mlcommons · sarthakpati · Nov 14, 2023 · Nov 7, 2023 · Nov 7, 2023 · Nov 7, 2023
@@ -1,4 +1,4 @@
-FROM mcr.microsoft.com/devcontainers/python:3.8-bullseye
+FROM mcr.microsoft.com/devcontainers/python:3.9-bullseye
 
 # Copy environment.yml (if found) to a temp location so we update the environment. Also
 # copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
     steps:
       - uses: actions/checkout@v2
       - uses: psf/black@stable

@@ -26,7 +26,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.8'
+        python-version: 3.9
     # This second step is unnecessary but highly recommended because
     # It will cache database and saves time re-downloading it if database isn't stale.
     - name: Cache pip

@@ -60,11 +60,11 @@ jobs:
         key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install dependencies and package
       if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
       run: |

@@ -61,11 +61,11 @@ jobs:
         key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install dependencies and package
       if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
       run: |

@@ -40,7 +40,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.8'
+        python-version: 3.9
     - name: Check dev version
       run: | # Get current canonical version, append current date as an identifier
         currentVer=$(python -c "from GANDLF import version; print(version)")

@@ -61,11 +61,11 @@ jobs:
         key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install dependencies and package
       if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
       run: |

@@ -1,27 +1,29 @@
-FROM ubuntu:18.04
+FROM ubuntu:20.04
 LABEL github="https://github.com/mlcommons/GaNDLF"
 LABEL docs="https://mlcommons.github.io/GaNDLF/"
 LABEL version=1.0
 
 # Install fresh Python and dependencies for build-from-source
-RUN apt-get update && apt-get install -y python3.8 python3-pip libjpeg8-dev zlib1g-dev python3-dev libpython3.8-dev libffi-dev libgl1
-RUN python3.8 -m pip install --upgrade pip
+RUN apt-get update && apt-get install -y software-properties-common
+RUN add-apt-repository ppa:deadsnakes/ppa
+RUN apt-get update &&  apt-get install -y  python3.9 python3-pip libjpeg8-dev zlib1g-dev python3-dev libpython3.8-dev libffi-dev libgl1
+RUN python3.9 -m pip install --upgrade pip
 # EXPLICITLY install cpu versions of torch/torchvision (not all versions have +cpu modes on PyPI...)
-RUN python3.8 -m pip install torch==1.13.1+cpu torchvision==0.14.1+cpu torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cpu
-RUN python3.8 -m pip install openvino-dev==2023.0.1 opencv-python-headless mlcube_docker
+RUN python3.9 -m pip install torch==1.13.1+cpu torchvision==0.14.1+cpu torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cpu
+RUN python3.9 -m pip install openvino-dev==2023.0.1 opencv-python-headless mlcube_docker
 
 # Do some dependency installation separately here to make layer caching more efficient
 COPY ./setup.py ./setup.py
-RUN python3.8 -c "from setup import requirements; file = open('requirements.txt', 'w'); file.writelines([req + '\n' for req in requirements]); file.close()" \
-    && python3.8 -m pip install -r ./requirements.txt
+RUN python3.9 -c "from setup import requirements; file = open('requirements.txt', 'w'); file.writelines([req + '\n' for req in requirements]); file.close()" \
+    && python3.9 -m pip install -r ./requirements.txt
 
 COPY . /GaNDLF
 WORKDIR /GaNDLF
-RUN python3.8 -m pip install -e .
+RUN python3.9 -m pip install -e .
 # Entrypoint forces all commands given via "docker run" to go through python, CMD forces the default entrypoint script argument to be gandlf_run
 # If a user calls "docker run gandlf:[tag] gandlf_anonymize", it will resolve to running "python gandlf_anonymize" instead.
 # CMD is inherently overridden by args to "docker run", entrypoint is constant.
-ENTRYPOINT python3.8
+ENTRYPOINT python3.9
 CMD gandlf_run
 
 # The below force the container commands to run as a nonroot user with UID > 10000.

@@ -1,30 +1,33 @@
-FROM pytorch/pytorch:1.13.1-cuda11.6-cudnn8-runtime
+FROM nvidia/cuda:11.6.2-devel-ubuntu20.04
 LABEL github="https://github.com/mlcommons/GaNDLF"
 LABEL docs="https://mlcommons.github.io/GaNDLF/"
 LABEL version=1.0
 
 # Install instructions for NVIDIA Container Toolkit allowing you to use the host's GPU: https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html
 # Note that to do this on a Windows host you need experimental feature "CUDA on WSL" -- not yet stable.
+ENV DEBIAN_FRONTEND=noninteractive 
 
