Merge pull request #21 from scijava/better-imports

Better imports

Author: ctrueden

jgo/__init__.py

@@ -1 +1,2 @@
-from .jgo import resolve_dependencies
+from .jgo import resolve_dependencies, jgo_main as main
+from .util import main_from_endpoint, maven_scijava_repository, add_jvm_args_as_necessary

jgo/__main__.py

@@ -1,3 +1,3 @@
 import jgo
 if __name__ == '__main__':
-    jgo.jgo_main()
+    jgo.main()

jgo/util.py

@@ -0,0 +1,71 @@
+import psutil
+import sys
+
+from .jgo import jgo_main as main
+
+def add_jvm_args_as_necessary(argv, gc_option='-XX:+UseConcMarkSweepGC'):
+    """
+
+    Extend existing ``argv`` with reasonable default values for garbage collection and max heap size.
+    If ``-Xmx`` is not specified in ``argv``, set max heap size to half the system's memory.
+
+    :param argv: arugment vector
+    :param gc_option: Use this garbage collector settings, if any.
+    :return: ``argv`` with
+    """
+    if gc_option and 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 = '{}{}'.format(max(total_memory // (1024**exponent) // 2, 1), memory_unit)
+
+    argv = ['-Xmx{}'.format(max_heap_size)] + argv
+
+    return argv
+
+def maven_scijava_repository():
+    return 'https://maven.imagej.net/content/groups/public'
+
+
+def main_from_endpoint(
+        primary_endpoint,
+        argv=sys.argv[1:],
+        repositories={'imagej.public': maven_scijava_repository()},
+        primary_endpoint_version=None,
+        primary_endpoint_main_class=None,
+        secondary_endpoints=()):
+    """
+    Convenience method to populate appropriate argv for jgo. This is useful to distribute Java programs as Python modules.
+
+    For example, to run paintera with slf4j logging bindings, call
+    ``
+    main_from_endpoint(
+        'org.janelia.saalfeldlab:paintera',
+        primary_endpoint_version='0.8.1',
+        secondary_endpoints=('org.slf4j:slf4j-simple:1.7.25',),
+    )
+    ``
+
+    :param primary_endpoint: The primary endpoint of the Java program you want to run.
+    :param repositories: Any maven repository that holds the required jars. Defaults to {'imagej.public': maven_scijava_repository()}.
+    :param primary_endpoint_version: Will be appended to ``primary_endpoint`` if it does not evaluate to ``False``
+    :param primary_endpoint_main_class: Will be appended to ``primary_endpoitn`` if it does not evaluate to ``False``.
+    :param secondary_endpoints: Any other endpoints that should be added.
+    :return: ``None``
+    """
+    double_dash_index  = [i for (i, arg) in enumerate(argv) if arg == '--'][0] if '--' in argv else -1
+    jgo_and_jvm_argv   = ([] if double_dash_index < 0 else argv[:double_dash_index]) + ['--ignore-jgorc']
+    repository_strings = ['-r'] + ['{}={}'.format(k, v) for (k, v) in repositories.items()]
+    primary_endpoint   = primary_endpoint + ':{}'.format(primary_endpoint_version) if primary_endpoint_version else primary_endpoint
+    primary_endpoint   = primary_endpoint + ':{}'.format(primary_endpoint_main_class) if primary_endpoint_main_class else primary_endpoint
+    endpoint           = ['+'.join((primary_endpoint,) + secondary_endpoints)]
+    paintera_argv      = argv if double_dash_index < 0 else argv[double_dash_index+1:]
+    argv               = add_jvm_args_as_necessary(jgo_and_jvm_argv) + repository_strings + endpoint + paintera_argv
+
+    main(argv=argv)