Merge branch 'development' into experimental

pyneuroml/analysis/__init__.py

@@ -158,6 +158,8 @@ def generate_current_vs_frequency_curve(
     :param simulator: simulator to use
     :type simulator: str
     :param num_processors: number of processors to use for analysis
+        This option is only used with NetPyNE which can use MPI for
+        parallelising simulations. For other simulators, this is unused.
     :type num_processors: int
     :param include_included: include included files
     :type include_included: bool

pyneuroml/pynml.py

@@ -103,9 +103,16 @@ def generate_interactive_plot(*args, **kwargs):
             )
 
 
+# read from env variable if found
+try:
+    java_max_memory = os.environ["JNML_MAX_MEMORY_LOCAL"]
+except KeyError:
+    java_max_memory = "400M"
+
+
 DEFAULTS = {
     "v": False,
-    "default_java_max_memory": "400M",
+    "default_java_max_memory": java_max_memory,
     "nogui": False,
 }  # type: dict[str, typing.Any]
 
@@ -2497,7 +2504,9 @@ def run_jneuroml(
     :param target_file: LEMS or NeuroML file to run jnml on
     :type target_file: str
     :param max_memory: maximum memory allowed for use by the JVM
-    :type max_memory: bool
+        Note that the default value of this can be overridden using the
+        JNML_MAX_MEMORY_LOCAL environment variable
+    :type max_memory: str
     :param exec_in_dir: working directory to execute LEMS simulation in
     :type exec_in_dir: str
     :param verbose: toggle whether jnml should print verbose information

setup.cfg

@@ -60,6 +60,7 @@ console_scripts =
         *.md
         *.xsl
         *.hoc
+        TEMPLATE.channel.nml
 
 [options.extras_require]
 neuron =