I've found the solution:anaconda - graphviz - can't import after installation
I want to use graphviz and follow the commend in https://anaconda.org/anaconda/graphviz
run following in terminal
conda install -c anaconda graphviz
However no matter in Jupyter Notebook, python or Pycharm to import graphviz, it always shows
ModuleNotFoundError: No module named 'graphviz'
How to solve this problem? Thank you.
PS:
when run which python in terminal: it return /opt/anaconda3/bin/python, therefore I use anaconda environment by default. And I have only one environment in anaconda that is root.
when I run conda list in terminal, I can find this line :
graphviz 2.40.1 hefbbd9a_2
I found a weird thing:
my pip and conda use the same environment:
run :which pip
get : /opt/anaconda3/bin/pip
run : which conda
get : /opt/anaconda3/bin/conda
However when I run pip list, I cannot find graphviz and many other packages which shows in conda list. For these packages show in conda list but not in pip list, I also cannot import them no matter in Jupyter notebook, python, pycharm etc. Why this happens?
After using "conda install attrs", other package installations are working fine without any http connection or ModuleNotFoundError errors. Please try and let me know.
Since yesterday I've had this error when I try to import packages on anaconda :
ImportError: Missing required dependencies ['numpy']
I have tried un-installing Anaconda and Python, switching to Python 2.7 but nothing works it's still the same error, here is the code I get :
Any help is really appreciated thanks !
I had this same issue immediately after upgrading pandas to 0.19.2. I fixed it with the following install/uninstall sequence from the windows cmd line:
pip uninstall pandas -y
pip uninstall numpy -y
pip install pandas
pip install numpy
This also broke my matplotlib install so I uninstalled/installed that as well.
Very odd behavior for a seemingly routine upgrade.
What happens if you try to import numpy?
Have you tried'
pip install --upgrade numpy
pip install --upgrade pandas
I had to install this other package:
sudo apt-get install libatlas-base-dev
Seems like it is a dependency for numpy but the pip or apt-get don't install it automatically for whatever reason.
I had this problem with last version of numpy 1.16.x
Problem resolved with
python3 -m pip uninstall numpy
python3 -m pip install numpy==1.14.0
Did you install miniconda and pandas without dependencies?
Try installing numpy first with conda install numpy or pip install numpy.
If you're on Windows you can get pre-compiled versions of most libraries that require compilation from here.
On Windows 10 Anaconda3-5.3.0-Windows-x86_64 I had the Missing required dependencies ['numpy'] error when running scripts as so, %HOMEPATH%\AppData\Local\Continuum\anaconda3\python.exe pandas_script_foo.py.
In my case the error was caused by missing Anaconda package PATH definitions when running Anaconda python.exe in a windows cmd.exe session. The numpy package is not missing. It just can't be found on the PATH.
The Anaconda installation includes windows shortcuts that give examples of configuring the PATH per script run. See the shortcuts in the %HOMEPATH%\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Anaconda3 (64-bit) directory for examples.
See the %HOMEPATH%\AppData\Local\Continuum\anaconda3\cwp.py script to see how Anaconda configures PATH.
Below is an example windows BAT file that calls cwp.py to setup PATH, and then run a python script. Its a copy of the commands the Anaconda jupyter-lab shortcut executes.
%HOMEPATH%\AppData\Local\Continuum\anaconda3\python.exe ^
%HOMEPATH%\AppData\Local\Continuum\anaconda3\cwp.py ^
%HOMEPATH%\AppData\Local\Continuum\anaconda3 ^
%HOMEPATH%\AppData\Local\Continuum\anaconda3\python.exe ^
%HOMEPATH%\AppData\Local\Continuum\anaconda3\Scripts\jupyter-lab-script.py
If you need to execute python scripts on Anaconda with the conveniance of running a BAT file, the above BAT file example should do the trick.
The data manipulation capabilities of pandas are built on top of the numpy library. In a way, numpy is a dependency of the pandas library. If you want to use pandas, you have to make sure you also have numpy. When you install pandas using pip, it automatically installs numpy. If it doesn't, try the following
pip install -U numpy pandas
For conda
conda install numpy pandas
I also faced the same issue. It happened to me after I upgraded my numpy library.
It was resolved in my case by upgrading my pandas library as well after upgrading my numpy library using the below command:
pip install --upgrade pandas
Try:
sudo apt-get install libatlas-base-dev
It should work now.
Else, try uninstall and reinstall numpy and pandas.
I had the same issue. It was because I had multiple versions of numpy installed. Remove all versions by repeatedly using:
pip uninstall numpy
Then re-install it with the command:
pip install numpy
First, try to import numpy on it's own, like so:
import numpy as np
I got this message:
ImportError: Something is wrong with the numpy installation. While importing
we detected an older version of numpy in
['/home/michael/.local/lib/python3.6/site-packages/numpy']. One method of
fixing this is to repeatedly uninstall numpy until none is found, then
reinstall this version.
So do what it says, keep uninstalling numpy until there is none, and then reinstall.
This worked for me.
