Hotfix: reintroduces content from PR #3 that was accidentally deleted

.env.TEMPLATE

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+DEFAULT_ENV=dev
+
+# if 0, doesn't open a browser to the frontend webapp on a normal stack launch
+DO_OPEN_BROWSER=1
+
+POSTGRES_USER=molevolvr
+POSTGRES_PASSWORD=
+POSTGRES_DB=molevolvr

.gitignore

@@ -1 +1,2 @@
+/.env
 .DS_Store

README.md

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+# MolEvolvR Stack
+
+This repo contains the implementation of the MolEvolvR stack, i.e.:
+- `app`: the frontend webapp, written in React
+- `backend`: a backend written in [Plumber](https://www.rplumber.io/index.html)
+- `cluster`: the containerized SLURM "cluster" on which jobs are run
+- `services`: a collection of services on which the stack relies:
+    - `postgres`: configuration for a PostgreSQL database, which stores job information
+
+Most of the data processing is accomplished via the `MolEvolvR` package, which
+is currently available at https://github.com/JRaviLab/molevol_scripts. The stack
+simply provides a user-friendly interface for accepting and monitoring the
+progress of jobs, and orchestrates running the jobs on SLURM. The jobs
+themselves call methods of the package at each stage of processing.
+
+## Running the Stack in Development
+
+To run the stack, you'll need to [install Docker and Docker Compose](https://www.docker.com/).
+
+First, copy `.env.TEMPLATE` to `.env` and fill in the necessary values. You
+should supply a random password for the `POSTGRES_PASSWORD` variable. Of note
+is the `DEFAULT_ENV` variable, which gives `run_stack.sh` a default environment
+in which to operate; in development, this should be set to `dev`.
+
+Then, you can run the following command to bring up the stack:
+
+```bash
+./run_stack.sh
+```
+
+This will start the stack in development mode, which automatically reloads the
+backend or frontend when there are changes to their source.
+
+You should then be able to access the frontend at `http://localhost:5173`.
+
+## Production
+
+To run the stack in production, you can run the following
+
+```bash
+./run_stack.sh prod
+```
+
+This will start the stack in production mode.

backend/docker/Dockerfile

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+# syntax=docker/dockerfile:1.7
+
+# this Dockerfile should be used with the ./backend/ folder as the context
+# and ./backend/docker/Dockerfile as the dockerfile
+
+FROM rocker/tidyverse:4.3
+
+# install ccache, a compiler cache
+RUN apt-get update && apt-get install -y ccache
+
+# install some common cmd line tools
+RUN apt-get update && apt-get install -y curl
+
+# acquire drip, a plumber auto-reloader, and install
+ENV DRIP_URL="https://rdrip.netlify.app/builds/drip_0.1.0_linux_amd64.zip"
+RUN mkdir -p /tmp/software/ && \
+    wget -L -O /tmp/software/drip.zip ${DRIP_URL} && \
+    unzip /tmp/software/drip.zip -d /tmp/software && \
+    mv /tmp/software/drip /usr/local/bin && \
+    chmod +x /usr/local/bin/drip
+
+# acquire atlas, a schema manager
+RUN curl -sSf https://atlasgo.sh | sh
+
+# configure ccache env vars
+ENV PATH="/usr/lib/ccache:${PATH}"
+ENV CCACHE_DIR="/tmp/ccache"
+
+# install dependencies into the image
+COPY ./docker/install.R /tmp/install.r
+RUN   Rscript /tmp/install.r
+
+# RUN --mount=type=cache,target=/usr/local/lib/R/site-library \
+#     Rscript /tmp/install.r
+
+WORKDIR /app
+
+# copy the app into the image
+COPY . /app
+
+# run the app
+CMD ["/app/launch_api.sh"]

backend/docker/install.R

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+# install packages depended on by the molevolvr API server
+install.packages(
+    c(
+        "plumber",    # REST API framework
+        "DBI",        # Database interface
+        "RPostgres",  # PostgreSQL-specific impl. for DBI
+        "dbplyr",     # dplyr for databases
+        "box"         # allows R files to be referenced as modules
+    ),
+    Ncpus = 6
+)

backend/dummy.R

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+# Load the plumber package
+library(plumber)
+
+#* @get /
+function() {
+  "Hello, world!"
+}

backend/entrypoint.R

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+options(box.path = "/app")
+
+box::use(
+  plumber[plumb],
+  server/tcp_utils[wait_for_port]
+)
+
+# receive the target port as the env var API_PORT, or 9050 if unspecified
+target_port <- as.integer(Sys.getenv("API_PORT", unset=9050))
+
+# workaround for https://github.com/siegerts/drip/issues/3, in which
+# reloading fails due to the port being in use. we just wait, polling
+# occasionally, for up to 60 seconds for the port to become free.
+if (wait_for_port(target_port, poll_interval = 1, verbose = TRUE)) {
+  pr <- plumb("./dummy.R")$run(
+    host="0.0.0.0",
+    port=target_port,
+    debug=TRUE
+  )
+}
+else {
+  stop(
+    paste0("Failed to start the API server; port ", target_port, " still occupied after wait timeout exceeded"
+  )
+}

