diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 3e61f9c4..9e3332f8 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -12,7 +12,7 @@ jobs: # needs: format_and_lint strategy: matrix: - python-version: ["3.11", "3.12"] + python-version: ["3.13"] extractor: [ "ctranspath", "chief-ctranspath", @@ -59,7 +59,7 @@ jobs: # needs: format_and_lint strategy: matrix: - python-version: ["3.11", "3.12"] + python-version: ["3.13"] steps: - uses: actions/checkout@v4 @@ -95,12 +95,12 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.13' - name: Install the code linting and formatting tool Ruff run: pipx install ruff - name: Lint code with Ruff - run: ruff check --output-format=github --target-version=py311 + run: ruff check --output-format=github --target-version=py313 - name: Check code formatting with Ruff - run: ruff format --diff --target-version=py311 + run: ruff format --diff --target-version=py313 # continue-on-error: true diff --git a/.python-version b/.python-version index e4fba218..24ee5b1b 100644 --- a/.python-version +++ b/.python-version @@ -1 +1 @@ -3.12 +3.13 diff --git a/README.md b/README.md index 9a0ed68b..062cbe0e 100644 --- a/README.md +++ b/README.md @@ -64,20 +64,42 @@ cd STAMP ``` ```bash -# GPU (CUDA) Installation (Using flash-attn on CUDA systems for gigapath and other models) +# GPU (CUDA) Installation (excluding conchv1_5, gigapath and musk) -# And then this for all models: -uv sync --extra build --extra gpu +uv sync --extra gpu source .venv/bin/activate ``` ```bash -# CPU-only Installation (excluding COBRA, Gigapath (and flash-attn)) +# CPU-only Installation (excluding conchv1_5, gigapath and musk) uv sync --extra cpu source .venv/bin/activate ``` +> [!CAUTION] +> In the next step we will build [flash-attn](https://github.com/dao-ailab/flash-attention), this might take an extended amount of time and consume a lot of RAM and CPU time! +> +> Please make sure you have [Nvidia CUDA Toolkit 13.0](https://developer.nvidia.com/cuda-13-0-2-download-archive) installed! You must use Nvidia Driver version 580 or newer! +> +> The `nvcc --version` command must indicate that 13.0 is installed and is currently in PATH: `Cuda compilation tools, release 13.0, V13.0.88`. +> +> If you get another version or `Command 'nvcc' not found`, add it to the PATH: +> ```bash +> export CUDA_HOME=/usr/local/cuda-13.0 +> export PATH="${CUDA_HOME}/bin:$PATH" +> ``` +> +> Run `nvcc --version` to ensure flash-attn will be built for CUDA 13.0 + + +```bash +# GPU (CUDA) Installation - building flash-attn for supporting conchv1_5, gigapath and musk + +MAX_JOBS=2 uv sync --extra gpu_all # to speed up the build time increase max_jobs! This might use more RAM! +source .venv/bin/activate +``` + If you encounter errors during installation please read Installation Troubleshooting [below](#installation-troubleshooting). ### Additional Dependencies diff --git a/pyproject.toml b/pyproject.toml index ce840af8..8df5ab01 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ authors = [ ] description = "A protocol for Solid Tumor Associative Modeling in Pathology" readme = "README.md" -requires-python = ">=3.11" +requires-python = ">=3.13,<3.14" classifiers = [ "Programming Language :: Python :: 3", @@ -23,31 +23,30 @@ classifiers = [ ] dependencies = [ - "beartype>=0.21.0", - "einops>=0.8.1", - "h5py>=3.14.0", - "jaxtyping>=0.3.2", - "lightning>=2.5.2", - "matplotlib>=3.10.5", - "numpy>=2.2.2", - "opencv-python>=4.12.0.88", - "openpyxl>=3.1.5", - "openslide-bin>=4.0.0.8", - "openslide-python>=1.4.2", - "packaging>=25.0", - "pandas>=2.3.1", - "pillow>=11.3.0", - "pydantic>=2.11.7", - "pyyaml>=6.0.2", - "scikit-learn>=1.6.1", - "scipy>=1.16.1", - "torch>=2.7.1,<2.8.0", - "torchmetrics>=1.6.0", - "torchvision>=0.22.1", - "tqdm>=4.67.1", - "timm>=1.0.19", - "transformers>=4.55.0", - "lifelines>=0.28.0", + "beartype~=0.22.9", + "einops~=0.8.2", + "h5py~=3.16.0", + "jaxtyping~=0.3.9", + "lightning~=2.6.1", + "matplotlib~=3.10.8", + "numpy~=2.4.3", + "opencv-python~=4.13.0.92", + "openpyxl~=3.1.5", + "openslide-bin~=4.0.0.13", + "openslide-python~=1.4.3", + "packaging~=26.0", + "pandas~=2.3.3", + "pillow~=12.1.1", + "pydantic~=2.12.5", + "pyyaml~=6.0.3", + "scikit-learn~=1.8.0", + "scipy~=1.17.1", + "torchmetrics~=1.9.0", + "tqdm~=4.67.3", + "timm~=1.0.25", + "transformers~=4.57.6", + "lifelines~=0.30.3", + "huggingface-hub~=0.36.2" ] [project.optional-dependencies] @@ -58,14 +57,13 @@ build = [ "ninja" ] flash-attention = [ - "flash-attn>=2.8.3", + "flash-attn==2.8.3", ] conch = [ "huggingface-hub>=0.26.2", "conch @ git+https://github.com/KatherLab/CONCH", ] conch1_5_cpu = [ - "transformers>=4.45.2", "einops-exts==0.0.4", ] conch1_5 = [ @@ -99,19 +97,21 @@ virchow2 = [ "torch>=2.0.0", ] cobra = [ - "stamp[flash-attention]", - "causal-conv1d>=1.5.3.post1", - "mamba-ssm>=2.2.6.post3", + "causal-conv1d @ https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.6.1.post4/causal_conv1d-1.6.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_x86_64.whl ; sys_platform == 'linux' and platform_machine == 'x86_64' and python_version == '3.13' and extra == 'cobra'", + "causal-conv1d @ https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.6.1.post4/causal_conv1d-1.6.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_aarch64.whl ; sys_platform == 'linux' and platform_machine == 'aarch64' and python_version == '3.13' and extra == 'cobra'", + "mamba-ssm @ https://github.com/state-spaces/mamba/releases/download/v2.3.1/mamba_ssm-2.3.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_x86_64.whl ; sys_platform == 'linux' and platform_machine == 'x86_64' and python_version == '3.13'", + "mamba-ssm @ https://github.com/state-spaces/mamba/releases/download/v2.3.1/mamba_ssm-2.3.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_aarch64.whl ; sys_platform == 'linux' and platform_machine == 'aarch64' and python_version == '3.13'", + "cobra @ git+http://github.com/KatherLab/COBRA.git@49d231191db5a9c2ea37a2398dd922c8c9ee9cdb", - "jinja2>=3.1.4", - "triton" + "jinja2>=3.1.4", + "triton", ] prism_cpu = [ "sacremoses==0.1.1", "environs==11.0.0", ] prism = [ - "stamp[prism_cpu, flash-attention]", + "stamp[prism_cpu]", ] madeleine = [ "madeleine @ git+https://github.com/mahmoodlab/MADELEINE.git@de7c85acc2bdad352e6df8eee5694f8b6f288012" @@ -127,7 +127,7 @@ plip_cpu = [ "transformers>=4.45.2" ] plip = [ - "stamp[plip_cpu, flash-attention]", + "stamp[plip_cpu]", ] mcp = [ "fastmcp>=2.11.2", @@ -135,8 +135,21 @@ mcp = [ # Blanket target -cpu = ["stamp[conch,ctranspath,uni,virchow2,chief_ctranspath,conch1_5_cpu,prism_cpu,madeleine,musk_cpu,plip_cpu]"] -gpu = ["stamp[conch,ctranspath,uni,virchow2,chief_ctranspath,conch1_5,prism,madeleine,musk,plip,gigapath,cobra]"] +cpu = [ + "torch~=2.10.0", + "torchvision~=0.25.0", + "stamp[conch,ctranspath,uni,virchow2,chief_ctranspath,conch1_5_cpu,prism_cpu,madeleine,musk_cpu,plip_cpu]" +] +gpu = [ + "torch~=2.10.0", + "torchvision~=0.25.0", + "stamp[conch,ctranspath,uni,virchow2,chief_ctranspath,conch1_5_cpu,prism,madeleine,plip,musk_cpu,cobra]" +] +gpu_all = [ + "torch~=2.10.0", + "torchvision~=0.25.0", + "stamp[conch,ctranspath,uni,virchow2,chief_ctranspath,musk,gigapath,conch1_5,prism,madeleine,plip,cobra]" +] all = ["stamp[cpu]"] [project.scripts] @@ -148,11 +161,11 @@ all = ["stamp[cpu]"] [dependency-groups] dev = [ - "huggingface-hub>=0.34.3", - "ipykernel>=6.30.1", - "pyright>=1.1.403", - "pytest>=8.4.1", - "ruff>=0.12.7", + "huggingface-hub~=0.36.2", + "ipykernel~=7.2.0", + "pyright~=1.1.408", + "pytest~=9.0.2", + "ruff>=0.15.7", ] [build-system] @@ -173,28 +186,41 @@ lint.ignore = ["F722"] # https://docs.kidger.site/jaxtyping/faq/#flake8-or-ruff- [tool.uv] conflicts = [ - [ - { extra = "cpu" }, - { extra = "gpu" } - ] + [ + { extra = "cpu" }, + { extra = "gpu" }, + ], + [ + { extra = "cpu" }, + { extra = "gpu_all" }, + ], ] build-constraint-dependencies = [ - "torch<2.8", - "torchvision<0.23", + "torch==2.10.0", + "torchvision==0.25.0", ] [tool.uv.sources] torch = [ - { index = "pytorch-cu128", marker = "sys_platform != 'darwin'" } + { index = "pytorch-cpu", extra = "cpu" }, + { index = "pytorch-cu130", extra = "gpu" }, + { index = "pytorch-cu130", extra = "gpu_all" }, ] torchvision = [ - { index = "pytorch-cu128", marker = "sys_platform != 'darwin'" } + { index = "pytorch-cpu", extra = "cpu" }, + { index = "pytorch-cu130", extra = "gpu" }, + { index = "pytorch-cu130", extra = "gpu_all" }, ] [[tool.uv.index]] -name = "pytorch-cu128" -url = "https://download.pytorch.org/whl/cu128" +name = "pytorch-cpu" +url = "https://download.pytorch.org/whl/cpu" +explicit = true + +[[tool.uv.index]] +name = "pytorch-cu130" +url = "https://download.pytorch.org/whl/cu130" explicit = true @@ -210,7 +236,7 @@ requires-dist = [ "scikit-learn", "tqdm", "transformers", - "xformers; sys_platform != 'darwin'" # xformers is not supported on macOS + "xformers; (sys_platform == 'linux' and platform_machine == 'x86_64') or (sys_platform == 'win32' and platform_machine == 'AMD64')" ] @@ -221,23 +247,7 @@ requires-dist = [ "einops", ] - -[[tool.uv.dependency-metadata]] -name = "mamba-ssm" -requires-dist = [ - "setuptools", -] - -[[tool.uv.dependency-metadata]] -name = "causal-conv1d" -requires-dist = [ - "setuptools", - "torch" -] - [tool.uv.extra-build-dependencies] -cobra = [{ requirement = "torch", match-runtime = true }] flash-attn = [{ requirement = "torch", match-runtime = true }] -mamba-ssm = [{ requirement = "torch", match-runtime = true }] gigapath = [{ requirement = "torch", match-runtime = true }] conch = [{ requirement = "torch", match-runtime = true }] diff --git a/src/stamp/modeling/deploy.py b/src/stamp/modeling/deploy.py index e0444f15..035769f2 100644 --- a/src/stamp/modeling/deploy.py +++ b/src/stamp/modeling/deploy.py @@ -53,7 +53,9 @@ def load_model_from_ckpt(path: Union[str, Path]): hparams["task"], hparams["supported_features"], ModelName(hparams["model_name"]) ) - return LitModelClass.load_from_checkpoint(path, model_class=ModelClass) + return LitModelClass.load_from_checkpoint( + path, model_class=ModelClass, weights_only=False + ) def deploy_categorical_model_( diff --git a/src/stamp/modeling/train.py b/src/stamp/modeling/train.py index a55ec1e3..61944624 100644 --- a/src/stamp/modeling/train.py +++ b/src/stamp/modeling/train.py @@ -557,7 +557,9 @@ def train_model_( # Reload the best model using the same class as the input model ModelClass = type(model) - return ModelClass.load_from_checkpoint(model_checkpoint.best_model_path) + return ModelClass.load_from_checkpoint( + model_checkpoint.best_model_path, weights_only=False + ) def _compute_class_weights_and_check_categories( diff --git a/src/stamp/preprocessing/extractor/keep.py b/src/stamp/preprocessing/extractor/keep.py index 4adc964e..c0377793 100644 --- a/src/stamp/preprocessing/extractor/keep.py +++ b/src/stamp/preprocessing/extractor/keep.py @@ -4,9 +4,14 @@ """ try: + import json + + import timm import torch + import torch.nn as nn + from huggingface_hub import hf_hub_download + from safetensors.torch import load_file from torchvision import transforms - from transformers import AutoModel except ModuleNotFoundError as e: raise ModuleNotFoundError( "keep dependencies not installed." @@ -17,19 +22,81 @@ from stamp.preprocessing.extractor import Extractor -class KEEPWrapper(torch.nn.Module): - def __init__(self, model) -> None: +class KEEPImageModel(nn.Module): + def __init__(self, vision_config: dict, projection_dim: int) -> None: super().__init__() - self.model = model + + self.visual = timm.create_model( + "vit_large_patch16_224", + pretrained=False, + img_size=vision_config["img_size"], + patch_size=vision_config["patch_size"], + init_values=vision_config["init_values"], + num_classes=vision_config["num_classes"], + dynamic_img_size=vision_config.get("dynamic_img_size", True), + ) + + self.visual_head = nn.Sequential( + nn.Linear(self.visual.num_features, projection_dim), + nn.GELU(), + nn.Linear(projection_dim, projection_dim), + ) + + def encode_image(self, image_inputs: torch.Tensor) -> torch.Tensor: + vision_features = self.visual(image_inputs) + return torch.nn.functional.normalize(self.visual_head(vision_features), dim=-1) def forward(self, batch: torch.Tensor) -> torch.Tensor: - return self.model.encode_image(batch) + return self.encode_image(batch) -def keep() -> Extractor[KEEPWrapper]: - """Extracts features from slide tiles using the KEEP tile encoder.""" - model = AutoModel.from_pretrained("Astaxanthin/KEEP", trust_remote_code=True) +def _remap_layerscale_keys(sd: dict[str, torch.Tensor]) -> dict[str, torch.Tensor]: + remapped = {} + for k, v in sd.items(): + if ".ls1.weight" in k or ".ls2.weight" in k: + k = k.replace(".weight", ".gamma") + remapped[k] = v + return remapped + + +def _load_keep_image_model() -> KEEPImageModel: + repo_id = "Astaxanthin/KEEP" + + config_path = hf_hub_download( + repo_id=repo_id, + filename="config.json", + repo_type="model", + ) + weights_path = hf_hub_download( + repo_id=repo_id, + filename="model.safetensors", + repo_type="model", + ) + + with open(config_path) as f: + cfg = json.load(f) + + model = KEEPImageModel( + vision_config=cfg["vision_config"], + projection_dim=cfg["projection_dim"], + ) + + sd = load_file(weights_path) + sd = { + k: v + for k, v in sd.items() + if k.startswith("visual.") or k.startswith("visual_head.") + } + sd = _remap_layerscale_keys(sd) + + model.load_state_dict(sd, strict=False) model.eval() + return model + + +def keep() -> Extractor[KEEPImageModel]: + """Extracts features from slide tiles using the KEEP tile encoder.""" + model = _load_keep_image_model() transform = transforms.Compose( [ @@ -43,7 +110,7 @@ def keep() -> Extractor[KEEPWrapper]: ) return Extractor( - model=KEEPWrapper(model), + model=model, transform=transform, identifier=ExtractorName.KEEP, ) diff --git a/src/stamp/preprocessing/extractor/ticon.py b/src/stamp/preprocessing/extractor/ticon.py index 02aac13e..cda97ced 100644 --- a/src/stamp/preprocessing/extractor/ticon.py +++ b/src/stamp/preprocessing/extractor/ticon.py @@ -35,6 +35,8 @@ def __init__( dim: int, init_values: float = 1e-5, inplace: bool = False, + device=None, + dtype=None, ) -> None: super().__init__() self.inplace = inplace diff --git a/uv.lock b/uv.lock index beb0a251..6c467462 100644 --- a/uv.lock +++ b/uv.lock @@ -1,73 +1,43 @@ version = 1 revision = 3 -requires-python = ">=3.11" +requires-python = "==3.13.*" resolution-markers = [ - "(python_full_version >= '3.15' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (python_full_version >= '3.13' and platform_python_implementation != 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')", - "python_full_version >= '3.13' and python_full_version < '3.15' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu'", - "(python_full_version >= '3.14' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu') or (python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu') or (python_full_version >= '3.13' and platform_python_implementation != 'CPython' and sys_platform == 'linux' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu')", - "python_full_version == '3.13.*' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu'", - "(python_full_version >= '3.14' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu') or (python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu') or (python_full_version >= '3.13' and platform_python_implementation != 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu')", - "python_full_version == '3.13.*' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu'", - "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (python_full_version == '3.12.*' and platform_python_implementation != 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')", - "python_full_version == '3.12.*' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu'", - "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu') or (python_full_version == '3.12.*' and platform_python_implementation != 'CPython' and sys_platform == 'linux' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu')", - "python_full_version == '3.12.*' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu'", - "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu') or (python_full_version == '3.12.*' and platform_python_implementation != 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu')", - "python_full_version == '3.12.*' and platform_machine == 'aarch64' and platform_python_implementation == 'CPython' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu'", - "python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu'", - "python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu'", - "python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu'", - "python_full_version >= '3.13' and sys_platform == 'darwin' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu'", - "python_full_version >= '3.13' and sys_platform == 'darwin' and extra == 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu'", - "python_full_version >= '3.13' and sys_platform == 'darwin' and extra != 'extra-5-stamp-cpu' and extra != 