Unable to Load ndx-ophys-devices Namespace to build ndx-microscopy Extension

[alessandratrapani]

I am trying to build the ndx-microscopy extension, which requires the namespace of another extension, ndx-ophys-devices. However, I encounter an error indicating that the ndx-ophys-devices namespace cannot be loaded.

Error Details

When running the tests, the following error occurs:

src/pynwb/tests/test_constructors.py:None (src/pynwb/tests/test_constructors.py)
..\..\..\..\..\anaconda3\envs\ndx-microscopy-env\Lib\site-packages\hdmf\spec\namespace.py:452: in __load_namespace
    inc_ns = self.get_namespace(s['namespace'])
..\..\..\..\..\anaconda3\envs\ndx-microscopy-env\Lib\site-packages\hdmf\utils.py:668: in func_call
    return func(args[0], **pargs)
..\..\..\..\..\anaconda3\envs\ndx-microscopy-env\Lib\site-packages\hdmf\spec\namespace.py:303: in get_namespace
    raise KeyError("'%s' not a namespace" % name)
E   KeyError: "'ndx-ophys-devices' not a namespace"

Code

ndx-microscopy/spec/ndx-microscopy.namespace.yaml

Lines 10 to 14 in 65ba204

	schema:
	- namespace: core
	- namespace: ndx-ophys-devices
	- source: ndx-microscopy.extensions.yaml
	version: 0.1.0

ndx-microscopy/src/pynwb/ndx_microscopy/__init__.py

Lines 22 to 23 in 65ba204

	from ndx_ophys_devices import ExcitationSource, Indicator, OpticalFilter, Photodetector

@rly could you help identify why the ndx-ophys-devices namespace is not being recognized?
After merging this PR I would like to work on the integration with NWBEP003

[rly]

ndx-ophys-devices does not seem to be available on PyPI. Either it needs to be a Python module that is a dependency of this package (and mentioned in pyproject.toml or setup.py and therefore installed by pip when ndx-microscopy is installed, or the ndx-ophys-devices spec files need to be included in this package and the classes instantiated in __init__.py.

If I clone ndx-ophys-devices and install it locally, then running pytest gives me:

ERROR src/pynwb/tests/test_constructors.py - ValueError: No specification for 'ExcitationLightPath' in namespace 'ndx-microscopy'
ERROR src/pynwb/tests/test_roundtrip.py - ValueError: No specification for 'ExcitationLightPath' in namespace 'ndx-microscopy'

so it seems like the namespace is recognized then.

[alessandratrapani]

Ah sorry I forgot to specify that this error occurred running the code in the add_ophys_device branch, not the main branch

[rly]

No problem. I guessed that. I see now that you added the GitHub link to ndx-ophys-devices into requirements-min.txt, but it actually needs to be in pyproject.toml or setup.py to be used. requirements-min.txt is only used in a particular GitHub actions workflow that checks whether the tests pass when installing the minimum versions of the packages that you specify in pyproject.toml or setup.py. Both lists need to be manually updated. Sorry that's confusing! I'll try to improve the documentation.

Separately you may want to use the latest ndx template for this extension which has a few improvements like having a project.toml which is more standard now. I'm happy to help you migrate this extension over to using that (I do it manually but I've done it enough times for other extensions that it's pretty quick). Let me know.

[alessandratrapani]

• I released ndx-ophys-devices on PyPi
• I migrated this extension to use the newer version of ndx-template --> Update with newer ndx-template version  #26
• I added ndx-ophys-devices to pyproject.toml and requirements-min.txt --> Update with newer ndx-template version  #26

But I still have the same issue not finding the namespace