rebase dev and add box utils

.github/pull_request_template.md

@@ -12,6 +12,6 @@ A few sentences describing the changes proposed in this pull request.
 - [ ] Breaking change (fix or new feature that would cause existing functionality to change).
 - [ ] New tests added to cover the changes.
 - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`.
-- [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests`.
+- [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests  --disttests`.
 - [ ] In-line docstrings updated.
 - [ ] Documentation updated, tested `make html` command in the `docs/` folder.

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ dev, main ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ dev ]
+  schedule:
+    - cron: '18 1 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'cpp', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://git.io/codeql-language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    # - name: Autobuild
+    #   uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    - name: Build
+      run: |
+        python -m pip install -r requirements-dev.txt
+        BUILD_MONAI=1 ./runtests.sh --build
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/cron-mmar.yml

@@ -37,6 +37,6 @@ jobs:
     - name: Loading MMARs
       run: |
         # clean up temporary files
-        $(pwd)/runtests.sh --clean
+        $(pwd)/runtests.sh --build --clean
         # run tests
         python -m tests.ngc_mmar_loading

.github/workflows/cron.yml

@@ -48,8 +48,8 @@ jobs:
         python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
         coverage xml
         if pgrep python; then pkill python; fi
     - name: Upload coverage
@@ -62,7 +62,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10"]  # 21.02 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.12"]  # 21.02 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -91,8 +91,8 @@ jobs:
         python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
         coverage xml
         if pgrep python; then pkill python; fi
     - name: Upload coverage
@@ -106,7 +106,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10"]  # 21.02 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.12"]  # 21.02 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -190,8 +190,8 @@ jobs:
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
         ngc --version
-        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --pytype --unittests --disttests  # unit tests with pytype checks, coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
         coverage xml
         if pgrep python; then pkill python; fi
     - name: Upload coverage

.github/workflows/integration.yml

@@ -34,7 +34,7 @@ jobs:
         which python
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
-        python -m pip install torch==1.10.0+cu111 torchvision==0.11.1+cu111 -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.10.1+cu111 torchvision==0.11.2+cu111 -f https://download.pytorch.org/whl/torch_stable.html
         python -m pip install -r requirements-dev.txt
     - name: Run integration tests
       run: |
@@ -46,8 +46,8 @@ jobs:
         python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --net
-        BUILD_MONAI=1 ./runtests.sh --unittests
+        BUILD_MONAI=1 ./runtests.sh --build --net
+        BUILD_MONAI=1 ./runtests.sh --build --unittests --disttests
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Add reaction

.github/workflows/pythonapp-gpu.yml

@@ -20,34 +20,36 @@ jobs:
       matrix:
         environment:
           - "PT17+CUDA102"
-          - "PT17+CUDA110"
           - "PT18+CUDA102"
-          - "PT18+CUDA110"
+          - "PT18+CUDA112"
           - "PT19+CUDA114"
+          - "PT110+CUDA115"
           - "PT110+CUDA102"
         include:
+          # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
           - environment: PT17+CUDA102
             pytorch: "torch==1.7.1 torchvision==0.8.2"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
-          - environment: PT17+CUDA110
-            # we explicitly set pytorch to -h to avoid pip install error
-            pytorch: "-h"
-            base: "nvcr.io/nvidia/pytorch:20.09-py3"
           - environment: PT18+CUDA102
             pytorch: "torch==1.8.1 torchvision==0.9.1"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
-          - environment: PT18+CUDA110
+          - environment: PT18+CUDA112
             # we explicitly set pytorch to -h to avoid pip install error
+            # 21.03: 1.9.0a0+df837d0
             pytorch: "-h"
-            base: "nvcr.io/nvidia/pytorch:21.02-py3"
+            base: "nvcr.io/nvidia/pytorch:21.03-py3"
           - environment: PT19+CUDA114
             # we explicitly set pytorch to -h to avoid pip install error
-            # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
             # 21.10: 1.10.0a0+0aef44c
             pytorch: "-h"
             base: "nvcr.io/nvidia/pytorch:21.10-py3"
+          - environment: PT110+CUDA115
+            # we explicitly set pytorch to -h to avoid pip install error
+            # 21.12: 1.11.0a0+b6df043
+            pytorch: "-h"
+            base: "nvcr.io/nvidia/pytorch:21.12-py3"
           - environment: PT110+CUDA102
-            pytorch: "torch==1.10.0 torchvision==0.11.1"
+            pytorch: "torch==1.10.1 torchvision==0.11.2"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
     container:
       image: ${{ matrix.base }}
@@ -61,7 +63,7 @@ jobs:
           [ ${{ matrix.environment }} = "PT18+CUDA102" ] || \
           [ ${{ matrix.environment }} = "PT110+CUDA102" ]
         then
-        PYVER=3.6 PYSFX=3 DISTUTILS=python3-distutils && \
+        PYVER=3.7 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \
           curl \
           pkg-config \
@@ -122,7 +124,7 @@ jobs:
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
         python -c "import monai; monai.config.print_config()"
         # build for the current self-hosted CI Tesla V100
-        BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --quick --unittests
+        BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --build --quick --unittests --disttests
         if [ ${{ matrix.environment }} = "PT110+CUDA102" ]; then
           # test the clang-format tool downloading once
           coverage run -m tests.clang_format_utils

