Otherwise only fonts with that character will work.

This was in the original to-do list ("support remote kernels"). I think this feature would be extremely helpful for people who need to run the code on remote servers. Is this feature still part of the roadmap for the near future :)?

Currently, autocompletion is only working for the first identifier within a line. For example: writing

  x = [1,2,3]
  x.a

starts autocompletion and suggest a.append.

However, the following does not work:

  x = [1,2,3]
  x.append(x.rev

I guess the reason for this is the getPrefix function in autocomplete-provider.coffee. This regexp searches for the FIRST identifier to autocomplete, instead of using the the last identifier before cursor position.

I was trying to use juypter-nodejs.

I started Atom from the command line.

'node' could not be spawned.
Is it installed and on your path?
If so please open an issue on the package spawning the process.

If I go back to the terminal session:

➜  ~  echo $PATH
/Users/sebinsua/.nvm/versions/io.js/v1.8.1/bin:/usr/local/sbin:/usr/local/heroku/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/share/python

It looks fine to me?

Is there any way I can salvage a still running python backend if Atom locked up completely (but hasn't crashed)? Can I connect the python session to a CLI somehow?

I have been running a program for a while now and I don't want to loose my results.

Info can be taken from #13

It would be nice to have the functionality to place variable watches directly in the code, just like it's possible in LightTable.

Most likely, this will require modifying the code that is sent to the kernel by adding a language specific call such as:

from IPython.display import display

n = 0
for x in xrange(300)
    n = x; display(n)  # watch on n should display [n = 200] for example

where the inline display is added before sending the code to the kernel. This is already possible manually. However instead of listing only the actual value of the variable, every single change is concatenated into a list.

This feature would also make it possible to change plots online as every change would be displayed automatically.

#52

I've got atom Version 0.209.0 (0.209.0) on Mac OS X 10.10.3.

I had hydrogen 0.3.3 installed. When I try to upgrade to 0.3.15 I get pkg-config command not found. I uninstalled hydrogen and tried installing from scratch. Same thing.

pkg-config appears to be fine at the terminal:

08:25 $ pkg-config 
Must specify package names on the command line
✘-1 ~ 
10:13 $ which pkg-config
/usr/local/bin/pkg-config

Here's the output from install:

Installing “[email protected]” failed.Hide output…

> [email protected] install /private/var/folders/1p/38rnnlmx6hz5n9w8d3h19ks40000gn/T/apm-install-dir-115512-2651-ztsswl/node_modules/Hydrogen/node_modules/zmq
> node-gyp rebuild


/bin/sh: pkg-config: command not found
gyp: Call to 'pkg-config libzmq --libs' returned exit status 127. while trying to load binding.gyp
gyp ERR! configure error 
gyp ERR! stack Error: `gyp` failed with exit code: 1
gyp ERR! stack     at ChildProcess.onCpExit (/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/configure.js:343:16)
gyp ERR! stack     at ChildProcess.emit (events.js:98:17)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (child_process.js:820:12)
gyp ERR! System Darwin 14.3.0
gyp ERR! command "node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /private/var/folders/1p/38rnnlmx6hz5n9w8d3h19ks40000gn/T/apm-install-dir-115512-2651-ztsswl/node_modules/Hydrogen/node_modules/zmq
gyp ERR! node -v v0.10.35
gyp ERR! node-gyp -v v1.0.2
gyp ERR! not ok 
npm ERR! Darwin 14.3.0
npm ERR! argv "/Applications/Atom.app/Contents/Resources/app/apm/bin/node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/Users/dwatson/.atom/.apm/.apmrc" "--userconfig" "/Users/dwatson/.atom/.apmrc" "install" "/private/var/folders/1p/38rnnlmx6hz5n9w8d3h19ks40000gn/T/d-115512-2651-jfwvhe/package.tgz" "--target=0.22.0" "--arch=x64"
npm ERR! node v0.10.35
npm ERR! npm  v2.5.1
npm ERR! code ELIFECYCLE

npm ERR! [email protected] install: `node-gyp rebuild`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the [email protected] install script 'node-gyp rebuild'.
npm ERR! This is most likely a problem with the zmq package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     node-gyp rebuild
npm ERR! You can get their info via:
npm ERR!     npm owner ls zmq
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR!     /private/var/folders/1p/38rnnlmx6hz5n9w8d3h19ks40000gn/T/apm-install-dir-115512-2651-ztsswl/npm-debug.log

To make things easier on users, we need to find a way to bundle up zmq (or improve things upstream).

If we bundle binaries though, we'll quickly be out of date (or so I assume), because Atom is constantly updating which also means updates to node necessitating updates to nan and zmq. If we force the development headers to be vendorized, that's a different story.

There's also the case of seeing what the Atom team thinks, including asking about zmq being part of Atom or electron directly.

I'm a MacPorts guy. Is it possible to remove the hard dependency on the Homebrew pkg-config and zmq? Or is that out of your control?

