Merge branch '1.8.0' into py310

Author: mcloughlin2

.github/workflows/lint.yml

@@ -10,6 +10,9 @@ jobs:
         python-version: ["3.9"]
 
     steps:
+      - name: Update apt cache
+        run: |
+          sudo apt-get update || sudo apt-get update --fix-missing
       - name: System Dependencies
         run: |
           sudo apt install -y build-essential \

.github/workflows/pytest.yml

@@ -18,6 +18,7 @@ jobs:
     steps:
       - name: System Dependencies
         run: |
+          sudo apt-get update
           sudo apt install -y build-essential \
             libcairo2-dev \
             pkg-config \
@@ -47,8 +48,8 @@ jobs:
       - name: pytest
         run: |
           # python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/unit
-          python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/modac/test/unit
-          cd atomsci/ddm/test/unit && python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv
+          cd atomsci/modac/test/unit && python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv
+          cd ../../../../atomsci/ddm/test/unit && python3.9 -m pytest -m "not moe_required" -n 2 --capture=sys --capture=fd --cov=atomsci -vv
         env:
           ENV: test
 
@@ -64,6 +65,7 @@ jobs:
     steps:
       - name: System Dependencies
         run: |
+          sudo apt-get update
           sudo apt install -y build-essential \
             libcairo2-dev \
             pkg-config \
@@ -110,6 +112,7 @@ jobs:
     steps:
       - name: System Dependencies
         run: |
+          sudo apt-get update
           sudo apt install -y build-essential \
             libcairo2-dev \
             pkg-config \
@@ -139,8 +142,8 @@ jobs:
       - name: pytest
         run: |
           # TODO: Run this test with pytest for paralell testing
-          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
           cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 1
+          echo 'done'
         env:
           ENV: test
 
@@ -156,6 +159,7 @@ jobs:
     steps:
       - name: System Dependencies
         run: |
+          sudo apt-get update
           sudo apt install -y build-essential \
             libcairo2-dev \
             pkg-config \
@@ -202,6 +206,7 @@ jobs:
     steps:
       - name: System Dependencies
         run: |
+          sudo apt-get update
           sudo apt install -y build-essential \
             libcairo2-dev \
             pkg-config \

atomsci/ddm/pipeline/model_wrapper.py

@@ -1491,7 +1491,6 @@ def train(self, pipeline):
         em = perf.EpochManager(self,
                                 prediction_type="hybrid",
                                 model_dataset=pipeline.data,
-                                transformers=self.transformers,
                                 is_ki=self.params.is_ki,
                                 production=self.params.production,
                                 ki_convert_ratio=self.params.ki_convert_ratio)
@@ -1532,7 +1531,7 @@ def train(self, pipeline):
                 valid_loss_ep /= (valid_data.n_ki + valid_data.n_bind)
 
             train_perf, valid_perf, test_perf = em.update_epoch(ei,
-                                train_dset=train_dset, valid_dset=valid_dset, test_dset=test_dset, fold='final')
+                                train_dset=train_dset, valid_dset=valid_dset, test_dset=test_dset)
 
             self.log.info("Epoch %d: training %s = %.3f, training loss = %.3f, validation %s = %.3f, validation loss = %.3f, test %s = %.3f" % (
                           ei, pipeline.metric_type, train_perf, train_loss_ep, pipeline.metric_type, valid_perf, valid_loss_ep,

atomsci/ddm/test/integrative/hybrid/test_hybrid.py

@@ -20,6 +20,26 @@ def clean():
         if os.path.isfile("./output/"+f):
             os.remove("./output/"+f)
 
+def test_is_hybrid():
+    """Test to see of the model pipeline is built correctly"""
+    with open("H1_hybrid.json", "r") as f:
+        hp_params = json.load(f)
+
+    script_dir = parse.__file__.strip("parameter_parser.py").replace("/pipeline/", "")
+    python_path = sys.executable
+    hp_params["script_dir"] = script_dir
+    hp_params["python_path"] = python_path
+    hp_params["descriptor_type"] = "rdkit_raw"
+
+    params = parse.wrapper(hp_params)
+    if not os.path.isfile(params.dataset_key):
+        params.dataset_key = os.path.join(params.script_dir, params.dataset_key)
+
+    print("Train a hybrid models with MOE descriptors")
+    pl = mp.ModelPipeline(params)
+
+    assert pl.params.model_type == 'hybrid'
+ 
 @pytest.mark.moe_required
 def test():
     """Test full model pipeline: Curate data, fit model, and predict property for new compounds"""

atomsci/ddm/test/integrative/integrative_batch_chunk_tests

@@ -41,7 +41,7 @@ for folder in "${folders[@]}"; do
         if [[ -f "$file" && "$folder" != "__pycache__/" ]]; then
             cd "$folder"
             echo "Testing $folder"
-            pytest --capture=sys --capture=fd --cov=atomsci -vv
+            pytest -m "not moe_required" --capture=sys --capture=fd --cov=atomsci -vv
             cd ..
         else
           echo "Skipping folder: $folder. Not a test directory."

atomsci/ddm/test/integrative/wenzel_NN/config_wenzel_fit_NN.json

@@ -35,6 +35,8 @@
 
     "comment": "Results",
     "comment": "----------------------------------------",    
-    "result_dir": "result"
+    "result_dir": "result",
+
+    "seed":0
 }