Merge branch 'main' of github.com:saeyslab/polygloty

.github/workflows/publish.yml

@@ -16,7 +16,6 @@ jobs:
  - name: Check out repository
  uses: actions/checkout@v4
 
-
  - name: Set up specific version of Python
  uses: actions/setup-python@v5
  with:
@@ -28,13 +27,11 @@ jobs:
  - name: Set up Quarto
  uses: quarto-dev/quarto-actions/setup@v2
 
- # - name: Install AWS CLI
- # uses: unfor19/install-aws-cli-action@v1
  - name: Cache usecase_data
  uses: actions/cache@v2
  with:
  path: |
- notebooks/usecase_data
+ book/usecase/data
  key: usecase_data_${{ runner.os }}
 
  - name: Make sure data is available
@@ -43,26 +40,7 @@ jobs:
  aws s3 cp \
  --no-sign-request \
  s3://openproblems-bio/public/neurips-2023-competition/sc_counts_reannotated_with_counts.h5ad \
- notebooks/usecase_data/sc_counts_reannotated_with_counts.h5ad
-
- # attempt with pixi:
-
- # - name: Install pixi
- # run: curl -fsSL https://pixi.sh/install.sh | bash
-
- # - name: Cache several folders
- # uses: actions/cache@v2
- # with:
- # path: |
- # _freeze
- # .pixi
- # key: pixi_${{ runner.os }}
-
- # - name: Set up dependencies
- # run: pixi install -e dev
-
- # - name: Render slides
- # run: pixi run render_slides
+ book/usecase/data/sc_counts_reannotated_with_counts.h5ad
 
  # attempt with renv
  - name: Set up renv

README.md

@@ -93,10 +93,3 @@ To use the environment, use the following command:
 source renv/python/virtualenvs/renv-python-3.12/bin/activate
 quarto preview
 ```
-
-Or to render the slides:
-
-```bash
-source renv/python/virtualenvs/renv-python-3.12/bin/activate
-quarto render
-```

_extensions/quarto-ext/fontawesome/_extension.yml

@@ -0,0 +1,7 @@
+title: Font Awesome support
+author: Carlos Scheidegger
+version: 1.1.0
+quarto-required: ">=1.2.269"
+contributes:
+ shortcodes:
+ - fontawesome.lua