Setup: MacOS High Sierra, Spyder 3.3.1, Python 2.7.15 64bits, Qt 5.9.4, PyQt5 5.9.2 on Darwin
I run the following code in the IPython console within Spyder:
In [1]: import os
In [2]: os.system("ls")
Out[2]: 0
In [3]: os.system("aasdasd")
Out[3]: 32512
I can see the output to stdout of the ls command in the bash shell where I run spyder, but not to stderr of the second os.system call that should print sh: asdasd: command not found.
Where does spyder redirect stderr to? Is there a way to see error messages like the one generated in the second case?
Thank you very much!
(Spyder maintainer here) This was fixed in spyder-kernels 0.3.0, the package that provides kernels for our consoles. And by fixed I mean that both stdout and stderr of external commands are now shown directly in our IPython consoles.
To update spyder-kernels, please close Spyder and run in a system terminal (xterm or Terminal.app, this doesn't work on Windows):
conda install spyder-kernels=0.*
if you use Anaconda (it's not available at the moment, but it should be shortly, please wait until it is), or
pip install spyder-kernels==0.*
if you use a custom Python installation.
Related
I need to set up virtual environments for each language that I use. To do this, I'm running the Ubuntu 20.04 LTS Windows Subsystem for Linux (WSL) on Windows 10. Within WSL, I'm using Anaconda, installed in /usr/local/Anaconda, to create conda virtual environments for each language (i.e. one environment contains all my Python stuff, another contains my R stuff, etc.).
Since WSL doesn't come with a GUI, I'm using Visual Studio Code's (VSCode) Jupyter Notebook Extension to run Jupyter Notebooks to see plots/graphics. So far, I managed to easily create conda environments for Python (with ipython and ipykernel) and R (with IRkernel) and run their code in a notebook via the extension. Each time I set up an environment, the extension is easily able to find the kernel, connect to it and run the code.
However, I've not been able to set up an environment for Julia. I followed the documentation on the Julia website for installing the kernel, which is successfully found by the extension. But, when I try running a cell, the extension says it is trying to connect to the kernel, only for it to timeout and fail.
Here are the steps I have taken so far:
Create a clean conda environment (conda create -n Julia && conda activate Julia)
Install the latest version of Julia (conda install -c conda-forge julia)
Install the latest version of Jupyter (conda install -c conda-forge jupyter)
Install the Julia kernel with the built-in Julia package manager (using Pkg; Pkg.add("IJulia"))
Build the IJulia package (using Pkg; Pkg.build("IJulia"))
Confirm the presence of the Julia kernel (jupyter kernelspec list) which indeed shows the presence of a Julia kernel
Reload the VSCode connection to WSL (Ctrl + Shift + P; >Reload Window)
Shut down WSL via CMD (wsl --shutdown) for changes to take effect and reconnect
After I restart VSCode and WSL, the extension shows an option to use the Julia kernel installed in my conda environment: Julia 1.7.2 (~/.conda/envs/Julia/bin/julia). But when I create a cell and run code in a notebook, the extension creates a popup saying that it is connecting to the kernel and after some time an error message shows up:
Failed to start the Kernel.
Unable to start Kernel `Julia 1.7.2` due to connection timeout.
View Jupyter log for further details
I can also see the kernel spec JSON file in ~/.local/share/jupyter/kernels/julia-1.7/kernel.json
{
"display_name": "Julia 1.7.2",
"argv": [
"/home/USER/.conda/envs/Julia/bin/julia",
"-i",
"--color=yes",
"--project=#.",
"/home/USER/.conda/envs/Julia/share/julia/packages/IJulia/AQu2H/src/kernel.jl",
"{connection_file}"
],
"language": "julia",
"env": {},
"interrupt_mode": "signal"
}
The log file starts showing problems here:
info 17:50:48.378: Process Execution: cwd: ~
cwd: ~
warn 17:50:48.893: StdErr from Kernel Process [91m[1mERROR: [22m[39m
warn 17:50:49.138: StdErr from Kernel Process LoadError:
warn 17:50:49.795: StdErr from Kernel Process ArgumentError: Package IJulia not found in current path:
- Run `import Pkg; Pkg.add("IJulia")` to install the IJulia package.
The extension says it cannot find the IJulia kernel. This perplexes me because I can see the kernel spec in my home directory, the jupyter binary I installed from conda says that its there and the Jupyter Notebook extension can see the kernel. I have no explanation as to why the extension can see the kernel, match up the kernelspec but not be able to connect to it. Help would greatly be appreciated!
I'm fairly new to the Python scene. My problem is that when I launch a jupyter notebook from an Anaconda Powershell with my DataScience virtual environment activated, the notebook does not have my virtual environment in it's PATH, and therefore cannot find some packages (like plotly and progress). The same is true when I launch VS Code from Anaconda Navigator with DataScience activated. When I run import plotly in an interactive window, I get ModuleNotFoundError: No module named ‘plotly’. But when I run this line in the terminal within VS Code, it runs without error.
