slide2vec 7.1.0__tar.gz → 7.1.2__tar.gz

{slide2vec-7.1.0 → slide2vec-7.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 7.1.0
+Version: 7.1.2
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0
@@ -11,94 +11,51 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: hs2p[asap,cucim,openslide,sam2,tifffile,vips]>=6.1.0
 Requires-Dist: omegaconf
 Requires-Dist: matplotlib
-Requires-Dist: numpy<2
 Requires-Dist: pandas
 Requires-Dist: pillow
 Requires-Dist: rich
 Requires-Dist: torch
 Requires-Dist: torchvision
-Requires-Dist: transformers
+Requires-Dist: transformers<5,>=4.47
 Requires-Dist: wandb
 Requires-Dist: einops
-Requires-Dist: timm>=1.0.3
+Requires-Dist: einops-exts
+Requires-Dist: timm>=1.0.20
 Requires-Dist: huggingface_hub
-Provides-Extra: hoptimus
-Requires-Dist: torch>=2.0; extra == "hoptimus"
-Requires-Dist: torchvision>=0.15.0; extra == "hoptimus"
-Requires-Dist: xformers>=0.0.18; extra == "hoptimus"
-Provides-Extra: virchow
-Requires-Dist: timm>=1.0.3; extra == "virchow"
-Requires-Dist: torch>=2.0; extra == "virchow"
-Provides-Extra: uni
-Requires-Dist: torch>=2.0; extra == "uni"
-Requires-Dist: timm>=1.0.3; extra == "uni"
-Requires-Dist: xformers>=0.0.18; extra == "uni"
+Requires-Dist: packaging
 Provides-Extra: prism
-Requires-Dist: transformers~=4.53.0; extra == "prism"
-Requires-Dist: torch<2.8,>=2.3; extra == "prism"
-Requires-Dist: einops==0.8.0; extra == "prism"
-Requires-Dist: environs==11.0.0; extra == "prism"
-Requires-Dist: sacremoses==0.1.1; extra == "prism"
-Requires-Dist: xformers==0.0.31; extra == "prism"
+Requires-Dist: torch>=2.3; extra == "prism"
+Requires-Dist: environs; extra == "prism"
+Requires-Dist: sacremoses; extra == "prism"
 Provides-Extra: prism2
 Requires-Dist: torch>=2.3; extra == "prism2"
-Requires-Dist: transformers==4.51.3; extra == "prism2"
-Requires-Dist: safetensors; extra == "prism2"
-Requires-Dist: einops; extra == "prism2"
-Requires-Dist: flash-attn>=2.6.3; extra == "prism2"
-Provides-Extra: hibou
-Requires-Dist: scipy~=1.8.1; extra == "hibou"
-Requires-Dist: scikit-image~=0.19.3; extra == "hibou"
-Provides-Extra: moozy
-Requires-Dist: huggingface_hub<1.0,>=0.30.0; extra == "moozy"
+Requires-Dist: transformers<5,>=4.51; extra == "prism2"
 Provides-Extra: titan
-Requires-Dist: torch==2.0.1; extra == "titan"
-Requires-Dist: timm==1.0.3; extra == "titan"
-Requires-Dist: einops==0.6.1; extra == "titan"
-Requires-Dist: einops-exts==0.0.4; extra == "titan"
-Requires-Dist: transformers==4.46.0; extra == "titan"
+Requires-Dist: einops; extra == "titan"
+Requires-Dist: einops-exts; extra == "titan"
+Requires-Dist: timm>=1.0.3; extra == "titan"
+Requires-Dist: transformers<5,>=4.46; extra == "titan"
 Provides-Extra: waiv
-Requires-Dist: transformers<6,>=5.14; extra == "waiv"
-Requires-Dist: safetensors>=0.8; extra == "waiv"
-Requires-Dist: huggingface_hub==1.25.1; extra == "waiv"
+Requires-Dist: transformers>=4.57; extra == "waiv"
+Provides-Extra: flash-attn
+Requires-Dist: flash-attn>=2.6.3; extra == "flash-attn"
+Provides-Extra: xformers
+Requires-Dist: xformers; extra == "xformers"
 Provides-Extra: fm
-Requires-Dist: omegaconf>=2.3.0; extra == "fm"
-Requires-Dist: matplotlib; extra == "fm"
-Requires-Dist: numpy<2; extra == "fm"
-Requires-Dist: pandas; extra == "fm"
-Requires-Dist: pillow; extra == "fm"
-Requires-Dist: rich; extra == "fm"
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,tifffile,vips]>=6.1.0; extra == "fm"
-Requires-Dist: wandb; extra == "fm"
-Requires-Dist: torch<2.8,>=2.3; extra == "fm"
-Requires-Dist: torchvision>=0.18.0; extra == "fm"
-Requires-Dist: einops>=0.8.0; extra == "fm"
-Requires-Dist: timm>=1.0.20; extra == "fm"
-Requires-Dist: huggingface_hub<1.0,>=0.30.0; extra == "fm"
-Requires-Dist: environs; extra == "fm"
-Requires-Dist: einops-exts>=0.0.4; extra == "fm"
-Requires-Dist: transformers>=4.53; extra == "fm"
-Requires-Dist: sacremoses; extra == "fm"
-Requires-Dist: xformers>=0.0.31; extra == "fm"
-Requires-Dist: scipy>=1.8.1; extra == "fm"
-Requires-Dist: scikit-image>=0.19.3; extra == "fm"
-Requires-Dist: torchmetrics>=0.10.3; extra == "fm"
-Requires-Dist: fvcore; extra == "fm"
-Requires-Dist: iopath; extra == "fm"
-Requires-Dist: webdataset; extra == "fm"
-Requires-Dist: scikit-survival; extra == "fm"
-Requires-Dist: scikit-learn; extra == "fm"
+Requires-Dist: slide2vec[prism,prism2,titan,waiv]; extra == "fm"
 Requires-Dist: fairscale; extra == "fm"
-Requires-Dist: packaging==23.2; extra == "fm"
-Requires-Dist: ninja==1.11.1.1; extra == "fm"
-Requires-Dist: psutil<6; extra == "fm"
+Provides-Extra: cpu
+Requires-Dist: torch; extra == "cpu"
+Requires-Dist: torchvision; extra == "cpu"
+Provides-Extra: cu128
+Requires-Dist: torch; extra == "cu128"
+Requires-Dist: torchvision; extra == "cu128"
 Provides-Extra: docs
 Requires-Dist: sphinx>=8.1; extra == "docs"
 Requires-Dist: furo; extra == "docs"
@@ -131,6 +88,10 @@ pip install slide2vec
 
