I have a Jupyter notebook running inside an Anaconda virtual environment that won't recognize the statsmodels package. I've used both pip and conda, and I've reinstalled the whole environment several times in between restarting my computer. As you can see in this link, both pip and conda show that it is installed. However, I continue to get this error:
---> 43 import statsmodels.api as sm
ModuleNotFoundError: No module named 'statsmodels'
At first I thought it was the kernel, but that wouldn't explain why every other package I've installed is recognized properly.
The only thing I haven't done is tried it on another computer (I'm running Windows 10 x64). I just want to know if anyone can see something that I'm missing before I do so.
Thanks!
Edit:
I've tried the following commands to install it:
pip install statsmodels
conda install -c conda-forge statsmodels
conda install statsmodels
I've tried using each command individually, making sure to uninstall the previous installation. I've tried using only two at a time, with the same methodology. I've tried every permutation of the above installations, with a computer restart in between. I don't think the problem is that it's not installing. I have no clue why but Jupyter notebooks just isn't recognizing this one package.
I'm running all of my commands from an Anaconda command prompt, and I make sure to activate my focal virtual environment. I also run Jupyter lab by typing it directly into the command prompt and hitting enter (I make sure I've activated my environment).
I'll try running it on a different OS and update.
Thanks duffymo! My notebook wasn't using the correct kernel. I thought all I needed to do was run Jupyter lab from my virtual environment, but it needs to be purposefully added. I followed the directions shown here to add my conda environment to Jupyter lab:
How to add conda environment to jupyter lab
I could use some clarification regarding anaconda envs and the installed packages. I have just began using environments other than the base to keep my installations clean.
I just deleted my anaconda3 folder, installed it from scratch, made a new environment and tried to run a jupyter-notebook.
When reading excel via pandas I get the error Missing optional dependency 'xlrd'
prompting me to install xlrd via conda or pip.
So I open the terminal, activate the env I’m working in and install it using conda. I close the JN from the terminal, reopen it and run the same code. The problem persists.
I repeat the procedure, this time indicating the name of the env at the end. Problem persists.
I checked which python in the terminal, it is indeed the anaconda3/envs/newenv/bin/python
I do the same (in the new env) using pip. I use the command .../anaconda3/envs/newenv/bin/python -m pip install xlrd. I get the message Requirement already satisfied: xlrd in ./anaconda3/envs/newenv/lib/python3.7/site-packages (1.2.0).
I even tried installing the package inside the notebook using !conda install xlrd, still I get the same error.
Finally, I open Jupyter via the base env, and the package works there perfectly.
I have no idea why I can’t install this under the newenv, which was the point of having local envs after all.
Thanks heaps for your help!
You need to install the kernel in Jupyter to be able to use it.
jupyter kernelspec list
That command will give you the list of kernels you have. I am assuming it only shows you Python3
You will now need to install a kernel. Remember to do this while inside your virtual environment
python3 -m pip install ipykernel
python3 -m ipykernel install --user --name <your-new-kernel-name>
You should now see this in Jupyter notebook. Select the kernel in Jupyter and you should be good to go.
Another thing you may want to try is to install Jupyter while inside your virtual environment. While inside your virtual environment, you could do:
python3 -m pip install jupyter lab
and then while still inside your virtual environment, run jupyter after checking which jupyter. It should solve your problem as well.
I hope this question is not redundant, but I couldn’t find a solution on the internet so far. I’ve followed the github guide (https://github.com/fastai/fastai) to install the fastai library on my Anaconda environment. I want to use this library to tackle the ML course and solve other Kaggle competitions with it.
As per below, I’m opening my conda environment, selecting fastai and opening Jupyter Notebook:
When trying to run the packages in Jupyter, I still get an Import Error with No module named ‘fastai’. Any suggestions on what I’m doing wrong?
Had same issue. It looks like the problem is with "softlinks" fastai which are not working on Windows.
I fixed it with replacing that soflinks with real module fastai from root of repository. Just copied it to courses\dl1, courses\dl2, courses\dm1 and tutorials folders.
Prerry dirty. But works. Let me know how to fix it without copying.
Add a cell to the beginning of the notebook, !python -m pip install git+https://github.com/fastai/fastai.git
Edit:
Now that fastai is 1.0 and on pip, you probably just want to !python -m pip install fastai.
I prefer the !python -m pip syntax over just calling pip when mixing anaconda and pip, but it probably just reflects my system's python being messed up.
I had trouble making fastai_v1 work in jupyter lab, however it was working on the terminal. So the problem was with the virtual environment not being selected in the jupyter lab when it was launched.
