Merge branch 'dev' into pythonicworkflow

Author: KumoLiu

.github/workflows/blossom-ci.yml

@@ -34,8 +34,7 @@ jobs:
       (
         github.actor == 'Nic-Ma' ||
         github.actor == 'wyli' ||
-        github.actor == 'pxLi' ||
-        github.actor == 'YanxuanLiu' ||
+        github.actor == 'wendell-hom' ||
         github.actor == 'KumoLiu'
       )
     steps:

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -26,33 +26,30 @@ repos:
         args: ['--autofix', '--no-sort-keys', '--indent=4']
       - id: end-of-file-fixer
       - id: mixed-line-ending
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.3.5
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.0
     hooks:
     -   id: ruff
         args:
         - --fix
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
-        args: [--py37-plus]
-        name: Upgrade code excluding monai networks
+        args: [--py39-plus, --keep-runtime-typing]
+        name: Upgrade code with exceptions
         exclude: |
           (?x)(
               ^versioneer.py|
               ^monai/_version.py|
-              ^monai/networks/|  # no PEP 604 for torchscript tensorrt
-              ^monai/losses/  # no PEP 604 for torchscript tensorrt
+              ^monai/networks/| # avoid typing rewrites
+              ^monai/apps/detection/utils/anchor_utils.py| # avoid typing rewrites
+              ^tests/test_compute_panoptic_quality.py # avoid typing rewrites
           )
-      - id: pyupgrade
-        args: [--py37-plus, --keep-runtime-typing]
-        name: Upgrade monai networks
-        files: (?x)(^monai/networks/)
 
   - repo: https://github.com/asottile/yesqa
-    rev: v1.4.0
+    rev: v1.5.0
     hooks:
       - id: yesqa
         name: Unused noqa

CHANGELOG.md

@@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
-## [1.4.0] - 2024-10-14
+## [1.4.0] - 2024-10-17
 ## What's Changed
 ### Added
 * Implemented Conjugate Gradient Solver to generate confidence maps. (#7876)

CITATION.cff

@@ -6,7 +6,7 @@ title: "MONAI: Medical Open Network for AI"
 abstract: "AI Toolkit for Healthcare Imaging"
 authors:
   - name: "MONAI Consortium"
-date-released: 2024-10-14
+date-released: 2024-10-17
 version: "1.4.0"
 identifiers:
   - description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."

CONTRIBUTING.md

@@ -383,3 +383,8 @@ then make PRs to the `releasing/[version number]` to fix the bugs via the regula
 If any error occurs after the release process, first check out a new hotfix branch from the `main` branch,
 make a patch version release following the semantic versioning, for example, `releasing/0.1.1`.
 Make sure the `releasing/0.1.1` is merged back into both `dev` and `main` and all the test pipelines succeed.
+
+
+<p align="right">
+  <a href="#introduction">⬆️ Back to Top</a>
+</p>

README.md

@@ -16,11 +16,11 @@
 [![codecov](https://codecov.io/gh/Project-MONAI/MONAI/branch/dev/graph/badge.svg?token=6FTC7U1JJ4)](https://codecov.io/gh/Project-MONAI/MONAI)
 [![monai Downloads Last Month](https://assets.piptrends.com/get-last-month-downloads-badge/monai.svg 'monai Downloads Last Month by pip Trends')](https://piptrends.com/package/monai)
 
-MONAI is a [PyTorch](https://pytorch.org/)-based, [open-source](https://github.com/Project-MONAI/MONAI/blob/dev/LICENSE) framework for deep learning in healthcare imaging, part of [PyTorch Ecosystem](https://pytorch.org/ecosystem/).
-Its ambitions are:
-- developing a community of academic, industrial and clinical researchers collaborating on a common foundation;
-- creating state-of-the-art, end-to-end training workflows for healthcare imaging;
-- providing researchers with the optimized and standardized way to create and evaluate deep learning models.
+MONAI is a [PyTorch](https://pytorch.org/)-based, [open-source](https://github.com/Project-MONAI/MONAI/blob/dev/LICENSE) framework for deep learning in healthcare imaging, part of the [PyTorch Ecosystem](https://pytorch.org/ecosystem/).
+Its ambitions are as follows:
+- Developing a community of academic, industrial and clinical researchers collaborating on a common foundation;
+- Creating state-of-the-art, end-to-end training workflows for healthcare imaging;
+- Providing researchers with the optimized and standardized way to create and evaluate deep learning models.
 
 
 ## Features

monai/__init__.py

@@ -11,12 +11,12 @@
 
 from __future__ import annotations
 
+import logging
 import os
 import sys
-import logging
 import warnings
-from ._version import get_versions
 
+from ._version import get_versions
 
 old_showwarning = warnings.showwarning
 

monai/apps/detection/networks/retinanet_network.py

@@ -42,7 +42,7 @@
 import math
 import warnings
 from collections.abc import Callable, Sequence
-from typing import Any, Dict
+from typing import Any
 
 import torch
 from torch import Tensor, nn
@@ -330,7 +330,7 @@ def forward(self, images: Tensor) -> Any:
         features = self.feature_extractor(images)
         if isinstance(features, Tensor):
             feature_maps = [features]
-        elif torch.jit.isinstance(features, Dict[str, Tensor]):
+        elif torch.jit.isinstance(features, dict[str, Tensor]):
             feature_maps = list(features.values())
         else:
             feature_maps = list(features)

monai/apps/detection/transforms/array.py

@@ -15,7 +15,8 @@
 
 from __future__ import annotations
 
-from typing import Any, Sequence
+from collections.abc import Sequence
+from typing import Any
 
 import numpy as np
 import torch

monai/apps/generation/maisi/networks/autoencoderkl_maisi.py

@@ -13,7 +13,7 @@
 
 import gc
 import logging
-from typing import Sequence
+from collections.abc import Sequence
 
 import torch
 import torch.nn as nn