Merge branch 'Project-MONAI:dev' into add-gradient-accumulation-to-su…

…pervised-trainer
Project-MONAI · Mar 28, 2023 · 303a1a8 · 303a1a8
2 parents 2cc19bb + be3d138
commit 303a1a8
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diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -13,16 +13,12 @@ jobs:
     strategy:
       matrix:
         environment:
-          - "PT182+CUDA102"
           - "PT191+CUDA113"
           - "PT110+CUDA113"
           - "PT112+CUDA113"
           - "PTLATEST+CUDA118"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
-          - environment: PT182+CUDA102
-            pytorch: "torch==1.8.2 torchvision==0.9.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cu102"
-            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
           - environment: PT191+CUDA113
             pytorch: "torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu113"
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
@@ -34,7 +30,7 @@ jobs:
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
           - environment: PTLATEST+CUDA118
             pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu118"
-            base: "nvcr.io/nvidia/pytorch:22.12-py3"  # CUDA 11.8
+            base: "nvcr.io/nvidia/pytorch:23.02-py3"  # CUDA 11.8
     container:
       image: ${{ matrix.base }}
       options: "--gpus all"
@@ -43,47 +39,8 @@ jobs:
     - uses: actions/checkout@v3
     - name: apt install
       run: |
-        # FIXME: workaround for https://github.com/Project-MONAI/MONAI/issues/4200
-        apt-key del 7fa2af80 && rm -rf /etc/apt/sources.list.d/nvidia-ml.list /etc/apt/sources.list.d/cuda.list
         apt-get update
         apt-get install -y wget
-        wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
-        dpkg -i cuda-keyring_1.0-1_all.deb
-
-        if [ ${{ matrix.environment }} = "PT182+CUDA102" ]
-        then
-        PYVER=3.7 PYSFX=3 DISTUTILS=python3-distutils && \
-        apt-get update && apt-get install -y --no-install-recommends \
-          curl \
-          pkg-config \
-          python$PYVER \
-          python$PYVER-dev \
-          python$PYSFX-pip \
-          $DISTUTILS \
-          rsync \
-          swig \
-          unzip \
-          zip \
-          zlib1g-dev \
-          libboost-locale-dev \
-          libboost-program-options-dev \
-          libboost-system-dev \
-          libboost-thread-dev \
-          libboost-test-dev \
-          libgoogle-glog-dev \
-          libjsoncpp-dev \
-          cmake \
-          git && \
-        rm -rf /var/lib/apt/lists/* && \
-        export PYTHONIOENCODING=utf-8 LC_ALL=C.UTF-8 && \
-        rm -f /usr/bin/python && \
-        rm -f /usr/bin/python`echo $PYVER | cut -c1-1` && \
-        ln -s /usr/bin/python$PYVER /usr/bin/python && \
-        ln -s /usr/bin/python$PYVER /usr/bin/python`echo $PYVER | cut -c1-1` &&
-        curl -O https://bootstrap.pypa.io/get-pip.py && \
-        python get-pip.py && \
-        rm get-pip.py;
-        fi
     - name: Install the dependencies
       run: |
         which python
@@ -119,7 +76,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:22.09", "pytorch:22.11", "pytorch:22.12"]
+        container: ["pytorch:22.09", "pytorch:22.11", "pytorch:23.02"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -164,7 +121,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.12"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:22.09", "pytorch:22.11", "pytorch:23.02"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -264,7 +221,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:22.12-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:23.02-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:

diff --git a/.github/workflows/pythonapp-gpu.yml b/.github/workflows/pythonapp-gpu.yml
@@ -21,17 +21,12 @@ jobs:
     strategy:
       matrix:
         environment:
-          - "PT18+CUDA102"
           - "PT19+CUDA114DOCKER"
           - "PT110+CUDA111"
           - "PT112+CUDA118DOCKER"
           - "PT113+CUDA116"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
-          - environment: PT18+CUDA102
-            # pytorch 1.8.2 LTS
-            pytorch: "torch==1.8.2 torchvision==0.9.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cu102"
-            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
           - environment: PT19+CUDA114DOCKER
             # 21.10: 1.10.0a0+0aef44c
             pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
@@ -46,6 +41,10 @@ jobs:
           - environment: PT113+CUDA116
             pytorch: "torch==1.13.1 torchvision==0.14.1"
             base: "nvcr.io/nvidia/cuda:11.6.1-devel-ubuntu18.04"
+          - environment: PT114+CUDA120DOCKER
+            # 23.02: 1.14.0a0+44dac51
+            pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
+            base: "nvcr.io/nvidia/pytorch:23.02-py3"
     container:
       image: ${{ matrix.base }}
       options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true  # workaround for unsatisfied condition: cuda>=11.6
@@ -55,18 +54,13 @@ jobs:
     - name: apt install
       if: github.event.pull_request.merged != true
       run: |
-        # FIXME: workaround for https://github.com/Project-MONAI/MONAI/issues/4200
-        apt-key del 7fa2af80 && rm -rf /etc/apt/sources.list.d/nvidia-ml.list /etc/apt/sources.list.d/cuda.list
         apt-get update
         apt-get install -y wget
-        wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
-        dpkg -i cuda-keyring_1.0-1_all.deb
 