It looks like one of the dependencies (gyp) is not compatible with Python >= 3:

$ apm install hydrogen
Installing hydrogen to /Users/fonnescj/.atom/packages ✗

> [email protected] install /private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/apm-install-dir-115420-19773-pwklwc/node_modules/Hydrogen/node_modules/zmq
> node-gyp rebuild


gyp ERR! configure error 
gyp ERR! stack Error: Python executable "python" is v3.4.2, which is not supported by gyp.
gyp ERR! stack You can pass the --python switch to point to Python >= v2.5.0 & < 3.0.0.
gyp ERR! stack     at failPythonVersion (/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/configure.js:108:14)
gyp ERR! stack     at /Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/configure.js:97:9
gyp ERR! stack     at ChildProcess.exithandler (child_process.js:656:7)
gyp ERR! stack     at ChildProcess.emit (events.js:98:17)
gyp ERR! stack     at maybeClose (child_process.js:766:16)
gyp ERR! stack     at Socket.<anonymous> (child_process.js:979:11)
gyp ERR! stack     at Socket.emit (events.js:95:17)
gyp ERR! stack     at Pipe.close (net.js:466:12)
gyp ERR! System Darwin 14.4.0
gyp ERR! command "node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/apm-install-dir-115420-19773-pwklwc/node_modules/Hydrogen/node_modules/zmq
gyp ERR! node -v v0.10.35
gyp ERR! node-gyp -v v1.0.2
gyp ERR! not ok 
npm ERR! Darwin 14.4.0
npm ERR! argv "/Applications/Atom.app/Contents/Resources/app/apm/bin/node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/Users/fonnescj/.atom/.apm/.apmrc" "--userconfig" "/Users/fonnescj/.atom/.apmrc" "install" "/private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/d-115420-19773-1756kxc/package.tgz" "--target=0.22.0" "--arch=x64"
npm ERR! node v0.10.35
npm ERR! npm  v2.5.1
npm ERR! code ELIFECYCLE

npm ERR! [email protected] install: `node-gyp rebuild`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the [email protected] install script 'node-gyp rebuild'.
npm ERR! This is most likely a problem with the zmq package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     node-gyp rebuild
npm ERR! You can get their info via:
npm ERR!     npm owner ls zmq
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR!     /private/var/folders/z_/kgsm76k94s7_jhnkfydfnd380000gn/T/apm-install-dir-115420-19773-pwklwc/npm-debug.log

This is a problem with IRkernel. I opened two issues on this:

• IRkernel/IRkernel#137
• IRkernel/IRkernel#138

Waiting for them to be fixed.

FYI.

Currently messages from stdout and stderr of the kernels are logged to the console, but really we should be putting them somewhere with more visibility for the user.

Maybe a status bar error indicator that opens an editor with all the messages?

The following error shows upon installation (pkg-config is in fact installed and working, as far as I can tell):

[email protected] install /private/var/folders/wk/59lcnyg524q1zgyydwn8qgnr0000gn/T/apm-install-dir-11555-22648-1421byw/node_modules/Hydrogen/node_modules/zmq
node-gyp rebuild

/bin/sh: pkg-config: command not found
gyp: Call to 'pkg-config libzmq --libs' returned exit status 127. while trying to load binding.gyp
gyp ERR! configure error
gyp ERR! stack Error: gyp failed with exit code: 1
gyp ERR! stack at ChildProcess.onCpExit (/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/configure.js:343:16)
gyp ERR! stack at ChildProcess.emit (events.js:98:17)
gyp ERR! stack at Process.ChildProcess._handle.onexit (child_process.js:820:12)
gyp ERR! System Darwin 14.3.0
gyp ERR! command "node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /private/var/folders/wk/59lcnyg524q1zgyydwn8qgnr0000gn/T/apm-install-dir-11555-22648-1421byw/node_modules/Hydrogen/node_modules/zmq
gyp ERR! node -v v0.10.35
gyp ERR! node-gyp -v v1.0.2
gyp ERR! not ok
npm ERR! Darwin 14.3.0
npm ERR! argv "/Applications/Atom.app/Contents/Resources/app/apm/bin/node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/Users/javier/.atom/.apm/.apmrc" "--userconfig" "/Users/javier/.atom/.apmrc" "install" "/private/var/folders/wk/59lcnyg524q1zgyydwn8qgnr0000gn/T/d-11555-22648-y2knes/package.tgz" "--target=0.22.0" "--arch=x64"
npm ERR! node v0.10.35
npm ERR! npm v2.5.1
npm ERR! code ELIFECYCLE

npm ERR! [email protected] install: node-gyp rebuild
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the [email protected] install script 'node-gyp rebuild'.
npm ERR! This is most likely a problem with the zmq package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR! node-gyp rebuild
npm ERR! You can get their info via:
npm ERR! npm owner ls zmq
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR! /private/var/folders/wk/59lcnyg524q1zgyydwn8qgnr0000gn/T/apm-install-dir-11555-22648-1421byw/npm-debug.log

The log file npm-debug.log is not present, and neither is it's subfolder.

