Martin Kim

Bump minimum Python version to 3.9, test with 3.8 - 3.10.

1

Closes #1705. Changes include: - Remove `Literal` compatibility type

Fix links for breast cancer and mouse ob, add deprecation warning.

1

Closes #1707.

Update CI workflow to separate static code checking from pytest.

1

Closes #1341.

Replace custom `attrdict` with `ml_collections` implementation.

2

Closes #1690.

Continuing #1565 in a new staging branch.

See #2496

Incompability between Pandas <2 and >=2 saved models

2

Error occurs when a model is saved with Pandas =2 ``` scvi/model/base/_base_model.py:691: in load ) = _load_saved_files( scvi/model/base/_utils.py:68: in _load_saved_files model = torch.load(model_path, map_location=map_location) ../../.../python3.11/site-packages/torch/serialization.py:1014: in load return _load(opened_zipfile, ../../.../python3.11/site-packages/torch/serialization.py:1422:...

Reproducible script: ``` vae = SCANVAE(n_input=100, n_labels=1) x = torch.randint(0, 100, (10, 100), dtype=torch.float32) batch = torch.zeros(10, dtype=torch.long) labels = torch.zeros(10, dtype=torch.long) tensors = { REGISTRY_KEYS.X_KEY: x, REGISTRY_KEYS.BATCH_KEY: batch, REGISTRY_KEYS.LABELS_KEY:...