Merge pull request #107 from pythonhealthdatascience/dev

Dev

Author: amyheather

.gitignore

@@ -220,8 +220,8 @@ po/*~
 rsconnect/
 /.quarto/
 
-# Figure HTML generated by quarto
+# Quarto
 figure_*.html
-
 _site/
 **/*.quarto_ipynb
+site_libs/

CONTRIBUTING.md

@@ -104,4 +104,55 @@ If your name or contributions are missing from the README, or if you contributed
 @all-contributors please add @githubuser for ...
 ```
 
-Then list appropriate contribution types from [allcontributors.org/docs/en/emoji-key](https://allcontributors.org/docs/en/emoji-key) (e.g., code, review, doc, content, bug, ideas, infra).
+Then list appropriate contribution types from [allcontributors.org/docs/en/emoji-key](https://allcontributors.org/docs/en/emoji-key) (e.g., code, review, doc, content, bug, ideas, infra).
+
+<br>
+
+## Docker
+
+The GitHub action to build the website uses docker, as this avoids needing to install all the required Python and R packages and system dependencies with every deployment (unless there are environment changes).
+
+If you wish to build the docker image locally to test it out, run this command from the project directory:
+
+```{.bash}
+sudo docker build -t desrapbookdocker .
+```
+
+To view your available images, run:
+
+```{.bash}
+sudo docker images
+```
+
+Open the container interactively:
+
+```{.bash}
+sudo docker run -it desrapbookdocker /bin/bash
+```
+
+Restore R environment:
+
+```{.bash}
+Rscript -e "renv::restore()"
+```
+
+Edit the conda location in `.Renviron` (if present) to `RETICULATE_CONDA=/opt/conda/bin/conda`:
+
+```{.bash}
+apt-get update && apt-get install nano
+nano .Renviron
+```
+
+Build the website:
+
+```{.bash}
+quarto render
+```
+
+To close the container: `Ctrl+P` then `Ctrl+Q`.
+
+To delete the image:
+
+```{.bash}
+sudo docker image rm -f desrapbookdocker
+```

Dockerfile

@@ -18,21 +18,30 @@ RUN apt-get update && \
         python3-venv \
         build-essential \
         pandoc \
-        chromium-browser \
-        # Extra browser/system dependencies for Kaleido/Chromium
-        libnss3 \
+        # Required for chrome
+        fonts-liberation \
+        libasound2 \
         libatk-bridge2.0-0 \
+        libatk1.0-0 \
+        libatspi2.0-0 \
         libcups2 \
+        libdbus-1-3 \
+        libgbm1 \
+        libgtk-3-0 \
+        libnspr4 \
+        libnss3 \
+        libvulkan1 \
         libxcomposite1 \
         libxdamage1 \
-        libxfixes3 \
-        libxrandr2 \
-        libgbm1 \
         libxkbcommon0 \
-        libpango-1.0-0 \
-        libcairo2 \
-        libasound2 \
-        && rm -rf /var/lib/apt/lists/*
+        libxrandr2 \
+        xdg-utils \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install chrome (required by kaleido, which is used for plotly write_image)
+RUN wget -O /tmp/chrome.deb https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb && \
+    apt-get install -y --no-install-recommends /tmp/chrome.deb && \
+    rm /tmp/chrome.deb
 
 # Install Quarto CLI
 RUN wget -qO- https://quarto.org/download/latest/quarto-linux-amd64.deb > /tmp/quarto.deb && \

environment.yaml

@@ -6,6 +6,7 @@ dependencies:
   - flake8=7.3.0
   - itables=2.5.2
   - jupyter=1.1.1
+  - openssl=3.3.0
   - pandas=2.3.1
   - plotly=6.3.0
   - pip