fix(ci): cherry-pick fixes from development

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
       fail-fast: false
 
     steps:

pyneuroml/neuron/analysis/HHanalyse.py

@@ -4,17 +4,18 @@
 Implementation of the pynml-modchananalysis command
 """
 
-import typing
 import argparse
 import logging
 import re
 import subprocess
 import sys
 from math import log
+from typing import Optional
 
 import matplotlib.pyplot as pylab
 import neuron
 from pylab import *
+
 from pyneuroml.utils import get_state_color
 from pyneuroml.utils.cli import build_namespace
 
@@ -137,7 +138,7 @@ def remove_comments(txt):
     return clear_txt
 
 
-def get_states(txt: str) -> typing.List[str]:
+def get_states(txt: str) -> list[str]:
     """Get list of states from mod file text.
 
     :param txt: mod file text
@@ -157,7 +158,7 @@ def get_states(txt: str) -> typing.List[str]:
     return state_list
 
 
-def get_suffix(txt: str) -> typing.Optional[str]:
+def get_suffix(txt: str) -> Optional[str]:
     """Get suffix mod file text
 
     :param txt: mod file text

pyneuroml/utils/misc.py

@@ -7,7 +7,6 @@
 Copyright 2024 NeuroML contributors
 """
 
-
 import os
 
 from pyneuroml import JNEUROML_VERSION
@@ -25,3 +24,23 @@ def get_path_to_jnml_jar() -> str:
         "jNeuroML-%s-jar-with-dependencies.jar" % JNEUROML_VERSION,
     )
     return jar_path
+
+
+try:
+    from contextlib import chdir  # Python 3.11+
+except ImportError:
+    from contextlib import contextmanager
+
+    @contextmanager
+    def chdir(path):
+        """chdir context manager for python < 3.11
+
+        :param path: path to change to
+        :type path: str or os.PathLike
+        """
+        prev_cwd = os.getcwd()
+        os.chdir(path)
+        try:
+            yield
+        finally:
+            os.chdir(prev_cwd)

setup.cfg

@@ -32,7 +32,7 @@ install_requires =
     graphviz
     typing; python_version<"3.5"
     lxml
-    numpy<2.0.0
+    numpy
     sympy
     ppft[dill]
 

tests/neuron/test_neuron_utils.py

@@ -7,34 +7,31 @@
 Copyright 2023 NeuroML contributors
 """
 
-
-import unittest
 import logging
-import tempfile
-import pytest
 import pathlib
+import tempfile
+import unittest
 
+import pytest
 
 from pyneuroml.neuron import (
-    load_hoc_or_python_file,
-    morphinfo,
+    export_mod_to_neuroml2,
     get_utils_hoc,
     getinfo,
-    export_mod_to_neuroml2,
+    load_hoc_or_python_file,
+    morphinfo,
 )
 
 from . import load_olm_cell
 
-
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.DEBUG)
 
 
 class TestNeuronUtils(unittest.TestCase):
-
     """Test Neuron Utils"""
 
-    def test_hoc_loader(self):
+    def test_hoc_loader1(self):
         """Test hoc loader util function"""
         with tempfile.NamedTemporaryFile(mode="w", suffix=".hoc") as f:
             print(
@@ -47,6 +44,7 @@ def test_hoc_loader(self):
 
             self.assertTrue(load_hoc_or_python_file(f.name))
 
+    def test_hoc_loader2(self):
         with tempfile.NamedTemporaryFile(mode="w", suffix=".hoc") as f:
             print(
                 """
@@ -56,8 +54,10 @@ def test_hoc_loader(self):
                 flush=True,
             )
 
-            self.assertFalse(load_hoc_or_python_file(f.name))
+            with self.assertRaises(RuntimeError):
+                load_hoc_or_python_file(f.name)
 
+    def test_hoc_loader3(self):
         # loading python files is not yet implemented
         with tempfile.NamedTemporaryFile(mode="w", suffix=".py") as f:
             print(