Merge branch 'dev' into 6676_port_generative_losses

Signed-off-by: Mark Graham <markgraham539@gmail.com>

Author: marksgraham

.github/workflows/codeql-analysis.yml

@@ -64,6 +64,9 @@ jobs:
 
     - name: Build
       run: |
+        rm -rf /opt/hostedtoolcache/{node,go,Ruby,Java*}
+        ls -al /opt/hostedtoolcache
+        rm -rf /usr/share/dotnet/
         python -m pip install -U pip wheel
         python -m pip install -r requirements-dev.txt
         BUILD_MONAI=1 ./runtests.sh --build

.github/workflows/cron.yml

@@ -15,8 +15,8 @@ jobs:
         environment:
           - "PT191+CUDA113"
           - "PT110+CUDA113"
-          - "PT112+CUDA113"
-          - "PTLATEST+CUDA118"
+          - "PT113+CUDA113"
+          - "PTLATEST+CUDA121"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
           - environment: PT191+CUDA113
@@ -25,12 +25,12 @@ jobs:
           - environment: PT110+CUDA113
             pytorch: "torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113"
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
-          - environment: PT112+CUDA113
-            pytorch: "torch==1.12.1 torchvision==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu113"
+          - environment: PT113+CUDA113
+            pytorch: "torch==1.13.1 torchvision==0.14.1 --extra-index-url https://download.pytorch.org/whl/cu113"
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
-          - environment: PTLATEST+CUDA118
+          - environment: PTLATEST+CUDA121
             pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu118"
-            base: "nvcr.io/nvidia/pytorch:23.03-py3"  # CUDA 11.8
+            base: "nvcr.io/nvidia/pytorch:23.06-py3"  # CUDA 12.1
     container:
       image: ${{ matrix.base }}
       options: "--gpus all"
@@ -76,7 +76,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:22.09", "pytorch:22.11", "pytorch:23.03"]
+        container: ["pytorch:22.10", "pytorch:23.06"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -121,7 +121,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:22.09", "pytorch:22.11", "pytorch:23.03"]
+        container: ["pytorch:23.06"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -221,7 +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:23.03-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:23.06-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:

.github/workflows/docker.yml

@@ -85,12 +85,11 @@ jobs:
     container:
       image: docker://projectmonai/monai:latest
       options: "--shm-size=4g --ipc=host"
-    runs-on: ubuntu-latest
+    runs-on: [self-hosted, linux, X64, docker]
     steps:
     - name: Import
       run: |
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
-        echo $CUDA_VISIBLE_DEVICES
+        export OMP_NUM_THREADS=4 MKL_NUM_THREADS=4 CUDA_VISIBLE_DEVICES=  # cpu-only
         python -c 'import monai; monai.config.print_debug_info()'
         cd /opt/monai
         ls -al

.github/workflows/pythonapp-gpu.yml

@@ -25,7 +25,7 @@ jobs:
           - "PT110+CUDA111"
           - "PT112+CUDA118DOCKER"
           - "PT113+CUDA116"
-          - "PT114+CUDA120DOCKER"
+          - "PT210+CUDA121DOCKER"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
           - environment: PT19+CUDA114DOCKER
@@ -42,10 +42,10 @@ 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
-            # 23.03: 2.0.0a0+1767026
+          - environment: PT210+CUDA121DOCKER
+            # 23.06: 2.1.0a0+4136153
             pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
-            base: "nvcr.io/nvidia/pytorch:23.03-py3"
+            base: "nvcr.io/nvidia/pytorch:23.06-py3"
     container:
       image: ${{ matrix.base }}
       options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true  # workaround for unsatisfied condition: cuda>=11.6

CONTRIBUTING.md

@@ -151,6 +151,10 @@ make html
 ```
 The above commands build html documentation, they are used to automatically generate [https://docs.monai.io](https://docs.monai.io).
 
+The Python code docstring are written in
+[reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html) and
+the documentation pages can be in either [reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html) or [Markdown](https://en.wikipedia.org/wiki/Markdown).  In general the Python docstrings follow the [Google style](https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings).
+
 Before submitting a pull request, it is recommended to:
 - edit the relevant `.rst` files in [`docs/source`](./docs/source) accordingly.
 - build html documentation locally

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:23.03-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:23.06-py3
 FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="monai.contact@gmail.com"

docs/images/precision_options.png

@@ -6,6 +6,7 @@ itk>=5.2
 nibabel
 parameterized
 scikit-image>=0.19.0
+scipy>=1.7.1
 tensorboard
 commonmark==0.9.1
 recommonmark==0.6.0

docs/requirements.txt

@@ -45,6 +45,13 @@ Generic Interfaces
   :members:
   :special-members: __getitem__
 
+`GDSDataset`
+~~~~~~~~~~~~~~~~~~~
+.. autoclass:: GDSDataset
+  :members:
+  :special-members: __getitem__
+
+
 `CacheNTransDataset`
 ~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: CacheNTransDataset

docs/source/data.rst

@@ -58,6 +58,12 @@ Technical documentation is available at `docs.monai.io <https://docs.monai.io>`_
 
   installation
 
+.. toctree::
+  :maxdepth: 1
+  :caption: Precision and Performance
+
+  precision_performance
+
 .. toctree::
   :maxdepth: 1
   :caption: Contributing