'extra-5-stamp-gpu'", - "python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu'", - "python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux' and extra == 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"flash-attn" }, - { name = "transformers" }, ] conch1-5-cpu = [ { name = "einops-exts" }, - { name = "transformers" }, ] cpu = [ { name = "conch" }, @@ -3791,8 +3185,10 @@ cpu = [ { name = "madeleine" }, { name = "musk" }, { name = "sacremoses" }, - { name = "torch", version = "2.7.1", source = { registry = "https://pypi.org/simple" }, marker = "(sys_platform == 'darwin' and extra == 'extra-5-stamp-cpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')" }, - { name = "torch", version = "2.7.1+cu128", source = { registry = "https://download.pytorch.org/whl/cu128" }, marker = "(sys_platform != 'darwin' and extra == 'extra-5-stamp-cpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')" }, + { name = "torch", version = "2.10.0", source = { registry = "https://download.pytorch.org/whl/cpu" }, marker = "(sys_platform == 'darwin' and extra == 'extra-5-stamp-cpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (extra == 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extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu-all')" }, + { name = "cobra" }, + { name = "conch" }, + { name = "einops-exts" }, + { name = "environs" }, + { name = "fairscale" }, + { name = "gdown" }, + { name = "huggingface-hub" }, + { name = "jinja2" }, + { name = "madeleine" }, + { name = "mamba-ssm", version = "2.3.1", source = { url = "https://github.com/state-spaces/mamba/releases/download/v2.3.1/mamba_ssm-2.3.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_aarch64.whl" }, marker = "(platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu-all')" }, + { name = "mamba-ssm", version = "2.3.1", source = { url = "https://github.com/state-spaces/mamba/releases/download/v2.3.1/mamba_ssm-2.3.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_x86_64.whl" }, marker = 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(extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu-all')" }, + { name = "causal-conv1d", version = "1.6.1", source = { url = "https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.6.1.post4/causal_conv1d-1.6.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_x86_64.whl" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu-all')" }, { name = "cobra" }, { name = "conch" }, { name = "einops-exts" }, @@ -3829,17 +3248,17 @@ gpu = [ { name = "iopath" }, { name = "jinja2" }, { name = "madeleine" }, - { name = "mamba-ssm" }, + { name = "mamba-ssm", version = "2.3.1", source = { url = "https://github.com/state-spaces/mamba/releases/download/v2.3.1/mamba_ssm-2.3.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_aarch64.whl" }, marker = "(platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu-all')" }, + { name = "mamba-ssm", version = "2.3.1", source = { url = "https://github.com/state-spaces/mamba/releases/download/v2.3.1/mamba_ssm-2.3.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_x86_64.whl" }, marker = "(platform_machine == 'x86_64' and sys_platform == 'linux' and extra != 'extra-5-stamp-cpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu-all')" }, { name = "monai" }, { name = "musk" }, { name = "sacremoses" }, { name = "scikit-image" }, { name = "scikit-survival" }, - { name = "torch", version = "2.7.1", source = { registry = "https://pypi.org/simple" }, marker = "(sys_platform == 'darwin' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')" }, - { name = "torch", version = "2.7.1+cu128", source = { registry = "https://download.pytorch.org/whl/cu128" }, marker = "(sys_platform != 'darwin' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')" }, + { name = "torch", version = "2.10.0+cu130", source = { registry = "https://download.pytorch.org/whl/cu130" } }, + { name = "torchvision", version = "0.25.0+cu130", source = { registry = "https://download.pytorch.org/whl/cu130" } }, { name = "transformers" }, - { name = "triton", version = "3.3.1", source = { registry = "https://pypi.org/simple" }, marker = "(sys_platform == 'linux' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')" }, - { name = "triton", version = "3.4.0", source = { registry = "https://pypi.org/simple" }, marker = "(sys_platform != 