FROM rocker/geospatial:4.5

# ----- system deps -----

RUN apt-get update && \

apt-get install -y --no-install-recommends \

software-properties-common \

jags \

gsl-bin libgsl-dev \

htop \

gnupg2 \

libzmq3-dev \

libgmp-dev \

libssh-dev \

openjdk-21-jre \

openssh-client \

python3-dev \

python3-pip \

libmagick++-dev libmagickwand-dev libmagickcore-dev \

curl git ca-certificates && \

rm -rf /var/lib/apt/lists/*

# ----- R packages -----

RUN install2.r --error \

bench \

betapart \

rjags \

clustermq \

devtools \

furrr \

future \

future.apply \

future.batchtools \

landscapemetrics \

magick \

microbenchmark \

nlrx \

plotrix \

rasterVis \

rcdd \

Rcpp \

remotes \

RInside \

rslurm \

skimr \

ssh \

targets \

tidyverse \

usethis \

vegan \

withr

# ----- GitHub installs -----

RUN Rscript -e 'remotes::install_github("EFForTS-B10/[email protected]", upgrade = "never")' && \

Rscript -e 'remotes::install_github("ropensci/NLMR", upgrade = "never")' && \

Rscript -e 'remotes::install_github("ropensci/landscapetools", upgrade = "never")'

# ----- Persist JAVA_HOME and add to PATH -----

ENV JAVA_HOME=/usr/lib/jvm/java-21-openjdk-amd64

ENV PATH="${JAVA_HOME}/bin:${PATH}"

# ---------- InVEST 3.11.0 via micromamba (Python 3.9) ----------

ARG MAMBA_ROOT=/opt/conda

ENV MAMBA_ROOT_PREFIX=${MAMBA_ROOT}

ENV PATH=${MAMBA_ROOT}/envs/invest/bin:$PATH

# 1) micromamba

RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest \

| tar -xvj -C /usr/local/bin/ bin/micromamba --strip-components=1

# 2) env with compatible pins

RUN micromamba create -y \

-r ${MAMBA_ROOT} \

-n invest \

-c conda-forge \

python=3.9 \

natcap.invest==3.11.0 \

"numpy>=1.20,<1.24" \

"gdal>=3.2,<3.6" \

pip && \

micromamba clean -a -y

# 3) headless proof

RUN python -c "import natcap.invest as i; print(i.__version__)" && \

python -V && \

gdalinfo --version

# ---------- end InVEST ----------

# ---------- NetLogo multi-version (6.2.1, 6.4.0, 7.0.0) + NetVest ----------

ARG NETLOGO_ROOT=/opt/netlogo

ARG NETLOGO_NetVEST=6.2.1

ARG NETLOGO_6=6.4.0

ARG NETLOGO_7=7.0.0

# Choose 6.2.1 as the default for NetVEST

ENV NETLOGO_ROOT=${NETLOGO_ROOT} \

NETLOGO_DEFAULT=${NETLOGO_NetVEST} \

NETVEST_HOME=/opt/NetVest \

JAVA_TOOL_OPTIONS="-Djava.awt.headless=true"

# Fetch & install the three NetLogo versions

RUN set -eux; \

mkdir -p "${NETLOGO_ROOT}"; \

for v in ${NETLOGO_NetVEST} ${NETLOGO_6} ${NETLOGO_7}; do \

url="https://ccl.northwestern.edu/netlogo/${v}/NetLogo-${v}-64.tgz"; \

tmp="/tmp/netlogo-${v}.tgz"; \

dest="${NETLOGO_ROOT}/${v}"; \

echo "Downloading $url"; \

curl -L "$url" -o "$tmp"; \

mkdir -p "$dest"; \

tar -xzf "$tmp" -C "$dest" --strip-components=1; \

rm -f "$tmp"; \

done

# Canonical, read-only NetVest (works for Docker & Apptainer)

RUN git clone --depth 1 https://github.com/EFForTS-B10/NetVest.git "${NETVEST_HOME}" \

&& find "${NETVEST_HOME}" -type d -exec chmod a+rx {} \; \

&& find "${NETVEST_HOME}" -type f -exec chmod a+r {} \;

# To make a writable copy of NetVest, e.g. for development:

## mkdir -p "$HOME/NetVest"

## cp -rL /opt/NetVest/. "$HOME/NetVest/"

## or: git clone https://github.com/EFForTS-B10/NetVest.git "$HOME/NetVest"

# ---------- end NetLogo + NetVest ----------

# RStudio server tweak

RUN echo "session-timeout-minutes=0" >> /etc/rstudio/rsession.conf