Update update: json_lines is not supported by python versions < 3 - my issue had pretty much nothing to do with environments. I am now using 3.9.1 and all is gucci.
Update: After using which python in my jupyter notebook and in my Terminal, I see that they are both using the same environment. As such I am still at a loss as to why my notebook cannot find json_lines.
I have two python environments on my computer, a default one and one I have for running my jupyter notebook on. I am trying to install the library, json_lines to the latter environment. I am not used the Anaconda environment manager.
On my Mac's Terminal I used the general pip install command pip install json-lines, but when I try to execute the following line of Python import json_lines in my notebook, I still receive the following error ImportError: No module named json_lines.
As I suspect I am not installing to the correct environment, I tried installing the library from inside my notebook with the following, import sys; !{sys.executable} -m pip install jsonlines.
However, this has not changed my dilemma.
Is there some way I can specify from my Terminal which environment to install to? or is it likely I am encountering a different issue to what I suspect?
The package for json_lines in pip in json-lines. Hence you could install it as:
$ pip install json-lines
It may be appropriate to use an isolated python environment for your particular project if you want to use particular conda libraries but without the whole package. In this instance, you would be able to use virtualenv. This will allow you to create an isolated python environment.
$ pip3 install virtualenv
You can call virtualenv to create a virtual python environment with the working name e.g. myvenv.
$ virtualenv myvenv
From here, you can set your terminal to use this python version. If you are on *nix:
$ which python
/usr/bin/python
$ source myvenv/bin/activate
(myvenv)$ which python
/.../myvenv/bin/python
This article can help you out.
https://janakiev.com/blog/jupyter-virtual-envs/
You need to create a virtualenv which will be used by your notebooks.
Related
I installed Django on my Ubuntu 21.04 Software but when I use:
python manage.py runserver
I get an error massage :
No module named “Django”
But when I use :
python3 manage.py runserve
It works fine but my python —-version is 3.10.1 and python3 —version is 3.9.x
So what is the error and how I can run it with python only not python3
The issue here is that the python and python3 commands are pointing to two different Python installations/environments altogether.
It looks like you installed Django in your Python 3.9.x environment (the one which you access by typing python3).
On the other hand, your Python 3.10.1 environment (which you access by writing python) seems to have no Django installed.
The pip/pip3 commands are sometimes confusing, and may point to a different Python installation than the one you think they do. This depends entirely on how you set up your Python environments in your machine.
In order to access the pip of a specific Python environment, the best way is to run it as a module, e.g.:
python -m pip [...]
This guarantees that the pip you're using is the one associated with the Python environment you're evoking with the python command.
So in order to install Django on your Python 3.10.1 environment, you need to run:
python -m pip install django
If you use PIP3 to install the module, it will only be installed for Python3. If you use PIP to install the module, the system will use the Python version that is listed first in the PATH variable.
You have multiple Python instances on your machine. To avoid such a problems in the future, it is generally advised to use Virtualenv in Python, if you run code on your general-purpose device. (and have multiple Python instances on your machine)
In order to configure Virtualenv that run the following commands:
sudo apt install python3-venv python3-pip
python3 -m venv venv
Then you activate virtual environment:
source venv/bin/activate
Once the virtual environment is activated, you can install Python modules in this specific virtual environment, this way you will not have to mess up with issues such as the one you have described:
pip install django
and then if you run:
python manage.py runserver,
then it would be running in the context of the specific virtual environment.
I know it is not a direct answer to your problem, but I believe it will help you in avoiding such an issues in the future.
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 have the following version of python
import sys
print(sys.version)
3.6.5 | packaged by conda-forge | (default, Apr 6 2018, 13:44:09)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)]
I installed a package with the following command
pip install wfdb
It is succesfully installed because when I then write the command:
pip show wfdb
The following information appears
Location:
/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages
However, when I type the command import wfdb in Python notebook or the version of python in terminal, I get the following message
No module named 'wfdb'
Does it have to do with the path on which python is checking where the packages are? How to check this and how to change it?