 Many models need additional dependencies available through `pip install "slide2vec[fm]"`. See the [model installation guide](https://clemsgrs.github.io/slide2vec/models.html#model-installation) for model-specific extras, separate environments, and upstream packages.
 
+### Reproducible model environments
+
+The repository ships a `uv.lock` file that pins every package for each extra. From a checkout, `uv sync --extra cu128 --extra fm` installs the exact locked stack (use `--extra cpu` for CPU-only PyTorch). Add `--extra flash-attn` for PRISM2 and `gigapath-slide`. The Docker image is built from the same lock; its `SLIDE2VEC_EXTRAS` build argument selects the extras, for example `--build-arg SLIDE2VEC_EXTRAS="cu128"` for the base install only.
+
 For gated models such as Virchow2, request access on the model's Hugging Face page and authenticate with `hf auth login` or an `HF_TOKEN` environment variable.
 
 ## Embed a slide

{slide2vec-7.1.0 → slide2vec-7.1.2}/README.md

@@ -15,6 +15,10 @@ pip install slide2vec
 
 Many models need additional dependencies available through `pip install "slide2vec[fm]"`. See the [model installation guide](https://clemsgrs.github.io/slide2vec/models.html#model-installation) for model-specific extras, separate environments, and upstream packages.
 
+### Reproducible model environments
+
+The repository ships a `uv.lock` file that pins every package for each extra. From a checkout, `uv sync --extra cu128 --extra fm` installs the exact locked stack (use `--extra cpu` for CPU-only PyTorch). Add `--extra flash-attn` for PRISM2 and `gigapath-slide`. The Docker image is built from the same lock; its `SLIDE2VEC_EXTRAS` build argument selects the extras, for example `--build-arg SLIDE2VEC_EXTRAS="cu128"` for the base install only.
+
 For gated models such as Virchow2, request access on the model's Hugging Face page and authenticate with `hf auth login` or an `HF_TOKEN` environment variable.
 
