Updates

Author: ericspod

docs/source/installation.md

@@ -52,19 +52,20 @@ pip install monai
 MONAI supports the extras syntax such as `pip install 'monai[nibabel]'`. The options are
 
 ```text
-clearml, cucim, cupy, einops, fire, gdown, h5py, huggingface_hub, hyena, ignite, imagecodecs, itk, jsonschema, lmdb, lpips, matplotlib, metrics_reloaded, mlflow, nibabel, nni, onnx, openslide, optuna, pandas, pillow, polygraphy, psutil, pyamg, pybind11, pydicom, pynrrd, pytest, pynvml, pyyaml, requests, segment_anything, scipy, skimage, tensorboard, tensorboardX, tifffile, torchio, torchvision, tqdm, transformers, zarr
+clearml, cucim, cupy, einops, fire, gdown, h5py, huggingface_hub, hyena, ignite, imagecodecs, itk, jsonschema, lmdb, lpips, matplotlib, metrics_reloaded, mlflow, nibabel, nni, onnx, openslide, optuna, pandas, pillow, polygraphy, psutil, pyamg, pybind11, pydicom, pynrrd, pynvml, pyyaml, requests, segment_anything, scipy, skimage, tensorboard, tensorboardX, tifffile, torchio, torchvision, tqdm, transformers, zarr
 ```
 
-which correspond to the packages: `clearml`, `cucim` (`cucim-cu12` or `cucim-cu13`), `cupy`, `einops`, `fire`, `gdown`, `h5py`, `huggingface_hub`, `nvsubquadratic`, `omegaconf`, `pytorch-ignite`, `imagecodecs`, `itk`, `jsonschema`, `lmdb`, `lpips`, `matplotlib`, `MetricsReloaded`, `mlflow`, `nibabel`, `nni`, `filelock`, `onnx`, `onnxruntime`, `onnx_graphsurgeon`, `onnxscript`, `openslide-python`, `openslide-bin`, `optuna`, `pandas`, `pillow`, `polygraphy`, `psutil`, `pyamg`, `pybind11`, `pydicom`, `pynrrd`, `pytest`, `nvidia-ml-py`, `pyyaml`, `requests`, `segment_anything`, `scipy`, `scikit-image`, `tensorboard`, `tensorboardX`, `tifffile`, `torchio`, `torchvision`, `tqdm`, `transformers`, `zarr`.
+which correspond to the packages: `clearml`, `cucim` (`cucim-cu12` or `cucim-cu13`), `cupy-cuda13x`, `einops`, `fire`, `gdown`, `h5py`, `huggingface_hub`, `nvsubquadratic`, `omegaconf`, `pytorch-ignite`, `imagecodecs`, `itk`, `jsonschema`, `lmdb`, `lpips`, `matplotlib`, `MetricsReloaded`, `mlflow`, `nibabel`, `nni`, `filelock`, `onnx`, `onnxruntime`, `onnx_graphsurgeon`, `onnxscript`, `openslide-python`, `openslide-bin`, `optuna`, `pandas`, `pillow`, `polygraphy`, `psutil`, `pyamg`, `pybind11`, `pydicom`, `pynrrd`, `nvidia-ml-py`, `pyyaml`, `requests`, `segment_anything`, `scipy`, `scikit-image`, `tensorboard`, `tensorboardX`, `tifffile`, `torchio`, `torchvision`, `tqdm`, `transformers`, `zarr`.
 
-Almost all of these can be installed together with the `all` option. For development on MONAI, this should be accompanied by `testing` which will install the testing static checking packages.
+Almost all of these can be installed together with the `all` option. For development on MONAI, this should be accompanied by `testing` which will install the testing static checking packages. Cupy is omitted from `all` since the choice between
+Cuda 12 and 13 versions of the library can't be resolved when installing and must be manually installed.
 
 The `hyena` extra pulls in [`nvsubquadratic`](https://github.com/NVIDIA-BioNeMo/nvSubquadratic),
 required by `HyenaNDUNETR` / `HyenaMixer` / `HyenaTransformerBlock` (subquadratic
 O(N log N) alternatives to windowed self-attention). Install with
 `pip install 'monai[hyena]'`.
 
-The command  `pip install 'monai[all,hyena,testing]'` installs all the optional dependencies.
+The command  `pip install 'monai[all,hyena,testing]'` installs almost all the optional dependencies.
 
 When installing MONAI, the compiled extensions are not compiled by default. Set the environment variable `BUILD_MONAI` to `1` when invoking `pip` to compile these, see below for details.
 

pyproject.toml

@@ -71,8 +71,7 @@ all = [
   "lmdb",
   "lpips==0.1.4",
   "matplotlib>=3.6.3",
-  # TODO: change URL to https://github.com/Project-MONAI/MetricsReloaded@monai-support before finalising
-  "MetricsReloaded @ git+https://github.com/ericspod/MetricsReloaded@monai-support-fix",
+  "MetricsReloaded @ git+https://github.com/Project-MONAI/MetricsReloaded@monai-support",
   "mlflow>=2.12.2,<3.13",
   "nibabel",
   "ninja",
@@ -93,7 +92,6 @@ all = [
   "pybind11",
   "pydicom",
   "pynrrd",
-  "pytest",  # FIXME: CuPy 14.1.0 required this through polygraphy and trt_compiler https://github.com/Project-MONAI/MONAI/pull/8867
   "pytorch-ignite",
   "pyyaml",
   "requests",
@@ -114,7 +112,7 @@ cucim = [
   "cucim-cu12; platform_system == 'Linux' and python_version <= '3.10'",
   "cucim-cu13; platform_system == 'Linux' and python_version >= '3.11'"
 ]
-cupy = ["cupy"]
+cupy = ["cupy-cuda13x!=14.1.0"]  # not in all, the choice between cuda12x and cuda13x that can't be resolved here
 einops = ["einops"]
 fire = ["fire"]
 gdown = ["gdown>=4.7.3"]
@@ -146,7 +144,6 @@ pyamg = ["pyamg>=5.0.0,<5.3.0"]
 pybind11 = ["pybind11"]
 pydicom = ["pydicom"]
 pynrrd = ["pynrrd"]
-pytest = ["pytest"]
 pynvml = ["nvidia-ml-py"]
 pyyaml = ["pyyaml"]
 requests = ["requests"]