Thank you in advance,
Javier

While defining mappings between grammar names and kernel languages is good for cleaning up nonstandard language names, there are situations where you want to change the kernel being used manually:

1. Running some one-off code
2. Selecting which of several kernels for a particular language to use (e.g. python2 vs. python3)

To support these use cases, we should add some way of switching kernels.

I think it makes the most sense to replace the existing grammar -> kernel mapping config with this. The interaction might be something like this:

1. Open Command Palette
2. "Hydrogen: Select kernel for grammar " (Python Django)
3. Choose from all of the kernels, listed by their display_name (Python 3.4)
4. This mapping persists until it is changed again. Close Atom and reopen it to a Python Django file and it should load the Python 3.4 kernel.

Does this sound like a reasonable interaction?

So, I have a Python file open - fresh startup.

I select the first block of code I want to run - 2 import statements and 2 string variable definitions. Unfortunately, Hydrogen seems to go into an infinite loop, and the loading bar is displayed forever.

This doesn't happen if I have a fresh file and I evaluate the block line by line. But whenever this happens, interrupting or restarting the python kernel from Hydrogen doesn't seem to work.

I am running an Arch Linux System and I have installed iPython using the default package manager, however Hydrogen doesn't seem to find my installation. I don't understand how the whole "kernel" thing works with iPython, I just want the fancy functionality of Hydrogen. I'm sorry I posted this here but I didn't know where else to put it.

As you can see, there's no python kernel: in the bottom left.

Everything seems alright on OSX.

I just installed the node.js/javascript kernel restarted atom and rock on! This is awesome!

We could add node.js to the front page as well.

...or anything else that uses scripts (e.g. itorch.Plot)

jmp is an npm module for creating, parsing and replying to messages of the Jupyter Messaging Protocol.

When I try to install hydrogen I am getting the following error:

> [email protected] install /private/var/folders/3g/gp3lt1950195fs3kf27csb0h0000gn/T/apm-install-dir-11559-43382-ne5xq1/node_modules/Hydrogen/node_modules/zmq
> node-gyp rebuild


/bin/sh: pkg-config: command not found
gyp: Call to 'pkg-config libzmq --libs' returned exit status 127. while trying to load binding.gyp
gyp ERR! configure error 
gyp ERR! stack Error: `gyp` failed with exit code: 1
gyp ERR! stack     at ChildProcess.onCpExit (/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/configure.js:343:16)
gyp ERR! stack     at ChildProcess.emit (events.js:98:17)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (child_process.js:820:12)
gyp ERR! System Darwin 12.6.0
gyp ERR! command "node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /private/var/folders/3g/gp3lt1950195fs3kf27csb0h0000gn/T/apm-install-dir-11559-43382-ne5xq1/node_modules/Hydrogen/node_modules/zmq
gyp ERR! node -v v0.10.35
gyp ERR! node-gyp -v v1.0.2
gyp ERR! not ok 
npm ERR! Darwin 12.6.0
npm ERR! argv "/Applications/Atom.app/Contents/Resources/app/apm/bin/node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/Users/username/.atom/.apm/.apmrc" "--userconfig" "/Users/username/.atom/.apmrc" "install" "/private/var/folders/3g/gp3lt1950195fs3kf27csb0h0000gn/T/d-11559-43382-4rvrhq/package.tgz" "--target=0.22.0" "--arch=x64"
npm ERR! node v0.10.35
npm ERR! npm  v2.5.1
npm ERR! code ELIFECYCLE

npm ERR! [email protected] install: `node-gyp rebuild`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the [email protected] install script 'node-gyp rebuild'.
npm ERR! This is most likely a problem with the zmq package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     node-gyp rebuild
npm ERR! You can get their info via:
npm ERR!     npm owner ls zmq
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR!     /private/var/folders/3g/gp3lt1950195fs3kf27csb0h0000gn/T/apm-install-dir-11559-43382-ne5xq1/npm-debug.log

I do have brew-installed zeromq (4.0.5_2) and pkg-config (0.28). I am on OS X 10.8.5.
Plus, pkg-config is accessible from command line.

UI Theme: OneDark
Syntax Theme: Watson
Font: Fantasque Sans Mono (with default font there is not even rect char)

This is an amazing package. But when I try to use it. It display like this.
Some particular combination of UI theme and syntax theme may cause the backgroud and the font using the same color.
I'm using One Light + Chester Atom

I have tried other combinations, basically the 'light UI' works well with 'light syntax', and 'dark UI' works well with 'dark syntax'.

We could use fs.watch to track kernel installations (or other runtimes being launched, e.g. the notebook). To make this simpler, there are higher level watch libraries like https://github.com/mikeal/watch or https://github.com/bevry/watchr.

This would make it so it isn't just determined once on startup, but asynchronously throughout use.

Sorry about my poor English. I'm trying to report this by screenshot.
It happens when the codes are long enough and you scroll down.

This is to better accommodate kernels like IRkernel which output rich text (e.g. HTML) for even small results.

