I am trying to run the following in Jupyter notebook (with Python 2 if it makes a difference):
!head xyz.txt
and I get the following error:
'head' is not recognized as an internal or external command, operable
program or batch file.
Is there anything I need to import to be able to do this?
Might be useful for others.
Use ! followed by terminal command you want to execute. To run a shell command. E.g.,
! pip install some_package
to install the some_package.
An easier way to invoke terminal using jupyter-notebooks is to use magic function %%bash and use the jupyter cell as a terminal:
%%bash
head xyz.txt
pip install keras
git add model.h5.dvc data.dvc metrics.json
git commit -m "Second model, trained with 2000 images"
For Windows it would be %%cmd.
Write it at the beginning of the cell like this :
%%cmd
where python
myprogram "blabla" -x -y -z
You can start the cell with the magic % bash before the rest of your code. There is an example in this blog post, together with a list of some of the most useful magics.
Make sure you run your command in linux shell because there is non such command in windows.
Another option nowadays is the Jupyter kernel for Bash.
I had the same issue. Solved by running
!bash -c "head xyz.txt"
Related
I have ran the installation script by pasting this code:
$ curl https://bun.sh/install | bash
However, when I try to get the version of bun, it says it could not find it:
$ bun --version
Command 'bun' not found, did you mean:
command 'ben' from deb ben (0.9.0ubuntu2)
command 'bus' from deb atm-tools (1:2.5.1-4)
command 'zun' from deb python3-zunclient (4.0.0-0ubuntu1)
Try: sudo apt install <deb name>
I had the same issue running on Windows 10 WSL2 Ubuntu-22.04 with Bun v0.1.5.
The solution (and more detail just in case anyone needs it) below:
The executable for bun is in the directory "/home/username/.bun". You need to add this to your $PATH so that this can be found when typing bun commands such as "bun --help".
The bun setup process does not add this path so you need to do it yourself.
Two ways to do this :
(1) Manual method
Type in the terminal:
export BUN_INSTALL="/home/YOUR_USERNAME/.bun"
export PATH="$BUN_INSTALL/bin:$PATH"
Replacing YOUR_USERNAME with your real username (the current username can be found by typing 'whoami' in the terminal).
Note: This process will have to be REPEATED for every new shell you open.
(2) Automatic method
Edit the .bashrc file :
nano ~/.bashrc
at the end of this file add
BUN_INSTALL="/home/YOUR_USERNAME/.bun"
PATH="$BUN_INSTALL/bin:$PATH"
Replacing YOUR_USERNAME with your real username (the current username can be found by typing 'whoami' in the terminal).
(Remember to save your changes with Ctrl-O)
Note: You will NEED TO OPEN A NEW SHELL for this to work OR type 'source ~/.bashrc' to use in the current terminal.
You should now be able to run bun commands in any new shell.
The installation script says a message at the end telling you how to add bun to your PATH manually. Here is that output:
Manually add the directory to your $HOME/.bashrc (or similar)
BUN_INSTALL="/home/sno2/.bun"
PATH="$BUN_INSTALL/bin:$PATH"
I advise you re-run the installation command and copy the environment variables and add them to your PATH.
export BUN_INSTALL="/Users/manendra/.bun"
export PATH="$BUN_INSTALL/bin:$PATH"
add these to your .bashrc, .zshrc or you can use export command to use for current session.
Note: Change your username place of (manendra) "/Users/manendra/.bun"
Manually add the directory to ~/.bashrc (or similar):
export BUN_INSTALL="$HOME/.bun"
export PATH="$BUN_INSTALL/bin:$PATH"
From the installer, last message is:
To get started, run
exec /bin/zsh
bun --help
I've installed Cloud SDK on my windows 10 machine and I'm able to run commands like "gcloud", "gsutil" and "bq" on my command prompt. However, when I run "gsutil" or "bq" on Bash, this is the error I'm getting.
$ bq
bash: bq: command not found
Then I added this location to PATH C:\Users\User\AppData\Local\Google\Cloud SDK\google-cloud-sdk\bin, and afterwards I seem to be able to call gsutil and bq using gsutil.cmd and bq.cmd. But of course, I'd prefer calling bq / gsutil directly.
Has anyone has this problem before? Thank you!
I found one possible solution!
In Bash, go to the root bash folder by typing cd
Type touch .bashrc
write alias bq="bq.cmd" or alias gsutil="gsutil.cmd" or both
Press Esc and type :qa and Enter to save and exit
This tells Bash to remember bq as invoking bq.cmd, hence now I can invoke bq anywhere -- as far as I know.
If anyone has a better suggestion, please let me know! Thank you!
In the bash session itself, check what echo $PATH returns. It should inherit the path that was defined on Windows.
So open a new CMD session, and:
make sure the %PATH% does include C:\Users\User\AppData\Local\Google\Cloud SDK\google-cloud-sdk\bin,
then call C:\path\to\Git\bin\bash.exe to open a bash session
bq should work in such a shell session.
I have been trying to pip install psycopg2 for some time now
I have just updated to python 3.7.4, before this problem started.
