Improve .llm code coverage

.github/workflows/testing_latest.yml

@@ -52,12 +52,12 @@ jobs:
       - name: Install main package (Windows)
         if: ${{ steps.changed-files-specific.outputs.only_changed != 'true' && runner.os == 'Windows' }}
         run: |
-          uv pip install -e ".[test]"
+          uv pip install -e ".[test,rag]"
 
       - name: Install main package
         if: ${{ steps.changed-files-specific.outputs.only_changed != 'true' && runner.os != 'Windows' }}
         run: |
-          uv pip install -e ".[full,test]"
+          uv pip install -e ".[full,test,rag]"
 
       - name: Check installation
         if: steps.changed-files-specific.outputs.only_changed != 'true'
@@ -69,7 +69,7 @@ jobs:
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.only_changed != 'true'
-        timeout-minutes: 15
+        timeout-minutes: 30
         run: |
           uv run --no-project pytest --cov --cov-report=xml --durations 10
 

.github/workflows/testing_minimal.yml

@@ -60,4 +60,4 @@ jobs:
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         timeout-minutes: 15
         run: |
-          uv run --no-project pytest --durations 10
+          uv run --no-project pytest --ignore=test/llm --durations 10

.github/workflows/testing_nightly.yml

@@ -60,4 +60,4 @@ jobs:
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         timeout-minutes: 15
         run: |
-          uv run --no-project pytest --durations 10
+          uv run --no-project pytest --ignore=test/llm --durations 10

.github/workflows/testing_prev.yml

@@ -71,4 +71,4 @@ jobs:
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         timeout-minutes: 15
         run: |
-          uv run --no-project pytest --durations 10
+          uv run --no-project pytest --ignore=test/llm --durations 10

CHANGELOG.md

@@ -9,6 +9,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ### Changed
 
+- Improved `.llm` code coverage ([#10516](https://github.com/pyg-team/pytorch_geometric/pull/10516))
+
 ### Deprecated
 
 ### Removed

examples/llm/molecule_gpt.py

@@ -93,9 +93,10 @@ def get_clippable_params(params):
     # Create model ===============================================
     llm = LLM(
         # model_name='lmsys/vicuna-7b-v1.5',
-        model_name='TinyLlama/TinyLlama-1.1B-Chat-v0.1',
+        model_name='Qwen/Qwen3-0.6B',
         num_params=1,
         dtype=torch.bfloat16,
+        sys_prompt='You are an agent, answer my questions.',
     )
 
     graph_encoder = GINEConv(

pyproject.toml

@@ -65,6 +65,7 @@ rag=[
     "sentencepiece",
     "accelerate",
     "torchmetrics",
+    "peft",
 ]
 test=[
     "onnx",

test/datasets/test_protein_mpnn_dataset.py

@@ -1,7 +1,8 @@
 from torch_geometric.datasets import ProteinMPNNDataset
-from torch_geometric.testing import onlyOnline, withPackage
+from torch_geometric.testing import onlyLinux, onlyOnline, withPackage
 
 
+@onlyLinux
 @onlyOnline
 @withPackage('pandas')
 def test_protein_mpnn_dataset():

test/datasets/test_web_qsp_dataset.py

@@ -6,12 +6,7 @@
 
 from torch_geometric.datasets import WebQSPDataset
 from torch_geometric.datasets.web_qsp_dataset import KGQABaseDataset
-from torch_geometric.testing import (
-    onlyFullTest,
-    onlyOnline,
-    onlyRAG,
-    withPackage,
-)
+from torch_geometric.testing import onlyFullTest, onlyOnline, withPackage
 
 
 @pytest.mark.skip(reason="Times out")
@@ -144,7 +139,6 @@ def mock_load_dataset(path: str):
     return mock_load_dataset, ds
 
 
-@onlyRAG
 @withPackage("datasets", "pandas")
 def test_kgqa_base_dataset(tmp_path, monkeypatch):
 

test/llm/models/test_g_retriever.py

@@ -1,15 +1,16 @@
 import gc
 
+import pytest
 import torch
 
 from torch_geometric.llm.models import LLM, GRetriever
 from torch_geometric.nn import GAT
-from torch_geometric.testing import onlyRAG, withPackage
+from torch_geometric.testing import withPackage
 
 
-@onlyRAG
-@withPackage('transformers', 'sentencepiece', 'accelerate')
-def test_g_retriever() -> None:
+@withPackage('transformers', 'sentencepiece', 'accelerate', 'peft')
+@pytest.mark.parametrize('use_lora', [True, False])
+def test_g_retriever(use_lora: bool) -> None:
     llm = LLM(model_name='Qwen/Qwen3-0.6B', dtype=torch.float32,
               sys_prompt="You're an agent, answer my questions.")
 
@@ -25,6 +26,7 @@ def test_g_retriever() -> None:
     model = GRetriever(
         llm=llm,
         gnn=gnn,
+        use_lora=use_lora,
     )
     assert str(model) == ('GRetriever(\n'
                           '  llm=LLM(Qwen/Qwen3-0.6B),\n'
@@ -54,8 +56,7 @@ def test_g_retriever() -> None:
     torch.cuda.empty_cache()
 
 
-@onlyRAG
-@withPackage('transformers', 'sentencepiece', 'accelerate')
+@withPackage('transformers', 'sentencepiece', 'accelerate', 'peft')
 def test_g_retriever_many_tokens() -> None:
     llm = LLM(model_name='Qwen/Qwen3-0.6B', dtype=torch.float32,
               sys_prompt="You're an agent, answer my questions.")
@@ -73,6 +74,7 @@ def test_g_retriever_many_tokens() -> None:
         llm=llm,
         gnn=gnn,
         mlp_out_tokens=2,
+        use_lora=True,
     )
     assert str(model) == ('GRetriever(\n'
                           '  llm=LLM(Qwen/Qwen3-0.6B),\n'

test/llm/models/test_git_mol.py

@@ -14,11 +14,24 @@ def test_git_mol():
         [1, 2, 3, 4, 0, 6, 7, 8, 9, 5],
     ])
     edge_attr = torch.zeros(edge_index.size(1), 16, dtype=torch.long)
+    # batch size = 1
     batch = torch.tensor([0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
     smiles = ['CC(C)([C@H]1CC2=C(O1)C=CC3=C2OC(=O)C=C3)O']
     captions = ['The molecule is the (R)-(-)-enantiomer of columbianetin.']
     images = torch.randn(1, 3, 224, 224)
+    loss = model(x, edge_index, batch, edge_attr, smiles, images, captions)
+    assert loss >= 0
 
-    # Test train:
+    # batch size > 1
+    batch = torch.tensor([0, 0, 0, 0, 0, 1, 1, 1, 1, 1])
+    smiles = [
+        'CC(C)([C@H]1CC2=C(O1)C=CC3=C2OC(=O)C=C3)O',
+        'CCOc1ccccc1',
+    ]
+    captions = [
+        'The molecule is the (R)-(-)-enantiomer of columbianetin.',
+        'Ethoxybenzene is an aromatic ether.'
+    ]
+    images = torch.randn(2, 3, 224, 224)
     loss = model(x, edge_index, batch, edge_attr, smiles, images, captions)
     assert loss >= 0