.github/workflows/pythonapp-min.yml

@@ -51,11 +51,11 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==1.10.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.10.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
     - name: Install the dependencies
       run: |
         # min. requirements
-        python -m pip install torch==1.10.0
+        python -m pip install torch==1.10.1
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions
@@ -74,7 +74,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9]
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v2
@@ -101,7 +101,7 @@ jobs:
     - name: Install the dependencies
       run: |
         # min. requirements
-        python -m pip install torch==1.10.0
+        python -m pip install torch==1.10.1
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions

.github/workflows/pythonapp.yml

@@ -44,9 +44,9 @@ jobs:
     - name: Lint and type check
       run: |
         # clean up temporary files
-        $(pwd)/runtests.sh --clean
+        $(pwd)/runtests.sh --build --clean
         # Git hub actions have 2 cores, so parallize pytype
-        $(pwd)/runtests.sh --codeformat -j 2
+        $(pwd)/runtests.sh --build --codeformat -j 2
 
   quick-py3:  # full dependencies installed tests for different OS
     runs-on: ${{ matrix.os }}
@@ -87,10 +87,10 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==1.10.0+cpu torchvision==0.11.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.10.1+cpu torchvision==0.11.2+cpu -f https://download.pytorch.org/whl/torch_stable.html
     - name: Install the dependencies
       run: |
-        python -m pip install torch==1.10.0 torchvision==0.11.1
+        python -m pip install torch==1.10.1 torchvision==0.11.2
         cat "requirements-dev.txt"
         python -m pip install -r requirements-dev.txt
         python -m pip list

.github/workflows/release.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9]
     steps:
     - uses: actions/checkout@v2
       with:

.github/workflows/setupapp.yml

@@ -44,7 +44,7 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
         rm -rf $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/ruamel*
-        python -m pip install torch==1.10.0 torchvision==0.11.1
+        python -m pip install torch==1.10.1 torchvision==0.11.2
         python -m pip install -r requirements-dev.txt
     - name: Run unit tests report coverage
       run: |
@@ -59,8 +59,8 @@ jobs:
         python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
         coverage xml
         if pgrep python; then pkill python; fi
       shell: bash
@@ -74,7 +74,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9]
     steps:
     - uses: actions/checkout@v2
       with:
@@ -98,13 +98,13 @@ jobs:
     - name: Install the dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        python -m pip install torch==1.10.0 torchvision==0.11.1
+        python -m pip install torch==1.10.1 torchvision==0.11.2
         python -m pip install -r requirements-dev.txt
     - name: Run quick tests CPU ubuntu
       run: |
         python -m pip list
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        BUILD_MONAI=1 ./runtests.sh --quick --unittests
+        BUILD_MONAI=1 ./runtests.sh --build --quick --unittests --disttests
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.1.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -23,10 +23,10 @@ repos:
       - id: detect-private-key
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.29.0
+    rev: v2.31.0
     hooks:
       - id: pyupgrade
-        args: [--py36-plus]
+        args: [--py37-plus]
         name: Upgrade code
         exclude: |
           (?x)^(
@@ -35,7 +35,7 @@ repos:
           )$
 
   - repo: https://github.com/asottile/yesqa
-    rev: v1.2.3
+    rev: v1.3.0
     hooks:
       - id: yesqa
         name: Unused noqa

CONTRIBUTING.md

@@ -65,7 +65,7 @@ python -m pip install -U -r requirements-dev.txt
 
 License information: all source code files should start with this paragraph:
 ```
-# Copyright <Year> MONAI Consortium
+# Copyright (c) MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -113,7 +113,7 @@ or (for new features that would not break existing functionality):
 ```
 
 It is recommended that the new test `test_[module_name].py` is constructed by using only
-python 3.6+ build-in functions, `torch`, `numpy`, `coverage` (for reporting code coverages) and `parameterized` (for organising test cases) packages.
+python 3.7+ build-in functions, `torch`, `numpy`, `coverage` (for reporting code coverages) and `parameterized` (for organising test cases) packages.
 If it requires any other external packages, please make sure:
 - the packages are listed in [`requirements-dev.txt`](requirements-dev.txt)
 - the new test `test_[module_name].py` is added to the `exclude_cases` in [`./tests/min_tests.py`](./tests/min_tests.py) so that
@@ -228,7 +228,7 @@ Notably,
 for example, ``import monai.transforms.Spacing`` is the equivalent of ``monai.transforms.spatial.array.Spacing`` if
 ``class Spacing`` defined in file `monai/transforms/spatial/array.py` is decorated with ``@export("monai.transforms")``.
 
-For string definition, [f-string](https://www.python.org/dev/peps/pep-0498/) is recommended to use over `%-print` and `format-print` from python 3.6. So please try to use `f-string` if you need to define any string object.
+For string definition, [f-string](https://www.python.org/dev/peps/pep-0498/) is recommended to use over `%-print` and `format-print`. So please try to use `f-string` if you need to define any string object.
 
 #### Backwards compatibility
 MONAI is currently under active development, and with major version zero (following the [Semantic Versioning](https://semver.org/)).