-        if [ ${{ matrix.environment }} = "PT18+CUDA102" ] || \
-          [ ${{ matrix.environment }} = "PT110+CUDA111" ] || \
+        if [ ${{ matrix.environment }} = "PT110+CUDA111" ] || \
           [ ${{ matrix.environment }} = "PT113+CUDA116" ]
         then
-        PYVER=3.7 PYSFX=3 DISTUTILS=python3-distutils && \
+        PYVER=3.8 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \
           curl \
           pkg-config \
@@ -134,7 +128,7 @@ jobs:
         # build for the current self-hosted CI Tesla V100
         BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --build --disttests
         ./runtests.sh --quick --unittests
-        if [ ${{ matrix.environment }} = "PT18+CUDA102" ]; then
+        if [ ${{ matrix.environment }} = "PT113+CUDA116" ]; then
           # test the clang-format tool downloading once
           coverage run -m tests.clang_format_utils
         fi

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/pythonapp-min.yml
@@ -75,7 +75,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v3
@@ -120,7 +120,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        pytorch-version: ['1.8.2', '1.9.1', '1.10.2', '1.11.0', '1.12.1', 'latest']
+        pytorch-version: ['1.9.1', '1.10.2', '1.11.0', '1.12.1', '1.13', 'latest']
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v3
@@ -149,16 +149,8 @@ jobs:
         # min. requirements
         if [ ${{ matrix.pytorch-version }} == "latest" ]; then
           python -m pip install torch
-        elif [ ${{ matrix.pytorch-version }} == "1.8.2" ]; then
-          python -m pip install torch==1.8.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cpu
-        elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
-          python -m pip install torch==1.9.1
-        elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
-          python -m pip install torch==1.10.2
-        elif [ ${{ matrix.pytorch-version }} == "1.11.0" ]; then
-          python -m pip install torch==1.11.0
-        elif [ ${{ matrix.pytorch-version }} == "1.12.1" ]; then
-          python -m pip install torch==1.12.1
+        else
+          python -m pip install torch==${{ matrix.pytorch-version }}
         fi
         python -m pip install -r requirements-min.txt
         python -m pip list

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
@@ -149,7 +149,7 @@ jobs:
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=1.8 torchvision
+        python -m pip install torch>=1.9 torchvision
     - name: Check packages
       run: |
         pip uninstall monai

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
     steps:
     - uses: actions/checkout@v3
       with:
@@ -82,7 +82,7 @@ jobs:
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         password: ${{ secrets.TEST_PYPI }}
-        repository_url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/
 
   versioning:
     # compute versioning file from python setup.py

diff --git a/.github/workflows/setupapp.yml b/.github/workflows/setupapp.yml
@@ -76,7 +76,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10']
     steps:
     - uses: actions/checkout@v3
       with:
@@ -100,13 +100,13 @@ jobs:
     - name: Install the dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        python -m pip install torch==1.13.1 torchvision==0.14.1
         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 --build --quick --unittests --disttests
+        BUILD_MONAI=0 ./runtests.sh --build --quick --unittests --disttests
+        BUILD_MONAI=1 ./runtests.sh --build --quick --min
         coverage xml --ignore-errors
     - name: Upload coverage
       uses: codecov/codecov-action@v3

diff --git a/.gitignore b/.gitignore
@@ -135,6 +135,8 @@ tests/testing_data/endo.mp4
 tests/testing_data/ultrasound.avi
 tests/testing_data/train_data_stats.yaml
 tests/testing_data/eval_data_stats.yaml
+tests/testing_data/train_data_stats_by_case.yaml
+tests/testing_data/eval_data_stats_by_case.yaml
 tests/testing_data/CT_2D_head_fixed.mha
 tests/testing_data/CT_2D_head_moving.mha
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -32,12 +32,17 @@ repos:
     hooks:
       - id: pyupgrade
         args: [--py37-plus]
-        name: Upgrade code
+        name: Upgrade code excluding monai networks
         exclude: |
-          (?x)^(
-              versioneer.py|
-              monai/_version.py
-          )$
+          (?x)(
+              ^versioneer.py|
+              ^monai/_version.py|
+              ^monai/networks/  # no PEP 604 for torchscript tensorrt
+          )
+      - 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

