Merge pull request #4 from grst/grst-patch-1

Improve pytest setup
mikelkou · Aug 17, 2023 · c0e1973 · c0e1973
2 parents 04d6b3c + b302121
commit c0e1973
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diff --git a/tests/test_basic.py b/tests/test_basic.py
diff --git a/tests/test_fava.py b/tests/test_fava.py
@@ -0,0 +1,34 @@
+import os
+import pandas as pd
+import pytest
+from pathlib import Path
+
+from favapy import fava
+
+
+@pytest.fixture
+def data_dir() -> Path:
+    data_dir = os.environ.get("DATA_DIR")
+    if data_dir is None:
+        raise ValueError("DATA_DIR environment variable not set")
+    else:
+        return Path(data_dir)
+
+
+@pytest.fixture
+def test_dataset(data_dir) -> pd.DataFrame:
+    data_file_path = data_dir / "Example_dataset_GSE75748_sc_cell_type_ec.tsv"
+    return pd.read_csv(data_file_path, sep="\t").iloc[:100, :100]
+
+
+def test_favapy(test_dataset):
+    FAVA_network = fava.cook(
+        data=test_dataset,
+        log2_normalization=True,
+        hidden_layer=None,
+        latent_dim=None,
+        epochs=10,
+        batch_size=32,
+        interaction_count=100,
+    )
+    return FAVA_network