Merge pull request #221 from mims-harvard/avelez-dev

Conda tests via GH Actions

.github/workflows/conda-tests.yml

@@ -0,0 +1,45 @@
+# Docs for the Azure Web Apps Deploy action: https://github.com/Azure/webapps-deploy
+# More GitHub Actions for Azure: https://github.com/Azure/actions
+# More info on Python, GitHub Actions, and Azure App Service: https://aka.ms/python-webapps-actions
+
+name: Build Conda Environment And Run Python Tests 
+
+on:
+  push:
+    branches:
+      - main
+      - avelez-dev
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python version
+        uses: actions/setup-python@v1
+        with:
+          python-version: '3.9'
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          channels: bioconda, conda-forge, defaults
+          use-only-tar-bz2: true  
+          auto-update-conda: true
+          auto-activate-base: true
+
+      - name: Create and start Conda environment. Run tests.
+        run: |
+          echo "Creating Conda Environment from environment.yml"
+          conda env create -f environment.yml
+          conda activate tdc-conda-env
+          python run_tests.py
+          conda deactivate

environment.yml

@@ -10,11 +10,11 @@ dependencies:
   - python=3.9.13
   - pip=23.3.1
   - pandas=2.1.4
-  - rdkit=2023.9.5
   - requests=2.31.0
   - scikit-learn=1.3.0
   - seaborn=0.12.2
   - tqdm=4.65.0
   - pip:
     - cellxgene-census==1.10.2 
     - PyTDC==0.4.1
+    - rdkit==2023.9.5

run_tests.py

@@ -0,0 +1,9 @@
+import unittest
+
+if __name__ == '__main__':
+    loader = unittest.TestLoader()
+    start_dir = 'tdc/test'
+    suite = loader.discover(start_dir)
+
+    runner = unittest.TextTestRunner()
+    runner.run(suite)

tdc/test/dev_tests/chem_utils_test/test_molconverter.py

@@ -19,6 +19,7 @@ def setUp(self):
         print(os.getcwd())
         pass
 
+    @unittest.skip("dev test")
     def test_MolConvert(self):
         from tdc.chem_utils import MolConvert
 
@@ -34,6 +35,7 @@ def test_MolConvert(self):
 
         MolConvert.eligible_format()
 
+    # @unittest.skip("dev test")
     def tearDown(self):
         print(os.getcwd())
 

tdc/test/dev_tests/chem_utils_test/test_molfilter.py

@@ -19,12 +19,14 @@ def setUp(self):
         print(os.getcwd())
         pass
 
+    @unittest.skip("dev test")
     def test_MolConvert(self):
         from tdc.chem_utils import MolFilter
 
         filters = MolFilter(filters=["PAINS"], HBD=[0, 6])
         filters(["CCSc1ccccc1C(=O)Nc1onc2c1CCC2"])
 
+    # @unittest.skip("dev test")
     def tearDown(self):
         print(os.getcwd())
 

tdc/test/dev_tests/chem_utils_test/test_oracles.py

@@ -19,6 +19,7 @@ def setUp(self):
         print(os.getcwd())
         pass
 
+    @unittest.skip("dev test")
     def test_Oracle(self):
         from tdc import Oracle
 
@@ -34,6 +35,7 @@ def test_Oracle(self):
         oracle = Oracle(name="Hop")
         x = oracle(["CC(=O)OC1=CC=CC=C1C(=O)O", "C1=CC=C(C=C1)C=O"])
 
+    @unittest.skip("dev test")
     def test_distribution(self):
         from tdc import Evaluator
 

tdc/test/dev_tests/utils_tests/test_misc_utils.py

@@ -19,6 +19,7 @@ def setUp(self):
         print(os.getcwd())
         pass
 
+    @unittest.skip("dev test")
     def test_neg_sample(self):
         from tdc.multi_pred import PPI
 
