OPIL code completion not working in VS Code

[bjkeller]

Because the OPIL classes are generated, OPIL does not work with python code completion

The following are screen caps of VS Code with completions for sbol3. and opil.

In both cases, VS Code is showing (mostly) members of the respective packages, but for OPIL only the factory and other members that are in the opil code base are shown. Since the OPIL classes are generated they are not shown.

These screen captures are from https://github.com/aquariumbio/aquarium-opil in a VS Code dev container where I have installed opil. The resulting environment allows me to use code completion for pySBOL3, but not OPIL.

This particular configuration is somewhat convoluted, but to replicate it should be sufficient to create a virtual environment, pip install opil, start VS Code with Python extension (or some other editor able to use the virtual environment for code completion), and then edit a script with opil and sbol3 imported to see something similar.

[jakebeal]

@bjkeller I changed the title to be more descriptive, because when I first saw it, I thought you meant you didn't want to have code completion in OPIL.

[bjkeller]

Well, technically, it is working. It is just not reflective of the ontology classes

[bbartley]

Hi @bjkeller do you have any ideas what is required for code completion to work? In the Python interpreter, the generated classes all appear in the opil namespace:

>>> import opil
RDFLib Version: 5.0.0
>>> dir(opil)
['BooleanParameter', 'BooleanValue', 'CombinatorialDerivation', 'Component', 'Document', 'EnumeratedParameter', 'EnumeratedValue', 'ExperimentalRequest', 'Identified', 'IntegerParameter', 'IntegerValue', 'MeasureParameter', 'MeasureValue', 'Measurement', 'MeasurementType', 'Media', 'OPILFactory', 'Parameter', 'ParameterValue', 'ProtocolInterface', 'Query', 'SampleSet', 'ShaclValidator', 'Strain', 'StrateosOpilGenerator', 'StringParameter', 'StringValue', 'TimeInterval', 'TopLevel', 'URIParameter', 'URIValue', 'ValidationReport', 'VariableFeature', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', 'class_uri', 'generate_opil_from_strateos', 'help', 'inf', 'log', 'opil_factory', 'os', 'posixpath', 'rdflib', 'sbol', 'set_namespace', 'shacl_validator']

[bjkeller]

I'll look. I'm guessing that VS Code is somehow doing static analysis on the code b/c the Pylance extension is based on a static type checker

Can you see these in a different editor?

[bbartley]

@tramyn confirmed it doesn't work in PyCharm IDE either

[bjkeller]

The solution may be to add a .pyi file. See https://mypy.readthedocs.io/en/stable/stubs.html.

https://mypy.readthedocs.io/en/stable/stubgen.html

[jakebeal]

It looks like for PyCharm, at least, one can patch around this by generating a stub file (https://intellij-support.jetbrains.com/hc/en-us/community/posts/360003388099-Add-dynamic-created-classes-to-autocomplete-for-pycharm-2018, https://intellij-support.jetbrains.com/hc/en-us/community/posts/115000665110-auto-completion-for-dynamic-module-attributes-in-python).