Fix CI workflow bugs

- Mark tests with "cloud" and / or "benchmark" as needed
- Combine both "dev" and "benchmark" dependencies, was causing issues with the pytest due to imports (alternatively, use `try-except` block for optional dependency import)
- Replace pandas with polars in dev dependency (for benchmarking)

Author: kaitj

.github/scripts/run_benchmarks.py

@@ -14,7 +14,7 @@ def main():
     pytest.main(
         [
             "-m",
-            "benchmark",
+            "benchmark and not cloud",
             "--benchmark-save-data",
             f"--benchmark-json={args.output}",
             "--benchmark-time-unit=ms",

.github/workflows/benchmark.yaml

@@ -35,7 +35,7 @@ jobs:
           ref: ${{ matrix.target.ref }}
           submodules: true
       - uses: astral-sh/setup-uv@v8.1.0
-      - run: uv sync --group "benchmark" --extra "cloud"
+      - run: uv sync --extra "cloud"
       - name: Run benchmarks
         run: |
           uv run .github/scripts/run_benchmarks.py \ 
@@ -51,7 +51,6 @@ jobs:
     steps:
       - uses: actions/checkout@v6
       - uses: astral-sh/setup-uv@v8.1.0
-      - run: uv sync --group "benchmark"
       - uses: actions/download-artifact@v8
         with:
           pattern: benchmark-*

.github/workflows/ci.yaml

@@ -42,19 +42,19 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - run: uv sync --all-extras
 
-      - name: Run tests without cloudpathlib
+      - name: Run non-cloud tests
         run: |
           uv run pytest \
-            -m "not cloud" \
+            -m "not cloud and not benchmark" \
             --junitxml=pytest-cloudless.xml \
             --cov-report=xml:coverage.xml \
-            --cov bids2table \
+            --cov=bids2table \
             tests
 
-      - name: Run tests with cloudpathlib
+      - name: Run cloud tests
         run: |
           uv run pytest \
-            -m "cloud" \
+            -m "cloud and not benchmark" \
             --junitxml=pytest-cloud.xml \
             --cov-report=xml:coverage.xml \
             --cov=bids2table \

pyproject.toml

@@ -35,11 +35,11 @@ s3 = [
 pybids = ["pandas>=2.0.0"]
 
 [dependency-groups]
-benchmark = ["polars>=1.40.1", "pytest>=9.0.3", "pytest-benchmark>=5.2.3"]
 dev = [
     "pdoc>=16.0.0",
     "pre-commit>=4.6.0",
     "pytest>=9.0.3",
+    "pytest-benchmark>=5.2.3",
     "pytest-cov>=7.1.0",
     "ruff>=0.15.13",
 ]

tests/benchmarks/test_index.py

@@ -67,6 +67,7 @@ def _teardown(index_fpath: Path):
 
 
 @pytest.mark.benchmark
+@pytest.mark.cloud
 def test_openneuro(benchmark: BenchmarkFixture, tmp_path: Path) -> None:
     """Benchmark b2t2 with a subset of datasets on OpenNeuro."""
     workers = 4