fix bug with w- io mode

[h-mayorquin]

Motivation

@bendichter

The PR in #1748 introduced a bug where the io mode "w-" still tries to load the name space. See coments:
https://github.com/NeurodataWithoutBorders/pynwb/pull/1748/files#r1421748605
https://github.com/NeurodataWithoutBorders/pynwb/pull/1748/files#r1421748559

How to test the behavior?

Currently this fails in dev / main

from pathlib import Path
from pynwb import NWBHDF5IO
from pynwb.testing.mock.file import mock_NWBFile


nwbfile = mock_NWBFile()

file_path = Path('test.nwb')
if file_path.exists():
    file_path.unlink()

with NWBHDF5IO('test.nwb', 'w-') as io:
    io.write(nwbfile)


Traceback (most recent call last):
  File "/home/heberto/development/pynwb/build/error_test.py", line 13, in <module>
    with NWBHDF5IO('test.nwb', 'w-') as io:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heberto/miniconda3/envs/pynwb/lib/python3.11/site-packages/hdmf/utils.py", line 644, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heberto/development/pynwb/src/pynwb/__init__.py", line 269, in __init__
    super().load_namespaces(tm, path, file=file_obj, driver=driver)
  File "/home/heberto/miniconda3/envs/pynwb/lib/python3.11/site-packages/hdmf/utils.py", line 644, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heberto/miniconda3/envs/pynwb/lib/python3.11/site-packages/hdmf/backends/hdf5/h5tools.py", line 167, in load_namespaces
    open_file_obj = cls.__resolve_file_obj(path, file_obj, driver)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heberto/miniconda3/envs/pynwb/lib/python3.11/site-packages/hdmf/backends/hdf5/h5tools.py", line 142, in __resolve_file_obj
    file_obj = File(path, 'r', **file_kwargs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heberto/miniconda3/envs/pynwb/lib/python3.11/site-packages/h5py/_hl/files.py", line 567, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heberto/miniconda3/envs/pynwb/lib/python3.11/site-packages/h5py/_hl/files.py", line 231, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 106, in h5py.h5f.open
FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = 'test.nwb', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

The current PR fixes this.

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
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• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (0e45cd9) 91.97% compared to head (c3dcf87) 91.97%.

Additional details and impacted files

@@           Coverage Diff           @@
##              dev    #1795   +/-   ##
=======================================
  Coverage   91.97%   91.97%           
=======================================
  Files          27       27           
  Lines        2617     2618    +1     
  Branches      683      683           
=======================================
+ Hits         2407     2408    +1     
  Misses        138      138           
  Partials       72       72           

Flag	Coverage Δ
integration	71.23% <100.00%> (+0.01%)	⬆️
unit	83.65% <100.00%> (+<0.01%)	⬆️

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[bendichter]

Good catch

[bendichter]

lgtm. Could use a test if it's not too difficult to put one together

[h-mayorquin]

@bendichter

We could add the following test:

import unittest
import tempfile
from pathlib import Path
from pynwb import NWBHDF5IO
from pynwb.testing.mock.file import mock_NWBFile


class TestNWBHDF5IO(unittest.TestCase):
    def test_file_creation_and_deletion(self):
        io_modes_that_create_file = ["w", "w-", "x"]

        with tempfile.TemporaryDirectory() as temp_dir:
            temp_dir = Path(temp_dir)
            for io_mode in io_modes_that_create_file:
                file_path = temp_dir / f"test_io_mode={io_mode}.nwb"

                # Test file creation
                nwbfile = mock_NWBFile()
                with NWBHDF5IO(str(file_path), io_mode) as io:
                    io.write(nwbfile)


if __name__ == "__main__":
    unittest.main()

Could this be a good test? if so, where should it be?

[rly]

@h-mayorquin I think that test looks fine to cover this use case. Please add the test to this test class https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/tests/integration/hdf5/test_io.py#L19

[h-mayorquin]

@rly added the test.

[rly]

Thanks for adding the test. I marked this PR as ready for review. @h-mayorquin I hope that's OK. @bendichter please re-review.