Converting empty h.Vector object to ndarray results in TypeError and system exit w. Neuron 8.1

[espenhgn]

Context

Encountered some via some error in LFPy: LFPy/LFPy#414

Overview of the issue

In [1]: import numpy as np

In [2]: import neuron

In [3]: v = neuron.h.Vector()

In [4]: v.to_python()
Out[4]: []

In [5]: list(v)
Out[5]: []

In [6]: v.as_numpy()
Out[6]: array([], dtype=float64)

In [7]: np.array(v)
TypeError: float() argument must be a string or a real number, not 'hoc.HocObject'

Expected result/behavior

As far as I know both v.as_numpy() and np.array(v) should result in the same output, although the first syntax option may be preferable. IPython also shuts down (see below).

NEURON setup

• Version: 8.1.0 arm64 wheel from PyPI
• Installation method: pip
• OS + Version: macOS 11.6
• Compiler + Version: clang 12.0.1

% conda info

     active environment : lfpydev
    active env location : /Users/espenhagen/miniforge3/envs/lfpydev
            shell level : 1
       user config file : /Users/espenhagen/.condarc
 populated config files : /Users/espenhagen/miniforge3/.condarc
                          /Users/espenhagen/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.2.final.0
       virtual packages : __osx=11.6=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /Users/espenhagen/miniforge3  (writable)
      conda av data dir : /Users/espenhagen/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/espenhagen/miniforge3/pkgs
                          /Users/espenhagen/.conda/pkgs
       envs directories : /Users/espenhagen/miniforge3/envs
                          /Users/espenhagen/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.2 Darwin/20.6.0 OSX/11.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Logs

Full IPython trace:

In [7]: np.array(v)
TypeError: float() argument must be a string or a real number, not 'hoc.HocObject'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3361, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-7-ff0de560ad88>", line 1, in <cell line: 1>
    np.array(v)
ValueError: setting an array element with a sequence.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 1979, in showtraceback
    stb = value._render_traceback_()
AttributeError: 'ValueError' object has no attribute '_render_traceback_'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3301, in run_ast_nodes
    if await self.run_code(code, result, async_=asy):
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3378, in run_code
    self.showtraceback(running_compiled_code=True)
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 1981, in showtraceback
    stb = self.InteractiveTB.structured_traceback(etype,
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 1105, in structured_traceback
    return FormattedTB.structured_traceback(
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 999, in structured_traceback
    return VerboseTB.structured_traceback(
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 871, in structured_traceback
    formatted_exceptions += self.format_exception_as_a_whole(etype, evalue, etb, lines_of_context,
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 775, in format_exception_as_a_whole
    assert etb is not None
AssertionError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 1979, in showtraceback
    stb = value._render_traceback_()
AttributeError: 'AssertionError' object has no attribute '_render_traceback_'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 2900, in _run_cell
    return runner(coro)
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/async_helpers.py", line 129, in _pseudo_sync_runner
    coro.send(None)
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3098, in run_cell_async
    has_raised = await self.run_ast_nodes(code_ast.body, cell_name,
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3320, in run_ast_nodes
    self.showtraceback()
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 1981, in showtraceback
    stb = self.InteractiveTB.structured_traceback(etype,
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 1105, in structured_traceback
    return FormattedTB.structured_traceback(
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 999, in structured_traceback
    return VerboseTB.structured_traceback(
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 871, in structured_traceback
    formatted_exceptions += self.format_exception_as_a_whole(etype, evalue, etb, lines_of_context,
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 775, in format_exception_as_a_whole
    assert etb is not None
AssertionError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 1979, in showtraceback
    stb = value._render_traceback_()
AttributeError: 'AssertionError' object has no attribute '_render_traceback_'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/espenhagen/miniforge3/envs/lfpydev/bin/ipython", line 11, in <module>
    sys.exit(start_ipython())
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/__init__.py", line 123, in start_ipython
    return launch_new_instance(argv=argv, **kwargs)
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/traitlets/config/application.py", line 846, in launch_instance
    app.start()
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/terminal/ipapp.py", line 318, in start
    self.shell.mainloop()
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/terminal/interactiveshell.py", line 653, in mainloop
    self.interact()
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/terminal/interactiveshell.py", line 646, in interact
    self.run_cell(code, store_history=True)
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 2854, in run_cell
    result = self._run_cell(
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 2905, in _run_cell
    self.showtraceback(running_compiled_code=True)
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 1981, in showtraceback
    stb = self.InteractiveTB.structured_traceback(etype,
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 1105, in structured_traceback
    return FormattedTB.structured_traceback(
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 999, in structured_traceback
    return VerboseTB.structured_traceback(
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 871, in structured_traceback
    formatted_exceptions += self.format_exception_as_a_whole(etype, evalue, etb, lines_of_context,
  File "/Users/espenhagen/miniforge3/envs/lfpydev/lib/python3.10/site-packages/IPython/core/ultratb.py", line 775, in format_exception_as_a_whole
    assert etb is not None
AssertionError

If you suspect this is an IPython 8.1.1 bug, please report it at:
    https://github.com/ipython/ipython/issues
or send an email to the mailing list at ipython-dev@python.org

You can print a more detailed traceback right now with "%tb", or use "%debug"
to interactively debug it.

Extra-detailed tracebacks for bug-reporting purposes can be enabled via:
    %config Application.verbose_crash=True

[ramcdougal]

I agree that it's surprising that the np.array of an empty Vector doesn't work (it works for non-empty Vectors).

One point of clarification though: np.array(v) and v.as_numpy() are not interchangeable. The first makes a copy; the second shares memory. Consider:

>>> from neuron import h
>>> import numpy as np
>>> v = h.Vector([6, 5, 42])
>>> n = np.array(v)
>>> a = v.as_numpy()
>>> n[2]
42.0
>>> n[2] = 7
>>> v[2]
42.0
>>> a[2] = 7
>>> v[2]
7.0

i.e. changing a changes v and vice-versa, but n and v are independent.