I installed Anaconda (with Python 2.7), and installed Tensorflow in an environment called tensorflow. I can import Tensorflow successfully in that environment.
The problem is that Jupyter Notebook does not recognize the new environment I just created. No matter I start Jupyter Notebook from the GUI Navigator or from the command line within the tensorflow env, there is only one kernel in the menu called Python [Root], and Tensorflow cannot be imported. Of course, I clicked on that option multiple times, saved file, re-opened, but these did not help.
Strangely, I can see the two environments when I open the Conda tab on the front page of Jupyter. But when I open the Files tab, and try to new a notebook, I still end up with only one kernel.
I looked at this question:
Link Conda environment with Jupyter Notebook
But there isn't such a directory as ~/Library/Jupyter/kernels on my computer! This Jupyter directory only has one sub-directory called runtime.
I am really confused. Are Conda environments supposed to become kernels automatically? (I followed https://ipython.readthedocs.io/en/stable/install/kernel_install.html to manually set up the kernels, but was told that ipykernel was not found.)
I don't think the other answers are working any more, as conda stopped automatically setting environments up as jupyter kernels. You need to manually add kernels for each environment in the following way:
source activate myenv
python -m ipykernel install --user --name myenv --display-name "Python (myenv)"
As documented here:http://ipython.readthedocs.io/en/stable/install/kernel_install.html#kernels-for-different-environments
Also see this issue.
Addendum:
You should be able to install the nb_conda_kernels package with conda install nb_conda_kernels to add all environments automatically, see https://github.com/Anaconda-Platform/nb_conda_kernels
If your environments are not showing up, make sure you have installed
nb_conda_kernels in the environment with Jupyter
ipykernel and ipywidgets in the Python environment you want to access (note that ipywidgets is to enable some Juptyer functionality, not environment visibility, see related docs).
Anaconda's documentation states that
nb_conda_kernels should be installed in the environment from which
you run Jupyter Notebook or JupyterLab. This might be your base conda
environment, but it need not be. For instance, if the environment
notebook_env contains the notebook package, then you would run
conda install -n notebook_env nb_conda_kernels
Any other environments you wish to access in your notebooks must have
an appropriate kernel package installed. For instance, to access a
Python environment, it must have the ipykernel package; e.g.
conda install -n python_env ipykernel
To utilize an R environment, it must have the r-irkernel package; e.g.
conda install -n r_env r-irkernel
For other languages, their corresponding kernels must be installed.
In addition to Python, by installing the appropriatel *kernel package, Jupyter can access kernels from a ton of other languages including R, Julia, Scala/Spark, JavaScript, bash, Octave, and even MATLAB.
Note that at the time originally posting this, there was a possible cause from nb_conda not yet supporting Python 3.6 environments.
If other solutions fail to get Jupyter to recognize other conda environments, you can always install and run jupyter from within a specific environment. You may not be able to see or switch to other environments from within Jupyter though.
$ conda create -n py36_test -y python=3.6 jupyter
$ source activate py36_test
(py36_test) $ which jupyter
/home/schowell/anaconda3/envs/py36_test/bin/jupyter
(py36_test) $ jupyter notebook
Notice that I am running Python 3.6.1 in this notebook:
Note that if you do this with many environments, the added storage space from installing Jupyter into every environment may be undesirable (depending on your system).
The annoying thing is that in your tensorflow environment, you can run jupyter notebook without installing jupyter in that environment. Just run
(tensorflow) $ conda install jupyter
and the tensorflow environment should now be visible in Jupyter Notebooks started in any of your conda environments as something like Python [conda env:tensorflow].
I had to run all the commands mentioned in the top 3 answers to get this working:
conda install jupyter
conda install nb_conda
conda install ipykernel
python -m ipykernel install --user --name mykernel
Just run conda install ipykernel in your new environment, only then you will get a kernel with this env. This works even if you have different versions installed in each envs and it doesn't install jupyter notebook again. You can start youe notebook from any env you will be able to see newly added kernels.
Summary (tldr)
If you want the 'python3' kernel to always run the Python installation from the environment where it is launched, delete the User 'python3' kernel, which is taking precedence over whatever the current environment is with:
jupyter kernelspec remove python3
Full Solution
I am going to post an alternative and simpler solution for the following case:
You have created a conda environment
This environment has jupyter installed (which also installs ipykernel)
When you run the command jupyter notebook and create a new notebook by clicking 'python3' in the 'New' dropdown menu, that notebook executes python from the base environment and not from the current environment.
