Conda env not activated

I am a bit confused by the way environment.yml works.

I tried to install R and SageMath from conda-forge, with

name: sage-r-environment
channels:
  - conda-forge
dependencies:
  - python=2.7
  - sage
  - r-essentials

but when I launch the Jupyter server, neither R nor SageMath notebooks are available. SageMath also does not start from a terminal (it complains about some env variables not being set).

It seems that the reason is that the conda environment is not activated prior to launching the Jupyter server. The fix for me was to add a start file:

#!/bin/bash

source /srv/conda/bin/activate kernel
exec "$@"

Also, the fact that the environment is named kernel instead of sage-r-environment is surprising.

Demo repo is here: https://github.com/defeo/sage-r

Is this a bug, or am I doing something wrong?

[choldgraf]

hmmm that is strange - you shouldn’t need to do any source stuff in a start file. E.g. here’s the binder-examples conda repo:

https://github.com/binder-examples/conda/blob/master/environment.yml

Did you resolve this issue in the end, or still having problems with it? It feels like a bug to me…

[yuvipanda]

@minrk did a bunch of work recently around activating conda environments at startup. Not sure if that applies to postBuild though. You can set your first line to #!/bin/bash -l to run a login Shell, which should activate the environment for you