monai-weekly 1.7.dev2632__tar.gz → 1.7.dev2636__tar.gz

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2636}/PKG-INFO

@@ -1,15 +1,13 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.7.dev2632
+Version: 1.7.dev2636
 Summary: AI Toolkit for Healthcare Imaging
-Home-page: https://project-monai.github.io/
-Author: MONAI Consortium
-Author-email: monai.contact@gmail.com
+Author-email: MONAI Consortium <monai.contact@gmail.com>
 License: Apache License 2.0
+Project-URL: Homepage, https://project-monai.github.io/
 Project-URL: Documentation, https://monai.readthedocs.io/
 Project-URL: Bug Tracker, https://github.com/Project-MONAI/MONAI/issues
 Project-URL: Source Code, https://github.com/Project-MONAI/MONAI
-Platform: OS Independent
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Education
 Classifier: Intended Audience :: Science/Research
@@ -28,140 +26,170 @@ Classifier: Topic :: Software Development
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Typing :: Typed
 Requires-Python: >=3.10
-Description-Content-Type: text/markdown; charset=UTF-8
+Description-Content-Type: text/markdown
 License-File: LICENSE
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 Provides-Extra: all
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+Requires-Dist: packaging; extra == "testing"
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+Requires-Dist: pre-commit; extra == "testing"
+Requires-Dist: pycodestyle; extra == "testing"
+Requires-Dist: pyflakes; extra == "testing"
+Requires-Dist: pyrefly>=1.0.0; extra == "testing"
+Requires-Dist: ruff>=0.16.5; extra == "testing"
+Requires-Dist: tomli; extra == "testing"
+Requires-Dist: types-PyYAML; extra == "testing"
+Requires-Dist: types-setuptools; extra == "testing"
 Dynamic: license-file
 
 <p align="center">
@@ -207,7 +235,7 @@ MONAI works with the [currently supported versions of Python](https://devguide.p
 * Major releases of MONAI will have dependency versions stated for them. The current state of the `dev` branch in this repository is the unreleased development version of MONAI which typically will support current versions of dependencies and include updates and bug fixes to do so.
 * PyTorch support covers [the current version](https://github.com/pytorch/pytorch/releases) plus three previous minor versions. If compatibility issues with a PyTorch version and other dependencies arise, support for a version may be delayed until a major release.
 * Our support policy for other dependencies adheres for the most part to [SPEC0](https://scientific-python.org/specs/spec-0000), where dependency versions are supported where possible for up to two years. Discovered vulnerabilities or defects may require certain versions to be explicitly not supported.
-* See the `requirements*.txt` files for dependency version information.
+* See the `pyproject.toml` file for dependency version information.
 
 ## Installation
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2636}/README.md

@@ -41,7 +41,7 @@ MONAI works with the [currently supported versions of Python](https://devguide.p
 * Major releases of MONAI will have dependency versions stated for them. The current state of the `dev` branch in this repository is the unreleased development version of MONAI which typically will support current versions of dependencies and include updates and bug fixes to do so.
 * PyTorch support covers [the current version](https://github.com/pytorch/pytorch/releases) plus three previous minor versions. If compatibility issues with a PyTorch version and other dependencies arise, support for a version may be delayed until a major release.
 * Our support policy for other dependencies adheres for the most part to [SPEC0](https://scientific-python.org/specs/spec-0000), where dependency versions are supported where possible for up to two years. Discovered vulnerabilities or defects may require certain versions to be explicitly not supported.
-* See the `requirements*.txt` files for dependency version information.
+* See the `pyproject.toml` file for dependency version information.
 
