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Julia/Python bridge with IPython support.

Project description

PyJulia

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Experimenting with developing a better interface to Julia language that works with Python 2 & 3 and Julia v0.6+.

PyJulia is tested against Python versions 2.7, 3.5, 3.6, and 3.7.

Installation

Note: If you are using Python installed with Ubuntu or conda, PyJulia may not work with Julia ≥ 0.7. For workarounds, see Troubleshooting below. Same caution applies to any Debian-based and possibly other GNU/Linux distributions.

You will need to install PyCall in your existing Julia installation

julia> using Pkg  # for julia ≥ 0.7
julia> Pkg.add("PyCall")

Your python installation must be able to call command line program julia. If your installer does not add the Julia binary directory to your PATH, you will have to add it. An alias will not work.

Then finally you have to install PyJulia.

Note: If you are not familiar with pip and have some troubles with the following installation steps, we recommend going through the Tutorials in Python Packaging User Guide.

To get released versions you can use:

$ python3 -m pip install --user julia
$ python2 -m pip install --user julia  # If you need Python 2

where --user should be omitted if you are using virtual environment (virtualenv, venv, conda, etc.).

If you are interested in using the development version, you can install PyJulia directly from GitHub:

$ python3 -m pip install --user 'https://github.com/JuliaPy/pyjulia/archive/master.zip#egg=julia'

You may clone it directly to (say) your home directory.

$ git clone https://github.com/JuliaPy/pyjulia

then inside the pyjulia directory you need to run the python setup file

$ cd pyjulia
$ python3 -m pip install --user .
$ python3 -m pip install --user -e .  # If you want "development install"

The -e flag makes a development install, meaning that any change to PyJulia source tree will take effect at next python interpreter restart without having to reissue an install command.

See Testing below for how to run tests.

Usage

PyJulia provides a high-level interface which assumes a "normal" setup (e.g., julia program is in your PATH) and a low-level interface which can be used in a customized setup.

High-level interface

To call a Julia function in a Julia module, import the Julia module (say Base) with:

>>> from julia import Base

and then call Julia functions in Base from python, e.g.,

>>> Base.sind(90)

Other variants of Python import syntax also work:

>>> import julia.Base
>>> from julia.Base import Enums    # import a submodule
>>> from julia.Base import sin      # import a function from a module

The global namespace of Julia's interpreter can be accessed via a special module julia.Main:

>>> from julia import Main

You can set names in this module to send Python values to Julia:

>>> Main.xs = [1, 2, 3]

which allows it to be accessed directly from Julia code, e.g., it can be evaluated at Julia side using Julia syntax:

>>> Main.eval("sin.(xs)")

Low-level interface

If you need a custom setup for PyJulia, it must be done before importing any Julia modules. For example, to use the Julia executable named custom_julia, run:

>>> from julia import Julia
>>> jl = julia.Julia(runtime="custom_julia")

You can then use, e.g.,

>>> from julia import Base

IPython magic

In IPython (and therefore in Jupyter), you can directly execute Julia code using %%julia magic:

In [1]: %load_ext julia.magic
Initializing Julia interpreter. This may take some time...

In [2]: %%julia
   ...: Base.banner(IOContext(stdout, :color=>true))
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.0.1 (2018-09-29)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

Virtual environments

PyJulia can be used in Python virtual environments created by virtualenv, venv, and any tools wrapping them such as pipenv, provided that Python executable used in such environments are linked to identical libpython used by PyCall. If this is not the case, initializing PyJulia (e.g., import julia.Main) prints an informative error message with detected paths to libpython. See PyCall documentation for how to configure Python executable.

Note that Python environment created by conda is not supported.

Troubleshooting

Your Python interpreter is statically linked to libpython

If you use Python installed with Debian-based Linux distribution such as Ubuntu or install Python by conda, you might have noticed that PyJulia cannot be initialized properly with Julia ≥ 0.7. This is because those Python executables are statically linked to libpython. (See Limitations below for why that's a problem.)

If you are unsure if your python has this problem, you can quickly check it by:

$ ldd /usr/bin/python
        linux-vdso.so.1 (0x00007ffd73f7c000)
        libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007f10ef84e000)
        libc.so.6 => /usr/lib/libc.so.6 (0x00007f10ef68a000)
        libpython3.7m.so.1.0 => /usr/lib/libpython3.7m.so.1.0 (0x00007f10ef116000)
        /lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2 (0x00007f10efaa4000)
        libdl.so.2 => /usr/lib/libdl.so.2 (0x00007f10ef111000)
        libutil.so.1 => /usr/lib/libutil.so.1 (0x00007f10ef10c000)
        libm.so.6 => /usr/lib/libm.so.6 (0x00007f10eef87000)

in Linux where /usr/bin/python should be replaced with the path to your python command (use which python to find it out). In macOS, use otool -L instead of ldd. If it does not print the path to libpython like /usr/lib/libpython3.7m.so.1.0 in above example, you need to use one of the workaround below.

The easiest workaround is to use the python-jl command bundled in PyJulia. This can be used instead of normal python command for basic use-cases such as:

$ python-jl your_script.py
$ python-jl -c 'from julia.Base import banner; banner()'
$ python-jl -m IPython

See python-jl --help for more information.