Bubbles which only contain text (regardless of formatting) should have a multiline-result style bubble (pictured below) if they're larger than a single line, and should fit inline with no close button if they're small.

HTML results should also have the same close/new pane buttons as text ones if they only contain text.

A panel with a searchbox which displays all currently defined objects of the kernel would be useful.
The %who and %whos magics already provide a good interface for this, I don't know if they are available for other kernels aside from the python one.

Hey pal, when python spews out a really long string, sometimes the output popup exceeds the window width. Can dismiss with clear-results, but maybe the popup should have a maximum width?

We'll need/want to search the new Jupyter paths as well for kernelspecs, just as in https://github.com/jupyter/jupyter_core/blob/master/jupyter_core/paths.py

This is for the future release of the Jupyter packages (but my and the rest of the IPython/Jupyter team's likeliness to use this package).

I love the idea of this plugin.
I can't seem to get hydrogen to run on Jupyter's R kernel though (https://github.com/IRkernel/IRkernel)
When I enter a command and then try to evaluate it, i just get the 'working' animation, and it runs forever.

I realize that i'm asking about a (somewhat) underdeveloped kernel and that the problem may very well may not be on hydrogen's end. But I really don't have any way to know if it is hydrogen or something else since hydrogen is not reporting much in the way of errors or what it is doing at a given moment. Is there any way to get debugging information out of hydrogen? Outside of the sort of trial and error i described above, is there any way to figure out if hydrogen is actually successfully connecting with the intended kernel?

on my end:
I'm using the latest version of hydrogen (0.3.9), version 3.0.0 of ipython (jupyter), and the .3 version of the IRkernel.
I can also get the r kernel to work normally through a jupyter notebook or console.
I tested and was able to get hydrogen to work with python in atom.io

The autocomplete feature of the running kernel is quite beautiful. Now that autocomplete plus is part of Atom, it would be nice to somehow merge the autocomplete suggestions so you get the best of the static analysis and dynamic running kernel.

What did not work?
Bash kernel not found in Atom

What is should do?
Evaluate bash commands in Atom the same way it works for python

Steps to reproduce:

1. Install Hydrogen and tested that it is working with python kernel
2. Installed bash_kernel with pip install bash_kernel
3. Updated the language mapping to {"Shell Script": "bash"}
4. Restarted Atom from the command line
5. Tried to run a bash command in Atom, but received a error:

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

I'd love to see debugger integration, either via the cell / line magic %debug or with a separate keybinding to execute the given code with ipdb and use an interactive debugging session.

Unfortunately it looks like this right now:

%%debug
x = 0
y = 0

for x in xrange(200):
    y = x
    if y > 100:
        break

NOTE: Enter 'c' at the ipdb> prompt to continue execution.

�[1;32m�[0m(2)�[0;36m�[1;34m()�[0m

�[1;31m---------------------------------------------------------------------------�[0m
�[1;31mStdinNotImplementedError�[0m Traceback (most recent call last)
�[1;32m�[0m in �[0;36m�[1;34m()�[0m

�[1;32m/usr/lib/python2.7/bdb.pyc�[0m in �[0;36mtrace_dispatch�[1;34m(self, frame, event, arg)�[0m
�[0;32m 47�[0m �[1;32mreturn�[0m �[1;31m# None�[0m�[1;33m�[0m�[0m
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�[1;32m/usr/local/lib/python2.7/dist-packages/IPython/core/debugger.pyc�[0m in �[0;36minteraction�[1;34m(self, frame, traceback)�[0m
�[0;32m 276�[0m �[1;32mwhile�[0m �[0mTrue�[0m�[1;33m:�[0m�[1;33m�[0m�[0m
�[0;32m 277�[0m �[1;32mtry�[0m�[1;33m:�[0m�[1;33m�[0m�[0m
�[1;32m--> 278�[1;33m �[0mOldPdb�[0m�[1;33m.�[0m�[0minteraction�[0m�[1;33m(�[0m�[0mself�[0m�[1;33m,�[0m �[0mframe�[0m�[1;33m,�[0m �[0mtraceback�[0m�[1;33m)�[0m�[1;33m�[0m�[0m
�[0m�[0;32m 279�[0m �[1;32mexcept�[0m �[0mKeyboardInterrupt�[0m�[1;33m:�[0m�[1;33m�[0m�[0m
�[0;32m 280�[0m �[0mself�[0m�[1;33m.�[0m�[0mshell�[0m�[1;33m.�[0m�[0mwrite�[0m�[1;33m(�[0m�[1;34m'\n'�[0m �[1;33m+�[0m �[0mself�[0m�[1;33m.�[0m�[0mshell�[0m�[1;33m.�[0m�[0mget_exception_only�[0m�[1;33m(�[0m�[1;33m)�[0m�[1;33m)�[0m�[1;33m�[0m�[0m