 ## Embed a slide

slide2vec-7.1.2/pyproject.toml

@@ -0,0 +1,264 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "slide2vec"
+version = "7.1.2"
+description = "Embedding of whole slide images with Foundation Models"
+readme = "README.md"
+requires-python = ">=3.10"
+license = "Apache-2.0"
+authors = [
+    { name = "Clément Grisi", email = "clement.grisi@radboudumc.nl" },
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "hs2p[asap,cucim,openslide,sam2,tifffile,vips]>=6.1.0",
+    "omegaconf",
+    "matplotlib",
+    "pandas",
+    "pillow",
+    "rich",
+    "torch",
+    "torchvision",
+    # <5: Hibou's remote code imports transformers.onnx and
+    # pytorch_utils.find_pruneable_heads_and_indices, both removed in v5.
+    # >=4.47: PRISM's configuring_prism.py needs sub_configs / base_config_key.
+    "transformers>=4.47,<5",
+    "wandb",
+    "einops",
+    # TITAN remote code (used by the built-in conchv15 preset) imports it.
+    "einops-exts",
+    # first release that registers vit_base_patch16_dinov3
+    "timm>=1.0.20",
+    "huggingface_hub",
+    "packaging",
+]
+
+[project.urls]
+Homepage = "https://github.com/clemsgrs/slide2vec"
+"Bug Tracker" = "https://github.com/clemsgrs/slide2vec/issues"
+
+[project.scripts]
+slide2vec = "slide2vec.cli:entrypoint"
+
+# Rule for extras: lower bounds only. An exact or upper pin is kept only when it
+# is structural (the model's code breaks outside it); the reason sits next to
+# the pin. A model whose stack conflicts with the shared stack gets its own
+# extra and a uv conflict below. numpy<2 comes from hs2p[asap].
+[project.optional-dependencies]
+prism = [
+    # perceiver.py calls torch.nn.attention.sdpa_kernel with a list (absent in 2.2)
+    "torch>=2.3",
+    "environs",
+    "sacremoses",
+]
+prism2 = [
+    "torch>=2.3",
+    # the text (diagnostic) variant calls a Phi3Model helper whose signature
+    # changed in 4.52 and which 4.53 removed; slide2vec.encoders.models.prism2
+    # vendors it, so no upper bound. PRISM2 also imports flash_attn: add the
+    # flash-attn extra (CUDA only, so not pulled in here)
+    "transformers>=4.51,<5",
+]
+titan = [
+    "einops",
+    "einops-exts",
+    "timm>=1.0.3",
+    "transformers>=4.46,<5",
+]
+waiv = [
+    # phaet and mascaret load with zero missing keys at the pinned revisions
+    "transformers>=4.57",
+]
+# gigapath-slide needs flash-attn on GPUs with compute capability above 7
+flash-attn = [
+    "flash-attn>=2.6.3",
+]
+xformers = [
+    # optional: PRISM's PERCEIVER_MEM_EFF_ATTN path; gigapath-slide needs it
+    # on GPUs with compute capability 7 or below. Unpinned: each xformers
+    # build pins its torch.
+    "xformers",
+]
+fm = [
+    "slide2vec[prism,prism2,titan,waiv]",
+    # hard import in MUSK and gigapath-slide
+    "fairscale",
+]
+# torch wheel flavour for uv; when neither is selected torch comes from PyPI
+cpu = [
+    "torch",
+    "torchvision",
+]
+cu128 = [
+    "torch",
+    "torchvision",
+]
+docs = [
+    "sphinx>=8.1",
+    "furo",
+    "myst-parser",
+    "sphinx-copybutton",
+    "sphinx-autodoc-typehints",
+]
+testing = [
+    "pytest>=6.0",
+    "pytest-cov>=2.0",
+    "mypy>=0.910",
+    "flake8>=3.9",
+    "flake8-pyproject>=1.2.3",
+    "tox>=3.24",
+]
+
+[dependency-groups]
+dev = [
+    "pytest>=6.0",
+    "pytest-cov>=2.0",
+    "mypy>=0.910",
+    "flake8>=3.9",
+    "flake8-pyproject>=1.2.3",
+    "tox>=3.24",
+    # tests/test_encoder_plugins.py installs a plugin with `python -m pip`;
+    # uv environments ship without pip
+    "pip",
+]
+docs = [
+    "sphinx>=8.1",
+    "furo",
+    "myst-parser",
