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()

.gitignore

@@ -12,6 +12,7 @@ dev*
 # Files
 collect_env.py
 RUN_DSCRIPT.sh
+.coverage
 
 # File Types
 **/*.egg-info

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/)

coverage.txt

@@ -0,0 +1,58 @@
+============================= test session starts ==============================
+platform linux -- Python 3.12.11, pytest-9.0.2, pluggy-1.6.0
+rootdir: /mnt/home/ssledzieski/GitHub/D-SCRIPT
+configfile: pyproject.toml
+testpaths: dscript/tests
+plugins: anyio-4.12.0, cov-7.0.0
+collected 309 items / 2 deselected / 307 selected
+
+dscript/tests/test_alphabets.py ........................                 [  7%]
+dscript/tests/test_commands.py ..........                                [ 11%]
+dscript/tests/test_extract_3di.py ............                           [ 14%]
+dscript/tests/test_fasta.py .........                                    [ 17%]
+dscript/tests/test_foldseek.py .............                             [ 22%]
+dscript/tests/test_glider.py ........................................... [ 36%]
+.......                                                                  [ 38%]
+dscript/tests/test_language_model.py .........                           [ 41%]
+dscript/tests/test_load_worker.py .............                          [ 45%]
+dscript/tests/test_main.py .........................                     [ 53%]
+dscript/tests/test_models_contact.py .................                   [ 59%]
+dscript/tests/test_models_embedding.py ...........................       [ 68%]
+dscript/tests/test_models_interaction.py ............................    [ 77%]
+dscript/tests/test_par_writer.py ................                        [ 82%]
+dscript/tests/test_pretrained.py ....................                    [ 88%]
+dscript/tests/test_utils.py ..................................           [100%]
+
+================================ tests coverage ================================
+_______________ coverage: platform linux, python 3.12.11-final-0 _______________
+
+Name                                    Stmts   Miss  Cover   Missing
+---------------------------------------------------------------------
+dscript/__init__.py                         5      0   100%
+dscript/__main__.py                        35      1    97%   87
+dscript/alphabets.py                       49      0   100%
+dscript/commands/__init__.py                1      0   100%
+dscript/commands/embed.py                  32     13    59%   47-59, 63-65
+dscript/commands/evaluate.py              169    128    24%   112-154, 161-170, 180-291, 295-297
+dscript/commands/extract_3di.py            33      4    88%   55-58
+dscript/commands/par_worker.py             64     57    11%   22-121
+dscript/commands/par_writer.py             31      0   100%
+dscript/commands/predict_bipartite.py     199    143    28%   137-152, 155-159, 162-171, 174-176, 181-208, 220-418, 422-424
+dscript/commands/predict_block.py         289    243    16%   127-561, 565-567
+dscript/commands/predict_serial.py        176    136    23%   97-295, 299-301
+dscript/commands/train.py                 358    264    26%   265-301, 331-342, 394-454, 484-532, 537-831, 841-869, 873-875
+dscript/fasta.py                           44      6    86%   61-66
+dscript/foldseek.py                        35      1    97%   70
+dscript/glider.py                         185      3    98%   106-108
+dscript/language_model.py                  73     15    79%   31, 39, 61-63, 74, 85, 108-109, 129-134
+dscript/load_worker.py                     14      0   100%
+dscript/loading.py                         69     58    16%   15-34, 38-59, 63-85, 88-92
+dscript/models/__init__.py                  1      0   100%
+dscript/models/contact.py                  44      0   100%
+dscript/models/embedding.py                76      2    97%   143-144
+dscript/models/interaction.py              94      5    95%   201-206, 229
+dscript/pretrained.py                      88      1    99%   109
+dscript/utils.py                           66      0   100%
+---------------------------------------------------------------------
+TOTAL                                    2230   1080    52%
+================= 307 passed, 2 deselected in 94.25s (0:01:34) =================