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conftest.py
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conftest.py
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import pytest
import scvi
from scvi.model._utils import _init_library_size
from contrastive_vi.data.dataloaders.contrastive_dataloader import ContrastiveDataLoader
from contrastive_vi.model.contrastive_vi import ContrastiveVIModel
from tests.utils import get_next_batch
@pytest.fixture
def mock_adata():
adata = scvi.data.synthetic_iid(n_batches=2) # Same number of cells in each batch.
# Make number of cells unequal across batches to test edge cases.
adata = adata[:-3, :]
adata.layers["raw_counts"] = adata.X.copy()
ContrastiveVIModel.setup_anndata(
adata=adata,
batch_key="batch",
labels_key="labels",
layer="raw_counts",
)
return adata
@pytest.fixture
def mock_adata_manager(mock_adata):
return ContrastiveVIModel._setup_adata_manager_store[mock_adata.uns["_scvi_uuid"]]
@pytest.fixture
def mock_library_log_means_and_vars(mock_adata_manager):
return _init_library_size(mock_adata_manager, n_batch=2)
@pytest.fixture
def mock_library_log_means(mock_library_log_means_and_vars):
return mock_library_log_means_and_vars[0]
@pytest.fixture
def mock_library_log_vars(mock_library_log_means_and_vars):
return mock_library_log_means_and_vars[1]
@pytest.fixture
def mock_n_input(mock_adata):
return mock_adata.X.shape[1]
@pytest.fixture
def mock_n_batch(mock_adata):
return len(mock_adata.obs["batch"].unique())
@pytest.fixture
def mock_adata_background_indices(mock_adata):
return (
mock_adata.obs.index[(mock_adata.obs["batch"] == "batch_0")]
.astype(int)
.tolist()
)
@pytest.fixture
def mock_adata_background_label(mock_adata):
return 0
@pytest.fixture
def mock_adata_target_indices(mock_adata):
return (
mock_adata.obs.index[(mock_adata.obs["batch"] == "batch_1")]
.astype(int)
.tolist()
)
@pytest.fixture
def mock_adata_target_label(mock_adata):
return 1
@pytest.fixture
def mock_contrastive_dataloader(
mock_adata_manager, mock_adata_background_indices, mock_adata_target_indices
):
return ContrastiveDataLoader(
mock_adata_manager,
mock_adata_background_indices,
mock_adata_target_indices,
batch_size=32,
shuffle=False,
)
@pytest.fixture
def mock_contrastive_batch(mock_contrastive_dataloader):
return get_next_batch(mock_contrastive_dataloader)