Merge branch 'main' into dependabot/pip/urllib3-2.6.0

Author: SachidanandAlle

.github/workflows/blossom-ci.yml

@@ -63,7 +63,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           repository: ${{ fromJson(needs.Authorization.outputs.args).repo }}
           ref: ${{ fromJson(needs.Authorization.outputs.args).ref }}

.github/workflows/codeql-analysis.yml

@@ -49,11 +49,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -74,4 +74,4 @@ jobs:
     #    uses a compiled language
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4

.github/workflows/docker-plugin.yml

@@ -25,9 +25,9 @@ jobs:
     env:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: 3.10
       - name: clean up

.github/workflows/docker.yml

@@ -27,7 +27,7 @@ jobs:
     env:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Cleanup
         run: |
           echo Before Cleanup...

.github/workflows/pythonapp.yml

@@ -34,9 +34,9 @@ jobs:
         os: [windows-latest, ubuntu-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - if: runner.os == 'Linux'
@@ -56,9 +56,9 @@ jobs:
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -90,12 +90,12 @@ jobs:
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v6
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: cache weekly timestamp
@@ -152,9 +152,9 @@ jobs:
       matrix:
         python-version: ["3.10"]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: cache weekly timestamp

.github/workflows/release.yml

@@ -31,12 +31,12 @@ jobs:
     env:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v6
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: 3.10
       - name: Cache for pip
@@ -82,7 +82,7 @@ jobs:
           shell: bash
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: dist
           path: dist/

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ ci:
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: check-merge-conflict
   - id: trailing-whitespace
@@ -33,27 +33,27 @@ repos:
   - id: mixed-line-ending
 
 - repo: https://github.com/pycqa/isort
-  rev: 6.0.1
+  rev: 6.1.0
   hooks:
   - id: isort
     name: isort (python)
     args: ["--line-length=120", "--profile=black"]
 
 - repo: https://github.com/pycqa/isort
-  rev: 6.0.1
+  rev: 6.1.0
   hooks:
   - id: isort
     name: isort (python) (check)
     args: ["--line-length=120", "--profile=black", "--check"]
 
-- repo: https://github.com/psf/black
-  rev: 25.1.0
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 25.9.0
   hooks:
   - id: black
     args: ["--line-length=120"]
 
-- repo: https://github.com/psf/black
-  rev: 25.1.0
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 25.9.0
   hooks:
   - id: black
     name: black (check)
@@ -66,7 +66,7 @@ repos:
     args: ["--count", "--statistics", "--config=setup.cfg"]
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.16.1
+  rev: v1.18.2
   hooks:
   - id: mypy
     exclude: (^tests/|^plugins/)

README.md

@@ -14,7 +14,7 @@ limitations under the License.
 # MONAI Label
 [![License](https://img.shields.io/badge/license-Apache%202.0-green.svg)](https://opensource.org/licenses/Apache-2.0)
 [![CI Build](https://github.com/Project-MONAI/MONAILabel/workflows/build/badge.svg?branch=main)](https://github.com/Project-MONAI/MONAILabel/commits/main)
-[![Documentation Status](https://readthedocs.org/projects/monailabel/badge/?version=latest)](https://docs.monai.io/projects/label/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/monailabel/badge/?version=latest)](https://monai.readthedocs.io/projects/label/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/monailabel.svg)](https://badge.fury.io/py/monailabel)
 [![Azure DevOps tests (compact)](https://img.shields.io/azure-devops/tests/projectmonai/monai-label/10?compact_message)](https://dev.azure.com/projectmonai/monai-label/_test/analytics?definitionId=10&contextType=build)
 [![Azure DevOps coverage](https://img.shields.io/azure-devops/coverage/projectmonai/monai-label/10)](https://dev.azure.com/projectmonai/monai-label/_build?definitionId=10)
@@ -27,7 +27,7 @@ open-source and easy-to-install ecosystem that can run locally on a machine with
 and client work on the same/different machine. It shares the same principles
 with [MONAI](https://github.com/Project-MONAI).
 
-Refer to full [MONAI Label documentations](https://docs.monai.io/projects/label/en/latest/index.html) for more details or check out our [MONAI Label Deep Dive videos series](https://www.youtube.com/playlist?list=PLtoSVSQ2XzyD4lc-lAacFBzOdv5Ou-9IA).
+Refer to full [MONAI Label documentations](https://monai.readthedocs.io/projects/label/en/latest/index.html) for more details or check out our [MONAI Label Deep Dive videos series](https://www.youtube.com/playlist?list=PLtoSVSQ2XzyD4lc-lAacFBzOdv5Ou-9IA).
 
 Refer to [MONAI Label Tutorial](https://github.com/Project-MONAI/tutorials/tree/main/monailabel) series for application and viewer workflows with different medical image tasks. Notebook-like tutorials are created for detailed instructions.
 
