Merge pull request #141 from Project-MONAI/master

merge master

Author: Nic-Ma

.github/workflows/cron.yml

@@ -35,7 +35,7 @@ jobs:
         echo $CUDA_VISIBLE_DEVICES
         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")))'
-        ./runtests.sh --coverage
+        BUILD_MONAI=1 ./runtests.sh --coverage
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1
@@ -58,7 +58,7 @@ 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
-        ./runtests.sh --coverage --pytype
+        BUILD_MONAI=1 ./runtests.sh --coverage --pytype
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1

.github/workflows/pythonapp.yml

@@ -76,17 +76,17 @@ jobs:
         python -m pip install torch==1.4 -f https://download.pytorch.org/whl/cpu/torch_stable.html
         python -m pip install torchvision==0.5.0
         # min. requirements for windows instances
-        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:12]); f.close()"
+        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:13]); f.close()"
     - name: Install the dependencies
       run: |
         python -m pip install torch==1.4
         python -m pip install torchvision==0.5.0
         cat "requirements-dev.txt"
         python -m pip install -r requirements-dev.txt
         python -m pip list
-        SKIP_MONAI_BUILD=1 python setup.py develop
+        python setup.py develop
         python setup.py develop --uninstall
-        python setup.py develop  # compile the cpp extensions
+        BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions
       shell: bash
     - name: Run quick tests (CPU ${{ runner.os }})
       run: |
@@ -95,6 +95,56 @@ jobs:
       env:
         QUICKTEST: True
 
+  min-dep-py3:  # min dependencies installed
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest, macOS-latest, ubuntu-latest]
+    timeout-minutes: 20
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.x
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.x'
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "::set-output name=datew::$(date '+%Y-%V')"
+        echo "::set-output name=dir::$(pip cache dir)"
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v2
+      id: cache
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
+    - if: runner.os == 'windows'
+      name: Install torch cpu from pytorch.org (Windows only)
+      run: |
+        python -m pip install torch==1.4 -f https://download.pytorch.org/whl/cpu/torch_stable.html
+    - name: Install the dependencies
+      run: |
+        # min. requirements for windows instances
+        python -m pip install torch==1.4
+        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:6]); f.close()"
+        cat "requirements-dev.txt"
+        python -m pip install -r requirements-dev.txt
+        python -m pip list
+        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+      shell: bash
+    - name: Run quick tests (CPU ${{ runner.os }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -m tests.min_tests
+      env:
+        QUICKTEST: True
+
   GPU-quick-py3:  # GPU with full dependencies
     strategy:
       matrix:
@@ -170,11 +220,11 @@ jobs:
       run: |
         python -m pip list
         nvidia-smi
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        export CUDA_VISIBLE_DEVICES=$(coverage run -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
         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")))'
-        ./runtests.sh --quick
+        BUILD_MONAI=1 ./runtests.sh --quick
         if [ ${{ matrix.environment }} == "PT16+CUDA110" ]; then
           # test the clang-format tool downloading once
           coverage run -m tests.clang_format_utils
@@ -274,4 +324,7 @@ jobs:
     - name: Make html
       run: |
         cd docs/
-        make html
+        make clean
+        make html 2>&1 | tee tmp_log
+        if [[ $(grep -c "^WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; exit 1; fi
+      shell: bash

.github/workflows/setupapp.yml

@@ -43,7 +43,7 @@ jobs:
         echo $CUDA_VISIBLE_DEVICES
         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")))'
-        ./runtests.sh --coverage
+        BUILD_MONAI=1 ./runtests.sh --coverage
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1
@@ -83,65 +83,15 @@ jobs:
       run: |
         python -m pip list
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        ./runtests.sh --quick
+        BUILD_MONAI=1 ./runtests.sh --quick
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1
       with:
         fail_ci_if_error: false
         file: ./coverage.xml
 