To set my path to a specific python version I used the code below.
nano .bash_profile
I thought that it would now be easy for my system to identify the path of the newly installed python, as to enable it to install psycopg2. Then the below started happening.
The second line of system terminal or python terminal is now always showing:
-bash: zzzzz#: command not found on my terminal
No matter what I type on my terminal, I am always getting command not found
This would mean you literally have "zzzzz" somewhere in the bash_profile. Bash is seeing "zzzzz" as just another command to run at startup like the rest of the profile script. As there is nothing in your PATH matching that string, bash reports the issue back to you.
Either remove the extra line from your .bash_profile. OR use a terribly wasteful work-around!
ln -s /bin/true /bin/zzzzz
This will create a symbolic link to the "true" binary (all it ever does is return true) from zzzzz. Now bash can find zzzzz and run it during start up, which does nothing. No more error and an absurd work around. You should fix the file.
Does anyone know if it is possible to run an IPython/Jupyter notebook non-interactively from the command line and have the resulting .ipynb file saved with the results of the run. If it isn't already possible, how hard would it be to implement with phantomJS, something to turn the kernel on and off, and something to turn the web server on and off?
To be more specific, let's assume I already have a notebook original.ipynb and I want to rerun all cells in that notebook and save the results in a new notebook new.ipynb, but do this with one single command on the command line without requiring interaction either in the browser or to close the kernel or web server, and assuming no kernel or web server is already running.
example command:
$ ipython notebook run original.ipynb --output=new.ipynb
Yes it is possible, and easy, it will (mostly) be in IPython core for 2.0, I would suggest looking at those examples for now.
[edit]
$ jupyter nbconvert --to notebook --execute original.ipynb --output=new.ipynb
It is now in Jupyter NbConvert. NbConvert comes with a bunch of Preprocessors that are disabled by default, two of them (ClearOutputPreprocessor and ExecutePreprocessor) are of interest. You can either enabled them in your (local|global) config file(s) via c.<PreprocessorName>.enabled=True (Uppercase that's python), or on the command line with --ExecutePreprocessor.enabled=True keep the rest of the command as usual.
The --ExecutePreprocessor.enabled=True has convenient --execute alias that can be used on recent version of NbConvert. It can be combine with --inplace if desired
For example, convert to html after running the notebook headless :
$ jupyter nbconvert --to=html --execute RunMe.ipynb
converting to PDF after stripping outputs
$ ipython nbconvert --to=pdf --ClearOutputPreprocessor.enabled=True RunMe.ipynb
This (of course) does work with non-python kernels by spawning a <insert-your-language-here> kernel, if you set --profile=<your fav profile>. The conversion can be really long as it needs to rerun the notebook. You can do notebook to notebook conversion with the --to=notebook option.
There are various other options (timeout, allow errors, ...) that might need to be set/unset depending on use case. See documentation and of course jupyter nbconvert --help, --help-all, or nbconvert online documentation for more information.
Until this functionality becomes part of the core, I put together a little command-line app that does just what you want. It's called runipy and you can install it with pip install runipy. The source and readme are on github.
Run and replace original .ipynb file:
jupyter nbconvert --ExecutePreprocessor.timeout=-1 --to notebook --inplace --execute original.ipynb
To cover some features such as parallel workers, input parameters, e-mail sending or S3 input/output... you can install jupyter-runner
pip install jupyter-runner
Readme on github: https://github.com/omar-masmoudi/jupyter-runner
One more way is to use papermill, it has Command Line Interface
Usage example: (you need to specify output path for execution results to be stored)
papermill your_notebook.ipynb logs/yourlog.out.ipynb
You also can specify required params if you wish with -p flag for each param:
papermill your_notebook.ipynb logs/yourlog.out.ipynb -p env "prod" -p tests "e2e"
one more related to papermill reply - https://stackoverflow.com/a/55458141/2957102
You can just run the iPython-Notebook-server via command line:
ipython notebook --pylab inline
This will start the server in non-interactive mode and all output is printed below the code. You can then save the .ipynb-File which includes Code & Output.
As this post points out you can install Vimballs using the normal:
vim somevimball.vba
:so %
:q
But if you want to install a from the command line how do you do it? I ran a 'man vim' and it seems like the best "from source install" option was the '-S' option so I tried to install haskellmode with it:
wget 'http://projects.haskell.org/haskellmode-vim/vimfiles/haskellmode-20090430.vba'
vim -S haskellmode-20090430.vba
and that failed to work. It gave me the following error:
Error detected while processing function vimball#Vimball:
line 10:
(Vimball) The current file does not appear to be a Vimball!
press ENTER or type command to continue
It should be noted that using the first method I was able to successfully install the vimball. I have tried the second method on a few other vimballs and it has failed every time. Is there a way to install a vimball from the command line? It seems like a useful sort of task.
Oh, and I am running the following version of vim:
Version: 2:7.2.330-1ubuntu3
Thanks.
Use one of the following commands:
vim -c 'so %' -c 'q' somevimball.vba
or:
vim -c 'so % | q' somevimball.vba
For more information, see:
:help -c
:help :bar
Having seen this solution I decided to hide the messiness in a script that always should have existed, vim-install: http://github.com/robertmassaioli/vim-install