Confusing behavior of bash cell magics in Jupyter Notebook (Windows 10, Git Bash)
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I'm getting odd behavior when trying to use bash cell magics in Jupyter Notebooks on Windows 10, with Git Bash installed.
Cell magics seem to work fine for some bash programs (e.g. which, echo), but not others (e.g. head).
Use of a ! in lieu of bash cell magics works for some commands, but not others. This inconsistency kills notebook compatibility across different operating systems.
Does anyone have any insight into what's happening here?
Here are some examples:
Input:
%%bash
which bash
Output:
/bin/bash
Input:
!which bash
Output:
'which' is not recognized as an internal or external command, operable program or batch file.
Input:
%%bash
head file.csv
Output:
Input:
!head file.csv
Output:
Row,Column,*Target Name,*Sample Name
Input:
%%bash
echo pizza
Output:
pizza
Input:
!echo pizza
Output:
pizza
jupyter-notebook git-bash
asked Aug 9 '17 at 14:44
kubu4kubu4
688
add a comment |
I'm getting odd behavior when trying to use bash cell magics in Jupyter Notebooks on Windows 10, with Git Bash installed.
Cell magics seem to work fine for some bash programs (e.g. which, echo), but not others (e.g. head).
Use of a ! in lieu of bash cell magics works for some commands, but not others. This inconsistency kills notebook compatibility across different operating systems.
Does anyone have any insight into what's happening here?
Here are some examples:
Input:
%%bash
which bash
Output:
/bin/bash
Input:
!which bash
Output:
'which' is not recognized as an internal or external command, operable program or batch file.
Input:
%%bash
head file.csv
Output:
Input:
!head file.csv
Output:
Row,Column,*Target Name,*Sample Name
Input:
%%bash
echo pizza
Output:
pizza
Input:
!echo pizza
Output:
pizza
jupyter-notebook git-bash
asked Aug 9 '17 at 14:44
kubu4kubu4
688
I have a somewhat similar problem, did you ever get the to the bottom of this? stackoverflow.com/questions/51548928/…
– quantum285
Jul 26 '18 at 23:48
Nope! No progress. Admittedly, it's low priority, as the problem is being experienced by some undergrads in our lab. We've just made them switch to using lab computers running Ubuntu instead of their personal Windows laptops.
– kubu4
Jul 28 '18 at 4:26
I found that '!' uses the default windows shell whereas '%%bash' uses bash. So a workaround is to use '%%cmd' to use all of the commands you can use with '!' but then you face the problems that arise due to the difference between bash and batch. I've also taken the approach of using Ubuntu VMs also. Not sure if anything I said helps at all but just sharing..
– quantum285
Jul 29 '18 at 0:04
You say Git Bash is installed, but is Jupyter Notebook being launched from Git Bash or from another prompt, e.g., Anaconda?
– Karl Baker
Jan 4 at 7:34
Launching via Git Bash. Thanks for clarifying that point!
– kubu4
Jan 5 at 21:49
add a comment |
I'm getting odd behavior when trying to use bash cell magics in Jupyter Notebooks on Windows 10, with Git Bash installed.
Cell magics seem to work fine for some bash programs (e.g. which, echo), but not others (e.g. head).
Use of a ! in lieu of bash cell magics works for some commands, but not others. This inconsistency kills notebook compatibility across different operating systems.
Does anyone have any insight into what's happening here?
Here are some examples:
Input:
%%bash
which bash
Output:
/bin/bash
Input:
!which bash
Output:
'which' is not recognized as an internal or external command, operable program or batch file.
Input:
%%bash
head file.csv
Output:
Input:
!head file.csv
Output:
Row,Column,*Target Name,*Sample Name
Input:
%%bash
echo pizza
Output:
pizza
Input:
!echo pizza
Output:
pizza
jupyter-notebook git-bash
asked Aug 9 '17 at 14:44
kubu4kubu4
688
I'm getting odd behavior when trying to use bash cell magics in Jupyter Notebooks on Windows 10, with Git Bash installed.
Cell magics seem to work fine for some bash programs (e.g. which, echo), but not others (e.g. head).
Use of a ! in lieu of bash cell magics works for some commands, but not others. This inconsistency kills notebook compatibility across different operating systems.
Does anyone have any insight into what's happening here?
Here are some examples:
Input:
%%bash
which bash
Output:
/bin/bash
Input:
!which bash
Output:
'which' is not recognized as an internal or external command, operable program or batch file.
