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GitHub / microsoft / hi-ml

HI-ML toolbox for deep learning for medical imaging and Azure integration

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/microsoft%2Fhi-ml

Stars: 231
Forks: 51
Open Issues: 103

License: mit
Language: Python
Repo Size: 29.2 MB
Dependencies: 367

Created: almost 3 years ago
Updated: 17 days ago
Last pushed: about 1 month ago
Last synced: about 1 month ago

Commit Stats

Commits: 495
Authors: 23
Mean commits per author: 21.52
Development Distribution Score: 0.754
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/microsoft/hi-ml

Topics: ai, azure, azureml, deep-learning, health, healthcare, machine-learning, ml, mlops, python

Files

Readme

Dependencies

.github/actions/cancel_azureml_jobs/action.yml actions

actions/cache v3 composite
conda-incubator/setup-miniconda v2 composite

.github/actions/download_package_artifacts/action.yml actions

actions/download-artifact v2 composite

.github/actions/prepare_cpath_environment/action.yml actions

actions/cache v3 composite
conda-incubator/setup-miniconda v2 composite

.github/actions/prepare_himl_python_env/action.yml actions

actions/setup-python v4 composite

.github/actions/upload_package_artifacts/action.yml actions

actions/upload-artifact v2 composite

.github/workflows/check-pr-title.yml actions

naveenk1223/action-pr-title master composite

.github/workflows/codeql-analysis.yml actions

actions/checkout v3 composite
github/codeql-action/analyze v2 composite
github/codeql-action/autobuild v2 composite
github/codeql-action/init v2 composite

.github/workflows/cpath-pr.yml actions

./.github/actions/cancel_azureml_jobs * composite
./.github/actions/prepare_cpath_environment * composite
actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v3 composite
pypa/gh-action-pypi-publish v1.8.5 composite

.github/workflows/credscan.yml actions

actions/checkout v3 composite
github/codeql-action/upload-sarif v2 composite
microsoft/security-devops-action preview composite

.github/workflows/hi-ml-pr.yml actions

./.github/actions/cancel_azureml_jobs * composite
./.github/actions/download_package_artifacts * composite
./.github/actions/prepare_himl_python_env * composite
./.github/actions/upload_package_artifacts * composite
actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v3 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/multimodal-pr.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v3 composite

.devcontainer/Dockerfile docker

mcr.microsoft.com/vscode/devcontainers/miniconda 0-3 build

hi-ml-cpath/other/slide_image_loading/Dockerfile docker

mcr.microsoft.com/azureml/openmpi4.1.0-cuda11.1-cudnn8-ubuntu20.04 latest build

build_requirements.txt pypi

docutils ==0.16
myst-parser ==0.15.2
sphinx ==4.1.2
sphinx-argparse ==0.3.1
sphinx-autodoc-typehints ==1.12.0
sphinx-automodapi ==0.13
sphinx-rtd-theme ==1.0.0
twine ==3.3.0
wheel ==0.38.1

hi-ml/run_requirements.txt pypi

dataclasses-json ==0.5.2
hi-ml-azure >=0.1.8
jinja2 ==3.0.2
matplotlib >=3.4.3
opencv-python-headless >=4.5.1.48
pandas >=1.3.4
pillow ==9.3.0
protobuf <4.0
pytorch-lightning >=1.6.0,<1.7
rpdb >=0.1.6
torch >=1.9.0
torchvision >=0.10.0

hi-ml/setup.py pypi

line.strip *

hi-ml-azure/run_requirements.txt pypi

azure-ai-ml >=1.1.1
azure-storage-blob ==12.10.0
azureml-core >=1.42.0
azureml-dataset-runtime >=1.42.0
azureml-mlflow >=1.42.0
azureml-tensorboard >=1.42.0
azureml-train-core >=1.42.0
conda-merge >=0.1.5
mlflow >=1.29.0
pandas >=1.3.4
param >=1.12
protobuf <4.0
pysocks >=1.5.8
ruamel.yaml >=0.16.12
tensorboard >=2.6.0
typing-extensions >=4.3.0

hi-ml-azure/setup.py pypi

line.strip *

hi-ml-cpath/requirements_build.txt pypi

docutils ==0.16
myst-parser ==0.15.2
sphinx ==4.1.2
sphinx-autodoc-typehints ==1.12.0
sphinx-automodapi ==0.13
sphinx-rtd-theme ==1.0.0
twine ==3.3.0
wheel ==0.38.1

