Add Docker (#44)

* Run `golem::add_dockerfile_with_renv()`

* Rename files

* Clean up base Dockerfile

* Clean up main Dockerfile

* Remove dev dependencies from `renv.lock.prod`

* Update deployment instructions

* Update README; add overview and Deployment section

.Rbuildignore

@@ -11,3 +11,4 @@ $run_dev.*
 ^\.github$
 ^\.lintr$
 ^\.renvignore$
+^deploy$

README.md

@@ -7,6 +7,16 @@
 
 The goal of calypso is to provide a summary of OMOP data and display it in a public data catalogue
 
+## Overview
+
+1. [Installation](#installation)
+2. [Development](#development)
+    - [Set up](#set-up)
+    - [Updating the `renv` lockfile](#updating-the-renv-lockfile)
+    - [Design](#design)
+    - [Coding style](#coding-style)
+3. [Deployment](./deploy/README.md)
+
 ## Installation
 
 You can install the development version of calypso from within R like so:
@@ -120,3 +130,7 @@ lintr::lint_package()
 ```
 
 (or have it [run automatically in your IDE](https://lintr.r-lib.org/articles/editors.html)).
+
+## Deployment
+
+See the [deployment docs](./deploy/README.md).

deploy/Dockerfile

@@ -0,0 +1,16 @@
+FROM calypso_base:4.4.1
+
+WORKDIR /app
+COPY renv.lock.prod renv.lock
+
+RUN R -e 'renv::restore()'
+
+COPY calypso_*.tar.gz /app.tar.gz
+RUN R -e 'remotes::install_local("/app.tar.gz", upgrade="never")' && \
+    rm /app.tar.gz
+
+EXPOSE 3838
+CMD ["R", "-e", "options('shiny.port'=3838,shiny.host='0.0.0.0');library(calypso);calypso::run_app()"]
+
+# to build: docker build -t calypso .
+# to run: docker run -p 3838:3838 calypso

deploy/Dockerfile.base

@@ -0,0 +1,19 @@
+FROM rocker/shiny-verse:4.4.1
+SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
+
+RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
+
+# Set R options
+RUN echo "options(renv.config.pak.enabled = FALSE, repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" |\
+    tee /usr/local/lib/R/etc/Rprofile.site | \
+    tee /usr/lib/R/etc/Rprofile.site
+
+# Install renv
+RUN R -e 'install.packages("remotes")' && \
+    R -e 'remotes::install_version("renv", version = "1.0.7")'
+
+# Restore renv environment
+RUN mkdir /app
+WORKDIR /app
+COPY renv.lock.prod renv.lock
+RUN R -e 'renv::restore()'

deploy/README.md

@@ -0,0 +1,41 @@
+# Deploy
+
+## Build the package
+
+From the package root directory, run from `R`:
+
+```r
+pkgbuild::build(path = ".", dest_path = "deploy")
+```
+
+## Create `renv.lock.prod`
+
+From the package root directory, run from `R`:
+
+```r
+renv::snapshot(project = ".", lockfile = "./deploy/renv.lock.prod", type = "explicit")
+```
+
+## Build Docker images
+
+In the `deploy/` directory, run:
+
+```shell
+# Assuming R version 4.4.1
+docker build -f Dockerfile.base --platform=linux/amd64 -t calypso_base:4.4.1 .
+docker build -f Dockerfile --platform=linux/amd64 -t calypso:latest .
+```
+
+The `calypso_base` image acts as a cached image with most of the necessary dependencies installed,
+to speed up the build process of the `calypso` image. The base image is not intended to be run and
+is only expected to be rebuilt in case of major dependency changes.
+
+Note that the `calypso` image also includes a `renv::restore()` step, so any dependencies not present
+in the base image will still be installed.
+
+## Run Docker container
+
+```shell
+docker run -p 3838:3838 calypso:latest
+# then go to 127.0.0.1:80
+```