�[1;32m/usr/lib/python2.7/pdb.pyc�[0m in �[0;36minteraction�[1;34m(self, frame, traceback)�[0m
�[0;32m 208�[0m �[0mself�[0m�[1;33m.�[0m�[0msetup�[0m�[1;33m(�[0m�[0mframe�[0m�[1;33m,�[0m �[0mtraceback�[0m�[1;33m)�[0m�[1;33m�[0m�[0m
�[0;32m 209�[0m �[0mself�[0m�[1;33m.�[0m�[0mprint_stack_entry�[0m�[1;33m(�[0m�[0mself�[0m�[1;33m.�[0m�[0mstack�[0m�[1;33m[�[0m�[0mself�[0m�[1;33m.�[0m�[0mcurindex�[0m�[1;33m]�[0m�[1;33m)�[0m�[1;33m�[0m�[0m
�[1;32m--> 210�[1;33m �[0mself�[0m�[1;33m.�[0m�[0mcmdloop�[0m�[1;33m(�[0m�[1;33m)�[0m�[1;33m�[0m�[0m
�[0m�[0;32m 211�[0m �[0mself�[0m�[1;33m.�[0m�[0mforget�[0m�[1;33m(�[0m�[1;33m)�[0m�[1;33m�[0m�[0m
�[0;32m 212�[0m �[1;33m�[0m�[0m

�[1;32m/usr/lib/python2.7/cmd.pyc�[0m in �[0;36mcmdloop�[1;34m(self, intro)�[0m
�[0;32m 128�[0m �[1;32mif�[0m �[0mself�[0m�[1;33m.�[0m�[0muse_rawinput�[0m�[1;33m:�[0m�[1;33m�[0m�[0m
�[0;32m 129�[0m �[1;32mtry�[0m�[1;33m:�[0m�[1;33m�[0m�[0m
�[1;32m--> 130�[1;33m �[0mline�[0m �[1;33m=�[0m �[0mraw_input�[0m�[1;33m(�[0m�[0mself�[0m�[1;33m.�[0m�[0mprompt�[0m�[1;33m)�[0m�[1;33m�[0m�[0m
�[0m�[0;32m 131�[0m �[1;32mexcept�[0m �[0mEOFError�[0m�[1;33m:�[0m�[1;33m�[0m�[0m
�[0;32m 132�[0m �[0mline�[0m �[1;33m=�[0m �[1;34m'EOF'�[0m�[1;33m�[0m�[0m

�[1;32m/usr/local/lib/python2.7/dist-packages/IPython/kernel/zmq/kernelbase.pyc�[0m in �[0;36mraw_input�[1;34m(self, prompt)�[0m
�[0;32m 644�[0m �[1;32mif�[0m �[1;32mnot�[0m �[0mself�[0m�[1;33m.�[0m�[0m_allow_stdin�[0m�[1;33m:�[0m�[1;33m�[0m�[0m
�[0;32m 645�[0m raise StdinNotImplementedError(
�[1;32m--> 646�[1;33m �[1;34m"raw_input was called, but this frontend does not support input requests."�[0m�[1;33m�[0m�[0m
�[0m�[0;32m 647�[0m )
�[0;32m 648�[0m return self._input_request(prompt,

�[1;31mStdinNotImplementedError�[0m: raw_input was called, but this frontend does not support input requests.

Hey there,

Just wanted to say that this is awesome. I'm so glad someone started this up. I was waiting on the Big Split ™️ to settle before starting this up so I'm glad you took the initiative to kick this off. I'm assuming since I'm running from master on all the Jupyter repos that this isn't quite in the state to work with the coming release of the split off Jupyter and IPython packages. Currently I'm seeing the display waiting on output:

Since you're down the same path, I might as well mention a few bits of interest. The comms channels for IPython widgets are going to be wonderful to use though we'll end up needing them decoupled from the Notebook:

jupyter-widgets/ipywidgets#13

We'll likely need zmq to bring in the latest nan to stay up to date with iojs. I ran into this while tinkering with an Electron app to display output alongside a console.

JustinTulloss/zeromq.node#420 / JustinTulloss/zeromq.node#421

I've noticed a couple deprecations, but I'll ship a PR your way shortly.

Hi,

while the python kernel is working now (after starting atom from command line) the ruby kernel is still not responding. When I run "Run Hydrogen" on some code snippet like

  x = 6
  x

it starts computing but does not give any result. The last output from atom is

  [26252:0601/180536:INFO:CONSOLE(100)] "<IDS|MSG>,,{"msg_id":"41772bc9-cd43-4647-9e7a-303ef77a2589","username":"","session":0,"msg_type":"execute_request","version":"5.0"},{},{},{"code":"x=6\nx","silent":false,"store_history":true,"user_expressions":{},"allow_stdin":false}", source: /home/kaidu/.atom/packages/Hydrogen/lib/kernel.coffee (100)

Starting the ruby kernel from the ipython notebook (commandline) is working.

I am on Windows 8, Atom 0.200.0, and the installation fails with

Installing “[email protected]” failed.