hi-ml-cpath/requirements_run.txt pypi

coloredlogs ==15.0.1
cucim ==22.10.00
girder-client ==3.1.14
hi-ml *
ipykernel ==6.21.2
lightning-bolts ==0.4.0
monai-weekly ==1.2.dev2310
more-itertools ==8.10.0
numpy ==1.22.0
pillow ==9.3.0
pydicom ==2.3.0
scikit-image ==0.19.3
scipy ==1.7.3
seaborn ==0.10.1
simpleitk ==2.1.1.2
tifffile ==2022.10.10
timm ==0.6.12
torch ==1.11
torchmetrics ==0.10.2
torchstain ==1.3.0
umap-learn ==0.5.2
yacs ==0.1.8

hi-ml-cpath/requirements_test.txt pypi

black ==23.1.0 test
coverage ==7.1.0 test
flake8 ==6.0.0 test
mypy ==1.0.1 test
mypy-extensions ==1.0.0 test
pipdeptree ==2.5.0 test
pre-commit ==3.0.4 test
pycobertura ==3.0.0 test
pylint ==2.16.2 test
pytest ==7.2.1 test
pytest-cov ==4.0.0 test
pytest-rerunfailures ==11.1.1 test
pytest-timeout ==2.1.0 test

hi-ml-cpath/setup.py pypi

line.strip *

hi-ml-multimodal/requirements_build.txt pypi

docutils ==0.16
myst-parser ==0.15.2
setuptools ==65.5.1
sphinx ==4.1.2
sphinx-autodoc-typehints ==1.12.0
sphinx-automodapi ==0.13
sphinx-rtd-theme ==1.0.0
twine ==3.3.0
wheel ==0.38.1

hi-ml-multimodal/requirements_run.txt pypi

SimpleITK ==2.1.1
huggingface-hub ==0.6.0
pillow ==9.3.0
pydicom ==2.2.2
scikit-image ==0.18.1
timm ==0.6.5
torch ==1.9.0
torchvision >0.9,<=0.10.0
transformers ==4.17.0

hi-ml-multimodal/requirements_test.txt pypi

bump2version ==1.0.1 test
coverage ==6.3.2 test
flake8 ==5.0.2 test
ipykernel ==6.15.0 test
ipython ==7.34.0 test
mypy ==0.931 test
papermill ==2.3.4 test
pycobertura ==2.0.1 test
pytest ==6.2.2 test
pytest-cov ==2.11.1 test
pytest-rerunfailures ==10.2 test
pytest-timeout ==2.0.1 test
setuptools ==65.5.1 test

hi-ml-multimodal/setup.py pypi

new_project_template/requirements_build.txt pypi

docutils ==0.16
myst-parser ==0.15.2
setuptools ==65.5.1
sphinx ==4.1.2
sphinx-autodoc-typehints ==1.12.0
sphinx-automodapi ==0.13
sphinx-rtd-theme ==1.0.0
twine ==3.3.0
wheel ==0.38.1

new_project_template/requirements_run.txt pypi

param >=1.12

new_project_template/requirements_test.txt pypi

black ==22.1.0 test
coverage ==6.3.2 test
flake8 ==5.0.2 test
mypy ==0.931 test
pycobertura ==2.0.1 test
pylint ==2.15.0 test
pytest ==6.2.2 test
pytest-cov ==2.11.1 test
pytest-rerunfailures ==10.2 test
pytest-timeout ==2.0.1 test

new_project_template/setup.py pypi

line.strip *

pyproject.toml pypi

readthedocs_requirements.txt pypi

test_requirements.txt pypi

black ==23.1.0 test
coverage ==7.1.0 test
flake8-bugbear ==23.3.12 test
mypy ==1.0.1 test
pre-commit ==2.21.0 test
pycobertura ==3.0.0 test
pylint ==2.16.2 test
pytest ==7.2.1 test
pytest-cov ==4.0.0 test
pytest-rerunfailures ==11.1.1 test
pytest-timeout ==2.1.0 test
scikit-learn * test

docs/source/amulet/environment.yml conda

cudatoolkit 11.3.1.*
pip 22.2.2.*
python 3.9.13.*
pytorch 1.10.0.*
torchvision 0.10.0.*

