fix(ci): cherry-pick fixes from development

[sanjayankur31]

Pick fixes from development to make CI pass on master

[sanjayankur31]

A new failure related to tellurium, that needs investigation:

##   Tellurium validation example
pyNeuroML >>> CRITICAL - run_from_sedml_file failed with: in method 'ASTNode_replaceArgument', argument 3 of type 'ASTNode *'
pyNeuroML >>> CRITICAL - Args supplied: Namespace(version=False, verbose='INFO', java_max_memory='400M', nogui=False, input_files=['test_data/valid_doc_sedml.sedml'], sedml=False, neuron=None, run_tellurium=['-outputdir', 'none'], netpyne=None, eden=None, svg=False, png=False, dlems=False, vertex=False, xpp=False, dnsim=False, brian=False, brian2=False, moose=False, sbml=False, sbml_sedml=False, matlab=False, cvode=False, nineml=False, spineml=False, sbml_import=None, sbml_import_units=None, vhdl=None, graph=None, lems_graph=False, matrix=None, validate=False, validatev1=False, validate_sbml=False, validate_sbml_units=False, validate_sedml=False, swc=False)

[sanjayankur31]

It's something from tellurium:

$ pynml test_data/valid_doc_sedml.sedml -run-tellurium -outputdir none
pyNeuroML >>> CRITICAL - in method 'ASTNode_replaceArgument', argument 3 of type 'ASTNode *'
Traceback (most recent call last):
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/pyneuroml/tellurium/__init__.py", line 80, in run_from_sedml_file
    te.executeSEDML(
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/tellurium/sedml/tesedml.py", line 360, in executeSEDML
    factory.executePython()
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/tellurium/sedml/tesedml.py", line 591, in executePython
    code = self.toPython()
           ^^^^^^^^^^^^^^^
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/tellurium/sedml/tesedml.py", line 578, in toPython
    pysedml = template.render(c)
              ^^^^^^^^^^^^^^^^^^
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/jinja2/environment.py", line 1295, in render
    self.environment.handle_exception()
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/jinja2/environment.py", line 942, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/tellurium/sedml/templates/tesedml_template.template", line 68, in top-level template code
    {{ dataGeneratorToPython(doc, dg) }}
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/tellurium/sedml/tesedml.py", line 1840, in dataGeneratorToPython
    value = evaluableMathML(mathml, variables=variables, array=True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/tellurium/sedml/mathml.py", line 127, in evaluableMathML
    astnode.replaceArgument(key, libsbml.parseFormula(str(value)))
  File "/home/asinha/.local/share/virtualenvs/pynml-312/lib64/python3.12/site-packages/libcombine/__init__.py", line 3830, in replaceArgument
    return _libcombine.ASTNode_replaceArgument(self, bvar, arg)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: in method 'ASTNode_replaceArgument', argument 3 of type 'ASTNode *'

Needs debugging---isn't happening on development, so, it's likely a combination of library versions that's causing this.

[sanjayankur31]

Filed: sys-bio/tellurium#608

@pgleeson : not sure what to do here, disable this test for the moment? weirdly, not happening on development (or not yet)

[pgleeson]

Maybe pin to an earlier version of tellurium (or mathml/combine)..? Has helped in the past.