 ## Installation
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2636}/monai/__init__.py

@@ -62,8 +62,8 @@ PY_REQUIRED_MAJOR = 3
 PY_REQUIRED_MINOR = 9
 
 version_dict = get_versions()
-__version__: str = version_dict.get("version", "0+unknown")
-__revision_id__: str = version_dict.get("full-revisionid")
+__version__: str = str(version_dict.get("version", "0+unknown"))
+__revision_id__: str = str(version_dict.get("full-revisionid") or "")
 del get_versions, version_dict
 
 __copyright__ = "(c) MONAI Consortium"
@@ -136,4 +136,4 @@ except Exception:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "87060c45f8bbe7e1b677e0a9f872abce9890fb7f"
+__commit_id__ = "d1306f6d1996cffeb9d10984dd1c056b7fe2ed1d"

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2636}/monai/_version.py

@@ -1,5 +1,5 @@
 
-# This file was generated by 'versioneer.py' (0.23) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-08-09T02:43:34+0000",
+ "date": "2026-09-06T02:14:40+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "5a454eec9f1b95c6e263b40f7d237f1fdf8f654c",
- "version": "1.7.dev2632"
+ "full-revisionid": "917231cf0496c0a06cc1fe4c78822d570f8a2899",
+ "version": "1.7.dev2636"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2636}/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.dev2636}/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.dev2636}/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.dev2636}/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.dev2636}/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.dev2636}/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.dev2636}/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.dev2636}/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.dev2636}/monai/apps/nnunet/nnunetv2_runner.py

@@ -17,6 +17,8 @@ import os
 import re
 import shlex
 import subprocess
+import warnings
+from concurrent.futures import ThreadPoolExecutor
 from typing import Any
 
 import monai
@@ -274,6 +276,7 @@ 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,
@@ -709,7 +712,11 @@ class nnUNetV2Runner:  # noqa: N801
         **kwargs: Any,
     ) -> None:
         """
-        Create the line command for subprocess call for parallel training.
+        Launch subprocesses for parallel training.
+
+        The commands for each GPU run sequentially on that device, while different devices run in
+        parallel. Each stage waits for all of its devices to finish before the next stage starts.
+
         Note: to set the number of GPUs to use, use ``gpu_id_for_all`` instead of the `CUDA_VISIBLE_DEVICES`
         environment variable.
 
@@ -740,17 +747,19 @@ class nnUNetV2Runner:  # noqa: N801
                     f"log '.txt' inside '{os.path.join(self.nnunet_results, self.dataset_name)}'"
                 )
         for stage in all_cmds:
-            processes = []
-            for device_id in stage:
-                if not stage[device_id]:
-                    continue
-                cmd_str = "; ".join(shlex.join(cmd) for cmd, _ in stage[device_id])
-                env = stage[device_id][0][1]
-                logger.info(f"Current running command on GPU device {device_id}:\n{cmd_str}\n")
-                processes.append(subprocess.Popen(cmd_str, shell=True, env=env, stdout=subprocess.DEVNULL))
-            # finish this stage first
-            for p in processes:
-                p.wait()
+            device_cmds = [(device_id, gpu_cmds) for device_id, gpu_cmds in stage.items() if gpu_cmds]
+            if not device_cmds:
+                continue
+
+            def _run_device_commands(item):
+                device_id, gpu_cmds = item
+                for cmd, env in gpu_cmds:
+                    cmd_str = shlex.join(cmd)
+                    logger.info(f"Current running command on GPU device {device_id}:\n{cmd_str}\n")
+                    subprocess.Popen(cmd, shell=False, env=env, stdout=subprocess.DEVNULL).wait()
+
+            with ThreadPoolExecutor(max_workers=len(device_cmds)) as executor:
+                list(executor.map(_run_device_commands, device_cmds))
 
     def validate_single_model(self, config: str, fold: int, **kwargs: Any) -> None:
         """
@@ -995,7 +1004,16 @@ class nnUNetV2Runner:  # noqa: N801
 
         # apply postprocessing
         if run_postprocessing:
-            pp_fns, pp_fn_kwargs = load_pickle(self.best_configuration["best_model_or_ensemble"]["postprocessing_file"])
+            postprocessing_file = self.best_configuration["best_model_or_ensemble"]["postprocessing_file"]
+            warnings.warn(
+                f"unpickling postprocessing_file {postprocessing_file}: this path is read from "
+                "inference_information.json and is loaded with Python pickle without any allow list, "
+                "which gives whoever controls that file arbitrary code execution. Only proceed if the "
+                "inference_information.json is from a source you trust "
+                "(see https://github.com/Project-MONAI/MONAI/security/advisories/GHSA-8f32-8649-rv87).",
+                stacklevel=2,
+            )
+            pp_fns, pp_fn_kwargs = load_pickle(postprocessing_file)
             apply_postprocessing_to_folder(
                 folder_for_pp,
                 join(target_dir_base, "ensemble_predictions_postprocessed"),

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2636}/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.dev2636}/monai/apps/utils.py

@@ -166,20 +166,20 @@ def safe_extract_member(member, extract_to):
     return full_path
 
 
-def check_hash(filepath: PathLike, val: str | None = None, hash_type: str = "md5") -> bool:
+def check_hash(filepath: PathLike, val: str | None = None, hash_type: str = "sha256") -> bool:
     """
     Verify hash signature of specified file.
 
