Update dependencies (#518)

Author: j-adamczyk

Makefile

@@ -39,6 +39,10 @@ test: ## Run tests
 	  uv run pytest tests --ignore=tests/datasets ;\
 	fi
 
+test_with_datasets: ## Run tests, always including dataset tests
+	uv run ruff check
+	uv run pytest tests
+
 test-coverage: ## Run tests and calculate test coverage
 	-mkdir .tmp_coverage_files
 	uv run pytest --cov=skfp tests

pyproject.toml

@@ -26,11 +26,11 @@ requires-python = ">=3.10,<3.14"
 dependencies = [
     "descriptastorus>=2.0.0,<3",
     "e3fp>=1.2.6,<2",
-    "huggingface_hub>=0.20.0,<1",
+    "huggingface_hub>=0.20.0,<2",
     "joblib>=1.0.0,<2",
     "mordredcommunity>=2.0.0,<3",
     "numpy>=1.26.4,<3",
-    "pandas>=1.5.3,<3",
+    "pandas>=1.5.3,<4",
     "rdkit>=2023.9.6,<=2025.9.3",
     "scikit-learn>=1.6.0,<2",
     "scipy>=1.12.0,<2",

skfp/fingerprints/map.py

@@ -283,8 +283,8 @@ def _get_atom_pair_shingles(self, mol: Mol, atoms_envs: dict) -> set[bytes]:
 
     @staticmethod
     def _make_shingle(env_a: str | None, env_b: str | None, distance: int) -> str:
-        env_a = env_a if env_a else ""
-        env_b = env_b if env_b else ""
+        env_a = env_a or ""
+        env_b = env_b or ""
 
         if len(env_a) > len(env_b):
             larger_env: str = env_a

skfp/preprocessing/input_output/smiles.py

@@ -158,7 +158,7 @@ def transform_x_y(self, X, y, copy: bool = False) -> tuple[list[Mol], np.ndarray
     def _transform_batch(self, X: Sequence[str]) -> list[Mol]:
         with no_rdkit_logs() if self.suppress_warnings else nullcontext():
             require_strings(X)
-            replacements = self.replacements if self.replacements else {}
+            replacements = self.replacements or {}
             return [
                 MolFromSmiles(smi, sanitize=self.sanitize, replacements=replacements)
                 for smi in X