monai-weekly 1.7.dev2632__tar.gz → 1.7.dev2633__tar.gz

{monai_weekly-1.7.dev2632/monai_weekly.egg-info → monai_weekly-1.7.dev2633}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.7.dev2632
+Version: 1.7.dev2633
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://project-monai.github.io/
 Author: MONAI Consortium

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/__init__.py

@@ -136,4 +136,4 @@ except Exception:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "87060c45f8bbe7e1b677e0a9f872abce9890fb7f"
+__commit_id__ = "7f6bf2db52387d14ef867a79b888e7cc1b81c700"

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-08-09T02:43:34+0000",
+ "date": "2026-08-16T02:28:27+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "5a454eec9f1b95c6e263b40f7d237f1fdf8f654c",
- "version": "1.7.dev2632"
+ "full-revisionid": "17ff85f5808a658c19beac995edd5c28f1ee72a3",
+ "version": "1.7.dev2633"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/auto3dseg/auto_runner.py

@@ -790,6 +790,7 @@ class AutoRunner:
             nni_config_filename = os.path.abspath(os.path.join(self.work_dir, f"{name}_nni_config.yaml"))
             ConfigParser.export_config_file(nni_config, nni_config_filename, fmt="yaml", default_flow_style=None)
 
+            # pyrefly: ignore [redundant-cast]
             max_trial = min(self.hpo_tasks, cast(int, default_nni_config["maxTrialNumber"]))
             cmd = "nnictl create --config " + nni_config_filename + " --port 8088"
 
@@ -805,6 +806,7 @@ class AutoRunner:
                 n_trainings = len(import_bundle_algo_history(self.work_dir, only_trained=True))
 
             cmd = "nnictl stop --all"
+            # pyrefly: ignore [bad-argument-type]
             run_cmd(cmd.split(), check=True)
             logger.info(f"NNI completes HPO on {name}")
             last_total_tasks = n_trainings

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/deepedit/transforms.py

@@ -434,6 +434,7 @@ class AddInitialSeedPointDeepEditd(Randomizable, MapTransform):
         else:
             logger.info(f"Not slice IDs for label: {key_label}")
             sid = None
+        # pyrefly: ignore [unsupported-operation]
         self.sid[key_label] = sid
 
     def __call__(self, data: Mapping[Hashable, np.ndarray]) -> dict[Hashable, np.ndarray]:
@@ -561,6 +562,7 @@ class AddRandomGuidanceDeepEditd(Randomizable, MapTransform):
         self.guidance: dict[str, list[list[int]]] = {}
 
     def randomize(self, data=None):
+        # pyrefly: ignore [unsupported-operation]
         probability = data[self.probability]
         self._will_interact = self.R.choice([True, False], p=[probability, 1.0 - probability])
 
@@ -885,6 +887,7 @@ class AddInitialSeedPointMissingLabelsd(Randomizable, MapTransform):
         else:
             logger.info(f"Not slice IDs for label: {key_label}")
             sid = None
+        # pyrefly: ignore [unsupported-operation]
         self.sid[key_label] = sid
 
     def __call__(self, data: Mapping[Hashable, np.ndarray]) -> dict[Hashable, np.ndarray]:

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/deepgrow/dataset.py

@@ -175,6 +175,7 @@ def _save_data_2d(vol_idx, vol_image, vol_label, dataset_dir, relative_path):
             continue
 
         # For all Labels
+        # pyrefly: ignore [missing-attribute]
         unique_labels = np.unique(label.flatten())
         unique_labels = unique_labels[unique_labels != 0]
         unique_labels_count = max(unique_labels_count, len(unique_labels))

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/deepgrow/transforms.py

@@ -288,6 +288,7 @@ class AddRandomGuidanced(Randomizable, Transform):
         self._will_interact = None
 
     def randomize(self, data=None):
+        # pyrefly: ignore [unsupported-operation]
         probability = data[self.probability]
         self._will_interact = self.R.choice([True, False], p=[probability, 1.0 - probability])
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/detection/networks/retinanet_detector.py

@@ -525,6 +525,7 @@ class RetinaNetDetector(nn.Module):
             )
 