I used the below code to make it work. Replace 'myenv' with your virtual environment name.
source activate myevn
python -m ipykernel install --user --name myenv --display-name "Python (myenv)"
jupyter lab
more info here: Conda environments not showing up in Jupyter Notebook
I installed Jupyter notebooks in Ubuntu 14.04 via Anaconda earlier, and just now I installed TensorFlow. I would like TensorFlow to work regardless of whether I am working in a notebook or simply scripting. In my attempt to achieve this, I ended up installing TensorFlow twice, once using Anaconda, and once using pip. The Anaconda install works, but I need to preface any call to python with "source activate tensorflow". And the pip install works nicely, if start python the standard way (in the terminal) then tensorflow loads just fine.
My question is: how can I also have it work in the Jupyter notebooks?
This leads me to a more general question: it seems that my python kernel in Jupyter/Anaconda is separate from the python kernel (or environment? not sure about the terminology here) used system wide. It would be nice if these coincided, so that if I install a new python library, it becomes accessible to all the varied ways I have of running python.
Update
TensorFlow website supports five installations.
To my understanding, using Pip installation directly would be fine to import TensorFlow in Jupyter Notebook (as long as Jupyter Notebook was installed and there were no other issues) b/z it didn't create any virtual environments.
Using virtualenv install and conda install would need to install jupyter into the newly created TensorFlow environment to allow TensorFlow to work in Jupyter Notebook (see the following original post section for more details).
I believe docker install may require some port setup in the VirtualBox to make TensorFlow work in Jupyter Notebook (see this post).
For installing from sources, it also depends on which environment the source code is built and installed into. If it's installed into a freshly created virtual environment or an virtual environment which didn't have Jupyter Notebook installed, it would also need to install Jupyter Notebook into the virtual environment to use Tensorflow in Jupyter Notebook.
Original Post
To use tensorflow in Ipython and/or Jupyter(Ipython) Notebook, you'll need to install Ipython and Jupyter (after installing tensorflow) under the tensorflow activated environment.
Before install Ipython and Jupyter under tensorflow environment, if you do the following commands in terminal:
username$ source activate tensorflow
(tensorflow)username$ which ipython
(tensorflow)username$ /Users/username/anaconda/bin/ipython
(tensorflow)username$ which jupyter
(tensorflow)username$ /Users/username/anaconda/bin/jupyter
(tensorflow)username$ which python
(tensorflow)username$ /User/username//anaconda/envs/tensorflow/bin/python
This is telling you that when you open python from terminal, it is using the one installed in the "environments" where tensorflow is installed. Therefore you can actually import tensorflow successfully. However, if you are trying to run ipython and/or jupyter notebook, these are not installed under the "environments" equipped with tensorflow, hence it has to go back to use the regular environment which has no tensorflow module, hence you get an import error.
You can verify this by listing out the items under envs/tensorflow/bin directory:
(tensorflow) username$ ls /User/username/anaconda/envs/tensorflow/bin/
You will see that there are no "ipython" and/or "jupyer" listing out.
To use tensorflow with Ipython and/or Jupyter notebook, simply install them into the tensorflow environment:
(tensorflow) username$ conda install ipython
(tensorflow) username$ pip install jupyter #(use pip3 for python3)
After installing them, there should be a "jupyer" and a "ipython" show up in the envs/tensorflow/bin/ directory.
Notes:
Before trying to import tensorflow module in jupyter notebook, try close the notebook. And "source deactivate tensorflow" first, and then reactivate it ("source activate tensorflow") to make sure things are "on the same page". Then reopen the notebook and try import tensorflow. It should be import successfully (worked on mine at least).
i used these following which in virtualenv.
pip3 install --ignore-installed ipython
pip3 install --ignore-installed jupyter
This re-installs both ipython and jupyter notebook in my tensorflow virtual environment. You can verify it after installation by which ipython and which jupyter. The bin will be under the virtual env.
NOTE I am using python 3.*
I have another solution that you don't need to source activate tensorflow before using jupyter notebook every time.
Partion 1
Firstly, you should ensure you have installed jupyter in your virtualenv. If you have installed, you can skip this section (Use which jupyter to check). If you not, you could run source activate tensorflow, and then install jupyter in your virtualenv by conda install jupyter. (You can use pip too.)
Partion 2
1.From within your virtualenv, run
username$ source activate tensorflow
(tensorflow)username$ ipython kernelspec install-self --user
This will create a kernelspec for your virtualenv and tell you where it is:
(tensorflow)username$ [InstallNativeKernelSpec] Installed kernelspec pythonX in /home/username/.local/share/jupyter/kernels/pythonX
Where pythonX will match the version of Python in your virtualenv.