You would like it so that launching a new notebook with 'python3' within any environment executes the Python version from that environment and NOT the base
I am going to use the name 'test_env' for the environment for the rest of the solution. Also, note that 'python3' is the name of the kernel.
The currently top-voted answer does work, but there is an alternative. It says to do the following:
python -m ipykernel install --user --name test_env --display-name "Python (test_env)"
This will give you the option of using the test_env environment regardless of what environment you launch jupyter notebook from. But, launching a notebook with 'python3' will still use the Python installation from the base environment.
What likely is happening is that there is a user python3 kernel that exists. Run the command jupyter kernelspec list to list all of your environments. For instance, if you have a mac you will be returned the following (my user name is Ted).
python3 /Users/Ted/Library/Jupyter/kernels/python3
What Jupyter is doing here is searching through three different paths looking for kernels. It goes from User, to Env, to System. See this document for more details on the paths it searches for each operating system.
The two kernels above are both in the User path, meaning they will be available regardless of the environment that you launch a jupyter notebook from. This also means that if there is another 'python3' kernel at the environment level, then you will never be able to access it.
To me, it makes more sense that choosing the 'python3' kernel from the environment you launched the notebook from should execute Python from that environment.
You can check to see if you have another 'python3' environment by looking in the Env search path for your OS (see the link to the docs above). For me (on my mac), I issued the following command:
ls /Users/Ted/anaconda3/envs/test_env/share/jupyter/kernels
And I indeed had a 'python3' kernel listed there.
Thanks to this GitHub issue comment (look at the first response), you can remove the User 'python3' environment with the following command:
jupyter kernelspec remove python3
Now when you run jupyter kernelspec list, assuming the test_env is still active, you will get the following:
python3 /Users/Ted/anaconda3/envs/test_env/share/jupyter/kernels/python3
Notice that this path is located within the test_env directory. If you create a new environment, install jupyter, activate it, and list the kernels, you will get another 'python3' kernel located in its environment path.
The User 'python3' kernel was taking precedence over any of the Env 'python3' kernels. By removing it, the active environment 'python3' kernel was exposed and able to be chosen every time. This eliminates the need to manually create kernels. It also makes more sense in terms of software development where one would want to isolate themselves into a single environment. Running a kernel that is different from the host environment doesn't seem natural.
It also seems that this User 'python3' is not installed for everyone by default, so not everyone is confronted by this issue.
To add a conda environment to Jupyter:
In Anaconda Prompt :
run conda activate <env name>
run conda install -c anaconda ipykernel
run python -m ipykernel install --user --name=<env name>
** tested on conda 4.8.3 4.11.0
$ conda install nb_conda_kernels
(in the conda environment where you run jupyter notebook) will make all conda envs available automatically. For access to other environments, the respective kernels must be installed. Here's the ref.
This worked for me in windows 10 and latest solution :
1) Go inside that conda environment ( activate your_env_name )
2) conda install -n your_env_name ipykernel
3) python -m ipykernel install --user --name build_central --display-name "your_env_name"
(NOTE : Include the quotes around "your_env_name", in step 3)
The nb_conda_kernels package is the best way to use jupyter with conda. With minimal dependencies and configuration, it allows you to use other conda environments from a jupyter notebook running in a different environment. Quoting its documentation:
Installation
This package is designed to be managed solely using conda. It should be installed in the environment from which you run Jupyter Notebook or JupyterLab. This might be your base conda environment, but it need not be. For instance, if the environment notebook_env contains the notebook package, then you would run
conda install -n notebook_env nb_conda_kernels
Any other environments you wish to access in your notebooks must have an appropriate kernel package installed. For instance, to access a Python environment, it must have the ipykernel package; e.g.
conda install -n python_env ipykernel
To utilize an R environment, it
must have the r-irkernel package; e.g.
conda install -n r_env r-irkernel
For other languages, their corresponding kernels must be installed.
Then all you need to do is start the jupyter notebook server:
conda activate notebook_env # only needed if you are not using the base environment for the server
# conda install jupyter # in case you have not installed it already
jupyter
Despite the plethora of answers and #merv's efforts to improve them, it still hard to find a good one. I made this one CW, so please vote it to the top or improve it!
This is an old thread, but running this in Anaconda prompt, in my environment of interest, worked for me:
ipython kernel install --name "myenvname" --user
We have struggle a lot with this issue, and here's what works for us. If you use the conda-forge channel, it's important to make sure you are using updated packages from conda-forge, even in your Miniconda root environment.
