update infrastructure (#298)

* update R packages * attempt to remove python * update quarto and make fixes to styling * remove navbar color * simplify footer * add styling to buttons * update git submodule * update changelog
openproblems-bio · Dec 14, 2023 · e510487 · e510487
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diff --git a/.github/workflows/quarto_netlify.yml b/.github/workflows/quarto_netlify.yml
@@ -29,13 +29,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "4.2"
+          r-version: "4.3"
           use-public-rspm: true
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-
       - name: Set up environment
         run: |
           echo "LINUX_VERSION=$(uname -rs)" >> $GITHUB_ENV
@@ -54,12 +50,11 @@ jobs:
       - name: Install Quarto
         uses: quarto-dev/quarto-actions/setup@v2
         with:
-          version: 1.4.130
+          version: 1.4.527
 
       - name: Render with Quarto
         shell: bash -l {0}  
         run: |
-          source renv/python/virtualenvs/renv-python-3.10/bin/activate
           quarto render --profile evaluate_code
       
       ## push actions

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,17 @@
 # openproblems.bio unreleased
 
+## MINOR CHANGES
+
+
+* Several infrastructure updates (PR #298):
+
+  - Update R packages
+  - Remove Python from list of dependencies
+  - Update Quarto
+  - Fixes to styling
+  - Simplify footer
+  - Update openproblems-v2 submodule
+
 ## BUG FIXES
 
 * Updated the `openproblems-v2` submodule (PR #295). This fixes a deprecation error due to an update in ruamel.yaml.

diff --git a/_openproblems-v2 b/_openproblems-v2
diff --git a/_quarto.yml b/_quarto.yml
@@ -15,7 +15,7 @@ website:
   google-analytics: 'UA-178400615-1'
 
   page-footer:
-    left: "&copy; Open Problems 2023 with all data licensed under [CC-BY](https://creativecommons.org/licenses/by/2.0/). View on [GitHub](https://github.com/openproblems-bio/openproblems-v2). Made with [Quarto♥](https://quarto.org)."
+    left: "&copy; Open Problems 2023 with all data licensed under [CC-BY](https://creativecommons.org/licenses/by/2.0/)."
 
   navbar:
     logo: images/logo.png

diff --git a/events/2021-09_neurips/index.qmd b/events/2021-09_neurips/index.qmd
@@ -4,15 +4,15 @@ subtitle: Solving various multimodal integration tasks using ML
 description: |
   A NeurIPS Competition (2021)
 
-  [See on EvalAI](https://eval.ai/web/challenges/challenge-page/1111/overview){class="btn btn-primary" style="border: 1px solid white;"}
-  [Sign up for updates](https://docs.google.com/forms/d/e/1FAIpQLSe90Oky4-1b0HbdLsp5Yqo9juCd2mq-NlGHU9NHRW1ECok1xQ/viewform){class="btn btn-primary" style="border: 1px solid white;"}
+  [See on EvalAI](https://eval.ai/web/challenges/challenge-page/1111/overview){class="btn btn-primary"}
+  [Sign up for updates](https://docs.google.com/forms/d/e/1FAIpQLSe90Oky4-1b0HbdLsp5Yqo9juCd2mq-NlGHU9NHRW1ECok1xQ/viewform){class="btn btn-primary"}
 
-  [Watch the video](https://www.youtube.com/watch?v=ZXDILOyiy7A){class="btn btn-secondary" style="border: 1px solid white; font-size: 0.8rem; padding: 3px 10px;"}
-  [Read the documentation](/events/2021-09_neurips/documentation/index.qmd){class="btn btn-secondary" style="border: 1px solid white; font-size: 0.8rem; padding: 3px 10px;"}
-  [Download the data](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122){class="btn btn-secondary" style="border: 1px solid white; font-size: 0.8rem; padding: 3px 10px;"}
+  [Watch the video](https://www.youtube.com/watch?v=ZXDILOyiy7A){class="btn btn-secondary"}
+  [Read the documentation](/events/2021-09_neurips/documentation/index.qmd){class="btn btn-secondary"}
+  [Download the data](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122){class="btn btn-secondary"}
 
-  [Read the datasets paper (NeurIPS 2021)](https://datasets-benchmarks-proceedings.neurips.cc/paper/2021/hash/158f3069a435b314a80bdcb024f8e422-Abstract-round2.html){class="btn btn-secondary" style="border: 1px solid white; font-size: 0.8rem; padding: 3px 10px;"} 
-  [Read the competition paper (ICML 2022)](https://proceedings.mlr.press/v176/lance22a.html){class="btn btn-secondary" style="border: 1px solid white; font-size: 0.8rem; padding: 3px 10px;"}
+  [Read the datasets paper (NeurIPS 2021)](https://datasets-benchmarks-proceedings.neurips.cc/paper/2021/hash/158f3069a435b314a80bdcb024f8e422-Abstract-round2.html){class="btn btn-secondary"} 
+  [Read the competition paper (ICML 2022)](https://proceedings.mlr.press/v176/lance22a.html){class="btn btn-secondary"}
 title-block-banner-color: white
 title-block-banner: ../../images/heros/competition_dark.jpg
 page-layout: full

diff --git a/events/2022-08_neurips/index.qmd b/events/2022-08_neurips/index.qmd
@@ -4,7 +4,7 @@ subtitle: A competition on predicting multimodal expression across batches and t
 description: |
   A NeurIPS Competition (2022)
 
-  [See on Kaggle](https://www.kaggle.com/competitions/open-problems-multimodal){class="btn btn-primary" style="border: 1px solid white;"}
+  [See on Kaggle](https://www.kaggle.com/competitions/open-problems-multimodal){class="btn btn-primary"}
 date: "2022-08-15"
 start-date: "2022-08-15"
 end-date: "2022-11-15"

diff --git a/events/2023-08_neurips/index.qmd b/events/2023-08_neurips/index.qmd
@@ -2,7 +2,7 @@
 title: "NeurIPS 2023: Single-Cell Perturbation Prediction"
 subtitle: Generalizing experimental interventions to unseen contexts, a NeurIPS 2023 competition
 description: |
-  [Get Started on Kaggle](https://www.kaggle.com/competitions/open-problems-single-cell-perturbations){class="btn btn-primary" style="border: 1px solid white;"}
+  [Get Started on Kaggle](https://www.kaggle.com/competitions/open-problems-single-cell-perturbations){class="btn btn-primary"}
 date: "2023-08-30"
 start-date: "2023-09-11"
 end-date: "2023-11-30"