+    "sphinx-copybutton",
+    "sphinx-autodoc-typehints",
+]
+# encoder packages that are not on PyPI (musk, conch, gigapath-slide, sam2)
+models-git = [
+    "musk",
+    "conch",
+    "gigapath",
+    "sam-2",
+]
+
+[tool.uv]
+# ASAP and cucim are Linux-only. numpy<2 (from hs2p[asap]) has no wheels for
+# Python 3.13+, so the lock covers Python 3.10 to 3.12.
+environments = ["sys_platform == 'linux' and python_full_version < '3.13'"]
+# Lock-only: the cu128 index stops at torch 2.11. Hold the CPU and PyPI forks at
+# the same release so the CPU CI image tests the torch the CUDA image ships.
+# This is not part of the published metadata.
+constraint-dependencies = ["torch<2.12"]
+conflicts = [
+    [
+        { extra = "cpu" },
+        { extra = "cu128" },
+    ],
+]
+
+# flash-attn ships only an sdist whose build imports torch; declare its metadata
+# so uv can lock it without building it
+[[tool.uv.dependency-metadata]]
+name = "flash-attn"
+requires-dist = ["torch", "einops"]
+
+# flash-attn's setup.py imports torch, packaging, wheel and psutil. Build it in
+# an isolated environment that holds the same torch as the runtime environment.
+[tool.uv.extra-build-dependencies]
+flash-attn = [
+    { requirement = "torch", match-runtime = true },
+    "packaging",
+    "psutil",
+    "wheel",
+    "ninja",
+]
+
+[tool.uv.sources]
+torch = [
+    { index = "pytorch-cpu", extra = "cpu" },
+    { index = "pytorch-cu128", extra = "cu128" },
+]
+torchvision = [
+    { index = "pytorch-cpu", extra = "cpu" },
+    { index = "pytorch-cu128", extra = "cu128" },
+]
+musk = { git = "https://github.com/lilab-stanford/MUSK.git" }
+conch = { git = "https://github.com/Mahmoodlab/CONCH.git" }
+gigapath = { git = "https://github.com/prov-gigapath/prov-gigapath.git" }
+sam-2 = { git = "https://github.com/facebookresearch/sam2.git" }
+
+[[tool.uv.index]]
+name = "pytorch-cpu"
+url = "https://download.pytorch.org/whl/cpu"
+explicit = true
+
+[[tool.uv.index]]
+name = "pytorch-cu128"
+url = "https://download.pytorch.org/whl/cu128"
+explicit = true
+
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.packages.find]
+include = ["slide2vec*"]
+
+[tool.setuptools.package-data]
+slide2vec = ["py.typed", "cufile.json"]
+"slide2vec.configs" = ["*.yaml"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=slide2vec -m 'not gpu_integration'"
+testpaths = [
+    "tests",
+]
+markers = [
+    "heavy: real-weight foundation-model inference on CPU; minutes per test. Included in the PR suite and available separately through the manual heavy workflow (.github/workflows/nightly-heavy.yaml).",
+    "gpu_integration: real one-GPU versus multi-GPU parity; requires at least two visible CUDA devices. Run explicitly with `CUDA_VISIBLE_DEVICES=0,1 python -m pytest -m gpu_integration --no-cov`.",
+]
+
+[tool.mypy]
+mypy_path = "."
+check_untyped_defs = true
+disallow_any_generics = true
+ignore_missing_imports = true
+no_implicit_optional = true
+show_error_codes = true
+strict_equality = true
+warn_redundant_casts = true
+warn_return_any = true
+warn_unreachable = true
+warn_unused_configs = true
+no_implicit_reexport = true
+
+[tool.flake8]
+max-line-length = 160
+
+[tool.bumpver]
+current_version = "7.1.2"
+version_pattern = "MAJOR.MINOR.PATCH"
+commit = false
+tag = false
+push = false
+files = [
+    "pyproject.toml",
+    "slide2vec/__init__.py",
+    "docs/conf.py",
+]
+
+[tool.bumpver.file_patterns]
+"pyproject.toml" = [
+    '^current_version = "{version}"$',
+    '^version = "{version}"$',
+]
+"slide2vec/__init__.py" = [
+    '^__version__ = "{version}"$',
+]
+"docs/conf.py" = [
+    '^release = "{version}"$',
+]