2.Copy the new kernelspec somewhere useful. Choose a kernel_name for your new kernel that is not python2 or python3 or one you've used before and then:
(tensorflow)username$ mkdir -p ~/.ipython/kernels
(tensorflow)username$ mv ~/.local/share/jupyter/kernels/pythonX ~/.ipython/kernels/<kernel_name>
3.If you want to change the name of the kernel that IPython shows you, you need to edit ~/.ipython/kernels/<kernel_name>/kernel.json and change the JSON key called display_name to be a name that you like.
4.You should now be able to see your kernel in the IPython notebook menu: Kernel -> Change kernel and be able so switch to it (you may need to refresh the page before it appears in the list). IPython will remember which kernel to use for that notebook from then on.
Reference.
Here is what I did to enable tensorflow in Anaconda -> Jupyter.
Install Tensorflow using the instructions provided at
Go to /Users/username/anaconda/env and ensure Tensorflow is installed
Open the Anaconda navigator and go to "Environments" (located in the left navigation)
Select "All" in teh first drop down and search for Tensorflow
If its not enabled, enabled it in the checkbox and confirm the process that follows.
Now open a new Jupyter notebook and tensorflow should work
Your Anaconda install probably went to different directory than your Python install
For instance on my machine I can find location here
yaroslavvb-macbookpro:~ yaroslavvb$ which ipython
/Users/yaroslavvb/anaconda/bin/ipython
When you type python, it tries to find it in PATH going in left-to-right order. So you may have another version of python in a folder before Anaconda folder, and it'll use that. To fix, you can do export PATH=.... to change the path, and put Anaconda directory in front, so that it takes python from there instead of the default, ie
export PATH=/Users/yaroslavvb/anaconda/bin:$PATH
I installed PIP with Conda conda install pip instead of apt-get install python-pip python-dev.
Then installed tensorflow
use Pip Installation:
# Ubuntu/Linux 64-bit, CPU only, Python 2.7
$ export TF_BINARY_URL=https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-0.9.0-cp27-none-linux_x86_64.whl
# Ubuntu/Linux 64-bit, GPU enabled, Python 2.7
# Requires CUDA toolkit 7.5 and CuDNN v4. For other versions, see "Install from sources" below.
$ export TF_BINARY_URL=https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow-0.9.0-cp27-none-linux_x86_64.whl
...
pip install --upgrade $TF_BINARY_URL
Then it will work in jupyter notebook.
The accepted answer (by Zhongyu Kuang) has just helped me out. Here I've create an environment.yml file that enables me to make this conda / tensorflow installation process repeatable.
Step 1 - create a Conda environment.yml File
environment.yml looks like this:
name: hello-tensorflow
dependencies:
- python=3.6
- jupyter
- ipython
- pip:
- https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow_gpu-1.1.0-cp36-cp36m-linux_x86_64.whl
Note:
Simply replace the name to whatever you want. (mine is hello-tensorflow)
Simply replace the python version to whatever you want. (mine is 3.6)
Simply replace the tensorflow pip install URL to whatever you want (mine is the Tensorflow URL where Python 3.6 with GPU support)
Step 2 - create the Conda environment
With the environment.yml being in the current path you are on, this command creates the environment hello-tensorflow (or whatever you have renamed it to):
conda env create -f environment.yml
Step 3: source activate
Activate the newly created environment:
source activate hello-tensorflow
Step 4 - which python / jupyter / ipython
which python...
(hello-tensorflow) $ which python
/home/johnny/anaconda3/envs/hello-tensorflow/bin/python
which jupyter...
(hello-tensorflow) $ which jupyter
/home/johnny/anaconda3/envs/hello-tensorflow/bin/jupyter
which ipython...
(hello-tensorflow) $ which ipython
/home/johnny/anaconda3/envs/hello-tensorflow/bin/ipython
Step 5
You should now be able to import tensorflow from python, jupyter (console / qtconsole / notebook, etc.) and ipython.
I think your question is very similar with the question post here. Windows 7 jupyter notebook executing tensorflow. As Yaroslav mentioned, you can try
conda install -c http://conda.anaconda.org/jjhelmus tensorflow .
I had a similar issue when using a custom Ubuntu 16 image. The problem was related to an existing version of numpy that was already installed on my system.