Note that python-jl works by launching Python interpreter inside Julia. Importantly, it means that PyJulia has to be installed in the Python environment with which PyCall is configured. That is to say, following commands must work for python-jl to be usable:

julia> using PyCall

julia> pyimport("julia")
PyObject <module 'julia' from '/.../julia/__init__.py'>

In fact, you can simply use PyJulia inside the Julia REPL, if you are comfortable with working in it:

julia> using PyCall

julia> py"""
       from julia import Julia
       Julia(init_julia=False)

       from your_module_using_pyjulia import function
       function()
       """

Alternatively, you can use pyenv to build Python with --enable-shared option. Of course, manually building from Python source distribution with the same configuration also works.

$ PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.6.6
Downloading Python-3.6.6.tar.xz...
-> https://www.python.org/ftp/python/3.6.6/Python-3.6.6.tar.xz
Installing Python-3.6.6...
Installed Python-3.6.6 to /home/USER/.pyenv/versions/3.6.6

$ ldd ~/.pyenv/versions/3.6.6/bin/python3.6 | grep libpython
        libpython3.6m.so.1.0 => /home/USER/.pyenv/versions/3.6.6/lib/libpython3.6m.so.1.0 (0x00007fca44c8b000)

For more discussion, see: https://github.com/JuliaPy/pyjulia/issues/185

Segmentation fault in IPython

You may experience segmentation fault when using PyJulia in old versions of IPython. You can avoid this issue by updating IPython to 7.0 or above. Alternatively, you can use IPython via Jupyter (e.g., jupyter console) to workaround the problem.

How it works

PyJulia loads the libjulia library and executes the statements therein. To convert the variables, the PyCall package is used. Python references to Julia objects are reference counted by Python, and retained in the PyCall.pycall_gc mapping on the Julia side (the mapping is removed when reference count drops to zero, so that the Julia object may be freed).

Limitations

Mismatch in valid set of identifiers

Not all valid Julia identifiers are valid Python identifiers. Unicode identifiers are invalid in Python 2.7 and so PyJulia cannot call or access Julia methods/variables with names that are not ASCII only. Although Python 3 allows Unicode identifiers, they are more aggressively normalized than Julia. For example, ϵ (GREEK LUNATE EPSILON SYMBOL) and ε (GREEK SMALL LETTER EPSILON) are identical in Python 3 but different in Julia. Additionally, it is a common idiom in Julia to append a ! character to methods which mutate their arguments. These method names are invalid Python identifers. PyJulia renames these methods by subsituting ! with _b. For example, the Julia method sum! can be called in PyJulia using sum_b(...).

Pre-compilation mechanism in Julia 1.0

There was a major overhaul in the module loading system between Julia 0.6 and 1.0. As a result, the "hack" supporting the PyJulia to load PyCall stopped working. For the implementation detail of the hack, see: https://github.com/JuliaPy/pyjulia/tree/master/julia/fake-julia

For the update on this problem, see: https://github.com/JuliaLang/julia/issues/28518

Ctrl-C does not work / terminates the whole Python process

Currently, initializing PyJulia (e.g., by from julia import Main) disables KeyboardInterrupt handling in the Python process. If you are using normal python interpreter, it means that canceling the input by Ctrl-C does not work and repeatedly providing Ctrl-C terminates the whole Python process with the error message WARNING: Force throwing a SIGINT. Using IPython 7.0 or above is recommended to avoid such accidental shutdown.

It also means that there is no safe way to cancel long-running computations or I/O at the moment. Sending SIGINT with Ctrl-C will terminate the whole Python process.

For the update on this problem, see: https://github.com/JuliaPy/pyjulia/issues/211

No threading support

PyJulia cannot be used in different threads since libjulia is not thread safe. However, you can use multiple threads within Julia. For example, start IPython by JULIA_NUM_THREADS=4 ipython and then run:

In [1]: %load_ext julia.magic
Initializing Julia interpreter. This may take some time...

In [2]: %%julia
   ...: a = zeros(10)
   ...: Threads.@threads for i = 1:10
   ...:     a[i] = Threads.threadid()
   ...: end
   ...: a
Out[3]: array([1., 1., 1., 2., 2., 2., 3., 3., 4., 4.])

PyJulia does not release GIL

PyJulia does not release the Global Interpreter Lock (GIL) while calling Julia functions since PyCall expects the GIL to be acquired always. It means that Python code and Julia code cannot run in parallel.

Testing

PyJulia can be tested by simply running tox:

$ tox

The full syntax for invoking tox is

[PYJULIA_TEST_REBUILD=yes] [JULIA_EXE=<julia>] tox [options] [-- pytest options]
  • PYJULIA_TEST_REBUILD: Be careful using this environment variable! When it is set to yes, your PyCall.jl installation will be rebuilt using the Python interpreter used for testing. The test suite tries to build back to the original configuration but the precompilation would be in the stale state after the test. Note also that it does not work if you unconditionally set PYTHON environment variable in your Julia startup file.

  • JULIA_EXE: julia executable to be used for testing.

  • Positional arguments after -- are passed to pytest.

For example,

$ PYJULIA_TEST_REBUILD=yes JULIA_EXE=~/julia/julia tox -e py37 -- -s

means to execute tests with

  • PyJulia in shared-cache mode
  • julia executable at ~/julia/julia
  • Python 3.7
  • pytest's capturing mode turned off

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