{slide2vec-7.1.0 → slide2vec-7.1.2}/slide2vec/__init__.py

@@ -36,7 +36,7 @@ from slide2vec.encoders import (
 )
 
 
-__version__ = "7.1.0"
+__version__ = "7.1.2"
 
 __all__ = [
     "Model",

{slide2vec-7.1.0 → slide2vec-7.1.2}/slide2vec/api.py

@@ -7,7 +7,7 @@ import warnings
 from dataclasses import dataclass, field, replace
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Any, Callable, Mapping, Protocol, Sequence
+from typing import Any, Callable, Mapping, NamedTuple, Protocol, Sequence
 
 import torch
 from hs2p import (
@@ -261,9 +261,12 @@ class ExecutionOptions:
     #: (capped by CPU / SLURM limit, then split across the resolved GPU count).
     #: Image-only routes safely use zero when auto selection happens after model loading.
     num_workers_per_gpu: int | None = None
-    #: Tiling worker count. ``None`` means auto (capped by CPU / SLURM limit).
+    #: Tiling worker count. ``None`` means auto. The field keeps the requested value;
+    #: :meth:`resolved_num_preprocessing_workers` gives the count a run uses, capped by the
+    #: CPU / SLURM limit.
     num_preprocessing_workers: int | None = None
-    #: Number of GPUs to use. ``None`` defaults to all available GPUs.
+    #: Number of GPUs to use. ``None`` means all available GPUs. The field keeps the
+    #: requested value; :meth:`resolved_num_gpus` gives the count a run uses.
     num_gpus: int | None = None
     #: Forward-pass dtype — ``"fp16"``, ``"bf16"``, ``"fp32"``,
     #: or ``None`` (auto-determined from the model preset).
@@ -313,11 +316,9 @@ class ExecutionOptions:
         )
 
