Over the past couple years I’ve
pip installed lots of things without knowing what I was doing. All of a sudden, I am getting this error when I run a snippet in a Python 2.7 Jupyter Notebook:
ImportError: No module named matplotlib
When I run this in Terminal:
which -a python python 3… I get:
Sams-MacBook-Pro-2:~ sambrand$ which -a python python3 //anaconda/bin/python /usr/local/bin/python /usr/bin/python /usr/local/bin/python
I think this is showing that I have Python in a few places, which might explain why my standard libraries (eg. matplotlib) aren’t being found in the Python environment that I want to use.
My ideal result:
Ultimately, I just want to clean up my environment and start from scratch so that I can use Keras, Tensorflow, and all Anaconda packages with Python 3 as my default when I open a Jupyter Notebook.
Additionally, I’d like any subsequent
pip install from the terminal to update what I’m using in Jupyter.
From what I gather, this kind of bewilderment about Python environment is a fairly common issue, so I hope this post proves helpful.
Having a lot of python versions on the same machine is quite a common situation. To clean up your
python you need to do the following steps:
Keep in mind that as for OSX 10.15, “native”
pythonversion in still 2.7. It lives in
/usr/bin/. (Actual path is
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/but it’s the same thing.) If you want to roll back to the clean system
pythonenvironment, you need to delete everything else.
First of all you need to find all other pythons. On my machine it was like this:
$ which -a python python3 /Users/yura/anaconda3/bin/python # <- Anaconda /opt/local/bin/python # <- ports /opt/local/bin/python # <- ports /opt/local/bin/python # <- ports /opt/local/bin/python # <- ports /usr/bin/python # <- "native" ~/anaconda3/bin/python3 # <- Anaconda /Library/Frameworks/Python.framework/Versions/3.5/bin/python3 # <- python3 for OSX /usr/local/bin/python3 # <- python3 for OSX```
As you may see, I had installed more stuff from
mac ports, I had
python3 for Mac downloaded and installed by hands, and also I had badly installed Anaconda (it is not seen from here, but that installation had wrong access rights). Also, you may have something from
homebrew, which I don’t use. It will also appear in
/usr/local/bin. Well, let’s get started!
$ rm -rf ~/anaconda3
remove everything from
$ sudo rm -rf /Library/Frameworks/Python.Framework/
remove everything from
/Applications/Python*/, which you may installed manually:
$ sudo rm -rf /Applications/Python*
remove all the symlinks from
$ sudo rm /usr/local/bin/python*
remove all packages installed by
$ rm -rf ~/Library/Python/
And finally, you may also remove all
port-related files, they are in
/opt/local/bin/python*. WARNING: it may break some other
portpackages! So the most accurate way to do it is to use
portitself (but you may skip this step in order to leave untouched the other software from ports):
$ sudo port uninstall python*
That’s it! Now you have only a system
python2.7. You can download Anaconda and install it:
$ sh Anaconda3-*-MacOSX-x86_64.sh
Now you have a new
python3. To check this open a new terminal and try:
$ python --version Python 3.6.5 :: Anaconda, Inc.
matplotliband all the other scientific stuff like
pandasetc is already there:
$ python -c "import matplotlib as mpl; print(mpl.__version__)" 2.2.2
The best practice to keep it ‘clean’ is to use virtual environments. You can use
conda to do it.
From terminal run:
conda create -n envs_name python=3.6
After that you need to activate it, this is like saying “do the following only in my virtual environment and not on the global one”:
source activate envs_name pip install keras pip install tensorflow pip install ipykernel
The ipykernel let’s you manage your environments inside Jupyter.
It’s really easy and convenient.
It took me hours, and I haven’t “cleaned” my environment, but I was able to get Python 3, Keras, Tensorflow, and Anaconda running in a Jupyter notebook by following these steps:
- Delete Anaconda from computer
- Install Anaconda from the web
- Install Python 3 from the web
Pip install Kerasfrom Terminal (for some reason Keras wasn’t shown in Anaconda Navigator, as recommended in this post)
Pip install Tensorflowfrom Terminal
Jupyter Notebookfrom Terminal
I got this error “no module named Keras’. I was doing !pip install keras and !pip install tensorflow (in that order) from Jupyter Notebook. After I did the following the error went away.
- Opened CMDexe prompt from Anaconda navigator
- pip install Tensorflow
- pip install Keras
Now in jupyternotebook from keras import Sequential worked fine