         # 4. Generate anchors and store it in self.anchors: List[Tensor]
+        # pyrefly: ignore [bad-argument-type]
         self.generate_anchors(images, head_outputs)
         # num_anchor_locs_per_level: List[int], list of HW or HWD for each level
         num_anchor_locs_per_level = [x.shape[2:].numel() for x in head_outputs[self.cls_key]]
@@ -535,6 +536,7 @@ class RetinaNetDetector(nn.Module):
             # reshape to Tensor sized(B, sum(HWA), self.num_classes) for self.cls_key
             # or (B, sum(HWA), 2* self.spatial_dims) for self.box_reg_key
             # A = self.num_anchors_per_loc
+            # pyrefly: ignore [bad-argument-type]
             head_outputs[key] = self._reshape_maps(head_outputs[key])
 
         # 6(1). If during training, return losses

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/detection/transforms/array.py

@@ -257,10 +257,14 @@ class ZoomBox(Transform):
                 diff = od - zd
                 half = abs(diff) // 2
                 if diff > 0:  # need padding (half, diff - half)
+                    # pyrefly: ignore [bad-index, unsupported-operation]
                     zoomed_boxes[:, axis] = zoomed_boxes[:, axis] + half
+                    # pyrefly: ignore [bad-index, unsupported-operation]
                     zoomed_boxes[:, axis + spatial_dims] = zoomed_boxes[:, axis + spatial_dims] + half
                 elif diff < 0:  # need slicing (half, half + od)
+                    # pyrefly: ignore [bad-index, unsupported-operation]
                     zoomed_boxes[:, axis] = zoomed_boxes[:, axis] - half
+                    # pyrefly: ignore [bad-index, unsupported-operation]
                     zoomed_boxes[:, axis + spatial_dims] = zoomed_boxes[:, axis + spatial_dims] - half
         return zoomed_boxes
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/detection/transforms/box_ops.py

@@ -186,7 +186,9 @@ def flip_boxes(
     _flip_boxes: NdarrayTensor = boxes.clone() if isinstance(boxes, torch.Tensor) else deepcopy(boxes)  # type: ignore[assignment]
 
     for axis in flip_axes:
+        # pyrefly: ignore [bad-index, unsupported-operation]
         _flip_boxes[:, axis + spatial_dims] = spatial_size[axis] - boxes[:, axis] - TO_REMOVE
+        # pyrefly: ignore [bad-index, unsupported-operation]
         _flip_boxes[:, axis] = spatial_size[axis] - boxes[:, axis + spatial_dims] - TO_REMOVE
 
     return _flip_boxes

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/generation/maisi/networks/autoencoderkl_maisi.py

@@ -246,7 +246,9 @@ class MaisiConvolution(nn.Module):
 
         # update padding length if necessary
         padding = 3
+        # pyrefly: ignore [unsupported-operation]
         if padding % self.stride > 0:
+            # pyrefly: ignore [unsupported-operation]
             padding = (padding // self.stride + 1) * self.stride
         if self.print_info:
             logger.info(f"Padding size: {padding}")

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/nnunet/nnunetv2_runner.py

@@ -274,6 +274,7 @@ class nnUNetV2Runner:  # noqa: N801
                 modality = [modality]
 
             create_new_dataset_json(
+                # pyrefly: ignore [bad-argument-type]
                 modality=modality,
                 num_foreground_classes=num_foreground_classes,
                 num_input_channels=num_input_channels,

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/apps/pathology/transforms/post/dictionary.py

@@ -403,6 +403,7 @@ class GenerateInstanceCentroidd(MapTransform):
         d = dict(data)
         for key in self.key_iterator(d):
             offset = d[self.offset_key] if self.offset_key else None
+            # pyrefly: ignore [bad-argument-type]
             centroid = self.converter(d[key], offset)
             key_to_add = f"{key}_{self.centroid_key_postfix}"
             if key_to_add in d:

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/auto3dseg/operations.py

@@ -149,4 +149,5 @@ class SummaryOperations(Operations):
         Args:
             data: input data
         """
+        # pyrefly: ignore [missing-attribute]
         return {k: v(data[k], **kwargs).tolist() for k, v in self.data.items() if (callable(v) and k in data)}

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/auto3dseg/seg_summarizer.py

@@ -208,6 +208,7 @@ class SegSummarizer(Compose):
 
         for analyzer in self.summary_analyzers:
             if callable(analyzer):
+                # pyrefly: ignore [missing-attribute]
                 report.update({analyzer.stats_name: analyzer(data)})
 
         return report

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/bundle/reference_resolver.py

