I am running IPython Notebook on Enthought's Canopy 64 bit distribution, Ubuntu 14.04.
I've tried install libtiff, but when I import it in IPython Notebook, the kernel always dies at the import statement. What could possibly be causing this? Canopy is my default Python distribution, my paths all seem like they're set up appropriately, although I'm convinced that something in my Python setup is borked.
Any advice is appreciated.
EDIT: I'll be more specific. Output of sys.path:
['',
'/home/joe/Enthought/Canopy_64bit/User/src/svn',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python27.zip',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/plat-linux2',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/lib-tk',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/lib-old',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/lib-dynload',
'/home/joe/Enthought/Canopy_64bit/User/lib/python2.7/site-packages',
'/home/joe/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/PIL',
'/home/joe/opencv-2.4.9',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/site-packages',
'/home/joe/Canopy/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/site-packages/IPython/extensions']
As for how to install Python packages, I assume I go to ~/Enthought/Canopy_64bit/User/lib/python2.7/site-packages and run pip, setup.py, or a shell script, per the specific package's instructions. Is that correct? The article that I linked has the following line: "To install a package which is not available in the Canopy / EPD repository, follow standard Python installation procedures from the OS command line.", which seems to imply that I install per package instructions.
In .bashrc, I have the following:
VIRTUAL_ENV_DISABLE_PROMPT=1 source /home/joe/Enthought/Canopy_64bit/User/bin/activate
export PYTHONHOME=/home/joe/Enthought/Canopy_64bit/User/bin
export PATH=/home/joe/Enthought/Canopy_64bit/User/bin
export PYTHONPATH=/home/joe/Enthought/Canopy_64bit/User/bin
From what I understand of the linked articles, this means I'm setting Canopy User as my default Python distribution. I'm sure I'm doing something a bit over my head here, but I can't understand what else I need to do to fix this issue.
Worse yet, now I'm getting an "ImportError: No module named site" with these .bashrc settings, when trying to start IPython notebook or python from the command line. I can run only from the Canopy GUI.
Closing this. I made it harder than necessary.
It turns out, the PYTHONHOME and PYTHONPATH .bashrc variables were causing some conflicts. Commenting them out seems to have resolved the issue.
Installing outside packages does, indeed, happen from the home (~) directory.
Related
I am on Ubuntu 20.04 and have both Python2 and Python3 installed natively. I have also installed Python through miniforge, a variant of miniconda. In VSCode I have both the MS Python extension and Pylance installed.
I use the miniforge python for my coding. This works perfectly fine in PyCharm.
However in VSCode, when I try to execute the same file I get errors. After investigating it seems that VSCode is picking native Python2 - even though I have the miniforge Python selected. In this picture it can be seen that the status bar at the bottom states Python interpreter selected is Python3. But the output window shows that the python interpreter is Python2.
A more confusing thing is when I use VSCode for Jupyter notebook files then it picks up the interpreter correctly and I have no issues.
I have checked both User and Workspace settings, and they all point to Python3. How can I fix this for standard .py files?
I prefer VSCode to PyCharm, but will need to use PyCharm till this is resolved.
It seems that your system console cannot see python3. You need to put the python3 in the PATH variable, before python2. Like:
PATH=path/to/python3:path/to/python2:$PATH
Also, make sure that the environment containing python3 is activated before command prompt appears. It can be done in bash_profile by adding a line like
conda activate my_env_with_python3
Try changing the settings "Python:Python path", "Python:default interpreter path" and "Python:conda path" also.
I have just bumped into something similar. The Run code option resulted in the file being run with the default interpreter instead of the venv-based one with necessary packages installed.
The fix was simply to use "Run python file" instead:
The run-code behavior must be customizable, something is mentioned e.g. here: Run Code vs Run Python File in Terminal for VSCODE but I didn't bother.
import numpy
is not working. This started because I couldn't get PyQt5 to work on my home computer. In the Spyder IDE, I can import modules and get everything working fine, but in VS Code, I can't import basic modules. I'm on Windows 10 with Python 3.7. I've Googled a lot and have tried these:
Uninstall Anaconda and VS Code, and reinstall both
In VS Code, press Ctrl+Shift+P, Select Interpreter, and select Python 3.7.1 64-bit ('base':conda), ~\Anaconda3\python.exe
I saw on another similar question that python3.dll may be missing from one of my Anaconda directories, but it is indeed there.
Add environment variable to PATH by going to System Properties > Advanced tab > Environment Variables... > under System Path, Edit, New > C:\Users\myname\Anaconda3\Scripts
Once I did #4 above, the new error message in VS Code when importing numpy is DLL load failed: The specified module could not be found. And in the terminal, I see: The term 'conda' is not recognized as the name of the cmdlet, ...
One thing I notice is in a Python prompt (not Anaconda) I type:
import sys
print(sys.version)
The output is 3.7.2, while in VS Code, the Select Interpreter (see above #2) says Python 3.7.1. Not sure if this is important.
