As a sanity check, I ran cd scvi-tools && pytest within my new build environment and got the following:
============================================================================================================================================================ short test summary info ============================================================================================================================================================
FAILED tests/models/test_pyro.py::test_pyro_bayesian_save_load - AssertionError:
====================================================================================================================================== 1 failed, 162 passed, 6 skipped, 689 warnings in 532.95s (0:08:52) =======================================================================================================================================
Can I safely ignore this?
Please see below:
vscode ➜ /workspaces/scvi_work/scvi-tools (mk) $ pytest --lf
===================================================== test session starts ======================================================
platform linux -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /workspaces/scvi_work/scvi-tools
collected 125 items / 124 deselected / 1 selected f
run-last-failure: rerun previous 1 failure (skipped 4 files)
tests/models/test_pyro.py . [100%]
======================================================= warnings summary =======================================================
../../../home/vscode/.local/lib/python3.8/site-packages/torchvision/transforms/functional_pil.py:228
/home/vscode/.local/lib/python3.8/site-packages/torchvision/transforms/functional_pil.py:228: DeprecationWarning: BILINEAR is deprecated and will be removed in Pillow 10 (2023-07-01). Use Resampling.BILINEAR instead.
interpolation: int = Image.BILINEAR,
../../../home/vscode/.local/lib/python3.8/site-packages/torchvision/transforms/functional_pil.py:295
/home/vscode/.local/lib/python3.8/site-packages/torchvision/transforms/functional_pil.py:295: DeprecationWarning: NEAREST is deprecated and will be removed in Pillow 10 (2023-07-01). Use Resampling.NEAREST or Dither.NONE instead.
interpolation: int = Image.NEAREST,
../../../home/vscode/.local/lib/python3.8/site-packages/torchvision/transforms/functional_pil.py:311
/home/vscode/.local/lib/python3.8/site-packages/torchvision/transforms/functional_pil.py:311: DeprecationWarning: NEAREST is deprecated and will be removed in Pillow 10 (2023-07-01). Use Resampling.NEAREST or Dither.NONE instead.
interpolation: int = Image.NEAREST,
../../../home/vscode/.local/lib/python3.8/site-packages/torchvision/transforms/functional_pil.py:328
/home/vscode/.local/lib/python3.8/site-packages/torchvision/transforms/functional_pil.py:328: DeprecationWarning: BICUBIC is deprecated and will be removed in Pillow 10 (2023-07-01). Use Resampling.BICUBIC instead.
interpolation: int = Image.BICUBIC,
tests/dataset/test_anndata.py:9
/workspaces/scvi_work/scvi-tools/tests/dataset/test_anndata.py:9: DeprecationWarning: Please use `csr_matrix` from the `scipy.sparse` namespace, the `scipy.sparse.csr` namespace is deprecated.
from scipy.sparse.csr import csr_matrix
tests/dataset/test_built_in_data.py:97
/workspaces/scvi_work/scvi-tools/tests/dataset/test_built_in_data.py:97: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.internet
tests/dataset/test_built_in_data.py:103
/workspaces/scvi_work/scvi-tools/tests/dataset/test_built_in_data.py:103: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.internet
tests/dataset/test_built_in_data.py:108
/workspaces/scvi_work/scvi-tools/tests/dataset/test_built_in_data.py:108: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.internet
tests/dataset/test_dataset10X.py:47
/workspaces/scvi_work/scvi-tools/tests/dataset/test_dataset10X.py:47: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.internet
tests/models/test_models.py:728
/workspaces/scvi_work/scvi-tools/tests/models/test_models.py:728: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.internet
tests/models/test_models.py:769
/workspaces/scvi_work/scvi-tools/tests/models/test_models.py:769: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.internet
tests/models/test_pyro.py::test_pyro_bayesian_save_load
/workspaces/scvi_work/scvi-tools/scvi/data/_built_in_data/_synthetic.py:28: FutureWarning: X.dtype being converted to np.float32 from int64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.
adata = AnnData(data)
tests/models/test_pyro.py::test_pyro_bayesian_save_load
tests/models/test_pyro.py::test_pyro_bayesian_save_load
/usr/local/python/lib/python3.8/site-packages/pytorch_lightning/trainer/configuration_validator.py:131: UserWarning: You passed in a `val_dataloader` but have no `validation_step`. Skipping val loop.
rank_zero_warn("You passed in a `val_dataloader` but have no `validation_step`. Skipping val loop.")
tests/models/test_pyro.py::test_pyro_bayesian_save_load
tests/models/test_pyro.py::test_pyro_bayesian_save_load
/usr/local/python/lib/python3.8/site-packages/pytorch_lightning/trainer/trainer.py:1933: PossibleUserWarning: The number of training batches (3) is smaller than the logging interval Trainer(log_every_n_steps=10). Set a lower value for log_every_n_steps if you want to see logs for the training epoch.
rank_zero_warn(
tests/models/test_pyro.py::test_pyro_bayesian_save_load
/home/vscode/.local/lib/python3.8/site-packages/torch/distributions/normal.py:85: UserWarning: Specified kernel cache directory could not be created! This disables kernel caching. Specified directory is /home/vscode/.cache/torch/kernels. This warning will appear only once per process. (Triggered internally at ../aten/src/ATen/native/cuda/jit_utils.cpp:860.)
return self.loc + self.scale * torch.erfinv(2 * value - 1) * math.sqrt(2)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================================= 1 passed, 124 deselected, 17 warnings in 14.12s ========================================