@@ -254,6 +254,7 @@ class ReferenceResolver:
         """
         for k, v in config.items() if isinstance(config, dict) else enumerate(config):
             sub_id = f"{id}{cls.sep}{k}" if id != "" else f"{k}"
+            # pyrefly: ignore [invalid-yield]
             yield k, sub_id, v
 
     @classmethod

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/bundle/scripts.py

@@ -1966,6 +1966,7 @@ def create_workflow(
         )
 
     if config_file is not None:
+        # pyrefly: ignore [unexpected-keyword]
         workflow_ = workflow_class(config_file=config_file, **_args)
     else:
         workflow_ = workflow_class(**_args)

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/bundle/workflows.py

@@ -224,6 +224,7 @@ class BundleWorkflow(ABC):
             desc: descriptions for the property.
         """
         if self.properties is None:
+            # pyrefly: ignore [bad-assignment]
             self.properties = {}
         if name in self.properties:
             logger.warning(f"property '{name}' already exists in the properties list, overriding it.")
@@ -329,6 +330,7 @@ class PythonicWorkflow(BundleWorkflow):
         elif name in self._props_vals:
             value = self._props_vals[name]
         elif name in self.parser.config[self.parser.meta_key]:  # type: ignore[index]
+            # pyrefly: ignore [missing-attribute]
             id = self.properties.get(name, None).get(BundlePropertyConfig.ID, None)
             value = self.parser[id]
         else:
@@ -621,6 +623,7 @@ class ConfigWorkflow(BundleWorkflow):
         else:
             ref = self.parser.get(ref_id, None)
         # for reference IDs that not refer to a property directly but using expressions, skip the check
+        # pyrefly: ignore [unsupported-operation]
         if ref is not None and not ref.startswith(EXPR_KEY) and ref != ID_REF_KEY + id:
             return False
         return True

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/data/box_utils.py

@@ -1035,8 +1035,8 @@ def spatial_crop_boxes(
     # convert to float32 since torch.clamp_ does not support float16
     boxes_t = boxes_t.to(dtype=COMPUTE_DTYPE)
 
-    roi_start_t = convert_to_dst_type(src=roi_start, dst=boxes_t, wrap_sequence=True)[0].to(torch.int16)
-    roi_end_t = convert_to_dst_type(src=roi_end, dst=boxes_t, wrap_sequence=True)[0].to(torch.int16)
+    roi_start_t = convert_to_dst_type(src=roi_start, dst=boxes_t, wrap_sequence=True)[0]
+    roi_end_t = convert_to_dst_type(src=roi_end, dst=boxes_t, wrap_sequence=True)[0]
     roi_end_t = torch.maximum(roi_end_t, roi_start_t)
 
     # makes sure the bounding boxes are within the patch

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/data/dataset.py

@@ -1648,6 +1648,7 @@ class GDSDataset(PersistentDataset):
                             item_k = kvikio_numpy.fromfile(
                                 f"{hashfile}-{k}-{i}", dtype=meta_i_k["dtype"], like=cp.empty(())
                             )
+                            # pyrefly: ignore [missing-attribute]
                             item_k = convert_to_tensor(item[i].reshape(meta_i_k["shape"]), device=f"cuda:{self.device}")
                             item[i].update({k: item_k, f"{k}_meta_dict": meta_i_k})
                     return item

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/data/grid_dataset.py

@@ -142,6 +142,7 @@ class PatchIterd:
         self, data: Mapping[Hashable, NdarrayTensor]
     ) -> Generator[tuple[Mapping[Hashable, NdarrayTensor], np.ndarray], None, None]:
         d = dict(data)
+        # pyrefly: ignore [missing-attribute]
         original_spatial_shape = d[first(self.keys)].shape[1:]
 
         for patch in zip(*[self.patch_iter(d[key]) for key in self.keys]):

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/data/image_reader.py

@@ -22,7 +22,7 @@ from abc import ABC, abstractmethod
 from collections.abc import Callable, Iterable, Iterator, Sequence
 from dataclasses import dataclass
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, TypeAlias
+from typing import TYPE_CHECKING, Any, TypeAlias  # pyrefly: ignore [missing-module-attribute]
 
 import numpy as np
 from torch.utils.data._utils.collate import np_str_obj_array_pattern