> [email protected] install C:\Users\buchner\AppData\Local\Temp\apm-install-dir-115421-4460-cnflq2\node_modules\Hydrogen\node_modules\zmq
> node-gyp rebuild


C:\Users\buchner\AppData\Local\Temp\apm-install-dir-115421-4460-cnflq2\node_modules\Hydrogen\node_modules\zmq>node "C:\Users\buchner\AppData\Local\atom\app-0.200.0\resources\app\apm\node_modules\npm\bin\node-gyp-bin\\..\..\node_modules\node-gyp\bin\node-gyp.js" rebuild 

gypnpm ERR! Windows_NT 6.2.9200
npm ERR! argv "C:\\Users\\buchner\\AppData\\Local\\atom\\app-0.200.0\\resources\\app\\apm\\bin\\\\node.exe" "C:\\Users\\buchner\\AppData\\Local\\atom\\app-0.200.0\\resources\\app\\apm\\node_modules\\npm\\bin\\npm-cli.js" "--globalconfig" "C:\\Users\\buchner\\.atom\\.apm\\.apmrc" "--userconfig" "C:\\Users\\buchner\\.atom\\.apmrc" "install" "C:\\Users\\buchner\\AppData\\Local\\Temp\\d-115421-4460-c5n6l2\\package.tgz" "--target=0.22.0" "--arch=ia32"
npm ERR! node v0.10.35
npm ERR! npm  v2.5.1
npm ERR! code ELIFECYCLE

npm ERR! [email protected] install: `node-gyp rebuild`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the [email protected] install script 'node-gyp rebuild'.
npm ERR! This is most likely a problem with the zmq package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     node-gyp rebuild
npm ERR! You can get their info via:
npm ERR!     npm owner ls zmq
npm ERR! There is likely additional logging output above.

Python 3.4.2, Ipython notebook 3.1.0, and zeromq 4.0.5 are installed via Anaconda/Miniconda.

[Enter steps to reproduce below:]

Happens on any python or Julia file whenever I try to run any code.

Atom Version: 0.199.0
System: Mac OS X 10.10.3
Thrown From: Hydrogen package, v0.1.3

Stack Trace

Uncaught TypeError: Cannot read property 'toLowerCase' of undefined

At /Users/sglyon/.atom/packages/Hydrogen/lib/kernel-manager.coffee:40

TypeError: Cannot read property 'toLowerCase' of undefined
  at /Users/sglyon/.atom/packages/Hydrogen/lib/kernel-manager.coffee:40:73
  at arrayFilter (/opt/homebrew-cask/Caskroom/atom/latest/Atom.app/Contents/Resources/app.asar/node_modules/babel-core/node_modules/lodash/index.js:1427:13)
  at Function.filter (/opt/homebrew-cask/Caskroom/atom/latest/Atom.app/Contents/Resources/app.asar/node_modules/babel-core/node_modules/lodash/index.js:6365:14)
  at Object.module.exports.KernelManager.getKernelInfoForLanguage (/Users/sglyon/.atom/packages/Hydrogen/lib/kernel-manager.coffee:39:29)
  at Object.module.exports.KernelManager.languageHasKernel (/Users/sglyon/.atom/packages/Hydrogen/lib/kernel-manager.coffee:48:16)
  at Object.module.exports.AtomRepl.run (/Users/sglyon/.atom/packages/Hydrogen/lib/main.coffee:138:26)
  at atom-text-editor.subscriptions.add.atom.commands.add.hydrogen:run (/Users/sglyon/.atom/packages/Hydrogen/lib/main.coffee:25:33)
  at CommandRegistry.module.exports.CommandRegistry.handleCommandEvent (/opt/homebrew-cask/Caskroom/atom/latest/Atom.app/Contents/Resources/app.asar/src/command-registry.js:238:29)
  at /opt/homebrew-cask/Caskroom/atom/latest/Atom.app/Contents/Resources/app.asar/src/command-registry.js:3:61
  at KeymapManager.module.exports.KeymapManager.dispatchCommandEvent (/opt/homebrew-cask/Caskroom/atom/latest/Atom.app/Contents/Resources/app.asar/node_modules/atom-keymap/lib/keymap-manager.js:519:16)
  at KeymapManager.module.exports.KeymapManager.handleKeyboardEvent (/opt/homebrew-cask/Caskroom/atom/latest/Atom.app/Contents/Resources/app.asar/node_modules/atom-keymap/lib/keymap-manager.js:354:22)
  at HTMLDocument.module.exports.WindowEventHandler.onKeydown (/opt/homebrew-cask/Caskroom/atom/latest/Atom.app/Contents/Resources/app.asar/src/window-event-handler.js:178:20)

Commands

     -0:02.2.0 hydrogen:run (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -0:00.2.0 editor:select-to-first-character-of-line (atom-text-editor.editor.vim-mode.insert-mode.is-focused)

