Best way to run Julia code in an IPython notebook (or Python code in an IJulia notebook)
Question:
My goal is to run only a few lines of Julia in an IPython notebook where the majority of the code will be Python for some experiments …
I found a nice example notebook here:
http://nbviewer.ipython.org/github/JuliaLang/IJulia.jl/blob/master/python/doc/JuliaMagic.ipynb
And now I am wondering how I would install the IPython extension for Julia (I am primarily using IPython 2.1) so that I can load it via
%load_ext julia.magic
I am also very new to julia and I am wondering if there is a performance benefit of “mixing numpy and julia” as shown in this notebook (over regular Python numpy or regular Julia code)
When I understand the concept correctly, I would use IJulia notebooks (which I set up successfully) if I am only interested in running Julia code?
I installed IJulia, and i can also run IJulia notebooks, but I actually only wanted to have a small portion of Julia code in my notebook, the rest should be Python / Cython.
Unfortunately, I read that magic functions are not yet fully supported: “One difference from IPython is that the IJulia kernel currently does not support “magics”, which are special commands prefixed with % or %% to execute code in a different language”
Is there a way to run Python code in IJulia notebooks?
Answers:
Run Julia inside an IPython notebook
Hack
In order to run Julia snippets (or other language) inside an IPython notebook, I just append the string 'julia' to the default list in the _script_magics_default method from the ScriptMagics class in:
/usr/lib/python3.4/site-packages/IPython/core/magics/script.py or/usr/lib/python2.7/site-packages/IPython/core/magics/script.py.
Example:
# like this:
defaults = [
'sh',
'bash',
'perl',
'ruby',
'python',
'python2',
'python3',
'pypy',
'julia', # add your own magic
]
- Example notebook (using Python3)
Julia Magic (Bi-directional)
To use %load_ext julia.magic, you would need to run the setup.py here:
Update (09/04/2014): the setup.py file has been moved to pyjulia.jl:
Which you get when Pkg.add("IJulia") clones the repo in your filesystem:
cd ~/.julia/v0.3/IJulia/python/
sudo python2 setup.py install
Currently this only works for me in Python2. Python3 complains about:
ImportError: No module named 'core'
when I try to load the extention, but installs without complains.
After installing it you can also do this from inside Python2:
from julia import Julia
j = Julia()
arr = j.run('[1:10]')
type(arr) # numpy.ndarray
Runing a script from your system shell
Use the shell mode syntax in a notebook cell:
!julia my_script.jl
Run Python inside IJulia notebook
Using PyCall
It’s not really running python code in the context you want, but you can also use Python libraries from within Julia:
using PyCall
@pyimport math
println(math.pi)
Runing a script from your system shell
Use the shell mode syntax in a notebook cell:
;python my_script.py
Another option is to use Beaker. They have a tutorial notebook available that mixes R and Python; using Julia is just as easy.
If you want to run a whole notebook of only julia (or where you call other languages only from julia), then there is a cleaner solution. First, launch julia and do
Pkg.add("IJulia")
to get the IJulia package. Then you can
ipython notebook --profile julia
and your notebook will have julia as the native (default) language.
h/t to David Sanders and his excellent julia tutorials that are written in IPython notebooks; video here.
To complete this good answer, Without any hack, and without modifying any system file, a simple solution is with the %%script magic:
In [1]: %%script julia
...: println("Hi from a Julia sub-process")
...: a = [1:10]
Be cautious that the cell was run in a sub-process, so whatever was done in it is not accessible by the rest of the IPython session:
In [2]: print("Hi from the main IPython process")
...: print(a) # <-- not available from the Julia code, will fail !
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-2-c5a4f3535135> in <module>()
----> 1 print(a)
NameError: name 'a' is not defined
A clean and nice method is described in this notebook: https://github.com/binder-examples/julia-python/blob/master/python-and-julia.ipynb.
It strongly uses IPython magic (%julia <julia code> inlined in Python, and %%julia cells), but the result is quite impressive: the two Python and Julia processes can use the same variables and memory.
