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Add support for marking and skipping slow tests, temporarily mark pydantic tests as slow #589

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Merged
pstjohn merged 7 commits into from
Jan 13, 2025
Merged

Add support for marking and skipping slow tests, temporarily mark pydantic tests as slow #589

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abb8258
temporarily disable pydantic tests
pstjohn Jan 10, 2025
b96e454
change to use pytest marks to skip slow tests
pstjohn Jan 10, 2025
0eeda59
fix skip_slow typo
pstjohn Jan 10, 2025
0618e6e
add cleanup job
pstjohn Jan 11, 2025
be176e9
Update unit-tests.yml
pstjohn Jan 11, 2025
27f4f15
Update unit-tests.yml
pstjohn Jan 11, 2025
9480af8
use ngc as bionemo data source
pstjohn Jan 12, 2025
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3 changes: 3 additions & 0 deletions sub-packages/bionemo-esm2/tests/bionemo/esm2/scripts/test_pydantic_train.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,9 @@ def dummy_parquet_train_val_inputs(tmp_path):
return train_cluster_path, valid_cluster_path


@pytest.mark.skip(
"TODO: These tests currently take an inordinate amount of time. See https://jirasw.nvidia.com/browse/BIONEMO-553"
)
def test_pretrain_pydantic_cli(dummy_protein_dataset, dummy_parquet_train_val_inputs, tmpdir):
result_dir = tmpdir.mkdir("results")
train_cluster_path, valid_cluster_path = dummy_parquet_train_val_inputs
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9 changes: 9 additions & 0 deletions sub-packages/bionemo-geneformer/tests/bionemo/geneformer/scripts/test_pydantic_train.py
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Expand Up @@ -42,6 +42,9 @@ def test_bionemo2_rootdir(data_path):
assert data_path.is_dir(), f"Test data directory is supposed to be a directory.\n{data_error_str}"


@pytest.mark.skip(
"TODO: These tests currently take an inordinate amount of time. See https://jirasw.nvidia.com/browse/BIONEMO-553"
)
def test_pretrain_cli_from_ckpt(tmpdir, data_path):
# Same as test_pretrain, but includes a checkpoint to initialize from.
result_dir = Path(tmpdir.mkdir("results"))
Expand Down Expand Up @@ -83,6 +86,9 @@ def test_pretrain_cli_from_ckpt(tmpdir, data_path):
assert (result_dir / "test-experiment").exists(), "Could not find test experiment directory."


@pytest.mark.skip(
"TODO: These tests currently take an inordinate amount of time. See https://jirasw.nvidia.com/browse/BIONEMO-553"
)
def test_pretrain_cli(tmpdir, data_path):
"""trains from scratch"""
# data_path: Path = load("single_cell/testdata-20240506") / "cellxgene_2023-12-15_small" / "processed_data"
Expand Down Expand Up @@ -123,6 +129,9 @@ def test_pretrain_cli(tmpdir, data_path):
assert (result_dir / "test-experiment").exists(), "Could not find test experiment directory."


@pytest.mark.skip(
"TODO: These tests currently take an inordinate amount of time. See https://jirasw.nvidia.com/browse/BIONEMO-553"
)
def test_finetune_cli(tmpdir, data_path):
"""Uses CLI to invoke the entrypoint"""
# data_path: Path = load("single_cell/testdata-20240506") / "cellxgene_2023-12-15_small" / "processed_data"
Expand Down