Use Jrun to manage (maven) Java dependencies

[hanslovsky]

Example:

import scyjava_config
import time

scyjava_config.add_endpoints('net.imagej:imagej')
scyjava_config.set_verbose(2)

from scyjava import jnius

ImageJ = jnius.autoclass('net.imagej.ImageJ')
ij = ImageJ()
ij.ui().showUI()

while True:
    time.sleep(0.5)

Fixes #3

[ctrueden]

Super cool!

A couple of questions:

1. I see that a substantial part of scyjava_config is a wrapper around jnius_config. Is it a goal to encapsulate the jnius dependency? If so, should we also wrap autoclass? As it stands, the jnius dependency still leaks.

2. Is this naming foo_config for module foo a standard thing with Python? It seems weird to me as a newcomer; I haven't seen it in core Python modules. What about nested modules like scyjava.config? Which one is better style-wise?

3. How do you see the type conversion logic I wrote fitting in? Do you have a preferred way of doing naming that would be Pythonic? Let me know and I'll start migrating the code.

[hanslovsky]

1. The goal is not to encapsulate the jnius dependency. For config purposes, I wanted to avoid having to import both scyjava_config and jnius_config so users can call scyjava_config.add_endpoint and scyjava_config.add_classpath instead of jnius_config.add_classpath.
2. It is not standard but necessary to avoid import scyjava before import scyjava_config, see for example this post on stackoverflow.
3. Not entirely sure as both imagej and imglyb are supposed to be downstream dependencies. Shouldn't they live in their own repositories?

[hanslovsky]

As for pythonic styles: I am not python expert, but I think if we follow PEP (lower case method names, underscores for readibility; camel case class names), we should be fine. I would probably not add j in front of Java class names and just use their unqualified name, e.g.

RandomAccessibleInterval = jnius.autoclass('net.imglib2.RandomAccessibleInterval')

[ctrueden]

@hanslovsky Thanks for the clarifications.

Shouldn't they live in their own repositories?

There are two layers of conversion logic: 1) stuff for converting between core Python and Java types, particularly collections; and 2) stuff for converting image data types. I kept them separated; the imagej/convert.py class on the smart-convert branch of imagej/imagej.py currently has the base conversion layer that I think belongs in scyjava.

Would you be willing to take a quick look and let me know where in scyjava you think makes sense for the functions currently in convert.py? Which .py file, with which function names? I really have no clue about Python naming, since I do not understand how Python modules are normally structured—when I look at https://github.com/imglib/imglyb/tree/master/imglyb I get confused, since I don't understand how those files line up with the import statements in calling code. I'm also happy to RTFM if there is one you recommend.

I would probably not add j in front of Java class names and just use their unqualified name

I agree. The reason I put the j is because collections has some classes with the same names as the Java ones, so there is a name clash. To avoid that, we can stick with import collections and then just reference the classes fully qualified like collections.Iterable etc.

Regarding this PR: all looks awesome; please merge whenever you want, or ping me if you would rather me do it.

[hanslovsky]

I am not a python expert either and usually I just follow my gut feeling for project structure. I also do not think that this matters too much for a small project like this. That being said, this is how I would proceed:

• Add convert.py with a few modifications:
  • convert seems like a good name to me, no objections here
  • Indicate methods that are meant to be private with leading underscore. There is no private in python but convention is that leading underscore means something like internal use. I assume everything but to_java and to_python can be considered private, no?
  • JavaNumber should be a method java_number rather than a class.
  • name all class object variables with their unqualified java name, prepend underscore if private
• Add line to __init__.py (has to come after the call to _init_jvm()): from .convert import to_java, to_python.

Further reading:
https://docs.python-guide.org/writing/structure/
https://python-packaging.readthedocs.io/en/latest/minimal.html

[ctrueden]

Thanks for the suggestions, @hanslovsky. I think I got it all complete and committed with 3bc7746 and c112aef!