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/data/wsi_datasets.py

@@ -250,8 +250,10 @@ class SlidingPatchWSIDataset(Randomizable, PatchWSIDataset):
                     self.offset_limits = None
                 elif isinstance(offset_limits, tuple):
                     if isinstance(offset_limits[0], int):
+                        # pyrefly: ignore [bad-assignment]
                         self.offset_limits = (offset_limits, offset_limits)
                     elif isinstance(offset_limits[0], tuple):
+                        # pyrefly: ignore [bad-assignment]
                         self.offset_limits = offset_limits
                     else:
                         raise ValueError(

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/data/wsi_reader.py

@@ -319,6 +319,7 @@ class BaseWSIReader(ImageReader):
         }
         return metadata
 
+    # pyrefly: ignore [bad-override]
     def get_data(
         self,
         wsi,

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/engines/evaluator.py

@@ -489,11 +489,13 @@ class EnsembleEvaluator(Evaluator):
                 if engine.amp:
                     with torch.autocast("cuda", **engine.amp_kwargs):
                         if isinstance(engine.state.output, dict):
+                            # pyrefly: ignore [no-matching-overload]
                             engine.state.output.update(
                                 {engine.pred_keys[idx]: engine.inferer(inputs, network, *args, **kwargs)}
                             )
                 else:
                     if isinstance(engine.state.output, dict):
+                        # pyrefly: ignore [no-matching-overload]
                         engine.state.output.update(
                             {engine.pred_keys[idx]: engine.inferer(inputs, network, *args, **kwargs)}
                         )

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/engines/trainer.py

@@ -774,4 +774,5 @@ class AdversarialTrainer(Trainer):
             engine.state.output[AdversarialKeys.DISCRIMINATOR_LOSS].backward()
             engine.state.d_optimizer.step()
 
+        # pyrefly: ignore [bad-return]
         return engine.state.output

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/fl/client/monai_algo.py

@@ -251,6 +251,7 @@ class MonaiAlgoStats(ClientAlgoStats):
             dataroot=self.workflow.dataset_dir,  # type: ignore
             hist_bins=hist_bins,
             hist_range=hist_range,
+            # pyrefly: ignore [bad-argument-type]
             output_path=output_path,
             histogram_only=self.histogram_only,
         )

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/handlers/mlflow_handler.py

@@ -234,6 +234,7 @@ class MLFlowHandler:
         self._log_params(attrs)
 
         if self.dataset_logger:
+            # pyrefly: ignore [bad-argument-type]
             self.dataset_logger(self.dataset_dict)
         else:
             self._default_dataset_log(self.dataset_dict)
@@ -257,6 +258,7 @@ class MLFlowHandler:
                     else:
                         raise e
 
+        # pyrefly: ignore [missing-attribute]
         if experiment.lifecycle_stage != mlflow.entities.LifecycleStage.ACTIVE:
             raise ValueError(f"Cannot set a deleted experiment '{self.experiment_name}' as the active experiment")
         self.experiment = experiment

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/inferers/inferer.py

@@ -841,6 +841,7 @@ class SliceInferer(SlidingWindowInferer):
 
         if isinstance(out, Mapping):
             for k in out.keys():
+                # pyrefly: ignore [unsupported-operation]
                 out[k] = out[k].unsqueeze(dim=self.spatial_dim + 2)
             return out
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/losses/image_dissimilarity.py

@@ -241,6 +241,7 @@ class GlobalMutualInformationLoss(_Loss):
         if self.kernel_type == "gaussian":
             self.register_buffer("preterm", 1 / (2 * sigma**2), persistent=False)
             self.register_buffer("bin_centers", bin_centers[None, None, ...], persistent=False)
+
         self.smooth_nr = float(smooth_nr)
         self.smooth_dr = float(smooth_dr)
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/metrics/utils.py

@@ -217,6 +217,7 @@ def get_mask_edges(
         or_vol = seg_pred | seg_gt
         if not or_vol.any():
             pred, gt = lib.zeros(seg_pred.shape, dtype=bool), lib.zeros(seg_gt.shape, dtype=bool)
+            # pyrefly: ignore [bad-return]
             return (pred, gt) if spacing is None else (pred, gt, pred, gt)
         channel_first = [seg_pred[None], seg_gt[None], or_vol[None]]
         if spacing is None and not use_cucim:  # cpu only erosion

