setting aside nfs-dependent tests

.gitignore

@@ -135,3 +135,6 @@ dmypy.json
 src/baskerville/scripts/borzoi_test_genes.py
 src/baskerville/pygene.py
 src/baskerville/snps_old.py
+
+# backup
+**/*.py~

tests/conftest.py

@@ -0,0 +1,19 @@
+import pytest
+from pathlib import Path
+
+def pytest_collection_modifyitems(config, items):    
+    if not config.getoption("--integration"):
+        skip_integration = pytest.mark.skip(reason="Integration test - use --integration to run")
+        for item in items:
+            test_path = Path(item.fspath)
+            if "integration" in test_path.parts:
+                item.add_marker(skip_integration)
+
+def pytest_addoption(parser):
+    print("Adding custom option")  # Debug print
+    parser.addoption(
+        "--integration",
+        action="store_true",
+        default=False,
+        help="run integration tests"
+    )

tests/integration/test_transfer_load.py

@@ -0,0 +1,49 @@
+import json
+import numpy as np
+import pandas as pd
+from baskerville import seqnn
+
+def test_housby():
+    model_file = "/home/yuanh/analysis/Borzoi_transfer/exp_10_10_23/hayflick/houlsby/latent_8/train/f0c0/train/model_best.h5"
+    targets_file = "tests/data/transfer/targets.txt"
+    params_file = "tests/data/transfer/json/model_houlsby.json"
+
+    # model params
+    with open(params_file) as params_open:
+        params = json.load(params_open)
+    params_model = params["model"]
+    params_model["verbose"] = False
+
+    # set strand pairs
+    targets_df = pd.read_csv(targets_file, index_col=0, sep="\t")
+    if "strand_pair" in targets_df.columns:
+        params_model["strand_pair"] = [np.array(targets_df.strand_pair)]
+    strand_pair = np.array(targets_df.strand_pair)
+
+    seqnn_model = seqnn.SeqNN(params_model)
+    seqnn_model.restore(model_file)
+
+    print("load model success!")
+
+
+def test_se4():
+    model_file = "/home/yuanh/analysis/Borzoi_transfer/exp_10_10_23/hayflick/houlsby_se/se2/train/f0c0/train/model_best.h5"
+    targets_file = "tests/data/transfer/targets.txt"
+    params_file = "tests/data/transfer/json/model_se4.json"
+
+    # model params
+    with open(params_file) as params_open:
+        params = json.load(params_open)
+    params_model = params["model"]
+    params_model["verbose"] = False
+
+    # set strand pairs
+    targets_df = pd.read_csv(targets_file, index_col=0, sep="\t")
+    if "strand_pair" in targets_df.columns:
+        params_model["strand_pair"] = [np.array(targets_df.strand_pair)]
+    strand_pair = np.array(targets_df.strand_pair)
+
+    seqnn_model = seqnn.SeqNN(params_model)
+    seqnn_model.restore(model_file)
+
+    print("load model success!")