Hydrogen: Multiple kernels inside one rich document

[ahsen1402]

Hi,

I am running hydrogen on MAC OS, and in the documentation I read that we can run "Multiple kernels inside one rich document", for now i want to run markdown and python but I can not make it work. Is there anywhere instruction how can one do this?

[n-riesco]

Here's an example.

[ahsen1402]

thanks but problem is I can not run it when I try to run it it gives me a kernel not found error, or grammar error.

[n-riesco]

Have you installed the kernels to run those languages? E.g.:

• IPython
• IJavascript
• IJulia
• IRkernel

You can get the list of installed kernels in your computer by running jupyter kernelspec list.

[ahsen1402]

Python kernel i have but there is no markdown kernel in jupyter but in the documentation the creator of hydrogen claims it is compatible with markdown so i prorably missing something maybe too easy

[n-riesco]

There is no need for a markdown kernel. Atom tells Hydrogen what the language is in each code block, and Hydrogen calls the appropriate kernel.

To run this example you need a Python kernel and a Javascript kernel. If your computer doesn't have the Javascript kernel installed, Hydrogen will fail when you try to run the Javascript code.

Also note that the Hydrogen command Run All doesn't work for markdown files.

[lgeiger]

@ahsen1402 In order to run a code block make sure to place the cursor inside the block of code you wish to run. Otherwise Hydrogen doesn't know which code to execute:

[ahsen1402]

Thanks I will retry, for such files can the file extension be anything such as py?

[n-riesco]

Thanks I will retry, for such files can the file extension be anything such as py?

Not sure why you'd want to do that. Atom and most programs will think a file with extension .py is a python file. Markdown files usually have he extension .md.

Having said that, it's possible to tell Atom that a file is a markdown files regardless of the file extension.
See here:

[ahsen1402]

Thanks for the fast comments I have installed the IRkernel and I see the kernel and it works in Jupyter, however in hydrogen

Python

x='this is a string'

R

x=14
x=matrix(0,3,5)

The second R code does not work and gives me an error

---

NameError Traceback (most recent call last)
in ()
----> 1 x=matrix(0,3,5)

NameError: name 'matrix' is not defined

Sorry my noobishnes but this tool is supercool i feel bad not to make it work :(

[n-riesco]

It looks like the R code was executed by the python kernel.

Does it work when the file has an .md extension?

[ahsen1402]

unfortunately it does not work with .md as well.

[ahsen1402]

@n-riesco maybe it is a kernel update issue where do i run Hydrogen: Update Kernels ? i cant seem to find this command.

[BenRussert]

Should be in your command palette. Ctrl shift p and search "update kernels"

On Fri, Apr 21, 2017, 12:02 PM ahsen1402 [e-mail] wrote:

@n-riesco https://github.com/n-riesco maybe it is a kernel update issue
where do i run Hydrogen: Update Kernels ? i cant seem to find this
command.

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[ahsen1402]

When i update kernels i get a message saying

Hydrogen Kernels upgraded:

R
Matlab
Python 3

but still

Python

x='this is a string'
print(x)

R

x=14
x=matrix(0,3,5)

the R portion gives me error

NameError                                 Traceback (most recent call last)
<ipython-input-15-f2e84b5fefc8> in <module>()
----> 1 x=matrix(0,3,5)

NameError: name 'matrix' is not defined

any more ideas? It looks like i have the kernel and hydrogen recognizes it.

[lgeiger]

@ahsen1402 What Atom language are you using? You can tell this by looking at the lower right hand corner of the status bar.

If you want to use multiple kernels inside the same file it should look similar to this:

[ahsen1402]

I tried them all phyton and github markdown, actually in github markdown i got an error saying

No kernel for language github markdown found
Check that the language for this file is set in Atom and that you have a Jupyter kernel installed for it.

[lgeiger]

I am using GitHub Markdown?

That's OK too.

I'm out ideas. Want to join our Slack channel? I'd be happy to pair with you there.

[ahsen1402]

would be great i would like this work very much.

[lgeiger]

We where able to figure it out. The problem was one has to install language-r to make it work.