backend/launch_api.sh

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+#!/bin/bash
+
+# pass off to drip to control serving and reloading the API
+drip

backend/server/tcp_utils.R

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+#' Utility functions for working with TCP ports
+
+#' Check if a port is in use
+#' @param port The port to check
+#' @param host The IP for which to check the port
+#' @return TRUE if the port is in use, FALSE otherwise
+is_port_in_use <- function(port, host = "127.0.0.1") {
+  connection <- try(suppressWarnings(socketConnection(host = host, port = port, timeout = 1, open = "r+")), silent = TRUE)
+  if (inherits(connection, "try-error")) {
+    return(FALSE)  # Port is not in use
+  } else {
+    close(connection)
+    return(TRUE)   # Port is in use
+  }
+}
+
+#' Wait for a port to become free
+#' @param port The port to wait for
+#' @param timeout The maximum time to wait in seconds
+#' @param poll_interval The interval between checks in seconds
+#' @param host The IP for which to check the port
+#' @param verbose Whether to print messages to the console
+#' @return TRUE if the port is free, FALSE if the timeout is reached
+wait_for_port <- function(port, timeout = 60, poll_interval = 5, host = "127.0.0.1", verbose = TRUE) {
+  start_time <- Sys.time()
+  end_time <- start_time + timeout
+
+  while (Sys.time() < end_time) {
+    if (!is_port_in_use(port, host)) {
+      if (verbose) { cat("Port", port, "is now free\n") }
+      return(TRUE)
+    }
+    if (verbose) { cat("Port", port, "is in use. Checking again in", poll_interval, "seconds...\n") }
+    Sys.sleep(poll_interval)
+  }
+
+  if (verbose) { 
+    cat(paste0("Timeout of ", timeout, "s reached, but port ", port, " is still in use, aborting\n"))
+  }
+  return(FALSE)
+}

cluster/README.md

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+# MolEvolvR Cluster
+
+This folder will eventually contain Dockerfiles for building images for a SLURM
+controller and worker nodes.

docker-compose.override.yml

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+services:
+  backend:
+    volumes:
+      - ./backend/:/app/
+      # - ./backend/api/:/app/api/
+      # - ./backend/schema/:/app/schema/
+      # - ./backend/entrypoint.R:/app/entrypoint.R
+      # - ./backend/run_tests.sh:/app/run_tests.sh
+    ports:
+      - "9050:9050"
+    environment:
+      - "POSTGRES_DEV_HOST=dev-db"
+      - "PLUMBER_DEBUG=1"
+    depends_on:
+      - "dev-db"
+
+  app:
+    build:
+      context: ./app
+      target: dev
+    volumes:
+      - ./app/src:/app/src
+    environment:
+      - 'VITE_API=http://localhost:9050'
+    ports:
+      - "5713:5713"
+
+  db:
+    ports:
+      - "5460:5432"
+
+  # used by atlas to create migrations
+  dev-db:
+    image: postgres:16
+    env_file:
+      - .env

docker-compose.prod.yml

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+volumes:
+  app_bundle:
+  caddy_data:
+  caddy_config:
+
+services:
+  app:
+    image: molevolvr-frontend
+    build:
+      context: ./app
+      target: release
+    volumes:
+      - app_bundle:/app/dist
+    depends_on:
+      - backend
+
+  caddy:
+    image: caddy:2
+    ports:
+      - "80:80"
+      - "443:443"
+    volumes:
+      - app_bundle:/srv
+      - ./services/caddy/Caddyfile:/etc/caddy/Caddyfile
+      - caddy_data:/data
+      - caddy_config:/config
+    depends_on:
+      - app

docker-compose.yml

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+services:
+  backend:
+    image: molevolvr-backend
+    platform: linux/amd64
+    build:
+      context: ./backend
+      dockerfile: ./docker/Dockerfile
+    env_file:
+      - .env
+    environment:
+      - API_PORT=9050
+      - "POSTGRES_HOST=db"
+    depends_on:
+      db:
+        condition: service_healthy
+
+  app:
+    image: molevolvr-frontend
+    build: ./app
+    depends_on:
+      - backend
+
+  db:
+    image: postgres:16
+    env_file:
+      - .env
+    healthcheck:
+      test: ["CMD-SHELL", "sh -c 'pg_isready -U ${POSTGRES_USER} -d ${POSTGRES_DB}'"]
+      interval: 30s
+      timeout: 60s
+      retries: 5
+      start_period: 80s