enforce python engine in wgs_data_catalog to ensure thread-safety in CI

Author: tristanpwdennis

.github/workflows/tests.yml

@@ -33,10 +33,4 @@ jobs:
         run: pip install "${{ matrix.numpy-version }}" .[dev]
 
       - name: Run unit tests
-        env:
-          OMP_NUM_THREADS: 1
-          OPENBLAS_NUM_THREADS: 1
-          MKL_NUM_THREADS: 1
-          VECLIB_MAXIMUM_THREADS: 1
-          NUMEXPR_NUM_THREADS: 1
         run: pytest -v tests --ignore tests/integration --typeguard-packages=malariagen_data,malariagen_data.anoph

malariagen_data/anoph/sample_metadata.py

@@ -992,7 +992,9 @@ def wgs_data_catalog(self, sample_set: base_params.sample_set):
         # Load data catalog.
         path = f"{self._base_path}/{release_path}/metadata/general/{sample_set}/wgs_snp_data.csv"
         with self._fs.open(path) as f:
-            df = pd.read_csv(f, na_values="")
+            df = pd.read_csv(
+                f, na_values="", engine="python"
+            )  # Force python engine to ensure thread-safety
 
         # Normalise columns.
         df = df[