Claude/expand test coverage

.github/workflows/autorun-tests.yml

@@ -15,18 +15,24 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+
+    - name: Set up Python 3.11
       uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
+        python-version: "3.11"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -e ".[test,dev]"
+        uv sync --extra test --extra dev
+
     - name: Lint and format with ruff
       run: |
-        ruff check . --statistics
-        ruff format .
+        uv run ruff check . --statistics
+        uv run ruff format .
+
     - name: Test with pytest
       run: |
-        pytest --cov=dscript --cov-report=xml --cov-report=term-missing
+        uv run pytest --cov=dscript --cov-report=xml --cov-report=term-missing

.github/workflows/docs-build.yml

@@ -14,27 +14,27 @@ permissions:
 jobs:
   docs-build:
     runs-on: ubuntu-22.04
-    
+
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
-      
+
     - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
         python-version: "3.11"
-        
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e ".[docs]"
-        
+
     - name: Build documentation
       working-directory: docs
       run: |
         # Build HTML documentation with warnings treated as errors
         sphinx-build -W -b html source build/html
-        
+
     - name: Check for build artifacts
       run: |
         # Verify that the documentation was built successfully
@@ -43,7 +43,7 @@ jobs:
           exit 1
         fi
         echo "Documentation build completed successfully"
-        
+
     - name: Upload documentation artifacts
       uses: actions/upload-artifact@v4
       if: always()

CHANGELOG.md

@@ -16,7 +16,7 @@
 - Improve method for loading embeddings
 - Modernized D-SCRIPT repository
 - Significantly updated unittest coverage
-- Migrate to loguru under the hood 
+- Migrate to loguru under the hood
 - Update pyproject, GitHub actions, and other continuous integration/installation
 - Linting and formatting with Ruff
 
@@ -27,7 +27,7 @@
 - Update pretrained API and docs to include Topsy-Turvy
 - Add retry decorator to get_pretrained if download fails
 - Add ability to set a random seed for training
-- Update `evaluate` code to also store metrics in a file 
+- Update `evaluate` code to also store metrics in a file
 
 ### v0.2.1: 2022-06-28 -- Bug fixes
 - Add biopython to setup.py

README.md

@@ -48,12 +48,12 @@ For inference, proteins can be divided into blocks to reduce memory usage for em
 ```bash
 #Example with 16 blocks, using (using 3/16th the maximum embedding memory), and a GPU
 dscript predict --pairs data/pairs/ecoli_test.tsv --embeddings ecoli_embed.h5 --outfile ecoli_test_predict --blocks 16 -d 0
-``` 
+```
 
 For more information on prediction modes, such as all-pair and bipartite predictions, see our [complete documentation](https://d-script.readthedocs.io/en/main/usage.html)
 
 ## References
  - The original D-SCRIPT model is described in the paper “[D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions](https://doi.org/10.1016/j.cels.2021.08.010).”
  - We have updated D-SCRIPT to incorporate network information ([Topsy Turvy](https://academic.oup.com/bioinformatics/article/38/Supplement_1/i264/6617505)) and structure information ([TT3D](https://academic.oup.com/bioinformatics/article/39/11/btad663/7332153))
- - The addition of Blocked, Multi-GPU Parallel Inference to D-SCRIPT is described in the application note “[Memory-Efficient, Accelerated Protein Interaction inference with Blocked, Multi-GPU D-SCRIPT](https://doi.org/10.1093/bioinformatics/btaf564).” 
+ - The addition of Blocked, Multi-GPU Parallel Inference to D-SCRIPT is described in the application note “[Memory-Efficient, Accelerated Protein Interaction inference with Blocked, Multi-GPU D-SCRIPT](https://doi.org/10.1093/bioinformatics/btaf564).”
  - [Documentation](https://d-script.readthedocs.io/en/main/)