From 7692535495d506dfbaffbcaef2fbc3f9c36f30a2 Mon Sep 17 00:00:00 2001
From: Dani Arribas-Bel <daniel.arribas.bel@gmail.com>
Date: Fri, 5 May 2023 12:02:38 +0100
Subject: [PATCH] Builder for gdsrpy:2.0 ready

---
 pystack/Dockerfile | 36 +++++++++++++++++-------------------
 1 file changed, 17 insertions(+), 19 deletions(-)

diff --git a/pystack/Dockerfile b/pystack/Dockerfile
index 001ff5b..2860fcb 100644
--- a/pystack/Dockerfile
+++ b/pystack/Dockerfile
@@ -1,29 +1,27 @@
-FROM darribas/gdsr:1.0
+FROM darribas/gdsr:2.0
 
 LABEL org.label-schema.license="GPL-2.0" \
       org.label-schema.vcs-url="https://github.com/gdsl-ul/gdsr" \
       org.label-schema.vendor="Geographic Data Science Lab" \
       maintainer="Dani Arribas-Bel <D.Arribas-Bel@liverpool.ac.uk>"
 
-# Install Miniconda
-RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    -O $HOME/miniconda.sh && \
- sh $HOME/miniconda.sh -b -p /opt/conda && \
- rm $HOME/miniconda.sh && \
- ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
- echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
- echo "conda activate base" >> $HOME/.bashrc && \
- find /opt/conda/ -follow -type f -name '*.a' -delete && \
- find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
- /opt/conda/bin/conda clean -afy
+# Install Mambaforge
+RUN wget -O Mambaforge.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" \
+ && bash Mambaforge.sh -b -p "/opt/conda" \
+ && echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/rstudio/.bashrc \
+ && echo ". /opt/conda/etc/profile.d/mamba.sh" >> /home/rstudio/.bashrc \
+ && echo "conda activate base" >> /home/rstudio/.bashrc
 ENV PATH="/opt/conda/bin:${PATH}"
+RUN cat /home/rstudio/.bashrc
+USER rstudio
+# Install GDS env
+RUN . /opt/conda/etc/profile.d/conda.sh \
+ && . /opt/conda/etc/profile.d/mamba.sh \
+ && conda activate \
+ && mamba create --name gds --file https://github.com/darribas/gds_env/raw/v9.1/gds_py/gds_py_explicit_ubuntu-latest.txt \
+ && mamba activate gds \
+ && pip install -r https://github.com/darribas/gds_env/raw/v9.1/gds_py/gds_py_pip.txt
 
-# Install GDS environment
-RUN conda env create -f https://github.com/darribas/gds_env/raw/v6.1/gds_py/gds_py.yml 
-RUN bash -c "source /opt/conda/etc/profile.d/conda.sh && \
-    conda activate gds  && \
-    pip install -r https://github.com/darribas/gds_env/raw/v6.1/gds_py/gds_py_pip.txt" 
-EXPOSE 8888
-
+USER root
 # Install reticulate
 RUN R -e "install.packages('reticulate', repos='https://cran.rstudio.com');"