@@ -182,8 +182,8 @@ In addition, you can find a table of the basic supported fields, modalities, vie
 <pre>pip install -U monailabel</pre>
 
 MONAI Label supports the following OS with **GPU/CUDA** enabled. For more details instruction, please see the installation guides.
-- [Ubuntu](https://docs.monai.io/projects/label/en/latest/installation.html)
-- [Windows](https://docs.monai.io/projects/label/en/latest/installation.html#windows)
+- [Ubuntu](https://monai.readthedocs.io/projects/label/en/latest/installation.html)
+- [Windows](https://monai.readthedocs.io/projects/label/en/latest/installation.html#windows)
 
 ### GPU Acceleration (Optional Dependencies)
 Following are the optional dependencies which can help you to accelerate some GPU based transforms from MONAI. These dependencies are enabled by default if you are using `projectmonai/monailabel` docker.
@@ -401,15 +401,15 @@ the [contributing guidelines](https://github.com/Project-MONAI/MONAILabel/blob/m
 ## Community
 
 Join the conversation on Twitter [@ProjectMONAI](https://twitter.com/ProjectMONAI) or join
-our [Slack channel](https://projectmonai.slack.com/archives/C031QRE0M1C).
+our [Slack channel](https://join.slack.com/t/projectmonai/shared_invite/zt-3hucgm02q-i8Bn9XofDZs2UGOH4jUl4w).
 
 Ask and answer questions over
 on [MONAI Label's GitHub Discussions tab](https://github.com/Project-MONAI/MONAILabel/discussions).
 
 ## Additional Resources
 
-- Website: https://monai.io/
-- API documentation: https://docs.monai.io/projects/label
+- Website: https://project-monai.github.io/
+- API documentation: https://monai.readthedocs.io/projects/label
 - Code: https://github.com/Project-MONAI/MONAILabel
 - Project tracker: https://github.com/Project-MONAI/MONAILabel/projects
 - Issue tracker: https://github.com/Project-MONAI/MONAILabel/issues

sample-apps/endoscopy/README.md

@@ -106,7 +106,7 @@ interactive and automated segmentation.
   </summary>
 This model is currently trained to segment **Tool** from 2D in-body images.
 
-- Network: This model uses the [BasicUNet](https://docs.monai.io/en/latest/networks.html#basicunet) as the default network.
+- Network: This model uses the [BasicUNet](https://monai.readthedocs.io/en/stable/networks.html#basicunet) as the default network.
 - Labels: `{ "Tool": 1 }`
 - Dataset: The model is pre-trained over few in-body Images related to Endoscopy
 - Inputs: 3 channels.
@@ -119,7 +119,7 @@ This model is currently trained to segment **Tool** from 2D in-body images.
   <summary>
   <strong>ToolTracking</strong> is based on UNet for automated segmentation. This model works for single label segmentation tasks.
   </summary>
-- Network: This model uses the [FlexibleUNet](https://docs.monai.io/en/latest/networks.html#flexibleunet) as the default network.
+- Network: This model uses the [FlexibleUNet](https://monai.readthedocs.io/en/stable/networks.html#flexibleunet) as the default network.
 - Labels: `{ "Tool": 1 }`
 - Dataset: The model is pre-trained over few in-body Images related to Endoscopy
 - Inputs: 1 channel for the image modality
@@ -130,7 +130,7 @@ This model is currently trained to segment **Tool** from 2D in-body images.
   <summary>
   <strong>InBody/OutBody</strong> is based on SEResNet50 for classification. This model determines if tool is present or not (in-body vs out-body).
   </summary>
-- Network: This model uses the [SEResNet50](https://docs.monai.io/en/latest/networks.html#seresnet50) as the default network.
+- Network: This model uses the [SEResNet50](https://monai.readthedocs.io/en/stable/networks.html#seresnet50) as the default network.
 - Labels: `{ "InBody": 0, "OutBody": 1 }`
 - Dataset: The model is pre-trained over few in-body Images related to Endoscopy
 - Inputs: 1 channel for the image modality

sample-apps/monaibundle/README.md

@@ -14,7 +14,7 @@ limitations under the License.
 # MONAI Bundle Application
 The MONAIBundle App allows you to easily pull any MONAI Bundle from the [MONAI Model Zoo](https://github.com/Project-MONAI/model-zoo/tree/dev/models) and import it into MONAI Label. However, it's important to note that any MONAI Bundle used with MONAI Label must meet the following constraints:
 
-- It must comply with the [MONAI Bundle Specification](https://docs.monai.io/en/latest/mb_specification.html).
+- It must comply with the [MONAI Bundle Specification](https://monai.readthedocs.io/en/stable/mb_specification.html).
 - For inference, the bundle must define either an `inference.json` or `inference.yaml` file, and it must include the keys described in the bundle.py file located in the `monailabel/tasks/infer/` directory.
 - For training, the bundle must define either a `train.json` or `train.yaml file`, and it must include the keys described in the bundle.py file located in the `monailabel/tasks/train/` directory.
 - For multi-GPU training, the bundle must define either a `multi_gpu_train.json` or `multi_gpu_train.yaml` file.