I need to use the command line in Jupyter Notebook in a virtual environment, but the commands don't execute in the environment itself. I'm using Anaconda Navigator to open Jupyter Notebook. For background, I use a Mac.
Whenever I do something like ! pip install xyz, it installs the package in the Anaconda directory for libraries (see the image). I made sure that the kernel is in the environment, so that's not the problem.
What's interesting is that if I try to import a package, I can only import packages from the environment itself, not the Anaconda libraries. In other words, installing packages doesn't occur in the environment, but importing packages does.
Image that shows the pip install
This wouldn't matter that much because I could download packages in the Terminal itself, but I also need to do things like in the image below in my virtual environment, which is not possible to do in the Terminal (or is it?).
Example of what I need to do
Any ideas on how to fix this?
EDIT: That error is fixed. However, I'm getting an error if I try to use a Python command: image of error. The first line just defines the file path for the script (the last item in the list is a .py file). I tried doing "%%python" followed by the command, but it doesn't work. Any ideas?
Related
I pip installed the sportsreference package in my command prompt and it shows successful. Yet when I try to call it in my Jupyter Notebook it says no module named sportsreference.
Any help on what I'm doing wrong?
The interpreter that your Jupyter uses to run the cells is not the one you installed that package into. Remember you can have not only different versions of Python interpreter, but also different virtual environments associated with each Python interpreter in your machine.
So either install the package in the interpreter that Jupyter uses, or run the Jupyter from the interpreter you've installed that package into.
The simplest solution is to install it in a Jupyter cell with:
!pip install <your_package_name>
the ! allows you to execute command.
To check which interpreter currently runs your code you can check the output of:
import sys
print(sys.executable)
can anyone help me understand using conda environment with visual studio code? I had activate the virtual environment (imageprocessing) with this:
conda activate imageprocessing
and the terminal seem to have been on virtual environment, so there's look like no problem with the PATH, it looks like this.
(imageprocessing) ../users/[project_folder_somewhere]
But when I open visual studio code and activate the kernel used for opening Notebooks there, exactly with the python from imageprocessing virtual environment, I keep needed to install the previously forged library, for example, Pillow. Which part that doesn't work out? Did I install Pillow package redundantly if I keep doing this? Does visual code doesn't integrated that well with conda even though it has been connected through the path? I used this feature for opening .ipynb files on Visual Studio Code because browser-based Jupyter Notebooks are too slow and messy directory than if using this (or so I thought?).
In VS Code, when we use different python environments, the locations where the modules are installed are different. Therefore, we need to be clear which python environment we are currently using. (We could check it with the command "python --version" in the VS Code terminal.)
When we use the conda environment, it comes with python, so we can use "pip" to install modules, or "conda" to install modules. The modules it installs are stored in: "...\anaconda3\envs\conda-name\lib\site-packages".
The command "pip show pillow" checks the installation position of the module:
In addition, after the installation is complete, it still shows that the module cannot be found. I noticed that there is a problem with the file name here. We need to rename "PIL" to "pillow", or use "import PIL"
Reference: conda-environment in VS Code.
Add:
I apologize in advance for my poor vocabulary - I do not know much about environments, paths, and things of the sort. I am on macOS Catalina.
I created a program using Spyder from Anaconda. My program uses packages like pandas and numpy which are built into Anaconda. I used to be able to run the program in Terminal with the command: $ python3 app.py.
However, I recently downloaded Python 3.9.1 from https://www.python.org/downloads/mac-osx/. Ever since then, I have been unable to run the program in Terminal because of missing package errors like
import numpy as np
ModuleNotFoundError: No module named 'numpy'
I went to my applications folder, right clicked on Python 3.9.1, and clicked Move To Trash. This did not solve my problem. I reinstalled Anaconda (I did not uninstall it - just simply installed again), but that also did not solve my problem. I am able to run the program in Spyder (from Anaconda), but I wish to run it in Terminal again.
I believe the solution is simple, but I am not sure what to do. I have tried searching and reading but I am not familiar with the terminology. I think I just need to reset the environment, but I am not sure.
Anaconda is used for creating closed enviorments, so you don't need to thrash your computer with global packages.
Imagine you have 2 different projects. Project A works only on python 3.2 and Project B works on 3.8.
That's where anaconda comes in.Managing enviorments with conda
conda create -n PROJECTA python=3.2
conda create -n PROJECTB python=3.8
Now activate env you wish to work with. For macOS
source activate PROJECTA
Now you should see (PROJECTA) instead of (base)
Now inside this PROJECTA you can install modules you require like
pip install numpy
and when executing .py file
move to dir with your app.py file and
python3 app.py
this will be opened in conda enviorment you created and activated, using modules you installed in this env.
You can still edit py file and execute it through shell, but it will throw errors if you try to run it from IDE without linking project to respected conda enviorment.
