fixed incorrect handling of conda environments

Dockerfile_jupyterhub

@@ -8,39 +8,22 @@ ARG env_name=rs-notebooks
 ADD *.ipynb /notebooks/
 ADD sample.geojson /notebooks/
 
-SHELL ["/bin/bash", "-l", "-c"]
-
 # creating environment
-ADD environment_jupyterlab.yml ${dest_yml}
-
-# this only seems to work when overring CMD with /bin/bash when runing docker run
-# or with shells spawned afterwards (e.g. from jupyterlab itself)
-# does not work for further RUN commands in the Dockerfile despite having used SHELL earlier
-RUN conda init bash
-RUN mamba init bash
-
+ADD environment_jupyterhub_lite.yml ${dest_yml}
 RUN mamba env create --file ${dest_yml} --name ${env_name}
 
-# leads to "your shell has not been properly configured despite having RUN conda init"
-RUN echo "conda activate ${env_name}" >> ~/.bashrc
-RUN echo "conda activate ${env_name}" >> ~/.profile
+# setting up shell to run in the correct environment
+SHELL ["conda", "run", "-n", "rs-notebooks", "/bin/bash", "-c"]
 
-ENV ENV_NAME ${env_name}
-
-# HOW DOES THIS TRANSFER TO JUPYTERHUB?
 # setting up jupyter lab to use bash as a terminal
 # this ensures that the right environment is activated in the terminal
 # should allow users to run pip installs from notebooks/jupyter lab terminal
 # without encountering issues with different environments
-RUN /opt/conda/envs/${env_name}/bin/jupyter lab --generate-config && \
-    echo 'c.NotebookApp.terminado_settings = { "shell_command": ["/bin/bash"] }' >> /root/.jupyter/jupyter_lab_config.py
+#RUN /opt/conda/envs/rs-notebooks/bin/jupyter lab --generate-config && \
+#RUN jupyter lab --generate-config && \
+#    echo 'c.NotebookApp.terminado_settings = { "shell_command": ["/bin/bash"] }' >> /root/.jupyter/jupyter_lab_config.py
 
 # setting up default landing folder
 WORKDIR /notebooks
 
-# this should work but doesn't. conda activate from .bashrc/.profile fails
-# so /opt/conda/envs/${ENV_NAME}/bin is not in $PATH
-#CMD jupyterhub-singleuser
-
-# this works but bypasses the conda activate issue for CMD by going into the path directly 
-CMD /opt/conda/envs/${ENV_NAME}/bin/jupyterhub-singleuser
+CMD jupyterhub-singleuser

Dockerfile_jupyterlab

@@ -8,38 +8,22 @@ ARG env_name=rs-notebooks
 ADD *.ipynb /notebooks/
 ADD sample.geojson /notebooks/
 
-SHELL ["/bin/bash", "-l", "-c"]
-
 # creating environment
 ADD environment_jupyterlab.yml ${dest_yml}
-
-#this only seems to work when overring CMD with /bin/bash when runing docker run
-#or with shells spawned afterwards (e.g. from jupyterlab itself)
-# does not work for further RUN commands in the Dockerfile despite having used SHELL earlier
-RUN conda init bash
-RUN mamba init bash
-
 RUN mamba env create --file ${dest_yml} --name ${env_name}
 
-# leads to "your shell has not been properly configured" despite having RUN conda init
-RUN echo "conda activate ${env_name}" >> ~/.bashrc
-RUN echo "conda activate ${env_name}" >> ~/.profile
-
-ENV ENV_NAME ${env_name}
+# setting up shell to run in the correct environment
+SHELL ["conda", "run", "-n", "rs-notebooks", "/bin/bash", "-c"]
 
 # setting up jupyter lab to use bash as a terminal
 # this ensures that the right environment is activated in the terminal
 # should allow users to run pip installs from notebooks/jupyter lab terminal
 # without encountering issues with different environments
-RUN /opt/conda/envs/${env_name}/bin/jupyter lab --generate-config && \
-    echo 'c.NotebookApp.terminado_settings = { "shell_command": ["/bin/bash"] }' >> /root/.jupyter/jupyter_lab_config.py
+#RUN /opt/conda/envs/rs-notebooks/bin/jupyter lab --generate-config && \
+RUN jupyter lab --generate-config
+RUN echo 'c.NotebookApp.terminado_settings = { "shell_command": ["/bin/bash"] }' >> /root/.jupyter/jupyter_lab_config.py
 
 # setting up default landing folder
 WORKDIR /notebooks
 
-# this should work but doesn't. conda activate from .bashrc/.profile fails
-# so /opt/conda/envs/${ENV_NAME}/bin is not in $PATH
-#CMD jupyter lab --ip 0.0.0.0 --no-browser --allow-root
-
-# this works but bypasses the conda activate issue for CMD by going into the path directly 
-CMD /opt/conda/envs/${ENV_NAME}/bin/jupyter lab --ip 0.0.0.0 --no-browser --allow-root
+CMD jupyter lab --ip 0.0.0.0 --no-browser --allow-root