I had the same issue while using Microsoft Visual Code with Python 3.7.3 64-bit('base':conda)as my python interpreter. Before running any code type the following three commands:
C:/ProgramData/Anaconda3/Scripts/activate #activate conda Scripts directory
conda activate base #activate conda
& C:/ProgramData/Anaconda3/python.exe #to run python
I have same problem.
I have got two version of numpy 1.16.6 and 1.15.4, fresh installed pandas did not work correctly.
I fixed it by uninstalling all versions of numpy and pandas and install the last versions.
$ pip uninstall numpy pandas -y
Uninstalling numpy-1.16.6:
Successfully uninstalled numpy-1.16.6
Uninstalling pandas-0.24.2:
Successfully uninstalled pandas-0.24.2
$ pip uninstall numpy pandas -y
Uninstalling numpy-1.15.4:
Successfully uninstalled numpy-1.15.4
Cannot uninstall requirement pandas, not installed
$ pip uninstall numpy pandas -y
Cannot uninstall requirement numpy, not installed
$ pip install numpy pandas
I had the same issue with anaconda package, it got updated.
anaconda {4.3.1 -> custom} ## I am not sure if this was the issue
Hit below command to know
conda list --revisions
what i did is just uninstall pandas with conda and re-install it
conda install pandas
Some new libs may also get installed with it.
It worked for me hope will do the same for you.
Uninstall all pip packages that you're having problems with. Manually remove all site-packages files. If you're using MacPorts, sudo port clean .
Then try reinstalling. Sometimes, there are files that should have been removed, but weren't if the installation was abruptly interrupted or something.
There could be an issue with conflicting versions of the package(s), as well as potentially issues with Pathing. Are you sure you've set the correct Path for your binaries? (/opt/local/bin, /anaconda2/bin, etc.)
Another issue could be some PYTHONPATH that's explicitly looking in the wrong place for the file.
I had a same issue recently with Anaconda with Python 3.7.
I solved this problem by downgrading python version to 3.6:
conda install python=3.6
and then by updating all the packages:
conda update --all
pandas is built on top of numpy so you need to have numpy to use the data manipulation feature, so install numpy first.
pip install numpy
This worked in my anaconda environment, but I do not know why conda does not work. For some reason conda uninstall was not sufficient. This only worked with conda remove.
conda remove pandas
conda remove numpy
conda install pip
pip install pandas
*With help from this answer
This raises the following import warning in python 3.6 and 3.7:
ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
If you with to ignore this warning (and maybe other ImportWarnings), add the following to your script before importing pandas:
import warnings
warnings.filterwarnings('ignore', category=ImportWarning, module='_bootstrap.py')
In my case even though I was using the above options of uninstall and installing using pip the code was still giving me same errors.
Finally, I created a vritual environment and Installed numpy and pandas using pip in my virtual env. Now the code is running.
Steps: for Anaconda3 - Please change according to your installation type:
[if you dont have virtual env package installed]
$ pip install virtualenv
[from command prompt go to the directory by c:\anadonda3\scripts
[write the following command to use virtual env to create a virtual env for you in your desired location]
$virtualenv c:\anaconda3\envs\my_virtual_env
[once created you will have to activate your virtual env]
$c:\anaconda3\envs\my_virtual_env\scripts activate
[now pip install numpy and pandas and other required packages using pip]
[once installations are done exit from the virtual env]
$c:\anaconda3\envs\my_virtual_env\scripts deactivate
now use the python.exe inside your virtual env folder to run the script and it will run even with python 3.7.
I am using Win10 and Conda, and this issue just append to me when upgrading python 3.7.2-h8c8aaf0_0 --> 3.7.2-h8c8aaf0_2.
I solved it by return to the previous version with
conda install python=3.7.2=h8c8aaf0_0
If you're running your program on PyCharm on Windows, there is a known bug, because PyCharm simply doesn't add env-related paths to PATH.
The issue is fixed in the 2019.1 Early Access Preview (EAP) build.
For me installing the EAP fixed the issue.
nothing worked for me ... except when I found this
I suspect that you have a local file called unittest.py that is getting imported instead of the standard module.
I was trying to upgrade my anaconda 2 with anaconda 3. I tried installing Anaconda3-2018.12-Windows-x86 and Anaconda3-2019.03-Windows-x86_64 on my Windows 10 machine and failed with this error. For me, using Anaconda3-4.4.0-Windows-x86_64 for anaconda 3 worked the trick after trying everything listed in answers here.
I fixed this using Anaconda by going to Environments > base(root), searching for numpy in the installed modules and clicking the tickbox alongside it and choosing > Mark for specific version installation > 1.14.0 (as suggested by another user on this thread). Then clicking Apply. Once it downgraded numpy I stopped getting errors when running py files on the command line.
Throughout this saga, I was still able to use https://pypi.org/project/auto-py-to-exe/ even when I was getting the numpy errors on the command line, but it was a hassle to create an exe every time I wanted to test a change. It's all sorted now. I guess there was a problem with numpy 1.16.4.
Anyway, I hope this helps someone who's using Anaconda as well.
The following worked for me.
