Cannot compile scaffold with latest main

[francesshei]

I just pulled the main branch and when running bsb compile --redo I get the following error:

Traceback (most recent call last):
  File "/Users/francescosheiban/.pyenv/versions/neuralenv/bin/bsb", line 8, in <module>
    sys.exit(handle_cli())
  File "/Users/francescosheiban/neuralenv/bsb/bsb/cli/__init__.py", line 10, in handle_cli
    handle_command(sys.argv[1:], exit=True)
  File "/Users/francescosheiban/neuralenv/bsb/bsb/cli/__init__.py", line 30, in handle_command
    namespace.handler(namespace, dryrun=dryrun)
  File "/Users/francescosheiban/neuralenv/bsb/bsb/cli/commands/__init__.py", line 97, in execute_handler
    self.handler(context)
  File "/Users/francescosheiban/neuralenv/bsb/bsb/cli/commands/_commands.py", line 135, in handler
    network = Scaffold(cfg)
  File "/Users/francescosheiban/neuralenv/bsb/bsb/core.py", line 130, in __init__
    self._bootstrap(config, storage, clear=clear)
  File "/Users/francescosheiban/neuralenv/bsb/bsb/core.py", line 163, in _bootstrap
    storage = Storage(config.storage.engine, config.storage.root)
  File "/Users/francescosheiban/neuralenv/bsb/bsb/storage/__init__.py", line 176, in __init__
    self._engine.__dict__[key] = interface(self._engine)
TypeError: Can't instantiate abstract class MorphologyRepository with abstract methods get_all_meta, set_all_meta, update_all_meta

Note, I have no morphologies defined in my network config JSON

[Helveg]

Oh, that must be because of #742 and #743 . I suppose you used git pull, did you also pip install -e . afterwards? It should install a newer compatible version of bsb-hdf5, if not I should fix it.

[francesshei]

Good catch! I didn't run pip install -e . after pulling because I had already installed it in editable mode, but this solved the issue! 👍🏼