So install Miniconda, and then do:
conda config --add channels conda-forge --force
conda update --all -y
conda install nb_conda_kernels -y
conda env create -f custom_env.yml -q --force
jupyter notebook
and your custom environment will show up in Jupyter as an available kernel, as long as ipykernel was listed for installation in your custom_env.yml file, like this example:
name: bqplot
channels:
- conda-forge
- defaults
dependencies:
- python>=3.6
- bqplot
- ipykernel
Just to prove it working with a bunch of custom environments, here's a screen grab from Windows:
I ran into this same problem where my new conda environment, myenv, couldn't be selected as a kernel or a new notebook. And running jupter notebook from within the env gave the same result.
My solution, and what I learned about how Jupyter notebooks recognizes conda-envs and kernels:
Installing jupyter and ipython to myenv with conda:
conda install -n myenv ipython jupyter
After that, running jupter notebook outside any env listed myenv as a kernel along with my previous environments.
Python [conda env:old]
Python [conda env:myenv]
Running the notebook once I activated the environment:
source activate myenv
jupyter notebook
hides all my other environment-kernels and only shows my language kernels:
python 2
python 3
R
This has been so frustrating, My problem was that within a newly constructed conda python36 environment, jupyter refused to load “seaborn” - even though seaborn was installed within that environment. It seemed to be able to import plenty of other files from the same environment — for example numpy and pandas but just not seaborn. I tried many of the fixes suggested here and on other threads without success. Until I realised that Jupyter was not running kernel python from within that environment but running the system python as kernel. Even though a decent looking kernel and kernel.json were already present in the environment. It was only after reading this part of the ipython documentation:
https://ipython.readthedocs.io/en/latest/install/kernel_install.html#kernels-for-different-environments
and using these commands:
source activate other-env
python -m ipykernel install --user --name other-env --display-name "Python (other-env)"
I was able to get everything going nicely. (I didn’t actually use the —user variable).
One thing I have not yet figured is how to set the default python to be the "Python (other-env)" one. At present an existing .ipynb file opened from the Home screen will use the system python. I have to use the Kernel menu “Change kernel” to select the environment python.
I had similar issue and I found a solution that is working for Mac, Windows and Linux. It takes few key ingredients that are in the answer above:
To be able to see conda env in Jupyter notebook, you need:
the following package in you base env:
conda install nb_conda
the following package in each env you create:
conda install ipykernel
check the configurationn of jupyter_notebook_config.py
first check if you have a jupyter_notebook_config.py in one of the location given by jupyter --paths
if it doesn't exist, create it by running jupyter notebook --generate-config
add or be sure you have the following: c.NotebookApp.kernel_spec_manager_class='nb_conda_kernels.manager.CondaKernelSpecManager'
The env you can see in your terminal:
On Jupyter Lab you can see the same env as above both the Notebook and Console:
And you can choose your env when have a notebook open:
The safe way is to create a specific env from which you will run your example of envjupyter lab command. Activate your env. Then add jupyter lab extension example jupyter lab extension. Then you can run jupyter lab
While #coolscitist's answer worked for me, there is also a way that does not clutter your kernel environment with the complete jupyter package+deps.
It is described in the ipython docs and is (I suspect) only necessary if you run the notebook server in a non-base environment.
conda activate name_of_your_kernel_env
conda install ipykernel
python -m ipykernel install --prefix=/home/your_username/.conda/envs/name_of_your_jupyter_server_env --name 'name_of_your_kernel_env'
You can check if it works using
conda activate name_of_your_jupyter_server_env
jupyter kernelspec list
First you need to activate your environment .
pip install ipykernel
Next you can add your virtual environment to Jupyter by typing:
python -m ipykernel install --name = my_env
Follow the instructions in the iPython documentation for adding different conda environments to the list of kernels to choose from in Jupyter Notebook. In summary, after installing ipykernel, you must activate each conda environment one by one in a terminal and run the command python -m ipykernel install --user --name myenv --display-name "Python (myenv)", where myenv is the environment (kernel) you want to add.
Possible Channel-Specific Issue
I had this issue (again) and it turned out I installed from the conda-forge channel; removing it and reinstalling from anaconda channel instead fixed it for me.
Update: I again had the same problem with a new env, this time I did install nb_conda_kernels from anaconda channel, but my jupyter_client was from the conda-forge channel. Uninstalling nb_conda_kernels and reinstalling updated that to a higher-priority channel.