Input:
%%bash
head file.csv
Output:
Input:
!head file.csv
Output:
Row,Column,*Target Name,*Sample Name
Input:
%%bash
echo pizza
Output:
pizza
Input:
!echo pizza
Output:
pizza
jupyter-notebook git-bash
jupyter-notebook git-bash
asked Aug 9 '17 at 14:44
kubu4kubu4
688
asked Aug 9 '17 at 14:44
kubu4kubu4
688
asked Aug 9 '17 at 14:44
kubu4kubu4
688
asked Aug 9 '17 at 14:44
kubu4kubu4
688
asked Aug 9 '17 at 14:44
kubu4kubu4
688
688
I have a somewhat similar problem, did you ever get the to the bottom of this? stackoverflow.com/questions/51548928/…
– quantum285
Jul 26 '18 at 23:48
Nope! No progress. Admittedly, it's low priority, as the problem is being experienced by some undergrads in our lab. We've just made them switch to using lab computers running Ubuntu instead of their personal Windows laptops.
– kubu4
Jul 28 '18 at 4:26
I found that '!' uses the default windows shell whereas '%%bash' uses bash. So a workaround is to use '%%cmd' to use all of the commands you can use with '!' but then you face the problems that arise due to the difference between bash and batch. I've also taken the approach of using Ubuntu VMs also. Not sure if anything I said helps at all but just sharing..
– quantum285
Jul 29 '18 at 0:04
You say Git Bash is installed, but is Jupyter Notebook being launched from Git Bash or from another prompt, e.g., Anaconda?
– Karl Baker
Jan 4 at 7:34
Launching via Git Bash. Thanks for clarifying that point!
– kubu4
Jan 5 at 21:49
add a comment |
I have a somewhat similar problem, did you ever get the to the bottom of this? stackoverflow.com/questions/51548928/…
– quantum285
Jul 26 '18 at 23:48
Nope! No progress. Admittedly, it's low priority, as the problem is being experienced by some undergrads in our lab. We've just made them switch to using lab computers running Ubuntu instead of their personal Windows laptops.
– kubu4
Jul 28 '18 at 4:26
I found that '!' uses the default windows shell whereas '%%bash' uses bash. So a workaround is to use '%%cmd' to use all of the commands you can use with '!' but then you face the problems that arise due to the difference between bash and batch. I've also taken the approach of using Ubuntu VMs also. Not sure if anything I said helps at all but just sharing..
– quantum285
Jul 29 '18 at 0:04
You say Git Bash is installed, but is Jupyter Notebook being launched from Git Bash or from another prompt, e.g., Anaconda?
– Karl Baker
Jan 4 at 7:34
Launching via Git Bash. Thanks for clarifying that point!
– kubu4
Jan 5 at 21:49
I have a somewhat similar problem, did you ever get the to the bottom of this? stackoverflow.com/questions/51548928/…
– quantum285
Jul 26 '18 at 23:48
I have a somewhat similar problem, did you ever get the to the bottom of this? stackoverflow.com/questions/51548928/…
– quantum285
Jul 26 '18 at 23:48
Nope! No progress. Admittedly, it's low priority, as the problem is being experienced by some undergrads in our lab. We've just made them switch to using lab computers running Ubuntu instead of their personal Windows laptops.
– kubu4
Jul 28 '18 at 4:26
Nope! No progress. Admittedly, it's low priority, as the problem is being experienced by some undergrads in our lab. We've just made them switch to using lab computers running Ubuntu instead of their personal Windows laptops.
– kubu4
Jul 28 '18 at 4:26
I found that '!' uses the default windows shell whereas '%%bash' uses bash. So a workaround is to use '%%cmd' to use all of the commands you can use with '!' but then you face the problems that arise due to the difference between bash and batch. I've also taken the approach of using Ubuntu VMs also. Not sure if anything I said helps at all but just sharing..
– quantum285
Jul 29 '18 at 0:04
I found that '!' uses the default windows shell whereas '%%bash' uses bash. So a workaround is to use '%%cmd' to use all of the commands you can use with '!' but then you face the problems that arise due to the difference between bash and batch. I've also taken the approach of using Ubuntu VMs also. Not sure if anything I said helps at all but just sharing..
– quantum285
Jul 29 '18 at 0:04
You say Git Bash is installed, but is Jupyter Notebook being launched from Git Bash or from another prompt, e.g., Anaconda?
– Karl Baker
Jan 4 at 7:34
You say Git Bash is installed, but is Jupyter Notebook being launched from Git Bash or from another prompt, e.g., Anaconda?
– Karl Baker
Jan 4 at 7:34
Launching via Git Bash. Thanks for clarifying that point!