     def __post_init__(self) -> None:
-        resolved_num_gpus = _default_num_gpus() if self.num_gpus is None else self.num_gpus
-        object.__setattr__(self, "num_gpus", resolved_num_gpus)
         object.__setattr__(self, "precision", normalize_precision_name(self.precision))
         object.__setattr__(self, "output_dtype", normalize_output_dtype(self.output_dtype))
-        if resolved_num_gpus < 1:
+        if self.num_gpus is not None and self.num_gpus < 1:
             raise ValueError("ExecutionOptions.num_gpus must be at least 1")
         if self.batch_size < 1:
             raise ValueError("ExecutionOptions.batch_size must be at least 1")
@@ -325,40 +326,62 @@ class ExecutionOptions:
             raise ValueError("ExecutionOptions.prefetch_factor must be at least 1")
         if self.num_workers_per_gpu is not None and self.num_workers_per_gpu < 0:
             raise ValueError("ExecutionOptions.num_workers_per_gpu must be non-negative")
+        if self.num_preprocessing_workers is not None and self.num_preprocessing_workers < 0:
+            raise ValueError("ExecutionOptions.num_preprocessing_workers must be non-negative")
         if self.on_image_mismatch not in IMAGE_MISMATCH_POLICIES:
             raise ValueError(
                 "ExecutionOptions.on_image_mismatch must be one of "
                 f"{', '.join(repr(policy) for policy in IMAGE_MISMATCH_POLICIES)}; "
                 f"got {self.on_image_mismatch!r}"
             )
+
+    def resolved_num_gpus(self) -> int:
+        """GPU count a run uses: :attr:`num_gpus`, or every visible GPU when it is ``None``."""
+        return self._machine_resolution.num_gpus
+
+    def resolved_num_preprocessing_workers(self) -> int:
+        """Tiling worker count a run uses: :attr:`num_preprocessing_workers`, or the CPU /
+        SLURM limit when it is ``None``, and never more than that limit."""
+        return self._machine_resolution.num_preprocessing_workers
+
+    def resolved_num_workers_per_gpu(self) -> int:
+        if self.num_workers_per_gpu is not None:
+            return self.num_workers_per_gpu
+        return max(1, cpu_worker_limit() // self.resolved_num_gpus())
+
+    @functools.cached_property
+    def _machine_resolution(self) -> "_MachineResolution":
+        # Resolved once per instance, on first use, so every reader in a run agrees and the
+        # log line is written once. The cache sits outside the dataclass fields: equality,
+        # hashing and repr see only what the caller asked for.
+        num_gpus = _default_num_gpus() if self.num_gpus is None else self.num_gpus
         cap = cpu_worker_limit()
-        cpu_count = os.cpu_count() or 1
-        slurm_limit = slurm_cpu_limit()
-        capped_num_preprocessing_workers = (
+        num_preprocessing_workers = (
             cap if self.num_preprocessing_workers is None else min(self.num_preprocessing_workers, cap)
         )
-        object.__setattr__(self, "num_preprocessing_workers", capped_num_preprocessing_workers)
-        logger = logging.getLogger(__name__)
-        cap_source = f"slurm_cpu_limit={slurm_limit}" if slurm_limit is not None else f"cpu_count={cpu_count}"
-        resolved_num_workers = self.resolved_num_workers_per_gpu()
-        num_workers_per_gpu_label = (
-            f"{resolved_num_workers} (requested=auto)"
-            if self.num_workers_per_gpu is None
-            else str(resolved_num_workers)
+        num_workers_per_gpu = (
+            max(1, cap // num_gpus) if self.num_workers_per_gpu is None else self.num_workers_per_gpu
+        )
+        slurm_limit = slurm_cpu_limit()
+        cap_source = (
+            f"slurm_cpu_limit={slurm_limit}" if slurm_limit is not None else f"cpu_count={os.cpu_count() or 1}"
         )
-        logger.info(
-            "ExecutionOptions: num_workers_per_gpu=%s, num_preprocessing_workers=%d "
+        logging.getLogger(__name__).info(
+            "ExecutionOptions: num_gpus=%s, num_workers_per_gpu=%s, num_preprocessing_workers=%d "
             "(preprocessing cap=%d via %s)",
-            num_workers_per_gpu_label,
-            capped_num_preprocessing_workers,
+            _auto_label(num_gpus, requested=self.num_gpus),
+            _auto_label(num_workers_per_gpu, requested=self.num_workers_per_gpu),
+            num_preprocessing_workers,
             cap,
             cap_source,
         )
+        return _MachineResolution(num_gpus=num_gpus, num_preprocessing_workers=num_preprocessing_workers)
 
-    def resolved_num_workers_per_gpu(self) -> int:
-        if self.num_workers_per_gpu is not None:
-            return self.num_workers_per_gpu
-        return max(1, cpu_worker_limit() // self.num_gpus)
+    def __getstate__(self) -> dict[str, Any]:
+        # A copy or an unpickled instance resolves again on the machine that uses it.
+        state = dict(self.__dict__)
+        state.pop("_machine_resolution", None)
+        return state
 
     def resolved_image_num_workers_per_gpu(self) -> int:
         """Resolve safe post-model-load image-transform workers for this rank."""
@@ -898,8 +921,9 @@ class Model:
         The dense counterpart of the pooled coordinate path: each ``SlideRegions`` names a
         slide + a set of level-0 ROI coordinates, and every ROI is read, encoded through the
         dense transform, and written to ``dense_embeddings/[<class>/]<sample_id>/<x>_<y>.pt``
-        plus a geometry sidecar. The run splits its ROIs across all visible GPUs
-        (``execution.num_gpus``); ``num_gpus=1`` encodes fully in-process. Resume is
+        plus a geometry sidecar. The run splits its ROIs across
+        ``execution.resolved_num_gpus()`` GPUs (all visible GPUs by default);
+        ``num_gpus=1`` encodes fully in-process. Resume is
         automatic — only ROIs whose sidecar has the same source-spacing declaration,
         resolved hs2p read plan and feature identity are skipped. Returns one
         :class:`~slide2vec.artifacts.DenseRegionArtifact` per input ROI.
@@ -932,10 +956,10 @@ class Model:
         **normalization-only** transform, padded up to the encoder's patch multiple, encoded
         — whole-image, or by sliding the encoder's native field and blending the token grids
         — and written to ``dense_image_embeddings/<sample_id>.pt`` plus a geometry sidecar.
-        The run splits its images across all visible GPUs (``execution.num_gpus``);
-        ``num_gpus=1`` encodes fully in-process. Resume is automatic: an image is skipped
-        only when its payload exists and its sidecar records the same normalized source
-        identity and complete extraction recipe. Returns one
+        The run splits its images across ``execution.resolved_num_gpus()`` GPUs (all
+        visible GPUs by default); ``num_gpus=1`` encodes fully in-process. Resume is
+        automatic: an image is skipped only when its payload exists and its sidecar records
+        the same normalized source identity and complete extraction recipe. Returns one
         :class:`~slide2vec.artifacts.DenseImageArtifact` per input image, in input order.
 