So I have run the following commands in various shell/terminal sessions:
import sys
print(sys.path)
In a VS Code terminal I get:
['', 'C:\\Users\\adiad\\Anaconda3\\envs\\DataScience\\python37.zip', 'C:\\Users\\adiad\\Anaconda3\\envs\\DataScience\\DLLs', 'C:\\Users\\adiad\\Anaconda3\\envs\\DataScience\\lib', 'C:\\Users\\adiad\\Anaconda3\\envs\\DataScience', 'C:\\Users\\adiad\\Anaconda3\\envs\\DataScience\\lib\\site-packages']
In an interactive window in VS Code I get:
['C:\\Users\\adiad\\AppData\\Local\\Temp\\04e2b30c-4fc3-4aa9-9567-3aba17081a73', 'C:\\Users\\adiad\\Anaconda3\\python37.zip', 'C:\\Users\\adiad\\Anaconda3\\DLLs', 'C:\\Users\\adiad\\Anaconda3\\lib', 'C:\\Users\\adiad\\Anaconda3', '', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages\\win32', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages\\win32\\lib', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages\\Pythonwin', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages\\IPython\\extensions', 'C:\\Users\\adiad\\.ipython']
In a jupyter notebook running in my browser I get:
['C:\\Users\\adiad\\Anaconda3\\envs\\test', 'C:\\Users\\adiad\\Anaconda3\\python37.zip', 'C:\\Users\\adiad\\Anaconda3\\DLLs', 'C:\\Users\\adiad\\Anaconda3\\lib', 'C:\\Users\\adiad\\Anaconda3', '', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages\\win32', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages\\win32\\lib', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages\\Pythonwin', 'C:\\Users\\adiad\\Anaconda3\\lib\\site-packages\\IPython\\extensions', 'C:\\Users\\adiad\\.ipython']
The IPython session don't appear to reference my virtual environment. So my question is: what do I need to do make IPython run with same environment as my terminal?
I found the following SO question which seems to answer my question, but I find it hard to believe that everyone is following this practice.
How to start an ipython shell(not notebook) within a conda or virtualenv
Here's my configuration:
conda version : 4.7.12
conda-build version : 3.18.8
python version : 3.7.3.final.0
virtual packages :
base environment : C:\Users\adiad\Anaconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/win-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : C:\Users\adiad\Anaconda3\pkgs
C:\Users\adiad\.conda\pkgs
C:\Users\adiad\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\adiad\Anaconda3\envs
C:\Users\adiad\.conda\envs
C:\Users\adiad\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.3 Windows/10 Windows/10.0.18362
After doing further digging, my problem ought to be filed under, "knowing enough to be dangerous." My problem was ultimately caused by the fact that the jupyter package hadn't yet been installed in my new environment. So whenever I attempted to launch an IPython session of some kind, either in VS Code or in a browser, the application would look in my environment and see that the IPython packages weren't installed. It would then look to other conda environments and use the "nearest" equivalent, which was the base environment. Hence, most of the packages would load, but not all.
The fix to my problem was:
conda install jupyter
Another simple fix:
Launch CMD.exe prompt on Anaconda Navigator
Install: conda install jupyter
And
Conda install plotly
I have a WSL environment running python and venv.
Besides that I have VSCode running in Windows with AREPL
I have no problem accessing my python venv including pip modules using the VSCode terminal. AREPL however seems to fail to recognize my pip plugins. My guess is that AREPL is using the Windows Python version to run the code instantly. However the WSL python venv does not generate a python.exe I could point my AREPL interpreter to.
So my question is:
Can I run AREPL on Windows VSCode to validate code that requires PIP modules that are NOT installed in Windows, but are installed on WSL within a venv.
I've tried Changing AREPL Python Path to either Python venv, WSL or Windows Python:
"D:\Scripting\Python\venvs\automation\bin\python"
"C:\Windows\System32\wsl.exe" (nothing happens as I type)
"C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.7_3.7.1264.0_x64__qbz5n2kfra8p0\python.exe" (generates error)
Error when using venv location:
Error in the AREPL extension!
Error running python with command: D:\Scripting\Python\venvs\automation\bin\python -u C:\Users\user\.vscode\extensions\almenon.arepl-1.0.16\node_modules\arepl-backend\python\python_evaluator.py
Error: spawn D:\Scripting\Python\venvs\automation\bin\python ENOENT
at Process.ChildProcess._handle.onexit (internal/child_process.js:232:19)
at onErrorNT (internal/child_process.js:407:16)
at process._tickCallback (internal/process/next_tick.js:63:19)
Are you sure you have installed python 3 and it is in your PATH?