-# Explicitly install python3.8 (this uses 11.1 for now, as PyTorch LTS 1.8.2 is built against it)
-RUN apt-get update && apt-get install -y python3.8 python3-pip libjpeg8-dev zlib1g-dev python3-dev libpython3.8-dev libffi-dev libgl1
-RUN python3.8 -m pip install --upgrade pip
-RUN python3.8 -m pip install torch==1.13.1+cu116 torchvision==0.14.1+cu116 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu116
-RUN python3.8 -m pip install openvino-dev==2023.0.1 opencv-python-headless mlcube_docker
+# Explicitly install python3.9 (this uses 11.1 for now, as PyTorch LTS 1.8.2 is built against it)
+RUN apt-get update && apt-get install -y software-properties-common
+RUN add-apt-repository ppa:deadsnakes/ppa
+RUN apt-get update &&  apt-get install -y  python3.9 python3-pip libjpeg8-dev zlib1g-dev python3-dev libpython3.8-dev libffi-dev libgl1
+RUN python3.9 -m pip install --upgrade pip
+RUN python3.9 -m pip install torch==1.13.1+cu116 torchvision==0.14.1+cu116 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu116
+RUN python3.9 -m pip install openvino-dev==2023.0.1 opencv-python-headless mlcube_docker
 
 # Do some dependency installation separately here to make layer caching more efficient
 COPY ./setup.py ./setup.py
-RUN python3.8 -c "from setup import requirements; file = open('requirements.txt', 'w'); file.writelines([req + '\n' for req in requirements]); file.close()" \
-    && python3.8 -m pip install -r ./requirements.txt
+RUN python3.9 -c "from setup import requirements; file = open('requirements.txt', 'w'); file.writelines([req + '\n' for req in requirements]); file.close()" \
+    && python3.9 -m pip install -r ./requirements.txt
 
 COPY . /GaNDLF
 WORKDIR /GaNDLF
-RUN python3.8 -m pip install -e .
+RUN python3.9 -m pip install -e .
 
 # Entrypoint forces all commands given via "docker run" to go through python, CMD forces the default entrypoint script argument to be gandlf_run
 # If a user calls "docker run gandlf:[tag] gandlf_anonymize", it will resolve to running "python gandlf_anonymize" instead.
 # CMD is inherently overridden by args to "docker run", entrypoint is constant.
-ENTRYPOINT python3.8
+ENTRYPOINT python3.9
 CMD gandlf_run
 
 # The below force the container commands to run as a nonroot user with UID > 10000.

@@ -6,24 +6,27 @@ LABEL version=1.0
 # Quick start instructions on using Docker with ROCm: https://github.com/RadeonOpenCompute/ROCm-docker/blob/master/quick-start.md
 
 # The base image contains ROCm, python 3.8 and pytorch already, no need to install those
-RUN python3 -m pip install --upgrade pip
-RUN python3.8 -m pip install torch==1.13.1+rocm5.2 torchvision==0.14.1+rocm5.2 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/rocm5.2
-RUN python3 -m pip install --upgrade pip && python3 -m pip install openvino-dev==2023.0.1 opencv-python-headless mlcube_docker
+RUN apt-get update && apt-get install -y software-properties-common
+RUN add-apt-repository ppa:deadsnakes/ppa
+RUN apt-get update &&  apt-get install -y  python3.9 python3-pip libjpeg8-dev zlib1g-dev python3-dev libpython3.8-dev libffi-dev libgl1
+RUN python3.9 -m pip install --upgrade pip
+RUN python3.9 -m pip install torch==1.13.1+rocm5.2 torchvision==0.14.1+rocm5.2 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/rocm5.2
+RUN python3.9 -m pip install --upgrade pip && python3.9 -m pip install openvino-dev==2023.0.1 opencv-python-headless mlcube_docker
 RUN apt-get update && apt-get install -y libgl1
 
 # Do some dependency installation separately here to make layer caching more efficient
 COPY ./setup.py ./setup.py
-RUN python3.8 -c "from setup import requirements; file = open('requirements.txt', 'w'); file.writelines([req + '\n' for req in requirements]); file.close()" \
-    && python3.8 -m pip install -r ./requirements.txt
+RUN python3.9 -c "from setup import requirements; file = open('requirements.txt', 'w'); file.writelines([req + '\n' for req in requirements]); file.close()" \
+    && python3.9 -m pip install -r ./requirements.txt
 
 COPY . /GaNDLF
 WORKDIR /GaNDLF
-RUN python3 -m pip install -e .
+RUN python3.9 -m pip install -e .
 