If you are using PyCharm Configure a Conda vir env in PyCharm
You must create separate environments for every projects or it will get messed up.
conda create -n name_of_environment python=3.6
You must not delete the python folder into trash rather uninstall it Python 3.9.1 and remove its path from the directory.
In short if you run python from terminal and it is not supporting your Installed anaconda packages . You should use anaconda prompt instead of CMD.
Because your anaconda is not added to path rather then it picks up the python 3.9 you have installed from Python 3.9.1 from https://www.python.org/downloads/mac-osx/. ( This is the python with separate environment then anaconda so it wont detect anaconda packages ).
When you run the cmd and enter python it runs the python that you downloaded and installed rather then Anaconda
At the time of installing anaconda it gives option to add conda variables to path you can select those at installing stage / or add manually
I want to follow along a course about deeplearning. This course has a github repo, where all of the codes are available. We need to use anaconda, create an environment based on the yaml file, and run a jupyter notebook within that environment.
There's even a test notebook to check whether the installation and environment creating process was successful. I have created the environment as the description said, the installation of the packages seemed to be good.
For the first few command, I get the required outputs, but the notebook doesn't seem to start from the correct environment, it gives me
C:\Users\user\Anaconda3\Lib\site-packages\jupyter.py
instead of
C:\Users\paperspace\Anaconda3\envs\ztdl\lib\site-packages\jupyter.py
And it can't find the packages that I have just installed before. For example, when it has to include sklearn it gives me:
No module named 'sklearn.__check_build._check_build'
Installing them from command line with pip/conda solves this.
I have tried to install manually ipykernel, nb_conda, jupyter as other posts say. I ran jupyter notebook after I activated the conda environment from the anaconda prompt. But none of these helped me. As I open the kernel menu, I can see that the proper ztdl anaconda environment is the active one.
I also removed anaconda from the %PATH%, and added it again afterwards with c:\Users\user\Anaconda3\ .
I have no idea what should I do to run the notebook within this given anaconda environment, so I can access the installed packages. Thanks in advance, any help is appreciated.
I updated the packages with conda update --all and was using jupyter to work. Before the update, everything was working, but now jupyter doesn't import any module beside the sys, os, copy and time. Numpy, matplotlib and theano are not being imported. But they are definitely in the conda list... the python version is 2.7.12
When I updated with conda, I remember that there was a message that numpy was being deprecieted due to conflicts. Now in the conda list I have numpy 1.11.1.
I'm new in python, so I don't understand the import error. Before uninstalling everything again, I would like to understand what the problem is to learn and of course to continue using jupyter ;)
I found this post https:// github.com/jupyter/notebook/issues/397 (sorry I can't link it, I'm new here) which seems to be a problem related to mine or similar, but I don't think I understand it so well... so before I break more I wanted to ask here!
Is jupyter badly "connected" to anaconda? How can I check where the packages are being searched? For any comment on this I would be very grateful!!
Here are the cells of jupyter:
cells of jupyter
and the Error I get:
ImportError
Thanks!
That import error is due to change in environment of the jupyter notebook. You might have installed the packages in one environment and you are running the jupyter notebook in another environment.
I have got two environments (envs) in my Anaconda folder. I have Anaconda3 folder to be specific).
(windows key+cmd) -> open the windows command prompt run as administrator.
Activate (name of the environment) -> eg.: activate tensorflow-gpu
Start installing packages using conda install
Note: For each environment you need to install all the packages you want to use, separately using the same process. This solution is for windows users, might work for linux users not sure though.
Additionally to make sure your conda environment is up to date run:
conda update conda
conda update anaconda
For more information: https://pradyumnamajumder.wordpress.com/2017/09/30/solution-to-the-python-packages-import-error-in-jupyter/
I followed the idea as in here and changed the file that launches the root jupyter command (cf. cat /dir_where_installed/anaconda2/bin/jupyter and the jupyter-notebook ( cf. cat /dir_where_installed/anaconda2/bin/jupyter-notebook).
It was set as in the anaconda environment conda info --envs as expected (both files had in the first line something like #! /dir_where_installed/anaconda2/bin/python), but for some reason after the update I did and even after installing again everything(!), jupyter wasn't taking that path, instead it was importing from the 'stock' python (apparently).
Anyway, I changed both lines with #! to take the path as in the output of which python.
Summary:
check path in cat /dir_where_installed/anaconda2/bin/jupyter and cat /dir_where_installed/anaconda2/bin/jupyter-notebook
which python out put should be something like /usr/bin/python
substitute the lines in both files starting with #! with #! /usr/bin/python
I'm not sure if this is a good idea, but it worked for me and now I can import all packages in jupyter. If anyone has any idea if this is a bad idea or a better solution, please let me know!