Config

{
  "core": {
    "themes": [
      "atom-dark-ui",
      "base16-eighties-dark"
    ],
    "disabledPackages": [
      "emmet",
      "linter-pyflakes",
      "rst-preview",
      "minimap",
      "notebook",
      "timekeeper"
    ],
    "PATH": "/usr/local/heroku/bin:/Users/sglyon/anaconda/bin:/Users/sglyon/src/julia/julia/usr/bin:/Users/sglyon/bin:/Users/sglyon/.cabal/bin:/usr/local/bin:/usr/local/sbin:/usr/texbin:/usr/local/gocode/bin:/Users/sglyon/google-cloud-sdk/bin:/Applications/Dynare/4.4.3/dynare  :/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin",
    "useReactEditor": true,
    "projectHome": "/Users/sglyon/School/NYU",
    "destroyEmptyPanes": false
  }
}

Installed Packages

# User
Hydrogen, v0.1.3
atom-django, v0.2.1
atomatigit, v1.3.0
autocomplete-paths, v1.0.2
base16-eighties-dark, v2.1.1
color-picker, v1.7.0
command-logger, v0.23.0
editor-stats, v0.17.0
language-julia, v0.8.1
language-latex, v0.6.1
language-matlab, v0.1.0
language-r, v0.2.0
language-restructuredtext, v0.5.0
linter, v0.12.2
project-manager, v1.15.5
remote-edit, v1.7.2
remote-sync, v2.4.1
script, v2.23.0
syntax-settings, v0.7.1
travis-ci-status, v0.14.1
vim-mode, v0.46.0
wakatime, v4.0.9

# Dev
No dev packages

[Enter steps to reproduce below:]

1. ...
2. ...

Atom Version: 0.201.0
System: Microsoft Windows Server 2008 R2 Standard
Thrown From: Hydrogen package, v0.3.7

Stack Trace

Uncaught Error: EBADF: bad file descriptor, write

At fs.js:657

Error: EBADF: bad file descriptor, write
  at Error (native)
  at Object.fs.writeSync (fs.js:657:20)
  at SyncWriteStream.write (fs.js:1906:6)
  at execSync (child_process.js:1372:20)
  at Object.<anonymous> (C:\Users\Administrator\.atom\packages\Hydrogen\lib\paths.coffee:10:12)
  at Object.<anonymous> (C:\Users\Administrator\.atom\packages\Hydrogen\lib\paths.coffee:3:1)
  at Module._compile (module.js:452:26)
  at Object.requireCoffeeScript (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\coffee-cash\lib\coffee-cash.js:85:19)
  at Module.load (module.js:347:32)
  at Function.Module._load (module.js:302:12)
  at Module.require (module.js:357:17)
  at require (module.js:376:17)
  at Object.<anonymous> (C:\Users\Administrator\.atom\packages\Hydrogen\lib\kernel-manager.coffee:6:17)
  at Object.<anonymous> (C:\Users\Administrator\.atom\packages\Hydrogen\lib\kernel-manager.coffee:1:1)
  at Module._compile (module.js:452:26)
  at Object.requireCoffeeScript (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\coffee-cash\lib\coffee-cash.js:85:19)
  at Module.load (module.js:347:32)
  at Function.Module._load (module.js:302:12)
  at Module.require (module.js:357:17)
  at require (module.js:376:17)
  at Object.<anonymous> (C:\Users\Administrator\.atom\packages\Hydrogen\lib\main.coffee:7:17)
  at Object.<anonymous> (C:\Users\Administrator\.atom\packages\Hydrogen\lib\main.coffee:1:1)
  at Module._compile (module.js:452:26)
  at Object.requireCoffeeScript (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\coffee-cash\lib\coffee-cash.js:85:19)
  at Module.load (module.js:347:32)
  at Function.Module._load (module.js:302:12)
  at Module.require (module.js:357:17)
  at require (module.js:376:17)
  at Package.module.exports.Package.requireMainModule (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\src\package.js:709:34)
  at Package.module.exports.Package.activateConfig (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\src\package.js:255:12)
  at PackageDetailView.module.exports.PackageDetailView.activate (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\settings-view\lib\package-detail-view.js:163:26)
  at PackageDetailView.module.exports.PackageDetailView.initialize (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\settings-view\lib\package-detail-view.js:146:12)
  at PackageDetailView.View (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\atom-space-pen-views\node_modules\space-pen\lib\space-pen.js:184:25)
  at new PackageDetailView (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\settings-view\lib\package-detail-view.js:38:54)
  at C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\settings-view\lib\settings-view.js:255:22
  at SettingsView.module.exports.SettingsView.getOrCreatePanel (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\settings-view\lib\settings-view.js:260:19)
  at SettingsView.module.exports.SettingsView.showPanel (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\settings-view\lib\settings-view.js:296:24)
  at space-pen-div.<anonymous> (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\settings-view\lib\package-card.js:214:26)
  at space-pen-div.jQuery.event.dispatch (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\jquery\dist\jquery.js:4435:9)
  at space-pen-div.elemData.handle (C:\Users\Administrator\AppData\Local\atom\app-0.201.0\resources\app.asar\node_modules\jquery\dist\jquery.js:4121:28)