 # Entrypoint forces all commands given via "docker run" to go through python, CMD forces the default entrypoint script argument to be gandlf_run
 # If a user calls "docker run gandlf:[tag] gandlf_anonymize", it will resolve to running "python gandlf_anonymize" instead.
 # CMD is inherently overridden by args to "docker run", entrypoint is constant.
-ENTRYPOINT python3
+ENTRYPOINT python3.9
 CMD gandlf_run
 
 

@@ -251,7 +251,7 @@ def get_metrics_mlcube_config(mlcube_config_file, entrypoint_script):
         mlcube_config = yaml.safe_load(f)
     if entrypoint_script:
         # modify the entrypoint to run a custom script
-        mlcube_config["tasks"]["evaluate"]["entrypoint"] = "python3.8 /entrypoint.py"
+        mlcube_config["tasks"]["evaluate"]["entrypoint"] = "python3.9 /entrypoint.py"
     mlcube_config["docker"]["build_strategy"] = "auto"
     return mlcube_config
 
@@ -315,7 +315,7 @@ def get_model_mlcube_config(mlcube_config_file, requires_gpu, entrypoint_script)
         device = "cuda" if requires_gpu else "cpu"
         mlcube_config["tasks"]["infer"][
             "entrypoint"
-        ] = f"python3.8 /entrypoint.py --device {device}"
+        ] = f"python3.9 /entrypoint.py --device {device}"
 
     return mlcube_config
     # Duplicate training task into one from reset (must be explicit) and one that resumes with new data

@@ -93,8 +93,8 @@ def __surface_distances(result, reference, voxelspacing=None, connectivity=1):
     Returns:
         float: The symmetric Hausdorff Distance between the object(s) in ```result``` and the object(s) in ```reference```. The distance unit is the same as for the spacing of elements along each dimension, which is usually given in mm.
     """
-    result = np.atleast_1d(result.astype(np.bool))
-    reference = np.atleast_1d(reference.astype(np.bool))
+    result = np.atleast_1d(result.astype(bool))
+    reference = np.atleast_1d(reference.astype(bool))
     if voxelspacing is not None:
         voxelspacing = _ni_support._normalize_sequence(voxelspacing, result.ndim)
         voxelspacing = np.asarray(voxelspacing, dtype=np.float64)

@@ -49,7 +49,7 @@ def run_gandlf(output_path, parameters_file):
         parameters_file (str): The path to the parameters file
     """
     exit_status = os.system(
-        f"python3.8 gandlf_generateMetrics -c {parameters_file} -i ./data.csv -o {output_path}"
+        f"python3.9 gandlf_generateMetrics -c {parameters_file} -i ./data.csv -o {output_path}"
     )
     exit_code = os.WEXITSTATUS(exit_status)
     sys.exit(exit_code)

@@ -24,7 +24,7 @@ def run_gandlf(output_path, parameters_file):
         parameters_file (str): The path to the parameters file
     """
     exit_status = os.system(
-        f"python3.8 gandlf_generateMetrics -c {parameters_file} -i ./data.csv -o {output_path}"
+        f"python3.9 gandlf_generateMetrics -c {parameters_file} -i ./data.csv -o {output_path}"
     )
     exit_code = os.WEXITSTATUS(exit_status)
     sys.exit(exit_code)

@@ -42,7 +42,7 @@ singularity:
 tasks:
   evaluate:
   # Runs metrics calculation on predictions
-    entrypoint: "python3.8 gandlf_generateMetrics"
+    entrypoint: "python3.9 gandlf_generateMetrics"
     parameters:
       inputs: {
         data_path: data/,

@@ -42,7 +42,7 @@ singularity:
 tasks:
   evaluate:
   # Runs metrics calculation on predictions
-    entrypoint: "python3.8 /entrypoint.py"
+    entrypoint: "python3.9 /entrypoint.py"
     parameters:
       inputs: {
         predictions: predictions/,

@@ -34,7 +34,7 @@ def run_gandlf(output_path, device):
         device (str): device to run on (i.e. CPU or GPU)
     """
     exit_status = os.system(
-        "python3.8 gandlf_run --train False "
+        "python3.9 gandlf_run --train False "
         f"--device {device} --config /embedded_config.yml "
         f"--modeldir /embedded_model/ -i ./data.csv -o {output_path}"
     )

@@ -25,7 +25,7 @@ def run_gandlf(output_path, device):
         parameters_file (str): The path to the parameters file
     """
     exit_status = os.system(
-        "python3.8 gandlf_run --train False "
+        "python3.9 gandlf_run --train False "
         f"--device {device} --config /embedded_config.yml "
         f"--modeldir /embedded_model/ -i ./data.csv -o {output_path}"
     )

