/pii/S0042682218302964},
+  url		= {https://www.sciencedirect.com/science/article/pii/S0042682218302964},
   abstract	= { Conjugating certain types of lentiviral vectors with targeting ligands can redirect the
 		  vectors to specifically transduce desired cell types. However, extensive genetic and/or
 		  biochemical manipulations are required for conjugation, which hinders applications for

diff --git a/_includes/protocol_links.md b/_includes/protocol_links.md
@@ -15,4 +15,4 @@
 
 ## Safety
 
-[Department Injury and Illness Prevention Program (IIPP) Manual)](http://www.bioeng.ucla.edu/dept-iipp/)
+[Department Injury and Illness Prevention Program (IIPP) Manual)](https://www.bioeng.ucla.edu/dept-iipp/)
diff --git a/_layouts/bibtemplate.html b/_layouts/bibtemplate.html
@@ -24,7 +24,7 @@
 {% endif %}
 
 {% if entry.abstract %}
-    <a onclick="toggle('{{entry.key}}_abstract')">[Abstract]</a>
+    <span onclick="toggle('{{entry.key}}_abstract')">[Abstract]</span>
 {% endif %}
 
 </span>

diff --git a/_posts/lit/1964-10-16-Strong-inference.markdown b/_posts/lit/1964-10-16-Strong-inference.markdown
@@ -3,7 +3,7 @@ layout: post
 title:  Strong Inference
 date:   1964-10-16 00:00:01
 categories: literature
-external-url: http://pages.cs.wisc.edu/~markhill/science64_strong_inference.pdf
+external-url: https://pages.cs.wisc.edu/~markhill/science64_strong_inference.pdf
 tags:
 - scientific method
 ---
diff --git a/_posts/lit/1995-07-27-protein-computer.md b/_posts/lit/1995-07-27-protein-computer.md
@@ -3,7 +3,7 @@ layout: post
 title:  Protein molecules as computational elements in living cells
 date:   1995-07-27 00:00:01
 categories: literature
-external-url: http://www.nature.com/doifinder/10.1038/376307a0
+external-url: https://www.nature.com/doifinder/10.1038/376307a0
 tags:
 - systems biology
 - modeling

diff --git a/_posts/lit/1999-05-01-FceR-model.md b/_posts/lit/1999-05-01-FceR-model.md
@@ -3,7 +3,7 @@ layout: post
 title:  Quantifying aggregation of IgE-FcϵRI by multivalent antigen
 date:   1999-05-01 00:00:01
 categories: literature
-external-url: http://linkinghub.elsevier.com/retrieve/pii/S0006349599773972
+external-url: https://linkinghub.elsevier.com/retrieve/pii/S0006349599773972
 tags:
 - Fc receptors
 - immunology

diff --git a/_posts/lit/2002-09-01-Biologist-radio.markdown b/_posts/lit/2002-09-01-Biologist-radio.markdown
@@ -3,7 +3,7 @@ layout: post
 title:  Can a biologist fix a radio?—Or, what I learned while studying apoptosis
 date:   2002-09-01 00:00:01
 categories: literature
-external-url: http://www.cell.com/cancer-cell/abstract/S1535-6108(02)00133-2
+external-url: https://www.cell.com/cancer-cell/abstract/S1535-6108(02)00133-2
 tags:
 - systems biology
 - modeling

diff --git a/_posts/lit/2005-01-01-Antedisciplinary-sci.markdown b/_posts/lit/2005-01-01-Antedisciplinary-sci.markdown
@@ -3,7 +3,7 @@ layout: post
 title:  “Antedisciplinary” Science
 date:   2005-01-01 00:00:01
 categories: literature
-external-url: http://dx.plos.org/10.1371/journal.pcbi.0010006
+external-url: https://dx.plos.org/10.1371/journal.pcbi.0010006
 tags:
 - scientific method
 ---
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,3 +4,4 @@ vendor @@
     .jekyll-cache
     .bundle
     _site
+    .ruby-version
Original file line number	Diff line number	Diff line change
Expand Up		@@ -15,4 +15,4 @@

		## Safety

		[Department Injury and Illness Prevention Program (IIPP) Manual)](http://www.bioeng.ucla.edu/dept-iipp/)
		[Department Injury and Illness Prevention Program (IIPP) Manual)](https://www.bioeng.ucla.edu/dept-iipp/)