You have (at least) 2 Python installations, one managed by Anaconda, the other what appears to be an official Python.org Mac build installed system-wide. The pip command on the command-line is the one tied to the Python.org Mac build.
pip is a script that is tied to a specific Python installation, and there can be multiple versions of the script installed in different locations, and is usually also installed with pipX and pipX.Y to match the X.Y version indicator of the Python version it is tied to. For Python 3.6, that means the same script would also be available as pip3 and pip3.6. (This also means that pip can be connected to Python 2 or Python 3, depending on your exact OS setup. It is not a given that pip, without a version number, installs into Python 2.x as some answers may claim).
Note that when you run a command without a path in your shell, (such as pip as opposed to /usr/bin/pip), you are asking your shell to find the command for you in a number of locations, listed in the PATH environment variable. The first location in the PATH list with that command is then fixed. which -a <command> would tell you all possible PATH-registered locations that the command can be found in. You can always use the full path to a command to bypass the PATH search path.
You can always verify what Python version the pip command is connected to with:
pip -V
which will output the version of pip and the location it is installed with. It'll print something like
pip pipX.pipY path/to/pythonX.Y/site-packages/pip (python X.Y)
where pipX.pipY is the pip version number and path/to/pythonX.Y tells you what Python installation this is for.
You can try to match this with the Python version by running
python -m site
which outputs the Python module search path for that Python version. Python can be run with python, pythonX and pythonX.Y too, and is subject to the same PATH search.
Note the -m switch there, that instructs Python to find a module in it's module search path and execute it as a script. Loads of modules support being run that way, including pip. This is important as that helps avoid having to search for a better pip command if you already can start the right Python version.
You have several good options here:
Since you are using Anaconda, you could look for a conda package for the same project. There is such a package for wfdb. Install it with
conda install wfdb
Anaconda aims to give you a wider software management experience that includes a broader set of software options than just the Python PyPI ecosystem, and conda packages usually manage more things than just the Python package.
Conda packages are usually maintained by a different set of developers from the package itself, so there may be a newer version available on PyPI (requiring pip install) than there is on Conda.
This is not an option for all Python packages, if there is no conda package you have to use pip. See Installing non-conda packages.
you can use the conda command to create a conda environment. Once you have an environment created, you can activate it with
source activate <name_of_cenv>
to alter your PATH settings. With the envirnoment 'active' the first directory listed on your PATH is the one for the conda environment and the pip command will be the one tied to that environment.
Note that a conda environment gives you an isolated environment for a specific project, keeping the library installation separate from the rest of your Python packages in the central site-packages location. If you want to install a package for all of your Anaconda Python projects, don't use a conda environment.
Use the Anaconda Python binary to run pip as a module; when you can run /path/to/python or pythoncommand to open the right Python version, you can use that same path to run /path/to/python -m pip ... instead of pip ... to be absolutely certain you are installing into the correct Python version.
Look for a better pip command, with which -a pip or which -a pip3.6, etc. But if you already know the Python binary, look in the same bin location for pip. If you have anaconda/bin/python, then there probably is a anaconda/bin/pip too.
As you can read here:
pip3 and pip would make a difference only when you are not using any
environment managers like virualenv (or) conda. Now as you are
creating a conda environment which has python==3.x, pip would be
equivalent to pip3.
For this reason it could be you did not activate your Conda environment before installing required packages and running your code.
Activate the new environment:
On Windows:
activate myenv
On macOS (this should be your option) and Linux:
source activate myenv
NOTE: Replace myenv with the name of the environment.
which python
gives the you the PATH to python
and then /path/to/python -m pip install thepackagetobeinstalled
Many thanks #MartijnPieters
You have installed python2.x package and you're using python3.x. Try:
pip3 install wfdb
If you don't have pip3 run:
[apt-get/yum] install python3-pip
You can see what packages you have currently installed by running:
pip freeze
and for python 3.x packages
pip3 freeze
Please remember each time you install a Python package, it will be placed in the directory for one particular Python version. Hence your error.