So make sure you've installed from the correct channels :)
I encountered this problem when using vscode server.
In the conda environment named "base", I installed the 1.2.0 version of opennmt-py, but I want to run jupyter notebook in the conda environment "opennmt2", which contains code using opennmt-py 2.0.
I solved the problem by reinstalling jupyter in conda(opennmt2).
conda install jupyter
After reinstalling, executing jupyter notebook in the opennmt2 environment will execute the newly installed jupyter
where jupyter
/root/miniconda3/envs/opennmt2/bin/jupyter
/root/miniconda3/bin/jupyter
For conda 4.5.12, what works for me is (my virtual env is called nwt)
conda create --name nwt python=3
after that I need to activate the virtual environment and install the ipykernel
activate nwt
pip install ipykernel
then what works for me is:
python -m ipykernel install --user --name env_name --display-name "name of your choosing."
As an example, I am using 'nwt' as the display name for the virtual env. And after running the commands above. Run 'jupyter notebook" in Anaconda Prompt again. What I get is:
Using only environment variables:
python -m ipykernel install --user --name $(basename $VIRTUAL_ENV)
I just wanted to add to the previous answers: in case installing nb_conda_kernels, ipywidgets and ipekernel dosen't work, make sure your version of Jupyter is up to date. My envs suddenly stopped showing up after a period of everything working fine, and it resumed working after I simply updated jupyter through the anaconda navigator.
In my case, using Windows 10 and conda 4.6.11, by running the commands
conda install nb_conda
conda install -c conda-forge nb_conda_kernels
from the terminal while having the environment active didn't do the job after I opened Jupyter from the same command line using conda jupyter notebook.
The solution was apparently to opened Jupyter from the Anaconda Navigator by going to my environment in Environments: Open Anaconda Navigator, select the environment in Environments, press on the "play" button on the chosen environment, and select 'open with Jupyter Notebook'.
Environments in Anaconda Navigator to run Jupyter from the selected environment
Related
There are many questions like this (e.g. Conda environments not showing up in Jupyter Notebook, Python: modul not found after Anaconda installation, https://askubuntu.com/questions/1271137/importing-anaconda-libraries-not-working). I have tried their solutions but to no avail.
In short, I have conda installed. I have installed jupyterlabs and nb_conda_kernels in my base environment. When I create a new conda env via a file, the environment is not listed in jupyter automatically. I can add it via
python -m ipykernel install --user --name <env-name>
but then after I restart jupyter and switch kernels, when I try to import a python module from it, it says module not found.
What do I need to do to fix this? I do not want to add jupyterlabs to every env.
NOTE:
when activating the env in the terminal the path is correct, e.g. /opt/anaconda/anaconda3/envs/<env-name>/bin
when using the env in the terminal, the pack is there.
when using the kernel in Jupyter, the module is not there.
I have started to learn how to work with creating new virtual environments. However whenever I try to launch a Jupyter Notebook I find that going through the dropdown menu and selecting the kernel name results in
Kernel starting, please wait...
followed by connection failed.
Very simply my approach is:
conda create --name py37 python==3.7.2
#activate
conda activate py37
conda install pandas
conda install ipykernel
ipython kernel install --user --display-name "guacamole"
Now when I locate the folder where the kernels are created:
C:\Users\User\AppData\Roaming\jupyter\kernels
What I find is that for the kernel.json file, when argv is set to "C:\Users\User\Anaconda3\python.exe" then my kernel loads fine in Jupyter
When argv is set to
"C:\Users\User\Anaconda3\envs\py37\python.exe" it fails to load.
Any suggestions would be really appreciated!
This ended up being very straight forward. While I feel a bit silly I didn't click at first I learnt a fair bit about virtual environments in the process!
All that was necessary was to simply run the following once I had activated the environment (in Anaconda prompt)
jupyter notebook
The problem was that I was running a jupyter notebook from a different location hence the clash. Hopefully this helps someone else.
You should be able to run jupyter notebook from any environment, and be able to select the kernel from the dropdown. No need to exit and change directory.
conda activate py37
python -m ipykernel install --user --name py37 --display-name "guacamole"
# then, to test
conda deactivate
jupyter notebook
I have a general misunderstanding of the concept of Python environments and am hoping to get clarification on a few questions here.
I use Python via Anaconda with Jupyter Notebook and have set up a few environments. But in the one or the other place a thinking error or something apparently made wrong.
