[Rdkit-discuss] Jupyter Could not find environment: my-rdkit-env

[Germano Massullo]

Hi there, I am experiencing some troubles in letting jupyter use rdkit
on Fedora 25
I installed Anaconda 4.4.0
then following [1] I runned

$ conda create -c rdkit -n my-rdkit-env rdkit
$ source activate my-rdkit-env

then

$ jupyter-notebook --ip foo_ip --port 8890

then from jupyter notebook

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors

but those imports return
====
CondaEnvironmentNotFoundError: Could not find environment: my-rdkit-env .
You can list all discoverable environments with `====`.
====

running
conda info --envs
I get
# conda environments:
#
my-rdkit-env * /home/user/.conda/envs/my-rdkit-env
root /opt/anaconda3


Thank you very much

[1]: http://www.rdkit.org/docs/Install.html

[Greg Landrum]

Hi,

This (or something like it) happens to me all the time: you need to install Jupyter in the new environment too.

The only reason what you are currently doing even halfway works is because you have Jupyter installed in the default conda environment and that is being used when you launch the notebook from the shell

________________________________
From: Germano Massullo <***@gmail.com>
Sent: Thursday, June 29, 2017 3:22:04 PM
To: rdkit-***@lists.sourceforge.net
Subject: [Rdkit-discuss] Jupyter Could not find environment: my-rdkit-env

Hi there, I am experiencing some troubles in letting jupyter use rdkit
on Fedora 25
I installed Anaconda 4.4.0
then following [1] I runned

$ conda create -c rdkit -n my-rdkit-env rdkit
$ source activate my-rdkit-env

then

$ jupyter-notebook --ip foo_ip --port 8890

then from jupyter notebook

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors

but those imports return
====
CondaEnvironmentNotFoundError: Could not find environment: my-rdkit-env .
You can list all discoverable environments with `====`.
====

running
conda info --envs
I get
# conda environments:
#
my-rdkit-env * /home/user/.conda/envs/my-rdkit-env
root /opt/anaconda3


Thank you very much

[1]: http://www.rdkit.org/docs/Install.html

[Germano Massullo]

Post by Greg Landrum
Hi,
This (or something like it) happens to me all the time: you need to
install Jupyter in the new environment too.
The only reason what you are currently doing even halfway works is
because you have Jupyter installed in the default conda environment
and that is being used when you launch the notebook from the shell

Thank you very much, it worked! I attach the complete commands list, so
that it could help any other users

Install Anaconda
then following [1] run

$ conda create -c rdkit -n my-rdkit-env rdkit
$ source activate my-rdkit-env
(missing line) $ conda install jupyter
then

$ jupyter-notebook --ip foo_ip --port 8890

then from jupyter notebook

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors


[1]: http://www.rdkit.org/docs/Install.html

[Michal Krompiec]

Hi Germano,
You can also install rdkit in the default environment:
conda install -c rdkit rdkit

Best,
Michal

Post by Germano Massullo
Hi there, I am experiencing some troubles in letting jupyter use rdkit
on Fedora 25
I installed Anaconda 4.4.0
then following [1] I runned
$ conda create -c rdkit -n my-rdkit-env rdkit
$ source activate my-rdkit-env
then
$ jupyter-notebook --ip foo_ip --port 8890
then from jupyter notebook
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors
but those imports return
====
CondaEnvironmentNotFoundError: Could not find environment: my-rdkit-env .
You can list all discoverable environments with `====`.
====
running
conda info --envs
I get
#
my-rdkit-env * /home/user/.conda/envs/my-rdkit-env
root /opt/anaconda3
Thank you very much
[1]: http://www.rdkit.org/docs/Install.html
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