Merge branch 'dev' into 7951-anchors-are-not-centered-on-grid-cells

Author: ericspod

.coderabbit.yaml

@@ -0,0 +1,53 @@
+# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json
+
+# This file configures CodeRabbit with the various options described in https://docs.coderabbit.ai/configure-coderabbit.
+# CodeRabbit also has a set of commands here: https://docs.coderabbit.ai/guides/commands/
+
+language: "en-US"
+early_access: false
+tone_instructions: "Be terse and to the point in all statements and commentary."
+reviews:
+  # chill is less verbose, assertive is more verbose with more nitpick feedback
+  profile: chill
+  high_level_summary: false
+  high_level_summary_placeholder: "@coderabbitai summary"
+  sequence_diagrams: false
+  auto_apply_labels: false
+  suggested_reviewers: false
+  changed_files_summary: false
+  suggested_labels: false
+  abort_on_close: true
+  poem: false
+  path_instructions:
+    - path: '**/*.md'
+      instructions: Remember that documentation must be updated with the latest information.
+    - path: '**/*.rst'
+      instructions: Remember that documentation must be updated with the latest information.
+    - path: '**/*.py'
+      instructions: >-
+        Review the Python code for quality and correctness. Ensure variable names adhere to PEP8 style guides, are
+        sensible and informative in regards to their function, though permitting simple names for loop and comprehension
+        variables. Ensure routine names are meaningful in regards to their function and use verbs, adjectives, and
+        nouns in a semantically appropriate way. Docstrings should be present for all definition which describe each
+        variable, return value, and raised exception in the appropriate section of the Google-style of docstrings.
+        Examine code for logical error or inconsistencies, and suggest what may be changed to addressed these. Suggest
+        any enhancements for code improving efficiency, maintainability, comprehensibility, and correctness. Ensure new
+        or modified definitions will be covered by existing or new unit tests.
+
+  auto_review:
+    # Automatic Review | Automatic code review
+    enabled: true
+    # Review draft PRs/MRs.
+    drafts: false
+    # ignore PRs with these in the title, these sorts of PRs should be drafts anyway
+    ignore_title_keywords:
+    - "WIP"
+    - "DO NOT MERGE"
+
+# opt out for now until it's clear this isn't too much info and is useful
+knowledge_base:
+  opt_out: true
+
+# chat is allowed
+chat:
+  auto_reply: true

.dockerignore

@@ -3,11 +3,15 @@
 __pycache__/
 docs/
 
+.vscode
+.git
+.mypy_cache
+.ruff_cache
+.pytype
 .coverage
 .coverage.*
 .coverage/
 coverage.xml
 .readthedocs.yml
-*.toml
 
 !README.md

.github/workflows/chatops.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: dispatch
-        uses: peter-evans/slash-command-dispatch@v4.0.0
+        uses: peter-evans/slash-command-dispatch@v5.0.2
         with:
           token: ${{ secrets.PR_MAINTAIN }}
           reaction-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql-analysis.yml

@@ -38,11 +38,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      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.
@@ -72,4 +72,4 @@ jobs:
         BUILD_MONAI=1 ./runtests.sh --build
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4

.github/workflows/conda.yml

@@ -21,17 +21,18 @@ jobs:
         os: [ubuntu-latest]
         python-version: ["3.9", "3.10"]
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 46 # equal to max + 3*std over the last 600 successful runs
     env:
       QUICKTEST: True
     steps:
     - if: runner.os == 'windows'
       name: Config pagefile (Windows only)
-      uses: al-cheb/configure-pagefile-action@v1.4
+      uses: al-cheb/configure-pagefile-action@v1.5
       with:
         minimum-size: 8GB
         maximum-size: 16GB
         disk-root: "D:"
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Clean up disk space
       run: |
         find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;

.github/workflows/cron-ngc-bundle.yml

@@ -17,16 +17,16 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: ~/.cache/pip

.github/workflows/cron.yml

@@ -32,7 +32,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: apt install
       run: |
         apt-get update
@@ -82,7 +82,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Install APT dependencies
       run: |
         apt-get update
@@ -131,7 +131,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Install the dependencies
@@ -233,7 +233,7 @@ jobs:
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Install MONAI
       id: monai-install
       run: |

.github/workflows/docker.yml

@@ -21,13 +21,13 @@ jobs:
     if: ${{ false }}  # disable docker build job  project-monai/monai#7450
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         # full history so that we can git describe
         with:
           ref: dev
           fetch-depth: 0
       - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.9'
       - shell: bash
@@ -37,7 +37,7 @@ jobs:
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: _version.py
           path: build/lib/monai/_version.py
@@ -53,11 +53,11 @@ jobs:
     needs: versioning_dev
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         ref: dev
     - name: Download version
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v6
       with:
         name: _version.py
     - name: docker_build

.github/workflows/integration.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: [self-hosted, linux, x64, command]
     steps:
     # checkout the pull request branch
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
@@ -22,7 +22,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: |
@@ -74,7 +74,7 @@ jobs:
       run: ./runtests.sh --build --net
 
     - name: Add reaction
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -89,7 +89,7 @@ jobs:
     runs-on: [self-hosted, linux, x64, command1]
     steps:
     # checkout the pull request branch
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
@@ -98,7 +98,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       id: cache
       with:
         path: |
@@ -154,7 +154,7 @@ jobs:
         python -m tests.test_integration_gpu_customization
 
     - name: Add reaction
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}

.github/workflows/pythonapp-gpu.yml

@@ -44,7 +44,7 @@ jobs:
       options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true  # workaround for unsatisfied condition: cuda>=11.6
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: apt install
       if: github.event.pull_request.merged != true
       run: |