install this package for testing

.github/workflows/ci-tests.yml

@@ -0,0 +1,42 @@
+# 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: Run Python Tests
+
+on:
+  push:
+  pull_request:
+    branches: ["main"]
+  workflow_dispatch:
+
+jobs:
+  pytester:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-22.04"]  # todo: add `, "macOS-14", "windows-2022"`
+            python-version: ["3.9", "3.10", "3.11"]
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python version
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install git-lfs
+        run: |
+          sudo apt-get install git-lfs
+          git lfs install
+
+      - name: Install package & dependencies
+        run: pip install . -U -r requires_test.txt
+
+      - name: Run tests
+        run: python run_tests.py

.github/workflows/codeql-analysis.yml

@@ -13,10 +13,10 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main"]
   pull_request:
     # The branches below must be a subset of the branches above
-    branches: [ "main" ]
+    branches: ["main"]
   schedule:
     - cron: '35 9 * * 0'
 

requirements.txt

@@ -8,7 +8,7 @@ numpy>=1.26.4,<2.0.0
 openpyxl>=3.0.10,<4.0.0
 pandas>=2.1.4,<3.0.0
 requests>=2.31.0,<3.0.0
-scikit-learn>=1.2.2
+scikit-learn>=1.2.2, <1.3.0
 seaborn>=0.12.2,<1.0.0
 tqdm>=4.65.0,<5.0.0
 transformers>=4.43.0,<4.51.0

requires_test.txt

@@ -0,0 +1,7 @@
+pytest==8.3.2
+
+mygene==3.2.2
+scvi-tools>=1.1.0, <1.3.0
+dgl==1.1.3
+torch_geometric==2.5.3
+torch==2.1.1

tdc/chem_utils/oracle/oracle.py

@@ -658,9 +658,8 @@ def SA(s):
 
 
 def load_gsk3b_model():
-    gsk3_model_path = "oracle/gsk3b.pkl"
-    if SKLEARN_VERSION >= version.parse("0.24.0"):
-        gsk3_model_path = "oracle/gsk3b_current.pkl"
+    # gsk3_model_path = "oracle/gsk3b.pkl"  # this was for `sklearn<=0.24`
+    gsk3_model_path = "oracle/gsk3b_current.pkl"
     return load_pickled_model(gsk3_model_path)