diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml index 51947cbc9..73d38eaaf 100644 --- a/.github/workflows/integration_tests.yml +++ b/.github/workflows/integration_tests.yml @@ -54,7 +54,6 @@ jobs: poetry env use '3.10' source $(poetry env info --path)/bin/activate poetry install --with test,dev --all-extras - pip install cupy-cuda12x env MPICC=/opt/openmpi-4.1.5/bin/mpicc python -m pip install git+https://github.com/mpi4py/mpi4py coverage run -m pytest -m integration_test && coverage xml && coverage report -m - name: Upload coverage to Codecov diff --git a/README.md b/README.md index 6ca024734..fd6dcafdf 100644 --- a/README.md +++ b/README.md @@ -45,10 +45,10 @@ DICOM images to create datasets. All optional dependencies can be installed with | xgboost | xgboost | Allows use of [XGBoost](https://xgboost.readthedocs.io/en/stable/) model | | torch | torch | Allows use of [PyTorch](https://pytorch.org/) models | | torchvision | torchvision | Allows use of [Torchvision](https://pytorch.org/vision/stable/index.html) library | -| torchxrayvision | torchxrayvision | Uses [torchxrayvision](https://mlmed.org/torchxrayvision/) library | -| monai | monai | Uses [monai](https://github.com/Project-MONAI/MONAI) to load and transform images | -| alibi | alibi | Uses [alibi](https://docs.seldon.io/projects/alibi/en/stable/) for additional explainability functionality | -| alibi-detect | alibi-detect | Uses [alibi-detect](https://docs.seldon.io/projects/alibi-detect/en/stable/) for dataset shift detection | +| torchxrayvision | torchxrayvision | Uses [TorchXRayVision](https://mlmed.org/torchxrayvision/) library | +| monai | monai | Uses [MONAI](https://github.com/Project-MONAI/MONAI) to load and transform images | +| alibi | alibi | Uses [Alibi](https://docs.seldon.io/projects/alibi/en/stable/) for additional explainability functionality | +| alibi-detect | alibi-detect | Uses [Alibi Detect](https://docs.seldon.io/projects/alibi-detect/en/stable/) for dataset shift detection | ## 🧑🏿‍💻 Developing diff --git a/cyclops/data/__init__.py b/cyclops/data/__init__.py index 57a85faba..d39588489 100644 --- a/cyclops/data/__init__.py +++ b/cyclops/data/__init__.py @@ -1,4 +1,5 @@ """Cyclops datasets package.""" + from cyclops.data.features import MedicalImage from cyclops.data.packaged_loading_scripts import medical_imagefolder from cyclops.data.slicer import SliceSpec diff --git a/docs/source/intro.rst b/docs/source/intro.rst index 71b463848..90bf78872 100644 --- a/docs/source/intro.rst +++ b/docs/source/intro.rst @@ -80,16 +80,16 @@ are listed in the sections below. | | | library | +-----------------------------+--------------------------+--------------+ | torchxrayvision | torchxrayvision | Uses | -| | | `torchxr | -| | | ayvision `__ | | | | library | +-----------------------------+--------------------------+--------------+ | monai | monai | Uses | -| | | `m | -| | | onai `__ | @@ -98,7 +98,7 @@ are listed in the sections below. | | | images | +-----------------------------+--------------------------+--------------+ | alibi | alibi | Uses | -| | | `alibi