docs/source/examples/1/environment.yml conda

pip 23.3.*
python 3.9.18.*

docs/source/examples/10/environment.yml conda

pip 23.3.*
python 3.9.18.*
scikit-learn

docs/source/examples/2/environment.yml conda

pip 23.3.*
python 3.9.18.*

docs/source/examples/3/environment.yml conda

pip 23.3.*
python 3.9.18.*

docs/source/examples/4/environment.yml conda

pip 23.3.*
python 3.9.18.*

docs/source/examples/5/environment.yml conda

pip 23.3.*
python 3.9.18.*
scikit-learn

docs/source/examples/6/environment.yml conda

pip 23.3.*
python 3.9.18.*
scikit-learn

docs/source/examples/7/environment.yml conda

pip 23.3.*
python 3.9.18.*
scikit-learn

docs/source/examples/8/environment.yml conda

pip 23.3.*
python 3.9.18.*
scikit-learn

hi-ml/environment.yml conda

_libgcc_mutex 0.1
_openmp_mutex 4.5
blas 2.16
bzip2 1.0.8
ca-certificates 2023.7.22
cudatoolkit 11.3.1
intel-openmp 2023.1.0
ld_impl_linux-64 2.40
libblas 3.8.0
libcblas 3.8.0
libffi 3.4.2
libgcc-ng 13.2.0
libgfortran-ng 7.5.0
libgfortran4 7.5.0
libgomp 13.2.0
liblapack 3.8.0
liblapacke 3.8.0
libnsl 2.0.1
libsqlite 3.44.0
libstdcxx-ng 13.2.0
libuuid 2.38.1
libuv 1.46.0
libzlib 1.2.13
mkl 2020.2
ncurses 6.4
openssl 3.1.4
pip 23.3.1
python 3.9.18.*
pytorch-mutex 1.0
readline 8.2
setuptools 68.2.2
tk 8.6.13
typing_extensions 4.8.0
xz 5.2.6
zlib 1.2.13

hi-ml/other/image_loading/environment.yml conda

pip 23.3.*
python 3.9.18.*

hi-ml/testhiml/environment.yml conda

cudatoolkit 11.3.1.*
pip 23.3.*
python 3.9.18.*
pytorch 1.10.0.*

hi-ml-azure/environment.yml conda

_libgcc_mutex 0.1
_openmp_mutex 5.1
ca-certificates 2023.08.22
ld_impl_linux-64 2.38
libffi 3.4.4
libgcc-ng 11.2.0
libgomp 11.2.0
libstdcxx-ng 11.2.0
ncurses 6.4
openssl 3.0.12
pip 23.3
python 3.9.18.*
readline 8.2
setuptools 68.0.0
sqlite 3.41.2
tk 8.6.12
xz 5.4.2
zlib 1.2.13

hi-ml-azure/src/health_azure/examples/environment.yml conda

pip 23.3.*
python 3.9.18.*

hi-ml-cpath/environment.yml conda

_libgcc_mutex 0.1
_openmp_mutex 4.5
blas 1.0
brotli-python 1.0.9
bzip2 1.0.8
ca-certificates 2023.08.22
cairo 1.16.0
certifi 2023.7.22
cffi 1.15.1
charset-normalizer 2.0.4
cudatoolkit 11.3.1
expat 2.5.0
ffmpeg 4.2.2
fontconfig 2.14.2
freetype 2.12.1
gdk-pixbuf 2.42.10
gettext 0.21.1
giflib 5.2.1
glib 2.78.1
glib-tools 2.78.1
gmp 6.2.1
gnutls 3.6.15
icu 73.1
idna 3.4
intel-openmp 2023.1.0
jpeg 9e
lame 3.100
lcms2 2.12
ld_impl_linux-64 2.38
lerc 3.0
libdeflate 1.17
libffi 3.4.4
libgcc-ng 13.2.0
libglib 2.78.1
libgomp 13.2.0
libiconv 1.17
libidn2 2.3.4
libnsl 2.0.0
libopus 1.3.1
libpng 1.6.39
libsqlite 3.44.0
libstdcxx-ng 13.2.0
libtasn1 4.19.0
libtiff 4.5.1
libunistring 0.9.10
libuuid 2.38.1
libuv 1.44.2
libvpx 1.7.0
libwebp 1.3.2
libwebp-base 1.3.2
libxcb 1.15
libxml2 2.10.4
libzlib 1.2.13
lz4-c 1.9.4
mkl 2023.1.0
mkl-service 2.4.0
mkl_fft 1.3.8
mkl_random 1.2.4
ncurses 6.4
nettle 3.7.3
openh264 2.1.1
openjpeg 2.5.0
openslide 3.4.1
openslide-python 1.2.0
openssl 3.0.12
pcre2 10.40
pillow 10.0.1
pip 23.3
pixman 0.40.0
pycparser 2.21
pyopenssl 23.2.0
pysocks 1.7.1
python 3.9.13.*
python_abi 3.9
pytorch 1.11.0
pytorch-mutex 1.0
readline 8.2
requests 2.31.0
setuptools 68.0.0
sqlite 3.41.2
tbb 2021.8.0
tk 8.6.12
torchvision 0.12.0
urllib3 1.26.18
x264 1!157.20191217
xz 5.4.2
zlib 1.2.13
zstd 1.5.5

hi-ml-cpath/other/slide_image_loading/environment.yml conda

pip 23.3.*
python 3.9.18.*

hi-ml-multimodal/environment.yml conda

cudatoolkit 11.1.*
pip 23.3.*
python 3.9.*
pytorch 1.9.0.*
torchvision 0.10.0.*

new_project_template/environment.yml conda

pip 23.3.*
python 3.9.18.*