'linux' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')" }, + { name = "triton" }, { name = "uni" }, { name = "wandb" }, { name = "webdataset" }, @@ -3860,7 +3279,6 @@ musk-cpu = [ { name = "musk" }, ] plip = [ - { name = "flash-attn" }, { name = "transformers" }, ] plip-cpu = [ @@ -3868,7 +3286,6 @@ plip-cpu = [ ] prism = [ { name = "environs" }, - { name = "flash-attn" }, { name = "sacremoses" }, ] prism-cpu = [ @@ -3881,8 +3298,9 @@ uni = [ ] virchow2 = [ { name = "huggingface-hub" }, - { name = "torch", version = "2.7.1", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'darwin' or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')" }, - { name = "torch", version = "2.7.1+cu128", source = { registry = "https://download.pytorch.org/whl/cu128" }, marker = "sys_platform != 'darwin' or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu')" }, + { name = "torch", version = "2.10.0", source = { registry = "https://download.pytorch.org/whl/cpu" }, marker = "(sys_platform == 'darwin' and extra == 'extra-5-stamp-cpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu-all')" }, + { name = "torch", version = "2.10.0+cpu", source = { registry = "https://download.pytorch.org/whl/cpu" }, marker = "(sys_platform != 'darwin' and extra == 'extra-5-stamp-cpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu') or (extra == 'extra-5-stamp-cpu' and extra == 'extra-5-stamp-gpu-all')" }, + { name = "torch", version = "2.10.0+cu130", source = { registry = "https://download.pytorch.org/whl/cu130" }, marker = "extra == 'extra-5-stamp-gpu' or extra == 'extra-5-stamp-gpu-all' or extra != 'extra-5-stamp-cpu'" }, ] [package.dev-dependencies] @@ -3896,91 +3314,93 @@ dev = [ [package.metadata] requires-dist = [ - { name = "beartype", specifier = ">=0.21.0" }, - { name = "causal-conv1d", marker = "extra == 'cobra'", specifier = ">=1.5.3.post1" }, + { name = "beartype", specifier = "~=0.22.9" }, + { name = "causal-conv1d", marker = "python_full_version == '3.13.*' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cobra'", url = "https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.6.1.post4/causal_conv1d-1.6.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_aarch64.whl" }, + { name = "causal-conv1d", marker = "python_full_version == '3.13.*' and platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cobra'", url = "https://github.com/Dao-AILab/causal-conv1d/releases/download/v1.6.1.post4/causal_conv1d-1.6.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_x86_64.whl" }, { name = "cobra", marker = "extra == 'cobra'", git = "http://github.com/KatherLab/COBRA.git?rev=49d231191db5a9c2ea37a2398dd922c8c9ee9cdb" }, { name = "conch", marker = "extra == 'conch'", git = "https://github.com/KatherLab/CONCH" }, - { name = "einops", specifier = ">=0.8.1" }, + { name = "einops", specifier = "~=0.8.2" }, { name = "einops-exts", marker = "extra == 'conch1-5-cpu'", specifier = "==0.0.4" }, { name = "environs", marker = "extra == 'prism-cpu'", specifier = "==11.0.0" }, { name = "fairscale", marker = "extra == 'gigapath'" }, { name = "fairscale", marker = "extra == 'musk-cpu'" }, { name = "fastmcp", marker = "extra == 'mcp'", specifier = ">=2.11.2" }, - { name = "flash-attn", marker = "extra == 'flash-attention'", specifier = ">=2.8.3" }, + { name = "flash-attn", marker = "extra == 'flash-attention'", specifier = "==2.8.3" }, { name = "fvcore", marker = "extra == 'gigapath'" }, { name = "gdown", marker = "extra == 'chief-ctranspath'", specifier = ">=5.2.0" }, { name = "gdown", marker = "extra == 'ctranspath'", specifier = ">=5.2.0" }, { name = "gigapath", marker = "extra == 'gigapath'", git = "https://github.com/KatherLab/prov-gigapath.git?rev=ec97baa5f071319680132e18868279b4cca877cc" }, - { name = "h5py", specifier = ">=3.14.0" }, + { name = "h5py", specifier = "~=3.16.0" }, { name = "hatchling", marker = "extra == 'build'" }, + { name = "huggingface-hub", specifier = "~=0.36.2" }, { name = "huggingface-hub", marker = "extra == 'conch'", specifier = ">=0.26.2" }, { name = "huggingface-hub", marker = "extra == 'uni'", specifier = ">=0.26.2" }, { name = "huggingface-hub", marker = "extra == 'virchow2'", specifier = ">=0.27.1" }, { name = "iopath", marker = "extra == 'gigapath'" }, - { name = "jaxtyping", specifier = ">=0.3.2" }, + { name = "jaxtyping", specifier = "~=0.3.9" }, { name = "jinja2", marker = "extra == 'cobra'", specifier = ">=3.1.4" }, - { name = "lifelines", specifier = ">=0.28.0" }, - { name = "lightning", specifier = ">=2.5.2" }, + { name = "lifelines", specifier = "~=0.30.3" }, + { name = "lightning", specifier = "~=2.6.1" }, { name = "madeleine", marker = "extra == 'madeleine'", git = "https://github.com/mahmoodlab/MADELEINE.git?rev=de7c85acc2bdad352e6df8eee5694f8b6f288012" }, - { name = "mamba-ssm", marker = "extra == 'cobra'", specifier = ">=2.2.6.post3" }, - { name = "matplotlib", specifier = ">=3.10.5" }, + { name = "mamba-ssm", marker = "python_full_version == '3.13.*' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'cobra'", url = "https://github.com/state-spaces/mamba/releases/download/v2.3.1/mamba_ssm-2.3.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_aarch64.whl" }, + { name = "mamba-ssm", marker = "python_full_version == '3.13.*' and platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'cobra'", url = "https://github.com/state-spaces/mamba/releases/download/v2.3.1/mamba_ssm-2.3.1+cu13torch2.10cxx11abiTRUE-cp313-cp313-linux_x86_64.whl" }, + { name = "matplotlib", specifier = "~=3.10.8" }, { name = "monai", marker = "extra == 'gigapath'" }, { name = "musk", marker = "extra == 'musk-cpu'", git = "https://github.com/lilab-stanford/MUSK.git?rev=e1699c27687f44bbf6d4adfcbb2abe89795d347f" }, { name = "ninja", marker = "extra == 'build'" }, - { name = "numpy", specifier = ">=2.2.2" }, - { name = "opencv-python", specifier = ">=4.12.0.88" }, - { name = "openpyxl", specifier = ">=3.1.5" }, - { name = "openslide-bin", specifier = ">=4.0.0.8" }, - { name = "openslide-python", specifier = ">=1.4.2" }, - { name = "packaging", specifier = ">=25.0" }, - { name = "pandas", specifier = ">=2.3.1" }, - { name = "pillow", specifier = ">=11.3.0" }, + { name = "numpy", specifier = "~=2.4.3" }, + { name = "opencv-python", specifier = "~=4.13.0.92" }, + { name = "openpyxl", specifier = "~=3.1.5" }, + { name = "openslide-bin", specifier = "~=4.0.0.13" }, + { name = "openslide-python", specifier = "~=1.4.3" }, + { name = "packaging", specifier = "~=26.0" }, + { name = "pandas", specifier = "~=2.3.3" }, + { name = "pillow", specifier = "~=12.1.1" }, { name = "psutil", marker = "extra == 'build'" }, - { name = "pydantic", specifier = ">=2.11.7" }, - { name = "pyyaml", specifier = ">=6.0.2" }, + { name = "pydantic", specifier = "~=2.12.5" }, + { name = "pyyaml", specifier = "~=6.0.3" }, { name = "sacremoses", marker = "extra == 'prism-cpu'", specifier = "==0.1.1" }, { name = "scikit-image", marker = "extra == 'gigapath'" }, - { name = "scikit-learn", specifier = ">=1.6.1" }, + { name = "scikit-learn", specifier = "~=1.8.0" }, { name = "scikit-survival", marker = "extra == 'gigapath'", specifier = ">=0.24.1" }, - { name = "scipy", specifier = ">=1.16.1" }, + { name = "scipy", specifier = "~=1.17.1" }, { name = "setuptools", marker = "extra == 'build'" }, - { name = "stamp", extras = ["conch", "ctranspath", "uni", "virchow2", "chief-ctranspath", "conch1-5", "prism", "madeleine", "musk", "plip", "gigapath", "cobra"], marker = "extra == 'gpu'" }, + { name = "stamp", extras = ["conch", "ctranspath", "uni", "virchow2", "chief-ctranspath", "conch1-5-cpu", "prism", "madeleine", "plip", "musk-cpu", "cobra"], marker = "extra == 'gpu'" }, { name = "stamp", extras = ["conch", "ctranspath", "uni", "virchow2", "chief-ctranspath", "conch1-5-cpu", "prism-cpu", "madeleine", "musk-cpu", "plip-cpu"], marker = "extra == 'cpu'" }, + { name = "stamp", extras = ["conch", "ctranspath", "uni", "virchow2", "chief-ctranspath", "musk", "gigapath", "conch1-5", "prism", "madeleine", "plip", "cobra"], marker = "extra == 'gpu-all'" }, { name = "stamp", extras = ["conch1-5-cpu", "flash-attention"], marker = "extra == 'conch1-5'" }, { name = "stamp", extras = ["cpu"], marker = "extra == 'all'" }, - { name = "stamp", extras = ["flash-attention"], marker = "extra == 'cobra'" }, { name = "stamp", extras = ["flash-attention"], marker = "extra == 'gigapath'" }, { name = "stamp", extras = ["musk-cpu", "flash-attention"], marker = "extra == 'musk'" }, - { name = "stamp", extras = ["plip-cpu", "flash-attention"], marker = "extra == 'plip'" }, - { name = "stamp", extras = ["prism-cpu", "flash-attention"], marker = "extra == 'prism'" }, - { name = "timm", specifier = ">=1.0.19" }, - { name = "torch", marker = "sys_platform != 'darwin'", specifier = ">=2.7.1,<2.8.0", index = "https://download.pytorch.org/whl/cu128" }, - { name = "torch", marker = "sys_platform == 'darwin'", specifier = ">=2.7.1,<2.8.0" }, - { name = "torch", marker = "sys_platform == 'darwin' and extra == 'chief-ctranspath'", specifier = ">=2.0.0" }, - { name = "torch", marker = "sys_platform == 'darwin' and extra == 'virchow2'", specifier = ">=2.0.0" }, - { name = "torch", marker = "sys_platform != 'darwin' and extra == 'chief-ctranspath'", specifier = ">=2.0.0", index = "https://download.pytorch.org/whl/cu128" }, - { name = "torch", marker = "sys_platform != 'darwin' and extra == 'virchow2'", specifier = ">=2.0.0", index = "https://download.pytorch.org/whl/cu128" }, - { name = "torchmetrics", specifier = ">=1.6.0" }, - { name = "torchvision", marker = "sys_platform != 'darwin'", specifier = ">=0.22.1", index = "https://download.pytorch.org/whl/cu128" }, - { name = "torchvision", marker = "sys_platform == 'darwin'", specifier = ">=0.22.1" }, - { name = "tqdm", specifier = ">=4.67.1" }, - { name = "transformers", specifier = ">=4.55.0" }, - { name = "transformers", marker = "extra == 'conch1-5-cpu'", specifier = ">=4.45.2" }, + { name = "stamp", extras = ["plip-cpu"], marker = "extra == 'plip'" }, + { name = "stamp", extras = ["prism-cpu"], marker = "extra == 'prism'" }, + { name = "timm", specifier = "~=1.0.25" }, + { name = "torch", marker = "extra == 'chief-ctranspath'", specifier = ">=2.0.0" }, + { name = "torch", marker = "extra == 'cpu'", specifier = "~=2.10.0", index = "https://download.pytorch.org/whl/cpu", conflict = { package = "stamp", extra = "cpu" } }, + { name = "torch", marker = "extra == 'gpu'", specifier = "~=2.10.0", index = "https://download.pytorch.org/whl/cu130", conflict = { package = "stamp", extra = "gpu" } }, + { name = "torch", marker = "extra == 'gpu-all'", specifier = "~=2.10.0", index = "https://download.pytorch.org/whl/cu130", conflict = { package = "stamp", extra = "gpu-all" } }, + { name = "torch", marker = "extra == 'virchow2'", specifier = ">=2.0.0" }, + { name = "torchmetrics", specifier = "~=1.9.0" }, + { name = "torchvision", marker = "extra == 'cpu'", specifier = "~=0.25.0", index = "https://download.pytorch.org/whl/cpu", conflict = { package = "stamp", extra = "cpu" } }, + { name = "torchvision", marker = "extra == 'gpu'", specifier = "~=0.25.0", index = "https://download.pytorch.org/whl/cu130", conflict = { package = "stamp", extra = "gpu" } }, + { name = "torchvision", marker = "extra == 'gpu-all'", specifier = "~=0.25.0", index = "https://download.pytorch.org/whl/cu130", conflict = { package = "stamp", extra = "gpu-all" } }, + { name = "tqdm", specifier = "~=4.67.3" }, + { name = "transformers", specifier = "~=4.57.6" }, { name = "transformers", marker = "extra == 'plip-cpu'", specifier = ">=4.45.2" }, { name = "triton", marker = "extra == 'cobra'" }, { name = "uni", marker = "extra == 'uni'", git = "https://github.com/KatherLab/uni.git?rev=f37c299eb0bffa0e585f120974082cfec6ee6d53" }, { name = "wandb", marker = "extra == 'gigapath'" }, { name = "webdataset", marker = "extra == 'gigapath'" }, ] -provides-extras = ["build", "flash-attention", "conch", "conch1-5-cpu", "conch1-5", "ctranspath", "chief-ctranspath", "gigapath", "uni", "virchow2", "cobra", "prism-cpu", "prism", "madeleine", "musk-cpu", "musk", "plip-cpu", "plip", "mcp", "cpu", "gpu", "all"] +provides-extras = ["build", "flash-attention", "conch", "conch1-5-cpu", "conch1-5", "ctranspath", "chief-ctranspath", "gigapath", "uni", "virchow2", "cobra", "prism-cpu", "prism", "madeleine", "musk-cpu", "musk", "plip-cpu", "plip", "mcp", "cpu", "gpu", "gpu-all", "all"] [package.metadata.requires-dev] dev = [ - { name = "huggingface-hub", specifier = ">=0.34.3" }, - { name = "ipykernel", specifier = ">=6.30.1" }, - { name = "pyright", specifier = ">=1.1.403" }, - { name = "pytest", specifier = ">=8.4.1" }, - { name = "ruff", specifier = ">=0.12.7" }, + { name = "huggingface-hub", specifier = "~=0.36.2" }, + { name = "ipykernel", specifier = "~=7.2.0" }, + { name = "pyright", specifier = "~=1.1.408" }, + { name 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