scvi-tools 1.2.0

[martinkim0]

• [ ] Bump version in pyproject.toml
• [ ] If patch release, backport version bump PR into the appropriate branch. Else, create a new branch off main with the appropriate rules
• [ ] Trigger a Docker image build in scvi-tools-docker targeting the release branch
• [ ] After image builds and pushes to the registry, run the tutorials using the new image
• [ ] Publish a new release on the tutorials repo off main after all tutorials changes have been merged
• [ ] Create a new branch off main in the main repo and run git submodule update --remote, and then merge the PR, with an appropriate backport as needed
• [ ] Run the release workflow
• [ ] Check that the version updates correctly on PyPI
• [ ] Build new Docker images with the stable and semantic versioning tags
• [ ] Check that the feedstock repo updates correctly
• [ ] (Optional) Post threads on Discourse and Twitter

[Rafael-Silva-Oliveira]

Hey @martinkim0 just out of curiosity, when is v 1.2 going to release? :) Would love to test the hyperparameter tuning with Ray for some label transferring

Thanks!

[martinkim0]

Hi @Rafael-Silva-Oliveira, right now it's looking like the end of the month. Regarding #2895, it's a deprecation warning, so it should be OK to use the current version of Ray hyperparameter tuning with no problem :)

[Rafael-Silva-Oliveira]

Hi @Rafael-Silva-Oliveira, right now it's looking like the end of the month. Regarding #2895, it's a deprecation warning, so it should be OK to use the current version of Ray hyperparameter tuning with no problem :)

Thank you for the reply, I think I'll wait for the new version since it just keeps giving me errors such as this one:

>>> results = tuner.fit(
...     adata=adata_to_annotate,
...     metric="validation_loss",
...     search_space=search_space,
...     num_samples=100,
...     max_epochs=20,
... )
2024-08-06 17:37:58,737 ERROR services.py:1329 -- Failed to start the dashboard , return code 1
2024-08-06 17:37:58,739 ERROR services.py:1354 -- Error should be written to 'dashboard.log' or 'dashboard.err'. We are printing the last 20 lines for you. See 'https://docs.ray.io/en/master/ray-observability/ray-logging.html#logging-directory-structure' to find where the log file is.
2024-08-06 17:37:58,740 ERROR services.py:1398 -- 
The last 20 lines of /mnt/scratch/tmp/ray/session_2024-08-06_17-37-49_487509_1278064/logs/dashboard.log (it contains the error message from the dashboard): 
  File "/mnt/work/RO_src/venv/stnav_venv/lib/python3.10/site-packages/ray/dashboard/dashboard.py", line 75, in run
    await self.dashboard_head.run()
  File "/mnt/work/RO_src/venv/stnav_venv/lib/python3.10/site-packages/ray/dashboard/head.py", line 325, in run
    modules = self._load_modules(self._modules_to_load)
  File "/mnt/work/RO_src/venv/stnav_venv/lib/python3.10/site-packages/ray/dashboard/head.py", line 219, in _load_modules
    head_cls_list = dashboard_utils.get_all_modules(DashboardHeadModule)
  File "/mnt/work/RO_src/venv/stnav_venv/lib/python3.10/site-packages/ray/dashboard/utils.py", line 121, in get_all_modules
    importlib.import_module(name)
  File "/usr/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/mnt/work/RO_src/venv/stnav_venv/lib/python3.10/site-packages/ray/dashboard/modules/dashboard_sdk.py", line 10, in <module>
    from pkg_resources import packaging
ImportError: cannot import name 'packaging' from 'pkg_resources' (/mnt/work/RO_src/venv/stnav_venv/lib/python3.10/site-packages/pkg_resources/__init__.py)
2024-08-06 17:38:02,984 INFO worker.py:1724 -- Started a local Ray instance.
[2024-08-06 17:38:04,337 E 1278064 1278064] core_worker.cc:215: Failed to register worker 01000000ffffffffffffffffffffffffffffffffffffffffffffffff to Raylet. IOError: [RayletClient] Unable to register worker with raylet. No such file or directory

Hopefully version 1.2.0 will improve usability as well!

Thanks

[raozuming]

Copied to #2992