Fix conda hook to work in both terminal and Jupyter Notebook (#2047)

* Fix conda hook to work in both terminal and Jupyter Notebook

* Fix hook for Jupyter Terminals

* Rename startup hook to have order of precedence

* Try to increase sleep

* Comment making env_name default in custom_environment

Author: mathbunnyru

docs/using/recipe_code/custom_environment.dockerfile

@@ -28,17 +28,16 @@ RUN "${CONDA_DIR}/envs/${env_name}/bin/python" -m ipykernel install --user --nam
 RUN "${CONDA_DIR}/envs/${env_name}/bin/pip" install --no-cache-dir \
     'flake8'
 
-# Creating a startup hook, which will activate our custom environment by default in Jupyter Notebook
-# More info about startup hooks: https://jupyter-docker-stacks.readthedocs.io/en/latest/using/common.html#startup-hooks
-# You can comment this section to keep the default environment in Jupyter Notebook
-USER root
-RUN activate_custom_env_script=/usr/local/bin/before-notebook.d/activate_custom_env.sh && \
-    echo "#!/bin/bash" > ${activate_custom_env_script} && \
-    echo "eval \"$(conda shell.bash activate "${env_name}")\"" >> ${activate_custom_env_script} && \
-    chmod +x ${activate_custom_env_script}
+# Uncomment this section to activate custom environment by default
+# Note: uncommenting this section makes "${env_name}" default both for Jupyter Notebook and Terminals
+# More information here: https://github.com/jupyter/docker-stacks/pull/2047
+# USER root
+# RUN \
+#     # This changes a startup hook, which will activate our custom environment for the process
+#     echo conda activate "${env_name}" >> /usr/local/bin/before-notebook.d/10activate-conda-env.sh && \
+#     # This makes the custom environment default in Jupyter Terminals for all users which might be created later
+#     echo conda activate "${env_name}" >> /etc/skel/.bashrc && \
+#     # This makes the custom environment default in Jupyter Terminals for already existing NB_USER
+#     echo conda activate "${env_name}" >> "/home/${NB_USER}/.bashrc"
 
 USER ${NB_UID}
-
-# Making this environment default in Terminal
-# You can comment this line to keep the default environment in a Terminal
-RUN echo "conda activate ${env_name}" >> "${HOME}/.bashrc"

images/docker-stacks-foundation/10activate-conda-env.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+# This registers the initialization code for the conda shell code
+# It also activates default environment in the end, so we don't need to activate it manually
+# Documentation: https://docs.conda.io/projects/conda/en/latest/dev-guide/deep-dives/activation.html
+eval "$(conda shell.bash hook)"

images/docker-stacks-foundation/Dockerfile

@@ -59,8 +59,9 @@ RUN chmod a+rx /usr/local/bin/fix-permissions
 # Enable prompt color in the skeleton .bashrc before creating the default NB_USER
 # hadolint ignore=SC2016
 RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
-   # Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
-   echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
+    # More information in: https://github.com/jupyter/docker-stacks/pull/2047
+    # and docs: https://docs.conda.io/projects/conda/en/latest/dev-guide/deep-dives/activation.html
+    echo 'eval "$(conda shell.bash hook)"' >> /etc/skel/.bashrc
 
 # Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
 # and make sure these dirs are writable by the `users` group.
@@ -135,6 +136,8 @@ USER root
 RUN mkdir /usr/local/bin/start-notebook.d && \
     mkdir /usr/local/bin/before-notebook.d
 
+COPY 10activate-conda-env.sh /usr/local/bin/before-notebook.d/
+
 # Switch back to jovyan to avoid accidental container runs as root
 USER ${NB_UID}
 

tests/base-notebook/test_start_container.py

@@ -48,7 +48,7 @@ def test_start_notebook(
         ports={"8888/tcp": host_port},
     )
     # sleeping some time to let the server start
-    time.sleep(1)
+    time.sleep(2)
     logs = running_container.logs().decode("utf-8")
     LOGGER.debug(logs)
     # checking that the expected command is launched