I installed Anaconda3 so I can create environments and install different packages in each environment. But I fail to understand the difference between the Python in
/usr/bin/python
and
/opt/anaconda3/bin/python
I can seem to access Python 3.6.5 Anaconda from both, why is that? And, what is the difference between both?
Furthermore, I would like to install packages to a single Python environment only.
When you are running python in the terminal, it is looking up your default path to your the python command. In this case, anaconda probably put a line in your shell profile specify the path to the anaconda version, which is why you are seeing it in the interpreter when you run python from either directory.
Secondly, you can set up a conda environment to download app specific dependencies without interfering with your default set up by
conda create --name myenv
source activate myenv
conda install packagename
This will install it in the myenv environment only. To deactivate the environment just run
source deactivate
Here is the documentation on that https://conda.io/docs/user-guide/tasks/manage-environments.html
Judging by your path, you are using Linux which comes with python installed. So /usr/bin/python is default and you have installed the other one later.
For the environments use https://conda.io/docs/user-guide/tasks/manage-environments.html to activate the desired environment, then you can pip install or conda install the packages and it will be places safely only in that environment. Note that spyder icon runs the root environment by default and you have to run it from terminal after activating one of the environments.
Edit:
I'm not sure why you want to use cd to change the python version. I suggest use aliases. I guess you are just changing the path but running the same version of the python anyway. Take a look at this question:
Two versions of python on linux. how to make 2.7 the default
I wanted to create a new virtual environment to install new packages. Following worked for me:
Commands are executed in Jupyter Notebook (OS: Ubuntu 16.04 LTS)
Upgrade pip:
!pip install --upgrade pip
Install virtual environment:
!pip install virtualenv
Select version of Python you want to use in new environment:
I wanted to create an environment with Python version 3. Naming it as Python3_xyz:
!virtualenv -p python3 Python3_xyz
After execution, this will create a folder with the same name in the current working directory (i.e. the location where Jupyter notebook is present)
Create a new option with the name of the created environment
And finally, run the following command:
!python -m ipykernel install --user --name=Python3_xyz
This will create a new option with the name Python3_xyz in the menu from where we create a new notebook.
NOTE: One can run above commands from the terminal as well just don't use '!' before the commands.
This question is bit dated, but since I faced a similar issue, what worked for me might help someone!
I did pip install requests from within my conda environment, but failed to import requests even after trying out everything.
What worked for me: run python -m pip install requests or python3 -m pip install requests within you environment. This installed requests successfully for me.
I have a MacBook Pro that came pre-installed with python2.7. I later installed python3 and ipython notebook. I installed pip too to install packages, and am able to install packages and run program from python3. However, for another project I need to run code in python2.7, and I am not sure how to install it in python2.7 folder.
I tried using pip for installing packages to 2.7, but it kept giving error saying package already exists. When I check for version of python using --version, I see 2 pythons installed. However, when I check for pip and pip3, both seem to be in th same folder.
Any tips on how to install packages in python2.7, without making any changes to 3.3? I am using python3 and ipython notebooks for another project.
viveks-mbp:~ vivekyadav$ which pip
/Library/Frameworks/Python.framework/Versions/3.3/bin/pip
viveks-mbp:~ vivekyadav$ which pip3
/Library/Frameworks/Python.framework/Versions/3.3/bin/pip3
viveks-mbp:~ vivekyadav$ which python
/usr/bin/python
viveks-mbp:~ vivekyadav$ which python3
/Library/Frameworks/Python.framework/Versions/3.3/bin/python3
You can use the virtualenv to create a kind of sandbox.
$ virtualenv <work-directory>
$ source <work-directory>/bin/activate
The last command initiate your virtual environment, totally isolated from the system. So every pip command will install the package inside this directory.
But you have to run your application inside the virtual environment too.