Merge pull request #392 from NeuroML/experimental

Use jnml jar 0.13.1; fixes to allow for cells with external morphology/biophysicalProperties

Author: pgleeson

.gitignore

@@ -177,3 +177,7 @@ arm64
 /examples/test_data/xppaut/wc_2.ode
 
 coverage.xml
+/examples/LEMS_NML2_Ex5_DetCell.sedml.omex
+/examples/hhcell.swc
+/examples/metadata.rdf
+/tests/utils/test_translation.net.nml

examples/LeakConductance.mod

@@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=LeakConductance type=ionChannelHH)
 COMMENT
 
     This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
-         org.neuroml.export  v1.10.0
-         org.neuroml.model   v1.10.0
-         jLEMS               v0.11.0
+         org.neuroml.export  v1.10.1
+         org.neuroml.model   v1.10.1
+         jLEMS               v0.11.1
 
 ENDCOMMENT
 

pyneuroml/__init__.py

@@ -12,7 +12,7 @@
     __version__ = importlib_metadata.version("pyNeuroML")
 
 
-JNEUROML_VERSION = "0.13.0"
+JNEUROML_VERSION = "0.13.1"
 
 # Define a logger for the package
 logging.basicConfig(

pyneuroml/io.py

@@ -34,6 +34,7 @@ def read_neuroml2_file(
     already_included: Optional[list] = None,
     optimized: bool = False,
     check_validity_pre_include: bool = False,
+    fix_external_morphs_biophys: bool = False,
 ) -> NeuroMLDocument:
     """Read a NeuroML2 file into a `nml.NeuroMLDocument`
 
@@ -49,6 +50,8 @@ def read_neuroml2_file(
     :type optimized: bool
     :param check_validity_pre_include: check each file for validity before including
     :type check_validity_pre_include: bool
+    :param fix_external_morphs_biophys: if a cell element has a morphology (or biophysicalProperties) attribute, as opposed to a subelement morphology/biophysicalProperties, substitute the external element into the cell element for ease of access
+    :type fix_external_morphs_biophys: bool
     :returns: nml.NeuroMLDocument object containing the read NeuroML file(s)
     """
     if already_included is None:
@@ -125,9 +128,14 @@ def read_neuroml2_file(
         for include in incl_to_remove:
             nml2_doc.includes.remove(include)
 
+        if fix_external_morphs_biophys:
+            from neuroml.utils import fix_external_morphs_biophys_in_cell
+            fix_external_morphs_biophys_in_cell(nml2_doc)
+
     return nml2_doc
 
 
+
 def write_neuroml2_file(
     nml2_doc: NeuroMLDocument,
     nml2_file_name: str,

pyneuroml/lib/jNeuroML-0.13.0-jar-with-dependencies.jar renamed to pyneuroml/lib/jNeuroML-0.13.1-jar-with-dependencies.jar

@@ -91,7 +91,7 @@ def summary(
 
     if nml2_doc is None:
         nml2_file_name = sys.argv[1]
-        nml2_doc = read_neuroml2_file(nml2_file_name, include_includes=verbose)
+        nml2_doc = read_neuroml2_file(nml2_file_name, include_includes=verbose, fix_external_morphs_biophys=True)
 
     info = nml2_doc.summary(show_includes=False)
 

pyneuroml/utils/info.py

@@ -1,6 +1,6 @@
 [metadata]
 name = pyNeuroML
-version = 1.2.15
+version = 1.3.0
 author = Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/NeuroML/pyNeuroML

setup.cfg

@@ -75,6 +75,8 @@ def test_rotate_cell(self):
         acell = neuroml.utils.component_factory("Cell", id="test_cell", validate=False)  # type: neuroml.Cell
 
         acell.set_spike_thresh("10mV")
+        acell.set_init_memb_potential("-70mV")
+        acell.set_specific_capacitance("1 uF_per_cm2")
 
         soma = acell.add_segment(
             prox=[0, 0, 0, 15],
@@ -159,6 +161,8 @@ def test_translate_cell_to_coords(self):
         """Test translate_cell_to_coords"""
         acell = neuroml.utils.component_factory("Cell", id="test_cell", validate=False)  # type: neuroml.Cell
         acell.set_spike_thresh("10mV")
+        acell.set_init_memb_potential("-70mV")
+        acell.set_specific_capacitance("1 uF_per_cm2")
         soma = acell.add_segment(
             prox=[10, 10, 10, 15],
             dist=[10, 10, 10, 15],