@@ -51,7 +51,7 @@ singularity:
 tasks:
   train:
   # Trains a new model, creating a model directory, or resumes training on an existing model.
-    entrypoint: "python3.8 gandlf_run --train True --device cpu"
+    entrypoint: "python3.9 gandlf_run --train True --device cpu"
     parameters:
       inputs: {
         # Path to a data csv such as that constructed by the "construct_csv" task.
@@ -67,7 +67,7 @@ tasks:
 
   infer:
   # Runs inference on some existing model given new data
-    entrypoint: "python3.8 gandlf_run --train False --device cpu"
+    entrypoint: "python3.9 gandlf_run --train False --device cpu"
     parameters:
       inputs: {
         # Path to a data csv such as that constructed by the "construct_csv" task.
@@ -84,7 +84,7 @@ tasks:
 
   construct_csv:
   # Constructs a data csv from a data directory that can be passed to future steps, to prevent issues with path translation between host and container.
-    entrypoint: "python3.8 gandlf_constructCSV --relativizePaths True"
+    entrypoint: "python3.9 gandlf_constructCSV --relativizePaths True"
     parameters:
       inputs: {
         # Do NOT change the position of the inputDir parameter! It is relevant due to MLCube mounting rules.
@@ -99,7 +99,7 @@ tasks:
 
   recover_config:
   # Extracts the config file from the embedded model (if any) in the MLCube.
-    entrypoint: "python3.8 gandlf_recoverConfig --mlcube internal"
+    entrypoint: "python3.9 gandlf_recoverConfig --mlcube internal"
     parameters: 
       outputs: {
         outputFile: {type: "file", default: "recovered_config.yml"},

@@ -51,7 +51,7 @@ singularity:
 tasks:
   train:
   # Trains a new model, creating a model directory, or resumes training on an existing model.
-    entrypoint: "python3.8 gandlf_run --train True --device cpu"
+    entrypoint: "python3.9 gandlf_run --train True --device cpu"
     parameters:
       inputs: {
         # Path to a data csv such as that constructed by the "construct_csv" task.
@@ -67,7 +67,7 @@ tasks:
 
   infer:
   # Runs inference on some existing model given new data
-    entrypoint: "python3.8 gandlf_run --train False --device cpu"
+    entrypoint: "python3.9 gandlf_run --train False --device cpu"
     parameters:
       inputs: {
         # Path to a data csv such as that constructed by the "construct_csv" task.
@@ -85,7 +85,7 @@ tasks:
 
   construct_csv:
   # Constructs a data csv from a data directory that can be passed to future steps, to prevent issues with path translation between host and container.
-    entrypoint: "python3.8 gandlf_constructCSV --relativizePaths True"
+    entrypoint: "python3.9 gandlf_constructCSV --relativizePaths True"
     parameters:
       inputs: {
         # Do NOT change the position of the inputDir parameter! It is relevant due to MLCube mounting rules.
@@ -100,7 +100,7 @@ tasks:
 
   recover_config:
   # Extracts the config file from the embedded model (if any) in the MLCube.
-    entrypoint: "python3.8 gandlf_recoverConfig --mlcube internal"
+    entrypoint: "python3.9 gandlf_recoverConfig --mlcube internal"
     parameters: 
       outputs: {
         outputFile: {type: "file", default: "recovered_config.yml"},

@@ -77,7 +77,7 @@ def run(self):
 requirements = [
     "torch==1.13.1",
     "black",
-    "numpy==1.22.0",
+    "numpy==1.25.0",
     "scipy",
     "SimpleITK!=2.0.*",
     "SimpleITK!=2.2.1",  # https://github.com/mlcommons/GaNDLF/issues/536
@@ -119,7 +119,7 @@ def run(self):
         version=__version__,
         author="MLCommons",
         author_email="gandlf@mlcommons.org",
-        python_requires=">=3.8",
+        python_requires=">=3.9, <=3.10",
         packages=find_packages(
             where=os.path.dirname(os.path.abspath(__file__)),
             exclude=toplevel_package_excludes,
@@ -149,7 +149,6 @@ def run(self):
             "License :: OSI Approved :: Apache Software License",
             "Natural Language :: English",
             "Operating System :: OS Independent",
-            "Programming Language :: Python :: 3.8",
             "Programming Language :: Python :: 3.9",
             "Programming Language :: Python :: 3.10",
             "Topic :: Scientific/Engineering :: Medical Science Apps.",