Commands

  2x -7:16.8.0 editor:newline (atom-text-editor.editor.is-focused)
  3x -7:02.6.0 core:backspace (atom-text-editor.editor.is-focused.autocomplete-active)
     -6:55.9.0 autocomplete-plus:confirm (atom-text-editor.editor.is-focused.autocomplete-active)
  6x -6:55.1.0 core:backspace (atom-text-editor.editor.is-focused)
     -6:43.5.0 autocomplete-plus:confirm (atom-text-editor.editor.is-focused.autocomplete-active)
 18x -5:15.8.0 core:backspace (atom-text-editor.editor.is-focused)
     -4:57.5.0 core:move-down (atom-text-editor.editor.is-focused.autocomplete-active)
     -4:51.1.0 core:move-up (atom-text-editor.editor.is-focused.autocomplete-active)
     -4:49.4.0 autocomplete-plus:confirm (atom-text-editor.editor.is-focused.autocomplete-active)
     -2:20.2.0 core:backspace (atom-text-editor.editor.is-focused)
  4x -2:19.6.0 core:move-right (atom-text-editor.editor.is-focused)
  3x -2:14.3.0 core:backspace (atom-text-editor.editor.is-focused)
 21x -2:09.7.0 core:select-up (atom-text-editor.editor.is-focused)
     -1:47.2.0 atom-beautify:beautify-editor (atom-text-editor.editor.is-focused)

Config

{
  "core": {
    "themes": [
      "one-dark-ui",
      "chester-atom-syntax"
    ],
    "disabledPackages": [
      "autocomplete-python"
    ]
  },
  "Hydrogen": {}
}

Installed Packages

# User
atom-beautify, v0.27.6
autocomplete-plus-python-jedi, v0.3.5
chester-atom-syntax, v0.1.1
language-r, v0.2.0
script, v2.23.0
web-browser, v1.4.4

# Dev
No dev packages

At present, stdout and execution results both look the same.

It would be nice to tint the background differently for stdout, errors, and returns.

fix-path may be able to make the path work when Atom is launched as an app. It won't fix problems with node-gyp during installation or update, though.

Hello, I am not able to figure out where I can see the output of the code that I execute, f.ex. this JS snippet:

console.log("Hello, Jupyter!");

Where can I see the Hello, Jupyter! output? Or is it impossible?

Thank you!

It's useful to have separate kernels in different files/projects if they are not related. It seems it's only possible to use one shared kernel of the same type currently.

Maybe give each running kernel a unique identifier (hash, PID, ...), this makes them distinguishable and would also give the user the opportunity to switch between them (if necessary).

I'd like to use this feature to run/debug several micro services for example, once #25 is implemented.

It would be great if we could set the working directory to be the file directory when a kernel is started.

We already do this if Python is started without a kernelspec, but we need to do this regardless. Otherwise we get ANSI color codes as in #42.

Anyone manage to get the ijavascript kernel working?
When I try to run JavaScript code in hydrogen is just hangs there waiting for results.

I'm getting no auto complete of dataframes/lists on the R kernel (using the $ symbol for referencing). Not sure if this hasn't been implemented yet or if I've borked something up.

steps to reproduce:

1. open a python file from the command line, e.g. atom foo.py
2. add # -*- coding: utf-8 -*- to the beginning of the file
3. move the cursor to the beginning of the file
4. choose hydrogen: run from the command palette or press ⌘-⌥-↩

Atom Version: 0.201.0
System: Mac OS X 10.10.4
Thrown From: Hydrogen package, v0.3.10

Stack Trace

Uncaught TypeError: Cannot read property '0' of null

At /Users/tscholak/.atom/packages/Hydrogen/lib/main.coffee:159

TypeError: Cannot read property '0' of null
    at /Users/tscholak/.atom/packages/Hydrogen/lib/main.coffee:186:54
    at /Users/tscholak/.atom/packages/Hydrogen/lib/main.coffee:231:56
    at /Users/tscholak/.atom/packages/Hydrogen/lib/config-manager.coffee:34:18
    at Object.module.exports.portfinder.findManyHelper (/Users/tscholak/.atom/packages/Hydrogen/lib/find-port.coffee:29:16)
    at /Users/tscholak/.atom/packages/Hydrogen/lib/find-port.coffee:36:26
    at Server.<anonymous> (/Users/tscholak/.atom/packages/Hydrogen/lib/find-port.coffee:19:20)
    at Server.g (events.js:257:16)
    at emitNone (events.js:67:13)
    at Server.emit (events.js:163:7)
    at net.js:1443:10

Commands

     -0:03.8.0 command-palette:toggle (atom-text-editor.editor.is-focused)
     -0:00.8.0 core:confirm (atom-text-editor.editor.mini.is-focused)
     -0:00.7.0 hydrogen:run (atom-text-editor.editor)

Config

{}

Installed Packages

# User
Hydrogen, v0.3.10

# Dev
No dev packages