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -18,7 +18,7 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3
   install:
     - requirements: docs/requirements.txt
 #  system_packages: true

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -117,7 +117,7 @@ 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 3.7+ build-in functions, `torch`, `numpy`, `coverage` (for reporting code coverages) and `parameterized` (for organising test cases) packages.
+python 3.8+ 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

diff --git a/Dockerfile b/Dockerfile
@@ -11,7 +11,7 @@
 
 # To build with a different base image
 # please run `docker build` using the `--build-arg PYTORCH_IMAGE=...` flag.
-ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:22.12-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:23.02-py3
 FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="[email protected]"

diff --git a/docs/images/python.svg b/docs/images/python.svg
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,5 +1,5 @@
 -f https://download.pytorch.org/whl/cpu/torch-1.12.1%2Bcpu-cp37-cp37m-linux_x86_64.whl
-torch>=1.8
+torch>=1.9
 pytorch-ignite==0.4.11
 numpy>=1.20
 itk>=5.2

diff --git a/docs/source/apps.rst b/docs/source/apps.rst
@@ -274,7 +274,13 @@ FastMRIReader
 
 `auto3dseg`
 -----------
-
 .. automodule:: monai.apps.auto3dseg
   :members:
   :imported-members:
+
+`nnUNet`
+--------
+.. automodule:: monai.apps.nnunet.__main__
+
+.. autoclass:: monai.apps.nnunet.nnUNetV2Runner
+  :members:
diff --git a/docs/source/bundle.rst b/docs/source/bundle.rst
@@ -37,6 +37,7 @@ Model Bundle
 `Scripts`
 ---------
 .. autofunction:: ckpt_export
+.. autofunction:: trt_export
 .. autofunction:: download
 .. autofunction:: load
 .. autofunction:: get_all_bundles_list

diff --git a/docs/source/installation.md b/docs/source/installation.md
@@ -19,7 +19,7 @@
 
 ---
 
-MONAI's core functionality is written in Python 3 (>= 3.7) and only requires [Numpy](https://numpy.org/) and [Pytorch](https://pytorch.org/).
+MONAI's core functionality is written in Python 3 (>= 3.8) and only requires [Numpy](https://numpy.org/) and [Pytorch](https://pytorch.org/).
 
 The package is currently distributed via Github as the primary source code repository,
 and the Python package index (PyPI). The pre-built Docker images are made available on DockerHub.

diff --git a/docs/source/transforms.rst b/docs/source/transforms.rst
@@ -88,6 +88,11 @@ Generic Interfaces
 .. autoclass:: RandomOrder
     :members:
 
+`SomeOf`
+^^^^^^^^^^^^^
+.. autoclass:: SomeOf
+    :members:
+
 Functionals
 -----------
 
@@ -2206,3 +2211,9 @@ Utilities
 
 .. automodule:: monai.transforms.utils_pytorch_numpy_unification
     :members:
+
+Lazy
+----
+.. automodule:: monai.transforms.lazy
+    :members:
+    :imported-members:
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -6,7 +6,7 @@ channels:
   - conda-forge
 dependencies:
   - numpy>=1.20
-  - pytorch>=1.8
+  - pytorch>=1.9
   - torchvision
   - pytorch-cuda=11.6
   - pip

diff --git a/monai/__init__.py b/monai/__init__.py
@@ -17,7 +17,7 @@
 from ._version import get_versions
 
 PY_REQUIRED_MAJOR = 3
-PY_REQUIRED_MINOR = 7
+PY_REQUIRED_MINOR = 8
 
 version_dict = get_versions()
 __version__: str = version_dict.get("version", "0+unknown")
@@ -50,6 +50,7 @@
         "(^(monai._C))",
         "(.*(__main__)$)",
         "(.*(video_dataset)$)",
+        "(.*(nnunet).*$)",
     ]
 )