Merge pull request #240 from mims-harvard/oracle_bug

Oracle bug -- fix #238

.gitignore

@@ -136,7 +136,7 @@ playground.ipynb
 test.ipynb
 file_structure.ipynb
 data/
-#oracle/
+oracle/
 
 # vim backup
 *~

environment.yml

@@ -24,7 +24,7 @@ dependencies:
   - pyg=2.5.0
   - pytorch=2.2.1
   - requests=2.31.0
-  - scikit-learn=1.3.0
+  - scikit-learn=1.2.2
   - seaborn=0.12.2
   - tqdm=4.65.0
   - torchaudio=2.2.1

requirements.txt

@@ -7,7 +7,7 @@ numpy==1.26.4
 openpyxl==3.0.10
 pandas==2.1.4
 requests==2.31.0
-scikit-learn==1.3.0
+scikit-learn==1.2.2
 seaborn==0.12.2
 tqdm==4.65.0
 cellxgene-census==1.10.2 

tdc/test/test_dataloaders.py

@@ -45,7 +45,7 @@ def test_pentelute(self):
 
     @unittest.skip(
         "test is taking up too much memory"
-    )  #FIXME: should probably create much smaller version and use that for the test
+    )  #FIXME: should probably create much smaller version and use that for the test. This test does pass locally, please rerun if changing anndata code.
     def test_h5ad_dataloader(self):
         from tdc.multi_pred.cellxgene import SingleCellPrediction
         from pandas import DataFrame

tdc/test/test_oracles.py

@@ -0,0 +1,47 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import division
+from __future__ import print_function
+
+import os
+import sys
+
+import unittest
+import shutil
+
+# temporary solution for relative imports in case TDC is not installed
+# if TDC is installed, no need to use the following line
+sys.path.append(
+    os.path.abspath(os.path.join(os.path.dirname(__file__), "../..")))
+# TODO: add verification for the generation other than simple integration
+
+
+class TestOracle(unittest.TestCase):
+
+    def setUp(self):
+        print(os.getcwd())
+        pass
+
+    def test_gsk3b(self):
+        from tdc import Oracle
+
+        oracle = Oracle(name='GSK3B')
+
+        x = oracle('CC(C)(C)[C@H]1CCc2c(sc(NC(=O)COc3ccc(Cl)cc3)c2C(N)=O)C1')
+        assert abs(x - 0.03) < 0.0001
+
+    def test_jnk3(self):
+        from tdc import Oracle
+
+        oracle = Oracle(name='JNK3')
+
+        x = oracle('C[C@@H]1CCN(C(=O)CCCc2ccccc2)C[C@@H]1O')
+        assert abs(x - 0.01) < 0.0001
+
+    # def tearDown(self):
+    #     print(os.getcwd())
+    #     shutil.rmtree(os.path.join(os.getcwd(), "data"))
+
+
+if __name__ == "__main__":
+    unittest.main()