jupyter finds wrong python binary with conda

[parsifal9]

Hi All, I am having a problem with jupyter finding the wrong version of python. But first

1. is this the right forum for this sort of problem?
2. I don't see a list of details to include in a report. Have I included useful info?

My set-up is

bash Anaconda3-5.1.0-Linux-x86_64.sh
conda env create --file environment.yml
source activate placer-env
conda install nb_conda

and anaconda is installed in /home/dun280/local/anaconda3/

I have been trying to get this to work with elpy mode in emacs. But now I have realized that the problem is something to do with jupyter's paths. The following code snippet shows the problem. In the virtual env, I can see the right jupyter and python but when I start "jupyter console" it picks up the wrong python.

tamar: echo $PATH
/home/dun280/local/anaconda3/bin:/home/dun280/local/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

tamar: which jupyter
/home/dun280/local/anaconda3/bin/jupyter
tamar: which python
/home/dun280/local/anaconda3/bin/python
tamar: python --version
Python 3.6.4 :: Anaconda, Inc.

tamar: source activate placer-env

(placer-env) tamar:  echo $PATH
/home/dun280/local/anaconda3/envs/placer-env/bin:/home/dun280/local/anaconda3/bin:/home/dun280/local/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

(placer-env) tamar: which jupyter
/home/dun280/local/anaconda3/envs/placer-env/bin/jupyter
(placer-env) tamar: jupyter --version
4.4.0

(placer-env) tamar: which python
/home/dun280/local/anaconda3/envs/placer-env/bin/python
(placer-env) tamar: python --version
Python 3.6.5

(placer-env) tamar: jupyter kernelspec list
Available kernels:
python3    /home/dun280/local/anaconda3/envs/placer-env/share/jupyter/kernels/python3

(placer-env) tamar: jupyter console
Jupyter console 5.2.0
Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 18:10:19) 
Type 'copyright', 'credits' or 'license' for more information
IPython 6.2.1 -- An enhanced Interactive Python. Type '?' for help.

See -- "jupyter console" has found Python 3.6.4, so I can't load all of the modules I have installed in the virtual env.

Bye

[parsifal9]

Hi All,

I have updated conda to see if that fixes the problem

conda update -n root conda
conda update --all

Now /home/dun280/local/anaconda3/bin has a python 3.6.5 binary

/home/dun280/Dropbox/learning/python-anaconda/placer/placer/Feature extraction
tamar:  echo $PATH
/home/dun280/local/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
tamar: which jupyter
/home/dun280/local/anaconda3/bin/jupyter
tamar: which python
/home/dun280/local/anaconda3/bin/python
tamar: python --version
Python 3.6.5
tamar: source activate placer-env
(placer-env) tamar:  echo $PATH
/home/dun280/local/anaconda3/envs/placer-env/bin:/home/dun280/local/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
(placer-env) tamar: which jupyter
/home/dun280/local/anaconda3/envs/placer-env/bin/jupyter
(placer-env) tamar: which python
/home/dun280/local/anaconda3/envs/placer-env/bin/python
(placer-env) tamar: python --version
Python 3.6.5
(placer-env) tamar: jupyter kernelspec list
Available kernels:
  python3    /home/dun280/local/anaconda3/envs/placer-env/share/jupyter/kernels/python3
(placer-env) tamar: jupyter console
Jupyter console 5.2.0
Python 3.6.5 | packaged by conda-forge | (default, Apr  6 2018, 13:39:56) 
Type 'copyright', 'credits' or 'license' for more information
IPython 6.4.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: import pandas as pd
In [2]: import fiona, fiona.crs
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-2-c04c0287504e> in <module>()
----> 1 import fiona, fiona.crs

ModuleNotFoundError: No module named 'fiona'

Now jupyter finds a "Python 3.6.5" but it is still the wrong python -- it does not find the modules installed in the virtual environment. However, if I just start python

(placer-env) tamar: python
Python 3.6.5 | packaged by conda-forge | (default, Apr  6 2018, 13:39:56) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas as pd
>>> import fiona, fiona.crs
>>> 

it can find them.