     Args:
         filepath: path of source file to verify hash value.
         val: expected hash value of the file.
-        hash_type: type of hash algorithm to use, default is `"md5"`.
+        hash_type: type of hash algorithm to use, default is `"sha256"`.
             The supported hash types are `"md5"`, `"sha1"`, `"sha256"`, `"sha512"`.
             See also: :py:data:`monai.apps.utils.SUPPORTED_HASH_TYPES`.
 
     """
     if val is None:
-        logger.info(f"Expected {hash_type} is None, skip {hash_type} check for file {filepath}.")
+        warnings.warn(f"No hash value provided for {filepath}; file integrity is NOT verified.", stacklevel=2)
         return True
     actual_hash_func = look_up_option(hash_type.lower(), SUPPORTED_HASH_TYPES)
 
@@ -204,7 +204,7 @@ def download_url(
     url: str,
     filepath: PathLike = "",
     hash_val: str | None = None,
-    hash_type: str = "md5",
+    hash_type: str = "sha256",
     progress: bool = True,
     **gdown_kwargs: Any,
 ) -> None:
@@ -217,7 +217,8 @@ def download_url(
             If undefined, `os.path.basename(url)` will be used.
         hash_val: expected hash value to validate the downloaded file.
             if None, skip hash validation.
-        hash_type: 'md5' or 'sha1', defaults to 'md5'.
+        hash_type: type of hash algorithm to use, default is `"sha256"`.
+            The supported hash types are `"md5"`, `"sha1"`, `"sha256"`, `"sha512"`.
         progress: whether to display a progress bar.
         gdown_kwargs: other args for `gdown` except for the `url`, `output` and `quiet`.
             these args will only be used if download from google drive.
@@ -315,7 +316,7 @@ def extractall(
     filepath: PathLike,
     output_dir: PathLike = ".",
     hash_val: str | None = None,
-    hash_type: str = "md5",
+    hash_type: str = "sha256",
     file_type: str = "",
     has_base: bool = True,
 ) -> None:
@@ -328,7 +329,7 @@ def extractall(
         output_dir: target directory to save extracted files.
         hash_val: expected hash value to validate the compressed file.
             if None, skip hash validation.
-        hash_type: 'md5' or 'sha1', defaults to 'md5'.
+        hash_type: type of hash algorithm to use, default is `"sha256"`.
         file_type: string of file type for decompressing. Leave it empty to infer the type from the filepath basename.
         has_base: whether the extracted files have a base folder. This flag is used when checking if the existing
             folder is a result of `extractall`, if it is, the extraction is skipped. For example, if A.zip is unzipped
@@ -394,7 +395,7 @@ def download_and_extract(
     filepath: PathLike = "",
     output_dir: PathLike = ".",
     hash_val: str | None = None,
-    hash_type: str = "md5",
+    hash_type: str = "sha256",
     file_type: str = "",
     has_base: bool = True,
     progress: bool = True,
@@ -410,7 +411,7 @@ def download_and_extract(
             default is the current directory.
         hash_val: expected hash value to validate the downloaded file.
             if None, skip hash validation.
-        hash_type: 'md5' or 'sha1', defaults to 'md5'.
+        hash_type: type of hash algorithm to use, default is `"sha256"`.
         file_type: string of file type for decompressing. Leave it empty to infer the type from url's base file name.
         has_base: whether the extracted files have a base folder. This flag is used when checking if the existing
             folder is a result of `extractall`, if it is, the extraction is skipped. For example, if A.zip is unzipped

{monai_weekly-1.7.dev2632 → monai_weekly-1.7.dev2636}/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)}