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/networks/blocks/hyena.py

@@ -98,21 +98,21 @@ class _DepthwiseFFTForward:
     _spatial_dims: int  # set by subclasses
     fft_chunk_size: int = 0  # 0 = no chunking; set in subclass __init__
 
-    def forward(self, x: torch.Tensor) -> torch.Tensor:
-        spatial = x.shape[2:]
+    def forward(self, input: torch.Tensor) -> torch.Tensor:
+        spatial = input.shape[2:]
         kernel_shape = self.weight.shape[2:]  # type: ignore[attr-defined]
         fft_dims = tuple(range(-self._spatial_dims, 0))
         fft_size = [s + k - 1 for s, k in zip(spatial, kernel_shape)]
-        in_dtype = x.dtype
+        in_dtype = input.dtype
 
         slices = (slice(None), slice(None)) + tuple(slice(k // 2, k // 2 + s) for s, k in zip(spatial, kernel_shape))
 
         chunk = getattr(self, "fft_chunk_size", 0)
-        if chunk > 0 and x.shape[1] > chunk:
+        if chunk > 0 and input.shape[1] > chunk:
             parts = []
-            for c0 in range(0, x.shape[1], chunk):
-                c1 = min(c0 + chunk, x.shape[1])
-                xc = x[:, c0:c1].float()
+            for c0 in range(0, input.shape[1], chunk):
+                c1 = min(c0 + chunk, input.shape[1])
+                xc = input[:, c0:c1].float()
                 kc = self.weight[c0:c1].squeeze(1).float()  # type: ignore[attr-defined]
                 kc = kc.flip(list(range(1, self._spatial_dims + 1)))
                 xc_fft = torch.fft.rfftn(xc, s=fft_size, dim=fft_dims)
@@ -125,7 +125,7 @@ class _DepthwiseFFTForward:
                 del out_c
             return torch.cat(parts, dim=1)
 
-        x_f32 = x.float()
+        x_f32 = input.float()
         k_f32 = self.weight.squeeze(1).float()  # type: ignore[attr-defined]
         # PyTorch ``F.conv*`` computes cross-correlation; FFT computes convolution.
         # Flip the kernel so the FFT output matches ``Conv{2,3}d`` exactly.

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/networks/nets/flexible_unet.py

@@ -61,9 +61,13 @@ class FlexUNetEncoderRegister:
                 "or implement all interfaces specified by it."
             )
 
+        # pyrefly: ignore [missing-attribute]
         name_string_list = name.get_encoder_names()
+        # pyrefly: ignore [missing-attribute]
         feature_number_list = name.num_outputs()
+        # pyrefly: ignore [missing-attribute]
         feature_channel_list = name.num_channels_per_output()
+        # pyrefly: ignore [missing-attribute]
         parameter_list = name.get_encoder_parameters()
 
         assert len(name_string_list) == len(feature_number_list) == len(feature_channel_list) == len(parameter_list)

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/networks/nets/milmodel.py

@@ -160,6 +160,7 @@ class MILModel(nn.Module):
                 ]
             )
             self.transformer = transformer_list
+            # pyrefly: ignore [unsupported-operation]
             nfc = nfc + 256
             self.attention = nn.Sequential(nn.Linear(nfc, 2048), nn.Tanh(), nn.Linear(2048, 1))
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/networks/nets/transchex.py

@@ -74,6 +74,7 @@ class BertPreTrainedModel(nn.Module):
             return load_tf_weights_in_bert(model, weights_path)
         old_keys = []
         new_keys = []
+        # pyrefly: ignore [missing-attribute]
         for key in state_dict.keys():
             new_key = None
             if "gamma" in key:
@@ -84,11 +85,13 @@ class BertPreTrainedModel(nn.Module):
                 old_keys.append(key)
                 new_keys.append(new_key)
         for old_key, new_key in zip(old_keys, new_keys):
+            # pyrefly: ignore [missing-attribute, unsupported-operation]
             state_dict[new_key] = state_dict.pop(old_key)
         missing_keys: list = []
         unexpected_keys: list = []
         error_msgs: list = []
         metadata = getattr(state_dict, "_metadata", None)
+        # pyrefly: ignore [missing-attribute]
         state_dict = state_dict.copy()
         if metadata is not None:
             state_dict._metadata = metadata