Any help? Everything works on my work computer fine, but it's just my home computer that is being difficult.
What ended up working for me is downgrading my Python installation from 3.7.1 to 3.6.4 with:
conda install python=3.6.4
Hope this helps someone out there.
On another question for the same problem, there was a suggestion that worked for me.
Put this on the variable path.
C:\Users\<Your user name>\Anaconda3\Library\bin
credit to user1024.
i installed simpleitk in anaconda using command
conda install -c simpleitk simpleitk then followed link https://github.com/SimpleITK/SimpleITKCondaRecipe to build it but it's not connecting to itk.org to build.
import SimpleITK as sitk on jupyter notebook is working but sitk.show() is not working. moreover when i tried to follow the commands from http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/Python_html/00_Setup.html,
from downloaddata import fetch_data, fetch_data_all not working.
even the command fetch_data_all(os.path.join('..','Data'), os.path.join('..','Data','manifest.json')) is not working. i am very new to simpleitk and don't know whether it is due to build not processed. please tell me how to solve my problems. i have been trying from many days, pl help me. moreover how to make imagej as default for simpleitk. i know lots of questions but i would be greatful if solved.
You seem to be having multiple problems, all of which have to do with installing a working environment and less specific to SimpleITK.
You installed SimpleITK using the conda install command, so there was no need to build it using the conda build command. Check that you have it installed correctly and see which version you have:
import SimpleITK as sitk
print(sitk.Version())
The functions fetch_data and fetch_data_all are part of a module found in the SimpleITK notebooks repository. To use the code from that repository you will need to clone it using git:
git clone https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks.git
Then you can run the notebooks or copy the relevant modules to your directory and work with them there.
The sitk.Show() command assumes that you have the ImageJ/Fiji program installed which is likely why it is not working (I am guessing here as you did not provide sufficient detail).
I'm trying to import a self-defined module in a Jupyter notebook using PyCharm (2016.1). However, I always get "ImportError: No module named xxx". Importing packages like NumPy or Matplotlib works fine. The self-defined module and the notebook are in the same directory and I've tried to set the directory as sources root. How can I fix this? Thanks a lot!
If you run the following in your notebook...
import sys
sys.path
...and you don't see the path to the directory containing the packages/modules, there are a couple ways around it. I can't speculate why this might happen in this example. I have seen some discrepancies in the results of sys.path when running Jupyter locally from PyCharm on OS X vs. on a managed Linux service.
An easy if hacky workaround is to set the sys path in your notebook to reflect where the packages/modules are rooted. For example, if your notebook was in a subdirectory from where the packages or modules are and sys.path only reflects that subdirectory:
import sys
sys.path.append("../")
The point is that sys.path must include the the directory the packages and modules are rooted in so the path you append will depend on the circumstances.
Perhaps a more proper solution, if you are using a virtualenv as your project interpreter, is to create a setup.py for your project and install the project as an editable package with pip. E.g. pip install -e . Then as long as Jupyter is running from that virtualenv there shouldn't be any issues with imports.
One ugly gotcha I ran into on OS X was Jupyter referencing the wrong virtualenv when started. This should also be apparent by inspecting the results of sys.path. I don't really know how I unintentionally managed set this but presume it was due to futzing around my first time getting Jupyter working in PyCharm. Instead of starting Jupyter with the local virtual env it would run with the one defined in ~/Library/Jupyter/kernels/.python/kernel.json. I was able to clear it by cleaning out that directory, e.g. rm -r ~/Library/Jupyter/kernels/.python.
As stated by Thomas in the comments make sure that your notebook serving path and project path are same. When you start your notebook in pycharm you should get something like this :
Serving notebooks from local directory: <path to your project root folder>
All my install for python were working pretty well since soon. Now, I have a weird issue that generates import errors for some of my Python scripts and when using Ipython those import performs as expected.
This issue does not depend on the working dir (tested this several times with the same result). And I didn't change anything in my .bashrc regarding PYTHONPATHs.
So this might be a noob question, but is there an option in Ipython to display everything Ipython is doing when I run a command, so that I can track which is the package Ipython succesfully imported?
The packages I have trouble with are actually yaml, matplotlib cloud Image. Is it possible that an update from 2.6 to 2.7 is responsible for that? (I work on OSX Lion and most of the packages are installed via macports and updated using the upgrade outdated command).
As I think I can probably fix this myself with the command I asked for, don't bother seeking further for package compatibility or anything if you got the Ipython command that might suits me.
The difference of imports between python and ipython resulted from a cross defined python reference library (when installing most of the python libraries with macports and some without any known ports with other package managers).
Reinstalling the whole python libraries using the process described in http://astrofrog.github.io/macports-python/
corrects the issue and it is preferable to install manually the libraries that don't have any known ports (for instance with a setup build/install process).