@@ -30,6 +31,7 @@ def test_neg_sample(self):
     #    data = ADME(name='Caco2_Wang')
     #    x = data.label_distribution()
 
+    @unittest.skip("dev test")
     def test_get_label_map(self):
         from tdc.multi_pred import DDI
         from tdc.utils import get_label_map
@@ -38,22 +40,26 @@ def test_get_label_map(self):
         split = data.get_split()
         get_label_map(name="DrugBank", task="DDI")
 
+    @unittest.skip("dev test")
     def test_balanced(self):
         from tdc.single_pred import HTS
 
         data = HTS(name="SARSCoV2_3CLPro_Diamond")
         data.balanced(oversample=True, seed=42)
 
+    @unittest.skip("dev test")
     def test_cid2smiles(self):
         from tdc.utils import cid2smiles
 
         smiles = cid2smiles(2248631)
 
+    @unittest.skip("dev test")
     def test_uniprot2seq(self):
         from tdc.utils import uniprot2seq
 
         seq = uniprot2seq("P49122")
 
+    @unittest.skip("dev test")
     def test_to_graph(self):
         from tdc.multi_pred import DTI
 
@@ -87,6 +93,7 @@ def test_to_graph(self):
         )
         # output: {'pyg_graph': the PyG graph object, 'index_to_entities': a dict map from ID in the data to node ID in the PyG object, 'split': {'train': df, 'valid': df, 'test': df}}
 
+    # @unittest.skip("dev test")
     def tearDown(self):
         print(os.getcwd())
 

tdc/test/dev_tests/utils_tests/test_splits.py

@@ -19,19 +19,22 @@ def setUp(self):
         print(os.getcwd())
         pass
 
+    @unittest.skip("dev test")
     def test_random_split(self):
         from tdc.single_pred import ADME
 
         data = ADME(name="Caco2_Wang")
         split = data.get_split(method="random")
 
+    @unittest.skip("dev test")
     def test_scaffold_split(self):
         ## requires RDKit
         from tdc.single_pred import ADME
 
         data = ADME(name="Caco2_Wang")
         split = data.get_split(method="scaffold")
 
+    @unittest.skip("dev test")
     def test_cold_start_split(self):
         from tdc.multi_pred import DTI
 
@@ -60,18 +63,21 @@ def test_cold_start_split(self):
             self.assertEqual(0, len(train_entity.intersection(test_entity)))
             self.assertEqual(0, len(valid_entity.intersection(test_entity)))
 
+    @unittest.skip("dev test")
     def test_combination_split(self):
         from tdc.multi_pred import DrugSyn
 
         data = DrugSyn(name="DrugComb")
         split = data.get_split(method="combination")
 
+    @unittest.skip("dev test")
     def test_time_split(self):
         from tdc.multi_pred import DTI
 
         data = DTI(name="BindingDB_Patent")
         split = data.get_split(method="time", time_column="Year")
 
+    @unittest.skip("dev test")
     def test_tearDown(self):
         print(os.getcwd())
 

tdc/test/test_benchmark.py

@@ -57,3 +57,6 @@ def test_ADME_evaluate_many(self):
 
         for my_group in self.group:
             self.assertTrue(my_group["name"] in results)
+
+if __name__ == "__main__":
+    unittest.main()

tdc/test/test_dataloaders.py

@@ -41,3 +41,6 @@ def test_generation(self):
     def tearDown(self):
         print(os.getcwd())
         shutil.rmtree(os.path.join(os.getcwd(), "data"))
+
+if __name__ == "__main__":
+    unittest.main()

tdc/test/test_functions.py

@@ -50,3 +50,6 @@ def tearDown(self):
             shutil.rmtree(os.path.join(os.getcwd(), "data"))
         if os.path.exists(os.path.join(os.getcwd(), "oracle")):
             shutil.rmtree(os.path.join(os.getcwd(), "oracle"))
+
+if __name__ == "__main__":
+    unittest.main()