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/networks/nets/vqvae.py

@@ -361,18 +361,22 @@ class VQVAE(nn.Module):
         else:
             downsample_parameters_tuple = downsample_parameters
 
+        # pyrefly: ignore [not-iterable]
         if not all(all(isinstance(value, int) for value in sub_item) for sub_item in downsample_parameters_tuple):
             raise ValueError("`downsample_parameters` should be a single tuple of integer or a tuple of tuples.")
 
         # check if downsample_parameters is a tuple of ints or a tuple of tuples of ints
+        # pyrefly: ignore [not-iterable]
         if not all(all(isinstance(value, int) for value in sub_item) for sub_item in upsample_parameters_tuple):
             raise ValueError("`upsample_parameters` should be a single tuple of integer or a tuple of tuples.")
 
         for parameter in downsample_parameters_tuple:
+            # pyrefly: ignore [bad-argument-type]
             if len(parameter) != 4:
                 raise ValueError("`downsample_parameters` should be a tuple of tuples with 4 integers.")
 
         for parameter in upsample_parameters_tuple:
+            # pyrefly: ignore [bad-argument-type]
             if len(parameter) != 5:
                 raise ValueError("`upsample_parameters` should be a tuple of tuples with 5 integers.")
 
@@ -396,6 +400,7 @@ class VQVAE(nn.Module):
             channels=channels,
             num_res_layers=num_res_layers,
             num_res_channels=num_res_channels,
+            # pyrefly: ignore [bad-argument-type]
             downsample_parameters=downsample_parameters_tuple,
             dropout=dropout,
             act=act,
@@ -408,6 +413,7 @@ class VQVAE(nn.Module):
             channels=channels,
             num_res_layers=num_res_layers,
             num_res_channels=num_res_channels,
+            # pyrefly: ignore [bad-argument-type]
             upsample_parameters=upsample_parameters_tuple,
             dropout=dropout,
             act=act,

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/networks/utils.py

@@ -601,6 +601,7 @@ def copy_model_state(
             dst_dict[dst_key] = val
             updated_keys.append(dst_key)
     for s in mapping if mapping else {}:
+        # pyrefly: ignore [unsupported-operation]
         dst_key = f"{dst_prefix}{mapping[s]}"
         if dst_key in dst_dict and dst_key not in to_skip:
             if dst_dict[dst_key].shape != src_dict[s].shape:

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/optimizers/novograd.py

@@ -112,6 +112,7 @@ class Novograd(Optimizer):
                 norm = torch.sum(torch.pow(grad, 2))
 
                 if exp_avg_sq == 0:
+                    # pyrefly: ignore [missing-attribute]
                     exp_avg_sq.copy_(norm)
                 else:
                     exp_avg_sq.mul_(beta2).add_(norm, alpha=1 - beta2)

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/transforms/croppad/array.py

@@ -1130,6 +1130,7 @@ class RandCropByPosNegLabel(Randomizable, TraceableTransform, LazyTransform, Mul
         self.bg_indices = bg_indices
         self.allow_smaller = allow_smaller
 
+    # pyrefly: ignore [bad-override]
     def randomize(
         self,
         label: torch.Tensor | None = None,
@@ -1319,6 +1320,7 @@ class RandCropByLabelClasses(Randomizable, TraceableTransform, LazyTransform, Mu
         self.warn = warn
         self.max_samples_per_class = max_samples_per_class
 
+    # pyrefly: ignore [bad-override]
     def randomize(
         self,
         label: torch.Tensor | None = None,

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/transforms/croppad/dictionary.py

@@ -19,7 +19,7 @@ from __future__ import annotations
 
 from collections.abc import Callable, Hashable, Mapping, Sequence
 from copy import deepcopy
-from typing import Any, TypeAlias, cast
+from typing import Any, TypeAlias, cast  # pyrefly: ignore [missing-module-attribute]
 
 import numpy as np
 import torch
@@ -1104,6 +1104,7 @@ class RandCropByPosNegLabeld(Randomizable, MapTransform, LazyTransform, MultiSam
         self.cropper.set_random_state(seed, state)
         return self
 
