Use base environment

Author: edoardob90

Dockerfile

@@ -32,30 +32,27 @@ RUN apt-get update && \
     rm -rf /var/lib/apt/lists/*
 
 # Copy the script to setup the environment
-RUN cp -a docker/setup_custom_env.py /opt/setup-scripts/ && \
-    chmod +x /opt/setup-scripts/setup_custom_env.py
+# RUN cp -a docker/setup_custom_env.py /opt/setup-scripts/ && \
+#     chmod +x /opt/setup-scripts/setup_custom_env.py
 
 # Copy the script to activate the Conda environment
-RUN cp -a docker/activate-custom-env.sh /usr/local/bin/before-notebook.d/
+# RUN cp -a docker/activate-custom-env.sh /usr/local/bin/before-notebook.d/
 
 # Switch back to the default notebook user
 USER ${NB_UID}
 
-# Set the working directory to the repository directory
-# WORKDIR ${HOME}/${BASENAME}
-
 # Create the Conda environment defined in environment.yml
-RUN mamba env create -f binder/environment.yml && \
+RUN mamba env update -f docker/environment.yml && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
 # Register the Jupyter kernel from the custom environment
-RUN /opt/setup-scripts/setup_custom_env.py ${BASENAME}
+# RUN /opt/setup-scripts/setup_custom_env.py ${BASENAME}
 
 # Copy the IPython configuration file (binder/postBuild script)
-RUN mkdir -p ${HOME}/.ipython/profile_default
-COPY binder/ipython_config.py ${HOME}/.ipython/profile_default/
+RUN mkdir -p ${HOME}/.ipython/profile_default && \
+    cp -a binder/ipython_config.py ${HOME}/.ipython/profile_default/
 
 # Set the environment variable IPYTHONDIR
 ENV IPYTHONDIR="${HOME}/.ipython"

docker/environment.yml

@@ -0,0 +1,23 @@
+---
+name: base
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - pip
+  - pip:
+      - numpy
+      - matplotlib
+      - pandas
+      - ipywidgets
+      - ipynbname
+      - jupyterlab
+      - pytest
+      - pytest-timeout
+      - markdown
+      - pre-commit
+      - geostatspy
+      - gstools
+      - scikit-learn
+      - attrs
+      - multiprocess