Update Dockerfile

Dockerfile

@@ -1,7 +1,9 @@
 # syntax=docker/dockerfile:1
 FROM rocker/r2u:22.04
 WORKDIR /code
+
 ARG DEBIAN_FRONTEND=noninteractive
+
 # ------------------------------------------------------------------------------
 # System deps (also needed if we have to compile any R package from source)
 # ------------------------------------------------------------------------------
@@ -12,7 +14,9 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \
     libopenblas-dev liblapack-dev \
     libjpeg-dev libpng-dev libtiff5-dev \
   && rm -rf /var/lib/apt/lists/*
+
 ENV LC_ALL=C.UTF-8 LANG=C.UTF-8 HF_HUB_DISABLE_TELEMETRY=1 PIP_NO_CACHE_DIR=1
+
 # ------------------------------------------------------------------------------
 # Try to install as many R packages as possible via Debian (blazing fast)
 # If any are missing from the repo, skip them and install later in R.
@@ -37,6 +41,7 @@ RUN set -eux; \
       fi; \
     done; \
     rm -rf /var/lib/apt/lists/*
+
 # ------------------------------------------------------------------------------
 # R fallback: install anything still missing (pak first for speed, then base R)
 # 'parallel' is part of base R; not needed here.
@@ -45,15 +50,19 @@ RUN set -eux; \
 # R fallback: install anything still missing (pak first, then base R)
 RUN Rscript - <<'RSCRIPT'
 options(Ncpus = parallel::detectCores())
+
 cran <- "https://cloud.r-project.org"
+
 # Required and optional packages
 req <- c(
   "shiny","dplyr","ggplot2","readr","ggExtra","DT","shinydashboard",
   "reticulate","remotes","data.table","stringdist","fastmatch",
   "stringr","Rfast","foreach","doParallel","digest"
 )
-opt <- c("text") # non-fatal if unavailable
+opt <- c("text")  # non-fatal if unavailable
+
 installed <- rownames(installed.packages())
+
 # Install required set: prefer pak (fast), fall back to install.packages
 need <- setdiff(req, installed)
 if (length(need)) {
@@ -64,19 +73,23 @@ if (length(need)) {
     pak::pak(need)
     TRUE
   }, error = function(e) FALSE)
+
   if (!ok) install.packages(need, repos = cran)
 }
+
 # Optional packages: best-effort only
 opt_need <- setdiff(opt, rownames(installed.packages()))
 if (length(opt_need)) {
   try(install.packages(opt_need, repos = cran), silent = TRUE)
 }
 RSCRIPT
+
 # ------------------------------------------------------------------------------
 # Install LinkOrgs from GitHub (retry once on transient errors)
 # ------------------------------------------------------------------------------
 RUN R -q -e "remotes::install_github('cjerzak/LinkOrgs-software/LinkOrgs', upgrade='never')" \
  || R -q -e "remotes::install_github('cjerzak/LinkOrgs-software/LinkOrgs', upgrade='never', dependencies=TRUE)"
+
 # ------------------------------------------------------------------------------
 # Miniforge (includes mamba by default) for Python ML backend
 # ------------------------------------------------------------------------------
@@ -103,12 +116,14 @@ RUN mamba create -y -n LinkOrgs_env python=3.11 pip && \
         /opt/conda/envs/LinkOrgs_env/bin/pip install jmp==0.0.4 && \
         /opt/conda/bin/conda clean -afy)
 ENV RETICULATE_PYTHON=/opt/conda/envs/LinkOrgs_env/bin/python
+
 # ------------------------------------------------------------------------------
 # App code
 # ------------------------------------------------------------------------------
 COPY . .
+
 # ------------------------------------------------------------------------------
 # Shiny entrypoint (honor HF $PORT; default 7860)
 # ------------------------------------------------------------------------------
 EXPOSE 7860
-CMD ["R", "--quiet", "-e", "port <- as.integer(Sys.getenv('PORT', '7860')); shiny::runApp('/code', host='0.0.0.0', port=port)"]
+CMD ["R", "--quiet", "-e", "port <- as.integer(Sys.getenv('PORT', '7860')); shiny::runApp('/code', host='0.0.0.0', port=port)"]