I initially tried
sudo pip3 install tensorflow
This resulted in the following exception:
Exception:
Traceback (most recent call last):
File "/anaconda/envs/py35/lib/python3.5/shutil.py", line 538, in move
os.rename(src, real_dst)
PermissionError: [Errno 13] Permission denied: '/anaconda/envs/py35/lib/python3.5/site-packages/numpy' -> '/tmp/pip-co73r3hm-uninstall/anaconda/envs/py35/lib/python3.5/site-packages/numpy'
The docs advise that if you encounter any issues with this command to try the following:
sudo pip3 install --upgrade \
https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-1.0.1-cp35-cp35m-linux_x86_64.whl
However, my system was unable to locate pip3
sudo: pip3 command not found
The ulitmate solution was to create a symlink for pip3
sudo ln -s /anaconda/envs/py35/bin/pip3.5 /usr/local/bin/pip3
Finally, the following command worked without trouble
sudo /usr/local/bin/pip3 install --upgrade \
https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-1.0.1-cp35-cp35m-linux_x86_64.whl
I verified the installation in the terminal and also verified a successful import in my Jupyter Notebook
import tensorflow as tf
I wonder if it is not enough to simply launch ipython from tensorflow environnement. That is
1) first activate tensorflow virtualenv with:
source ~/tensorflow/bin/activate
2) launch ipython under tensorflow environnement
(tensorflow)$ ipython notebook --ip=xxx.xxx.xxx.xxx
I found the solution from someone else's post. It is simple and works well!
http://help.pythonanywhere.com/pages/IPythonNotebookVirtualenvs
Just install the following in the Command Prompt and change kernel to Python 3 in Jupyter Notebook. It will import tensorflow successfully.
pip install tornado==4.5.3
pip install ipykernel==4.8.2
(Orginial post: https://github.com/tensorflow/tensorflow/issues/11851)
Jupyter Lab: ModuleNotFound tensorflow
For a future version of me or a colleague that runs into this issue:
conda install -c conda-forge jupyter jupyterlab keras tensorflow
Turns out jupyterlab is a plugin for jupyter.
So even if you are in an environment that has jupyter but not jupyterlab as well, if you try to run:
jupyter lab
then jupyter will look in the (base) environment for the jupyterlab plugin.
Then your imports in jupyter lab will be relative to that plugin and not your conda environment.
pip install tensorflow
This worked for me in my conda virtual environment.
I was trying to use conda install tensorflow in a conda virtual environment where jupyter notebooks was already installed, resulting in many conflicts and failure. But pip install worked fine.
conda info --envs
conda create --name py3-TF2.0 python=3
Proceed ([y]/n)? y
conda activate py3-TF2.0
conda install tensorflow
pip install --upgrade tensorflow
conda install -c anaconda ipykernel
python -m ipykernel install --user --name=py3-TF2.0
it is the best way but if it is required you should upgrade numpy with scipy as well
You can try "conda install tensorflow". This will install TensorFlow in your Anaconda directory.
Your local pip directory might not be shared with the Anaconda directory.
Thanks!
Open an Anaconda Prompt screen: (base) C:\Users\YOU>conda create -n tf tensorflow
After the environment is created type: conda activate tf
Prompt moves to (tf) environment, that is: (tf) C:\Users\YOU>
then install Jupyter Notebook in this (tf) environment:
conda install -c conda-forge jupyterlab - jupyter notebook
Still in (tf) environment, that is type
(tf) C:\Users\YOU>jupyter notebook
The notebook screen starts!!
A New notebook then can import tensorflow
FROM THEN ON
To open a session
click Anaconda prompt,
type conda activate tf
the prompt moves to tf environment
(tf) C:\Users\YOU>
then type (tf) C:\Users\YOU>jupyter notebook
When I do
import sys
sys.executable
I get '/usr/local/opt/python/bin/python2.7' in my ordinary python shell and '/usr/bin/python' in IPython or my jupyter notebook. I would like to force my jupyter notebook to use this same python that the shell is using. I have installed many modules and would like to be able to use the same ones in jupyter than I am using already in the shell. How can I do this?
The simplest way is to install IPython and Jupyter with the Python you want them to use. You can do this using pip:
path/to/python -m pip install jupyter
You could alternatively set up the IPython kernel to run with your desired Python without reinstalling the notebook. See the docs on installing kernels. This is more complicated than just installing everything again, though.
I had the same problem when using jupyter from a virtualenv.
In my case I had two kernels named python3. Doing a jupyter kernelspec list it reported only one kernel named python3 that pointed to an incorrect binary. I removed it using jupyter kernelpec remove python3 and magically appeared the correct one pointing to my activated virtualenv.
If you need to reinstall the kernel then, from the bin directory of the virtualenv you can do,
./python -m pip install ipykernel
sudo ./python -m ipykernel install