Merge pull request #450 from NeuroML/feat-provide-jnml-wrapper

Feat: provide `jnml` command that will use the bundled jar

Author: sanjayankur31

pyneuroml/runners.py

@@ -705,6 +705,7 @@ def run_jneuroml(
     report_jnml_output: bool = True,
     exit_on_fail: bool = False,
     return_string: bool = False,
+    output_prefix: str = " jNeuroML >>  ",
 ) -> typing.Union[typing.Tuple[bool, str], bool]:
     """Run jnml with provided arguments.
 
@@ -726,6 +727,8 @@ def run_jneuroml(
     :type exit_on_fail: bool
     :param return_string: toggle whether the output string should be returned
     :type return_string: bool
+    :param output_prefix: string to prefix the returned jNeuroML output with
+    :type output_prefix: str
 
     :returns: either a bool, or a Tuple (bool, str) depending on the value of
         return_string: True of jnml ran successfully, False if not; along with the
@@ -756,7 +759,7 @@ def run_jneuroml(
     try:
         command = f'java -Xmx{max_memory} {pre_jar} -jar  "{jar_path}" {pre_args} {target_file} {post_args}'
         retcode, output = execute_command_in_dir(
-            command, exec_in_dir, verbose=verbose, prefix=" jNeuroML >>  "
+            command, exec_in_dir, verbose=verbose, prefix=output_prefix
         )
 
         if retcode != 0:
@@ -919,7 +922,7 @@ def execute_command_in_dir_with_realtime_output(
         raise e
 
     if not p.returncode == 0:
-        logger.critical(
+        logger.error(
             "*** Problem running command (return code: %s): [%s]"
             % (p.returncode, command)
         )
@@ -990,14 +993,14 @@ def execute_command_in_dir(
         return return_string.decode("utf-8")
 
     except subprocess.CalledProcessError as e:
-        logger.critical("*** Problem running last command: %s" % e)
+        logger.error("*** Problem running last command: %s" % e)
 
         print("####################################################################")
         print("%s%s" % (prefix, e.output.decode().replace("\n", "\n" + prefix)))
         print("####################################################################")
         return (e.returncode, e.output.decode())
     except Exception as e:
-        logger.critical("*** Unknown problem running command: %s" % e)
+        logger.error("*** Unknown problem running command: %s" % e)
         return (-1, str(e))
 
 

pyneuroml/utils/jnmlwrapper.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+"""
+Simple wrapper around jNeuroML to allow users to use jnml using the version
+bundled in PyNeuroML
+
+File: pyneuroml/utils/jnmlwrapper.py
+
+Copyright 2025 NeuroML contributors
+Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
+"""
+
+import logging
+import os
+import sys
+
+from ..runners import run_jneuroml
+
+
+def __jnmlwrapper():
+    """Wrapper around jNeuroML jar shipped with PyNeuroML.
+
+    The following environment variables can be set:
+
+    - JNML_MAX_MEMORY_LOCAL: set the maximum memory available to the Java
+      Virtual Machine (default: 400M)
+
+    """
+    max_memory = os.getenv("JNML_MAX_MEMORY_LOCAL", "400M")
+    logging.getLogger("pyneuroml.runners").setLevel(logging.CRITICAL)
+
+    retstat, output = run_jneuroml(
+        pre_args=" ".join(sys.argv[1:]),
+        target_file="",
+        post_args="",
+        max_memory=max_memory,
+        report_jnml_output=False,
+        output_prefix="",
+        return_string=True,
+        exit_on_fail=False,
+    )
+
+    # if command ran successfully, print the output
+    # if it didn't, `run_jneuroml` will throw a critical error
+    if retstat is True:
+        print(output)
+        sys.exit(0)
+    else:
+        sys.exit(1)

setup.cfg

@@ -59,6 +59,7 @@ console_scripts =
     pynml-sonata          = neuromllite.SonataReader:main
     pynml-xpp             = pyneuroml.xppaut:main
     pynml-swc2nml         = pyneuroml.swc.ExportNML:main
+    jnml                  = pyneuroml.utils.jnmlwrapper:__jnmlwrapper
 
 [options.package_data]
 * =

test-ghactions.sh

@@ -28,7 +28,7 @@ echo "##   Testing all CLI tools"
 full_path=$(command -v pynml)
 bin_location=$(dirname $full_path)
 
-for f in ${bin_location}/pynml*
+for f in ${bin_location}/pynml* ${bin_location}/jnml
 do
     current_exec=$(basename $f)
     echo "-> Testing $current_exec runs"