– kubu4
Jan 5 at 21:49
Launching via Git Bash. Thanks for clarifying that point!
– kubu4
Jan 5 at 21:49
add a comment |
1 Answer
1
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votes
In my experience, as long as Jupyter is launched from a bash-compliant command line such as Git Bash (MingW64) or possibly Ubuntu on Windows, bash commands prepended with ! work in Jupyter Notebook, even on Windows systems.
I'm running windows 10 Pro with Python installed via Anaconda, and bash works when I launch Jupyter via Git Bash, but does not when I launch from the Anaconda prompt. For example:
>>> !ls
database.sqlite
Weather Data Clustering using k-Means.ipynb
>>>!pip show lxml | grep Version
Version: 4.1.0
answered Jan 4 at 7:45
Karl BakerKarl Baker
366115
add a comment |
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1 Answer
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votes
In my experience, as long as Jupyter is launched from a bash-compliant command line such as Git Bash (MingW64) or possibly Ubuntu on Windows, bash commands prepended with ! work in Jupyter Notebook, even on Windows systems.
I'm running windows 10 Pro with Python installed via Anaconda, and bash works when I launch Jupyter via Git Bash, but does not when I launch from the Anaconda prompt. For example:
>>> !ls
database.sqlite
Weather Data Clustering using k-Means.ipynb
>>>!pip show lxml | grep Version
Version: 4.1.0
answered Jan 4 at 7:45
Karl BakerKarl Baker
366115
add a comment |
In my experience, as long as Jupyter is launched from a bash-compliant command line such as Git Bash (MingW64) or possibly Ubuntu on Windows, bash commands prepended with ! work in Jupyter Notebook, even on Windows systems.
I'm running windows 10 Pro with Python installed via Anaconda, and bash works when I launch Jupyter via Git Bash, but does not when I launch from the Anaconda prompt. For example:
>>> !ls
database.sqlite
Weather Data Clustering using k-Means.ipynb
>>>!pip show lxml | grep Version
Version: 4.1.0
answered Jan 4 at 7:45
Karl BakerKarl Baker
366115
add a comment |
In my experience, as long as Jupyter is launched from a bash-compliant command line such as Git Bash (MingW64) or possibly Ubuntu on Windows, bash commands prepended with ! work in Jupyter Notebook, even on Windows systems.
I'm running windows 10 Pro with Python installed via Anaconda, and bash works when I launch Jupyter via Git Bash, but does not when I launch from the Anaconda prompt. For example:
>>> !ls
database.sqlite
Weather Data Clustering using k-Means.ipynb
>>>!pip show lxml | grep Version
Version: 4.1.0
answered Jan 4 at 7:45
Karl BakerKarl Baker
366115
In my experience, as long as Jupyter is launched from a bash-compliant command line such as Git Bash (MingW64) or possibly Ubuntu on Windows, bash commands prepended with ! work in Jupyter Notebook, even on Windows systems.
I'm running windows 10 Pro with Python installed via Anaconda, and bash works when I launch Jupyter via Git Bash, but does not when I launch from the Anaconda prompt. For example:
>>> !ls
database.sqlite
Weather Data Clustering using k-Means.ipynb
>>>!pip show lxml | grep Version
Version: 4.1.0
answered Jan 4 at 7:45
Karl BakerKarl Baker
366115
answered Jan 4 at 7:45
Karl BakerKarl Baker
366115
answered Jan 4 at 7:45
Karl BakerKarl Baker
366115
answered Jan 4 at 7:45
Karl BakerKarl Baker
366115
366115
add a comment |
add a comment |
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I have a somewhat similar problem, did you ever get the to the bottom of this? stackoverflow.com/questions/51548928/…
– quantum285
Jul 26 '18 at 23:48
Nope! No progress. Admittedly, it's low priority, as the problem is being experienced by some undergrads in our lab. We've just made them switch to using lab computers running Ubuntu instead of their personal Windows laptops.
– kubu4
Jul 28 '18 at 4:26
I found that '!' uses the default windows shell whereas '%%bash' uses bash. So a workaround is to use '%%cmd' to use all of the commands you can use with '!' but then you face the problems that arise due to the difference between bash and batch. I've also taken the approach of using Ubuntu VMs also. Not sure if anything I said helps at all but just sharing..
– quantum285
Jul 29 '18 at 0:04
You say Git Bash is installed, but is Jupyter Notebook being launched from Git Bash or from another prompt, e.g., Anaconda?
– Karl Baker
Jan 4 at 7:34
Launching via Git Bash. Thanks for clarifying that point!
– kubu4
Jan 5 at 21:49