Deleted the folders for numpy and pandas together with their contents completely from the site-packages folder. Check depending on whether you are using python2 or python3. Check the exact path as per your machine.
N.B handle with care "rm -rf" command. If you are not sure of what you are doing, please do it manually using any file explorer of your choice!!
rm -rf ~/anaconda2/envs/myenv/lib/pythonX/site-packages/pandas*
rm -rf ~/anaconda2/envs/myenv/lib/pythonX/site-packages/numpy*
Then i installed clean packages for pandas and numpy as usual with
pip install numpy
pip install pandas
I've got the same error recently. Before applying uninstall or install tools, try to update your Jupyter.
How? Go to 'Environments' and type on the Search Packages box 'pandas'. Afterwards, check the version (if that column shows a blue number with a diagonal arrow, it means that your pandas is out of date). Click on 'pandas' and a option will pop up (choose 'Apply' and wait for a couple of minutes to update the package). And then, make a quick test on any notebook to make sure that your Jupyter is running smoothly.
For those who couldn't solve with the above answers:
Ensure that you are running python3 with
$ python version
If not, install python3.
Then change default python to python3 with
$ alias python=python3
Next, close your jupyter lab/notebook environment and re-launch it with default python being python3.
build_exe_options = {"packages": ["os",'pandas','numpy']}
It works.
you are running python 3.7
create environment for python 3.6
python3.6 filename.py
I am trying to run some code using ortools on a python environment. I did not have troubles on a windows machine but I am having problems on mac (10.12.6). if in my virtual environment I run
pip freeze
or
conda list
ortools appears in my list of installed packages. But if I try to use it
ipython
from ortools.linear_solver import pywrapplp
I get an error saying that there's no module named ortools. If I go to
mac/anaconda3/envs/nameenv/lib/python3.6/site-packages I do have a folder called ortools with some python files including pywrapplp. Do you know what I am doing wrong ?
EDIT
following request from coments:
import os
os.getcwd()
returns '/Users/imac'
which ipython
/anaconda3/bin/ipython
Installing ortools is a bit of a headache. It was some days ago, I think I finally made it with
easy_install ortools
I think it is a problem with the path. I guess because I did not install it with conda it does not find the package. I got around writting:
sys.path.append('/anaconda3/envs/env_name/lib/python3.6/site-packages/')
at the begining of my ipynb. That way I can run ortools.
You could have several python interpreter installed (python2 and python3)
So if you want to use it with ipython, which seems to be bind on python3 in your case.
First check if you have pypi package ortools installed
ipython -m pip show ortools
If you got an error it means the package is not installed.
so you can easily install it using:
ipython -m pip install --user ortools
note: We provide Pypi ortools package (64 bits) for Manylinux, Windows and MacOS.
You can also rebuild it from source https://developers.google.com/optimization/introduction/installing/source
I'm having trouble running mayavi in python 3.3
When running my program with python3 (or python3.3) i get
from mayavi import mlab as ml
ImportError: No module named 'mayavi'
To get numpy and matplotlib to work, i used:
sudo apt-get install python3-"missing module"
But the usual way to install mayavi is just
sudo apt-get install mayavi2
And python3 doesn't find it....
Does anyone know a way to get mayavi to work with Python3?
Is it not supported yet?
I have tried both
import mayavi.mlab as ml
from mayavi import mlab as ml
Both give me the same error
Any clarification would be greatly appreciated :)
Mayavi can work with python 3 now. You will need VTK 7.0 or higher compiled for python 3 support. Then you can just install mayavi with pip. pip install mayavi
Installing vtk may prove somewhat difficult. You need to make sure to change the PYTHONPATH variable, and build vtk with tcl, tk, and python 3 support.
Today, Mayavi is not supported in python3.
http://www.vtk.org/Wiki/VTK/Python_Wrapping_FAQ
http://www.vtk.org/Wiki/VTK/Python_Wrapper_Enhancement#Python_3
See also this github issue:
https://github.com/enthought/mayavi/issues/84
I was able to get Mayavi2 to work with Python 3.6.4.
To set up Mayavi on ubuntu, do the following -
Install Anaconda/Miniconda distribution of python depending on your
needs(I used Miniconda 4.3.30). For more info look here
Run the following in terminal -
apt-get install -y libglib2.0-0 libxext6 libsm6 libxrender1 gtk3.0
conda install -y -c conda-forge qt vtk pyvtk pyside envisage mesalib mayavi
conda install -y -c ajsrk traitsui
Ideally , you wouldn't need the last line since traitsui will be installed as part of the dependencies in the previous step. However, I found an issue with this version of traitsui. So as a temporary fix, I have uploaded my version of traitsui into anaconda cloud; this can be used until the fix finds its way into the next release and is available in the conda-forge channel
To verify the installation start a terminal session and type 'mayavi2'
The best solution that I`ve found, is this. Even though, Mayavi will only work on Pyathon 3.5...
My solution is launching Spider from Anaconda 3 and then running the file mayavi2-script.py that can be found in the directory Anaconda/Scripts. It launches the 3D data visualizer as a pop-up window in Windows10.