Get back half of pipeline to run in docker

.github/workflows/python-package.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Install system
         run: |
           apt-get update -qqy
-          apt-get install -y git python3-pip libpq5 libpq-dev
+          apt-get install -y git python3-pip libpq5 libpq-dev r-base libtirpc-dev
       - uses: actions/checkout@v4
         with:
           submodules: 'true'

Dockerfile

@@ -15,8 +15,11 @@ FROM ghcr.io/osgeo/gdal:ubuntu-small-3.10.0
 RUN apt-get update -qqy && \
 	apt-get install -qy \
 		git \
+		cmake \
 		python3-pip \
+		r-base \
 		libpq-dev \
+		libtirpc-dev \
 	&& rm -rf /var/lib/apt/lists/* \
 	&& rm -rf /var/cache/apt/*
 
@@ -29,6 +32,10 @@ RUN pip install gdal[numpy]==3.10.0
 COPY requirements.txt /tmp/
 RUN pip install -r /tmp/requirements.txt
 
+RUN mkdir /root/R
+ENV R_LIBS_USER=/root/R
+RUN Rscript -e 'install.packages(c("lme4","lmerTest","emmeans"), repos="https://cloud.r-project.org")'
+
 COPY ./ /root/star
 WORKDIR /root/star
 RUN chmod 755 ./scripts/run.sh

requirements.txt

@@ -4,6 +4,7 @@ geopandas
 postgis
 psycopg2
 psutil
+pymer4
 pyproj
 scikit-image
 requests

scripts/run.sh

@@ -108,7 +108,7 @@ echo "Generating threat task list..."
 python3 ./utils/threats_generator.py --input ${DATADIR}/species-info --datadir ${DATADIR} --output ${DATADIR}/threatbatch.csv
 
 echo "Generating threat rasters..."
-littlejohn -j ${THREADS} -o ${DATADIR}/threatbatch.log -c ${DATADIR}/threatcatch.csv ${VIRTUAL_ENV}/bin/python3 -- ./threats/threat_processing.py
+littlejohn -j ${THREADS} -o ${DATADIR}/threatbatch.log -c ${DATADIR}/threatbatch.csv ${VIRTUAL_ENV}/bin/python3 -- ./threats/threat_processing.py
 
 echo "Summarising threats..."
 python3 ./threats/threat_summation.py --threat_rasters ${DATADIR}/threat_rasters --output ${DATADIR}/threat_results