My goal is to run only a few lines of Julia in an IPython notebook where the majority of the code will be Python for some experiments …
I found a nice example notebook here:
http://nbviewer.ipython.org/github/JuliaLang/IJulia.jl/blob/master/python/doc/JuliaMagic.ipynb
And now I am wondering how I would install the IPython extension for Julia (I am primarily using IPython 2.1) so that I can load it via
%load_ext julia.magic
I am also very new to julia and I am wondering if there is a performance benefit of “mixing numpy and julia” as shown in this notebook (over regular Python numpy or regular Julia code)
When I understand the concept correctly, I would use IJulia notebooks (which I set up successfully) if I am only interested in running Julia code?
I installed IJulia, and i can also run IJulia notebooks, but I actually only wanted to have a small portion of Julia code in my notebook, the rest should be Python / Cython.
Unfortunately, I read that magic functions are not yet fully supported: “One difference from IPython is that the IJulia kernel currently does not support “magics”, which are special commands prefixed with % or %% to execute code in a different language”
Is there a way to run Python code in IJulia notebooks?
Run Julia inside an IPython notebook
Hack
In order to run Julia snippets (or other language) inside an IPython notebook, I just append the string 'julia' to the default list in the _script_magics_default method from the ScriptMagics class in:
/usr/lib/python3.4/site-packages/IPython/core/magics/script.pyor/usr/lib/python2.7/site-packages/IPython/core/magics/script.py.
Example:
# like this:
defaults = [
'sh',
'bash',
'perl',
'ruby',
'python',
'python2',
'python3',
'pypy',
'julia', # add your own magic
]
- Example notebook (using Python3)
Julia Magic (Bi-directional)
To use %load_ext julia.magic, you would need to run the setup.py here:
Update (09/04/2014): the setup.py file has been moved to pyjulia.jl:
Which you get when Pkg.add("IJulia") clones the repo in your filesystem:
cd ~/.julia/v0.3/IJulia/python/
sudo python2 setup.py install
Currently this only works for me in Python2. Python3 complains about:
ImportError: No module named 'core'
when I try to load the extention, but installs without complains.
After installing it you can also do this from inside Python2:
from julia import Julia
j = Julia()
arr = j.run('[1:10]')
type(arr) # numpy.ndarray
Runing a script from your system shell
Use the shell mode syntax in a notebook cell:
!julia my_script.jl
Run Python inside IJulia notebook
Using PyCall
It’s not really running python code in the context you want, but you can also use Python libraries from within Julia:
using PyCall
@pyimport math
println(math.pi)
Runing a script from your system shell
Use the shell mode syntax in a notebook cell:
;python my_script.py
Another option is to use Beaker. They have a tutorial notebook available that mixes R and Python; using Julia is just as easy.
If you want to run a whole notebook of only julia (or where you call other languages only from julia), then there is a cleaner solution. First, launch julia and do
Pkg.add("IJulia")
to get the IJulia package. Then you can
ipython notebook --profile julia
and your notebook will have julia as the native (default) language.
h/t to David Sanders and his excellent julia tutorials that are written in IPython notebooks; video here.
To complete this good answer, Without any hack, and without modifying any system file, a simple solution is with the %%script magic:
In [1]: %%script julia
...: println("Hi from a Julia sub-process")
...: a = [1:10]
Be cautious that the cell was run in a sub-process, so whatever was done in it is not accessible by the rest of the IPython session:
In [2]: print("Hi from the main IPython process")
...: print(a) # <-- not available from the Julia code, will fail !
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-2-c5a4f3535135> in <module>()
----> 1 print(a)
NameError: name 'a' is not defined
A clean and nice method is described in this notebook: https://github.com/binder-examples/julia-python/blob/master/python-and-julia.ipynb.
It strongly uses IPython magic (%julia <julia code> inlined in Python, and %%julia cells), but the result is quite impressive: the two Python and Julia processes can use the same variables and memory.