         Every source is opened through hs2p. PNG/JPEG inputs use hs2p's one-level PIL reader
@@ -977,12 +1001,12 @@ class Model:
         set — and slide2vec neither tiles nor reads a slide. Each :class:`ImageSpec` is
         decoded, preprocessed with the encoder's **shipped** transform, encoded, and written
         to ``image_embeddings/<sample_id>.pt`` plus a provenance sidecar. The run splits its
-        images across all visible GPUs (``execution.num_gpus``); ``num_gpus=1`` encodes
-        fully in-process. Resume is automatic: an image is skipped only when its sidecar
-        records this ``output_format``, the requested ``image_path`` and the full feature
-        identity. A different recorded feature identity raises; a different recorded
-        ``image_path`` raises unless ``execution.on_image_mismatch="reencode"``; missing
-        provenance re-encodes. Returns
+        images across ``execution.resolved_num_gpus()`` GPUs (all visible GPUs by
+        default); ``num_gpus=1`` encodes fully in-process. Resume is automatic: an image is
+        skipped only when its sidecar records this ``output_format``, the requested
+        ``image_path`` and the full feature identity. A different recorded feature identity
+        raises; a different recorded ``image_path`` raises unless
+        ``execution.on_image_mismatch="reencode"``; missing provenance re-encodes. Returns
         one :class:`~slide2vec.artifacts.ImageEmbeddingArtifact` per input image, in input
         order.
 
@@ -1342,6 +1366,15 @@ def _default_num_gpus() -> int:
     return max(1, torch.cuda.device_count()) if torch.cuda.is_available() else 1
 
 
+class _MachineResolution(NamedTuple):
+    num_gpus: int
+    num_preprocessing_workers: int
+
+
+def _auto_label(resolved: int, *, requested: int | None) -> str:
+    return f"{resolved} (requested=auto)" if requested is None else str(resolved)
+
+
 def _require_output_dir_for_persistence(execution: ExecutionOptions, *, method_name: str) -> None:
     if execution.output_dir is None:
         raise ValueError(f"ExecutionOptions.output_dir is required for {method_name}")

{slide2vec-7.1.0 → slide2vec-7.1.2}/slide2vec/encoders/models/dinov3.py

@@ -36,9 +36,7 @@ def require_timm_for_dinov3() -> None:
     if Version(timm.__version__) < Version(_MIN_TIMM_VERSION):
         raise ImportError(
             f"dinov3-vitb16 requires timm>={_MIN_TIMM_VERSION} (the DINOv3 "
-            f"architectures were added in that release); found timm=={timm.__version__}. "
-            "Note that the 'titan' extra pins timm==1.0.3 and cannot be installed "
-            "alongside dinov3-vitb16."
+            f"architectures were added in that release); found timm=={timm.__version__}."
         )
 
 

{slide2vec-7.1.0 → slide2vec-7.1.2}/slide2vec/encoders/models/moozy/loading.py

@@ -79,7 +79,7 @@ def load_moozy_inference_components(device: torch.device) -> MoozyInferenceCompo
     except Exception as exc:
         raise RuntimeError(
             "huggingface_hub is required for bundled MOOZY inference support. "
-            "Install it with: pip install 'slide2vec[moozy]'"
+            "Install it with: pip install huggingface_hub"
         ) from exc
 
     checkpoint_path = hf_hub_download(repo_id=_HF_REPO_ID, filename=_HF_CHECKPOINT)