Merge branch 'main' into multiChannelSupport

Author: CavRiley

.github/ISSUE_TEMPLATE/human-ai-interaction-intake.md

@@ -0,0 +1,32 @@
+---
+name: Human-AI Interaction Intake
+about: Issues/questions related to the Human-AI Interaction Working Group
+title: "[HAI] "
+labels: Human-AI Interaction
+assignees: ''
+
+---
+
+## Short summary
+(One or two sentences describing the core idea or problem)
+
+## What is the idea or problem?
+(Brief description - vague is okay! We can refine together.)
+
+## Why does it matter?
+(Who benefits? What workflow or use case is affected?)
+
+## Any context, examples, or references?
+(Optional: links, screenshots, papers, existing tools, related repos)
+
+## How would you like to be involved?
+- [ ] I can contribute code or documentation
+- [ ] I can test or provide feedback
+- [ ] I want to follow the discussion
+- [ ] I have other ideas or expertise to share: _____________
+
+## Suggested milestone (optional)
+If you think this fits an existing [milestone](https://github.com/Project-MONAI/MONAILabel/milestones), mention it here. Otherwise, we'll help sort it during grooming.
+
+---
+*Note: If this issue needs broader WG input, you or a coordinator can move it to "Needs Discussion" to schedule it for a future WG meeting.*

.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

@@ -25,11 +25,11 @@ jobs:
     env:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     steps:
-      - uses: actions/checkout@v5
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.9
+          python-version: 3.10
       - name: clean up
         run: |
           sudo rm -rf /usr/share/dotnet

.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

@@ -31,14 +31,14 @@ 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
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+      - uses: actions/setup-node@v6
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.9
+          python-version: 3.10
       - name: Cache for pip
         uses: actions/cache@v4
         id: cache
@@ -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

docs/source/installation.rst

@@ -52,7 +52,7 @@ Prerequisites
 --------------------------
 MONAI Label supports both **Ubuntu** and **Windows** OS with GPU/CUDA enabled.
 
-Make sure you have python 3.8/3.9 version environment with PyTorch and CUDA installed. MONAI Label features on other python version are not verified.
+Make sure you have python 3.10+ version environment with PyTorch and CUDA installed. MONAI Label features on other python version are not verified.
 
 - Install `Python <https://www.python.org/downloads/>`_
 - Install the following Python libraries