Jrun python port



This is a notice that I am currently porting @ctrueden’s brilliant jrun to Python.
This means it

  • runs on Windows, and
  • can be distributed via conda very easily.

To get it, just run

conda install -c hanslovsky jrun

I recommend you use your system java and maven (these are currently not dependencies of the conda package) but they should be available through conda-forge if you need those:

conda install -c conda-forge openjdk maven

Any JavaFX application will not run with the conda-forge openjdk as it does not ship with JavaFX and, to the best of my knowledge, there is no JavaFX package on conda.


As an example use case, demonstrating @bogovicj’s BigWarp:

conda install -c hanslovsky jrun
$ jrun \
 -r imagej.public=https://maven.imagej.net/content/groups/public \
 sc.fiji:bigwarp_fiji:3.1.2-SNAPSHOT:@BigWarp \
 http://fiji.sc/site/logo.png \

The SNAPSHOT version is only required for a bug fix (if you omit the version, latest release is used).


Distributing your Java code through conda is super easy now, too. Just c&p and modify my Paintera conda recipe:

├── meta.yaml
└── paintera
    ├── paintera.py
    └── setup.py

paintera.py is as few lines as this:

import jrun.jrun
import os
import psutil
import sys

repositories = {
    'saalfeldlab'   : 'https://saalfeldlab.github.io/maven',
    'imagej.public' : 'https://maven.imagej.net/content/groups/public'

def add_jvm_args_as_necessary(argv):
    gc_option = '-XX:+UseConcMarkSweepGC'

    if not gc_option in argv:
        argv += [gc_option]

    for arg in argv:
        if '-Xmx' in arg:
            return argv

    total_memory  = psutil.virtual_memory().total
    exponent      = 3 if total_memory > 2*1024**3 else 2
    memory_unit   = 'G' if exponent == 3 else 'M'
    max_heap_size = os.getenv(
        '{}{}'.format(max(total_memory // (1024**exponent) // 2, 1), memory_unit))

    argv = ['-Xmx{}'.format(max_heap_size)] + argv

    return argv

def jrun_paintera():
    argv               = sys.argv[1:]
    double_dash_index  = [i for (i, arg) in enumerate(argv) if arg == '--'][0] if '--' in argv else -1
    jrun_and_jvm_argv  = [] if double_dash_index < 0 else argv[:double_dash_index]
    repository_strings = ['-r'] + ['{}={}'.format(k, v) for (k, v) in repositories.items()]
    endpoint           = ['org.janelia.saalfeldlab:paintera:0.1.1+{}'.format(os.getenv('PAINTERA_SLF4J_BINDING', 'org.slf4j:slf4j-simple'))]
    paintera_argv      = argv if double_dash_index < 0 else argv[double_dash_index+1:]
    argv               = add_jvm_args_as_necessary(jrun_and_jvm_argv) + repository_strings + endpoint + paintera_argv