Fix linting (snorkel-team#1696)

* Fix linting

* Reformat file

* Fix failing UTs

Author: humzaiqbal

snorkel/classification/multitask_classifier.py

@@ -360,17 +360,17 @@ def predict(
                 prob_dict_list[label_name].extend(prob_batch_dict[task_name])
                 gold_dict_list[label_name].extend(Y.cpu().numpy())
 
-        gold_dict: Dict[str, np.ndarray] = {}
-        prob_dict: Dict[str, np.ndarray] = {}
+        gold_dict: Dict[str, torch.Tensor] = {}
+        prob_dict: Dict[str, torch.Tensor] = {}
 
         for task_name in gold_dict_list:
-            gold_dict[task_name] = np.array(gold_dict_list[task_name])
-            prob_dict[task_name] = np.array(prob_dict_list[task_name])
+            gold_dict[task_name] = torch.Tensor(np.array(gold_dict_list[task_name]))
+            prob_dict[task_name] = torch.Tensor(np.array(prob_dict_list[task_name]))
 
         if return_preds:
-            pred_dict: Dict[str, np.ndarray] = defaultdict(list)
+            pred_dict: Dict[str, torch.Tensor] = defaultdict(np.ndarray)
             for task_name, probs in prob_dict.items():
-                pred_dict[task_name] = probs_to_preds(probs)
+                pred_dict[task_name] = torch.Tensor(probs_to_preds(probs.numpy()))
 
         results = {"golds": gold_dict, "probs": prob_dict}
 
@@ -431,9 +431,9 @@ def score(
             # Score and record metrics for each set of predictions
             for label_name, task_name in labels_to_tasks.items():
                 metric_scores = self.scorers[task_name].score(
-                    golds=results["golds"][label_name],
-                    preds=results["preds"][label_name],
-                    probs=results["probs"][label_name],
+                    golds=results["golds"][label_name].numpy(),
+                    preds=results["preds"][label_name].numpy(),
+                    probs=results["probs"][label_name].numpy(),
                 )
 
                 for metric_name, metric_value in metric_scores.items():

snorkel/labeling/apply/core.py

@@ -69,7 +69,7 @@ def _numpy_from_row_data(self, labels: List[RowData]) -> np.ndarray:
         if self._use_recarray:
             n_rows, _ = L.shape
             dtype = [(name, np.int64) for name in self._lf_names]
-            recarray = np.recarray(n_rows, dtype=dtype)
+            recarray: np.ndarray = np.recarray(n_rows, dtype=dtype)
             for idx, name in enumerate(self._lf_names):
                 recarray[name] = L[:, idx]
 

snorkel/labeling/model/label_model.py

@@ -60,7 +60,7 @@ class TrainConfig(Config):
     lr_scheduler: str = "constant"
     lr_scheduler_config: LRSchedulerConfig = LRSchedulerConfig()  # type: ignore
     prec_init: Union[float, List[float], np.ndarray, torch.Tensor] = 0.7
-    seed: int = np.random.randint(1e6)
+    seed: int = np.random.randint(1e6)  # type: ignore
     log_freq: int = 10
     mu_eps: Optional[float] = None
 
@@ -557,7 +557,9 @@ def _loss_mu(self, l2: float = 0) -> torch.Tensor:
         return loss_1 + loss_2 + self._loss_l2(l2=l2)
 
     def _set_class_balance(
-        self, class_balance: Optional[List[float]], Y_dev: np.ndarray
+        self,
+        class_balance: Optional[List[float]],
+        Y_dev: Optional[np.ndarray] = None,
     ) -> None:
         """Set a prior for the class balance.
 

snorkel/slicing/utils.py

@@ -36,7 +36,7 @@ def add_slice_labels(
 
     slice_names = S.dtype.names
 
-    Y_dict: Dict[str, np.ndarray] = dataloader.dataset.Y_dict  # type: ignore
+    Y_dict: Dict[str, torch.Tensor] = dataloader.dataset.Y_dict  # type: ignore
     labels = Y_dict[base_task.name]
 
     for slice_name in slice_names:

snorkel/utils/core.py

@@ -1,5 +1,5 @@
 import hashlib
-from typing import Dict, List
+from typing import Dict, List, Optional
 
 import numpy as np
 
@@ -69,7 +69,7 @@ def probs_to_preds(
             raise ValueError(
                 f"tie_break_policy={tie_break_policy} policy not recognized."
             )
-    return Y_pred.astype(np.int)
+    return Y_pred.astype(np.int_)
 
 
 def preds_to_probs(preds: np.ndarray, num_classes: int) -> np.ndarray:
@@ -129,7 +129,7 @@ def to_int_label_array(X: np.ndarray, flatten_vector: bool = True) -> np.ndarray
 
 
 def filter_labels(
-    label_dict: Dict[str, np.ndarray], filter_dict: Dict[str, List[int]]
+    label_dict: Dict[str, Optional[np.ndarray]], filter_dict: Dict[str, List[int]]
 ) -> Dict[str, np.ndarray]:
     """Filter out examples from arrays based on specified labels to filter.
 
@@ -195,7 +195,7 @@ def _get_mask(label_array: np.ndarray, filter_values: List[int]) -> np.ndarray:
     np.ndarray
         A boolean mask indicating whether to keep (1) or filter (0) each example
     """
-    mask = np.ones_like(label_array).astype(bool)
+    mask: np.ndarray = np.ones_like(label_array).astype(bool)
     for value in filter_values:
         mask *= np.where(label_array != value, 1, 0).astype(bool)
     return mask