Via anaconda prompt activate base I created a new environment conda create -c conda-forge --name TEST_env python=3.6 anaconda.
Afterwards selecting that via activate TEST_env and add a few libraries via conda install geopandas, conda install plotly etc. After that I registered the environment via python -m ipykernel install --user --name TEST_env.
If I then start jupyter notebook from the anaconda prompt and select TEST_env kernel and in a jupyter notebook I checked the call for geopandas:
import geopandas
print(geopandas.__file__)
it does not point to my environment folder C:\Users\User01\AppData\Local\Continuum\anaconda3\envs\TEST_env - but to C:\Users\User01\AppData\Roaming\Python\Python36\site-packages\geopandas\__init__.py.
Why is this the case? What did I forget or do wrong when setting up the environment?
Is there a possibility to adjust this retroactively or do I have to set up the environment again?
Thanks a lot!
Using Conda (4.8) on pyhthon 3.7, on Win10. I have scikit learn installed using conda conda install scikit-learn . Tried a few things: also installed it in the env conda install -n my_env scikit-learn. Also tried installing conda install -c anaconda ipython - nothing has worked.
I can list it:
scikit-learn 0.22 py37h6288b17_0
But in juypter notebook get error
from sklearn.datasets import fetch_lfw_pairs (tried couple other commands too)
ModuleNotFoundError: No module named 'sklearn'
But If I use Anaconda UI Navigator to launch notebook everything works fine
Update
I tried this command line option did not work for me, despite plenty effort and help & support from the community (as below). Meanwhile the Jupyter notebook can also be launched from the Anaconda UI itself. That always was working for me - no configuration or setup needed (none). I have not found any limitations etc with this yet (and you do get the exact same notebook). For advanced/unique use cases where you may need to fine tune your configuration cmd line could be helpful, I am not there.
Likely, you are loading the wrong kernel when you start your notebook.
Here is a barebones way to set up the environment:
conda create -n testenv python=3.7 -y
conda activate testenv
conda install scikit-learn
conda install ipython
conda install notebook
python -m ipykernel install --user --name testenv
When you click on new in the browser you will have an additional option next to python3, namely the kernel you just registered. I just tested this with anaconda 4.7 and I could import sklearn.
edit:
The code in the answer creates a new python environment. Then, it installs ipython and jupyter notebook in that environment and makes sure that this environment can be used with jupyter notebook (i.e. registering the ipykernel).
Now of course besides scikit learn, no other libraries have been installed within that specific environment.
So, if you want to use more libraries, you have to go to the command line, activate the environment, and install the libraries you want to use:
conda activate testenv
conda install scipy numpy matplotlib
To then run jupyter notebook from the environment, after you have installed all the things you want (and after having closed the command prompt or having deactivated the environment), you can do
conda activate testenv
jupyter notebook
in the command prompt.
Jupyterlab would usually use the environment inside which you launch it. For example:
If you activate my_env first and then do jupyter lab from terminal, it should detect the environment.
Incase it fails, go to Kernel -> Change Kernel and select the kernel you want to use.
Note: While creating a new kernel, I always use the display-name parameter which helps. You can do something like:
python -m ipykernel install --user --name my_env --display-name "Python (my_env)"
Hope this helps.
To fix this problem, you need to manually install this package in Anaconda.
How do I install? Open your Anaconda Prompt and run the below command:
conda install -c conda-forge scikit-learn
Then restart Jupyter Notebook and import this package.
I think the problem is that the environment is not activated. Try conda activate my_env first, and then type jupyter notebook.
The first thing you can do is:
import sys
print(sys.path)
Check if /path/to/anaconda/envs/my_env/lib/python3.7/site-packages exists in the path.
I find it useful to print the current sys.path so that I know where it is looking at.
conda info --envs
when testEnv exists:
conda activate testEnv
conda list scikit-learn
I have different Python environments on my Ubuntu machine:
/home/user/anaconda3/envs/untitled/bin/python
/home/user/anaconda3/bin/python
What is the easiest way to let an ipython / jupyter notebook work with either the first or the second python environment (if possible it would be good if I do not need to create a virtual environment for that)?
Looks like you already have two conda environments available on your machine. You could install the kernelspec for each one, and you should be able to use Jupyter with either.
# for /home/user/anaconda3/envs/my_env/bin/python
source activate my_env
python -m ipykernel install --user --name my_env --display-name "Python (my_env)"
source deactivate
And now you should see Python (my_env) as an available kernel in Jupyter.