-  min-dep-py3:  # min dependencies installed
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [windows-latest, macOS-latest, ubuntu-latest]
-    timeout-minutes: 20
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.x
-      uses: actions/setup-python@v1
-      with:
-        python-version: '3.x'
-    - name: Prepare pip wheel
-      run: |
-        which python
-        python -m pip install --upgrade pip wheel
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "::set-output name=datew::$(date '+%Y-%V')"
-        echo "::set-output name=dir::$(pip cache dir)"
-      shell: bash
-    - name: cache for pip
-      uses: actions/cache@v2
-      id: cache
-      with:
-        path: ${{ steps.pip-cache.outputs.dir }}
-        key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
-    - if: runner.os == 'windows'
-      name: Install torch cpu from pytorch.org (Windows only)
-      run: |
-        python -m pip install torch==1.4 -f https://download.pytorch.org/whl/cpu/torch_stable.html
-    - name: Install the dependencies
-      run: |
-        # min. requirements for windows instances
-        python -m pip install torch==1.4
-        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:5]); f.close()"
-        cat "requirements-dev.txt"
-        python -m pip install -r requirements-dev.txt
-        python -m pip list
-        SKIP_MONAI_BUILD=1 python setup.py develop  # no compile of extensions
-      shell: bash
-    - name: Run quick tests (CPU ${{ runner.os }})
-      run: |
-        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        python -m tests.min_tests
-      env:
-        QUICKTEST: True
-
-  install:
+  install:  # pip install from github url
     runs-on: ubuntu-latest
     steps:
     - name: Set up Python 3.7
@@ -158,14 +108,19 @@ jobs:
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install the default branch
-      run: |
-        pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
-    - name: Import
+    - name: Install the default branch no build
       run: |
+        BUILD_MONAI=0 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
         python -c 'import monai; monai.config.print_config()'
-    - name: Uninstall
+        cd $(python -c 'import monai; import os; print(os.path.dirname(monai.__file__))')
+        ls .
+        pip uninstall -y monai
+    - name: Install the default branch with build
       run: |
+        BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
+        python -c 'import monai; monai.config.print_config()'
+        cd $(python -c 'import monai; import os; print(os.path.dirname(monai.__file__))')
+        ls .
         pip uninstall -y monai
 
   docker:

MANIFEST.in

@@ -3,6 +3,3 @@ include monai/_version.py
 
 include README.md
 include LICENSE
-
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]

docs/source/conf.py

@@ -46,6 +46,7 @@
     "visualize",
     "utils",
     "inferers",
+    "optimizers",
 ]
 
 

docs/source/index.rst

@@ -57,6 +57,7 @@ Technical documentation is available at `docs.monai.io <https://docs.monai.io>`_
    losses
    networks
    metrics
+   optimizers
    data
    engines
    inferers

docs/source/installation.md

@@ -40,6 +40,10 @@ for the latest features:
 ```bash
 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
 ```
+or, to build with MONAI Cpp/CUDA extensions:
+```bash
+BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
+```
 this command will download and install the current master branch of [MONAI from
 GitHub](https://github.com/Project-MONAI/MONAI).
 
@@ -55,17 +59,25 @@ You can install it by running:
 ```bash
 cd MONAI/
 python setup.py develop
+```
+or, to build with MONAI Cpp/CUDA extensions and install:
+```bash
+cd MONAI/
+BUILD_MONAI=1 python setup.py develop
+# for MacOS
+BUILD_MONAI=1 CC=clang CXX=clang++ python setup.py develop
+```
 
-# For MacOS:
-# CC=clang CXX=clang++ python setup.py develop
-
-# To install without build
-# SKIP_MONAI_BUILD=1 python setup.py develop
-
-# To uninstall the package please run:
+To uninstall the package please run:
+```bash
+cd MONAI/
 python setup.py develop --uninstall
+
+# to further clean up the MONAI/ folder (Bash script)
+./runtests.sh --clean
 ```
-or simply adding the root directory of the cloned source code (e.g., ``/workspace/Documents/MONAI``) to your ``$PYTHONPATH``
+
+Alternatively, simply adding the root directory of the cloned source code (e.g., ``/workspace/Documents/MONAI``) to your ``$PYTHONPATH``
 and the codebase is ready to use (without the additional features of MONAI C++/CUDA extensions).
 
 

docs/source/optimizers.rst

@@ -0,0 +1,12 @@
+:github_url: https://github.com/Project-MONAI/MONAI
+
+.. _optimizers:
+
+Optimizers
+==========
+.. currentmodule:: monai.optimizers
+
+`Novograd`
+----------
+.. autoclass:: Novograd
+    :members:

monai/README.md

@@ -20,6 +20,8 @@
 
 * **networks**: contains network definitions, component definitions, and Pytorch specific utilities.
 
+* **optimizers**: classes defining optimizers.
+
 * **transforms**: defines data transforms for preprocessing and postprocessing.
 
 * **utils**: generic utilities intended to be implemented in pure Python or using Numpy,

monai/__init__.py

@@ -13,7 +13,9 @@
 import sys
 
 from ._version import get_versions
-from .utils.module import load_submodules
+
+PY_REQUIRED_MAJOR = 3
+PY_REQUIRED_MINOR = 6
 
 __version__ = get_versions()["version"]
 del get_versions
@@ -22,6 +24,15 @@
 
 __basedir__ = os.path.dirname(__file__)
 
+if not (sys.version_info.major == PY_REQUIRED_MAJOR and sys.version_info.minor >= PY_REQUIRED_MINOR):
+    raise RuntimeError(
+        "MONAI requires Python {}.{} or higher. But the current Python is: {}".format(
+            PY_REQUIRED_MAJOR, PY_REQUIRED_MINOR, sys.version
+        ),
+    )
+
+from .utils.module import load_submodules  # noqa: E402
+
 # handlers_* have some external decorators the users may not have installed
 # *.so files and folder "_C" may not exist when the cpp extensions are not compiled
 excludes = "(^(monai.handlers))|((\\.so)$)|(^(monai._C))"