You can download python here: https://www.python.org/downloads/
Error when using WSL:
Nothing happens
Error when using windows python:
Traceback (most recent call last):
line 1, in <module>
ModuleNotFoundError: No module named 'requests'
Maker of AREPL here! Sorry I didn't see this until recently, hopefully it will still be helpful. To use WSL python in windows vscode you can set your pythonpath to JUST wsl and your pythonoptions to ["python3", "-u"]. When you open it you will get ......
an error. Dang.
The problem is that the python-shell library I use uses path.join which joins the path to the arepl executor file with windows path separators, which doesn't work in WSL.
Instead of trying to run WSL python through windows vscode I suggest installing remote-wsl, opening a WSL vscode, installing the python and arepl extension there, and using that. I tested it and verified that it works.
My spyder version is 3.3.4 in anaconda( version 3.5), and my Ipython version is 7.4.0. Now my python version is 3.7.3 and I installed tensorflow of 1.13.1 version. When I open spyder and input the commands "import tensorflow as tf ",it is always running and I can not use function of tf. But I can use tensorflow in python through command prompt, I'm just not used to editing function in command prompt. So I want to know what is the reason that tensorflow doesn't work in spyder while running well in command prompt.
Here's a few links that I went to and did exactly what they said. I don't know what I'm doing wrong.
https://github.com/alexarchambault/jupyter-scala
https://github.com/ipython/ipython/wiki/IPython-kernels-for-other-languages
https://github.com/apache/incubator-toree
http://jcrudy.github.io/blog/html/2013/12/08/introduction_to_iscala.html
None of this is working. It may be some way that my node is configured. I just don't know. Please help.
I tried the following with Jupyterhub notebook and it works seamlessly:
# Step 1: Install spylon kernel
pip install spylon-kernel
# Step 2: create a kernel spec
python -m spylon_kernel install
# Step 3: start jupyter notebook
jupyter notebook
PS: to list all installed kernels, you can run the following command:
jupyter kernelspec list
You can use the information given here.
Ensure you have IPython 3 installed. ipython --version should return a
value >= 3.0. If it's not the case, a quick way of setting it up
consists in installing the Anaconda Python distribution, and then
running
$ pip install --upgrade "ipython[all]"
ipython --version should then return a value >= 3.0.
Download the Jupyter Scala binaries for Scala 2.10 (txz or zip) or
Scala 2.11 (txz or zip), and unpack them in a safe place. Then run
once the jupyter-scala program (or jupyter-scala.bat on Windows) it
contains. That will set-up the Jupyter Scala kernel for the current
user.
Check that Jupyter/IPython knows about Jupyter Scala by running
$ jupyter kernelspec list
This should print, among others, a line like
scala211
(or scala210 dependending on the Scala version you chose).
Then run either IPython console with
$ ipython console --kernel scala211
and start using the Jupyter Scala kernel straightaway, or run Jupyter
Notebook with
$ jupyter notebook
and create Scala 2.11 notebooks by choosing Scala 2.11 in the dropdown
in the upper right of the Jupyter Notebook start page.
Note: Since IPython has now been replaced by Jupyter, we replaced ipython in the above commands with jupyter.
I've just run:
conda create --name base2 --clone base to create an env just like base.
conda activate base2 to move to the new env.
conda install -c conda-forge spylon-kernel.
python -m spylon_kernel install --user. create a kernel spec for Jupyter notebook
jupyter-notebook
...and works just fine.
I'm using:
Anaconda 4.7.12
Jupyter-notebook 6.0.1
Ubuntu 18.04
ipykernel 5.1.3
ipython 7.9.0
ipython_genutils 0.2.0
jupyter_client 5.3.4
jupyter_core 4.6.0
traitlets 4.3.3
from def suma(a: Int) = a + 3
I can't add a comment to Heapify's answer, but his solution worked for JupyterLab on Windows without problems.
I cut and pasted his code into an Anaconda Powershell prompt
pip install spylon-kernel
python -m spylon_kernel install
jupyter notebook
And refreshed my anacopnda launcher and the spylon project option was available.
The answer for Linux can be found here.
Install Scala. Add these lines to ~/.bashrc
export SCALA_HOME=/usr/local/share/scala export
PATH=$PATH:$SCALA_HOME/bin:$PATH
Follow these instructions from the
GitHub site:
Download and unpack pre-packaged binaries Scala 2.11. Unpack each
downloaded archive(s), and, from a console, go to the bin
sub-directory of the directory it contains. Then run the following to
set-up the corresponding Scala kernel:
./jove-scala --kernel-spec
Make sure spark is installed in local along with SPARK_HOME is added or exported in .profile/environment file.
If not, you might get stuck with the following message:
"Intitializing Scala interpreter ..."
without any result.
For mac, I needed only to 3 commands to add Scala and run it with Spark (I had it already installed) on my Jupyter notebook
pip install spylon-kernel
python -m spylon_kernel install
ipython notebook
Once you run them on your terminal, you'll have spylon-kernel in your notebook, which can be used as your a Scala notebook.
spylon-kernel hasn't seen an update in years. These days its much better to use almond.