Merge pull request #434 from NeuroML/fix-pynml-archive

Fix pynml archive

Author: sanjayankur31

pyneuroml/archive/__init__.py

@@ -14,10 +14,10 @@
 import typing
 from zipfile import ZipFile
 
-from pyneuroml.utils import get_model_file_list
-from pyneuroml.utils.cli import build_namespace
 from pyneuroml.runners import run_jneuroml
 from pyneuroml.sedml import validate_sedml_files
+from pyneuroml.utils import get_model_file_list
+from pyneuroml.utils.cli import build_namespace
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -88,7 +88,7 @@ def cli(a: typing.Optional[typing.Any] = None, **kwargs: str):
     a = build_namespace(DEFAULTS, a, **kwargs)
 
     rootfile = a.rootfile
-    zipfile_extension = None
+    zipfile_extension = ".neux.zip"
 
     # first generate SED-ML file
     # use .omex as extension
@@ -99,7 +99,7 @@ def cli(a: typing.Optional[typing.Any] = None, **kwargs: str):
         run_jneuroml("", a.rootfile, "-sedml")
 
         rootfile = a.rootfile.replace(".xml", ".sedml")
-        zipfile_extension = ".omex"
+        zipfile_extension = ".omex.zip"
 
         # validate the generated file
         validate_sedml_files([rootfile])
@@ -119,7 +119,7 @@ def cli(a: typing.Optional[typing.Any] = None, **kwargs: str):
 def create_combine_archive(
     rootfile: str,
     zipfile_name: typing.Optional[str] = None,
-    zipfile_extension=".neux",
+    zipfile_extension=".neux.zip",
     filelist: typing.List[str] = [],
     extra_files: typing.List[str] = [],
 ):

tests/archive/test_archive.py

@@ -7,7 +7,6 @@
 Copyright 2023 NeuroML contributors
 """
 
-
 import logging
 import pathlib
 import unittest
@@ -109,7 +108,7 @@ def test_create_combine_archive(self):
             rootfile=dirname + "/HH_example_cell.nml",
             filelist=filelist,
         )
-        self.assertTrue(pathlib.Path(dirname + "/HH_example.neux").exists())
+        self.assertTrue(pathlib.Path(dirname + "/HH_example.neux.zip").exists())
 
         dirname = str(thispath.parent.parent.parent)
         filelist = []
@@ -119,7 +118,7 @@ def test_create_combine_archive(self):
             filelist=filelist,
         )
         self.assertTrue(
-            pathlib.Path(dirname + "/examples/LEMS_NML2_Ex5_DetCell.neux").exists()
+            pathlib.Path(dirname + "/examples/LEMS_NML2_Ex5_DetCell.neux.zip").exists()
         )
 
         dirname = str(thispath.parent.parent.parent)
@@ -130,5 +129,5 @@ def test_create_combine_archive(self):
             filelist=filelist,
         )
         self.assertTrue(
-            pathlib.Path(dirname + "/examples/NML2_SingleCompHHCell.neux").exists()
+            pathlib.Path(dirname + "/examples/NML2_SingleCompHHCell.neux.zip").exists()
         )