+    # pyrefly: ignore [bad-override]
     def randomize(
         self,
         label: torch.Tensor | None = None,
@@ -1266,6 +1267,7 @@ class RandCropByLabelClassesd(Randomizable, MapTransform, LazyTransform, MultiSa
         self.cropper.set_random_state(seed, state)
         return self
 
+    # pyrefly: ignore [bad-override]
     def randomize(
         self, label: torch.Tensor, indices: list[NdarrayOrTensor] | None = None, image: torch.Tensor | None = None
     ) -> None:

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/transforms/io/array.py

@@ -210,9 +210,7 @@ class LoadImage(Transform):
                 try:
                     self.register(the_reader(*args, **kwargs))
                 except OptionalImportError:
-                    warnings.warn(
-                        f"required package for reader {_r} is not installed, or the version doesn't match requirement."
-                    )
+                    raise
                 except TypeError:  # the reader doesn't have the corresponding args/kwargs
                     warnings.warn(f"{_r} is not supported with the given parameters {args} {kwargs}.")
                     self.register(the_reader())

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/transforms/lazy/utils.py

@@ -228,11 +228,13 @@ def resample(data: torch.Tensor, matrix: NdarrayOrTensor, kwargs: dict | None =
             img.affine = call_kwargs["dst_affine"]
             img = img.to(torch.float32)  # consistent with monai.transforms.spatial.functional.spatial_resample
             return img
+        # pyrefly: ignore [bad-argument-type, implicit-import]
         img = monai.transforms.crop_or_pad_nd(img, matrix_np, out_spatial_size, mode=call_kwargs["padding_mode"])
         img = img.to(torch.float32)  # consistent with monai.transforms.spatial.functional.spatial_resample
         img.affine = call_kwargs["dst_affine"]
         return img
 
+    # pyrefly: ignore [bad-argument-type, implicit-import]
     resampler = monai.transforms.SpatialResample(**init_kwargs)
     resampler.lazy = False  # resampler is a lazytransform
     with resampler.trace_transform(False):  # don't track this transform in `img`

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/transforms/transform.py

@@ -93,8 +93,10 @@ def _apply_transform(
     data = apply_pending_transforms_in_order(transform, data, lazy, overrides, logger_name)
 
     if isinstance(data, tuple) and unpack_parameters:
+        # pyrefly: ignore [not-callable]
         return transform(*data, lazy=lazy) if isinstance(transform, LazyTrait) else transform(*data)
 
+    # pyrefly: ignore [not-callable]
     return transform(data, lazy=lazy) if isinstance(transform, LazyTrait) else transform(data)
 
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/transforms/utility/dictionary.py

@@ -759,6 +759,7 @@ class FlattenSubKeysd(MapTransform):
             sub_keys = d[key].keys() if self.sub_keys is None else self.sub_keys
 
             # move all the sub-keys to the top level
+            # pyrefly: ignore [not-iterable]
             for sk in sub_keys:
                 # set the top-level key for the sub-key
                 sk_top = f"{self.prefix}_{sk}" if self.prefix else sk

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2633}/monai/transforms/utils.py

@@ -1284,10 +1284,14 @@ def keep_merge_components_with_points(
     features_neg, _ = label(img_neg_, connectivity=3, return_num=True)
 
     outs = np.zeros_like(img_pos_)
+    # pyrefly: ignore [missing-attribute]
     for bs in range(point_coords.shape[0]):
+        # pyrefly: ignore [bad-index]
         for i, p in enumerate(point_coords[bs]):
+            # pyrefly: ignore [bad-index]
             if point_labels[bs, i] in pos_val:
                 features = features_pos
+            # pyrefly: ignore [bad-index]
             elif point_labels[bs, i] in neg_val:
                 features = features_neg
             else:
@@ -1495,8 +1499,10 @@ def remove_small_objects(
         raise RuntimeError("Skimage required.")
 
     if by_measure:
+        # pyrefly: ignore [missing-attribute]
         sr = len(img.shape[1:])
         if isinstance(img, monai.data.MetaTensor):
+            # pyrefly: ignore [missing-attribute]
             _pixdim = img.pixdim
         elif pixdim is not None:
             _pixdim = ensure_tuple_rep(pixdim, sr)