medmlx 0.3.2__tar.gz

medmlx-0.3.2/.gitignore

@@ -0,0 +1,31 @@
+__pycache__/
+*.py[cod]
+.venv/
+*.egg-info/
+dist/
+build/
+.pytest_cache/
+.ruff_cache/
+.hypothesis/
+
+# Checkpoints and converted weights are never committed.
+checkpoints/
+weights/
+*.safetensors
+*.npz
+!tests/fixtures/*.npz
+!tests/fixtures/*/*.npz
+!tests/oracles/*.npz
+!packages/core/tests/fixtures/*/*.npz
+!packages/core/tests/oracles/*.npz
+!conversion/tests/fixtures/*.npz
+*.pt
+*.pth
+*.ckpt
+
+# Imaging data is never committed.
+data/
+*.nii
+*.nii.gz
+*.dcm
+.DS_Store

medmlx-0.3.2/LICENSE

@@ -0,0 +1,202 @@
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medmlx-0.3.2/PKG-INFO

@@ -0,0 +1,163 @@
+Metadata-Version: 2.5
+Name: medmlx
+Version: 0.3.2
+Summary: MedMLX Python API, CLI, and MCP for independent medical imaging runtimes
+Author: Joseph Sandoval, Alfredo Sandoval Jr.
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Classifier: Operating System :: MacOS :: MacOS X
+Requires-Python: <3.14,>=3.13
+Requires-Dist: medmlx-core==0.2.4
+Requires-Dist: packaging>=24
+Provides-Extra: all
+Requires-Dist: biomedparse-mlx==0.1.2; extra == 'all'
+Requires-Dist: fdg-pet-ct-mlx==0.2.2; extra == 'all'
+Requires-Dist: flexible-unet-mlx==0.2.2; extra == 'all'
+Requires-Dist: flexray-mlx==0.2.2; extra == 'all'
+Requires-Dist: lesiondiffusion-mlx==0.2.2; extra == 'all'
+Requires-Dist: lung-nodule-mlx==0.2.2; extra == 'all'
+Requires-Dist: medsam2-mlx==0.2.2; extra == 'all'
+Requires-Dist: mlx-generate==0.4.1; extra == 'all'
+Requires-Dist: mlx-reason-ct==0.3.3; extra == 'all'
+Requires-Dist: mlx-segment-ct==0.3.0; extra == 'all'
+Requires-Dist: mlxradiomics[io]==0.1.0.dev4; extra == 'all'
+Requires-Dist: nibabel<6,>=5.4.2; extra == 'all'
+Requires-Dist: nnunet-mlx==0.5.2; extra == 'all'
+Requires-Dist: radimagenet-mlx==0.2.2; extra == 'all'
+Requires-Dist: sam3-mlx[video]==0.1.5; extra == 'all'
+Requires-Dist: segresnet-mlx==0.2.2; extra == 'all'
+Requires-Dist: swin-unetr-mlx==0.2.2; extra == 'all'
+Requires-Dist: synthseg-mlx==0.2.2; extra == 'all'
+Requires-Dist: totalsegmentator-mlx==0.1.2.post1; extra == 'all'
+Requires-Dist: unest-mlx==0.2.3; extra == 'all'
+Provides-Extra: generate
+Requires-Dist: fdg-pet-ct-mlx==0.2.2; extra == 'generate'
+Requires-Dist: lesiondiffusion-mlx==0.2.2; extra == 'generate'
+Requires-Dist: mlx-generate==0.4.1; extra == 'generate'
+Requires-Dist: mlx-reason-ct==0.3.3; extra == 'generate'
+Requires-Dist: nibabel<6,>=5.4.2; extra == 'generate'
+Provides-Extra: mcp
+Requires-Dist: mcp<3,>=2.2; extra == 'mcp'
+Provides-Extra: segment
+Requires-Dist: biomedparse-mlx==0.1.2; extra == 'segment'
+Requires-Dist: flexible-unet-mlx==0.2.2; extra == 'segment'
+Requires-Dist: flexray-mlx==0.2.2; extra == 'segment'
+Requires-Dist: medsam2-mlx==0.2.2; extra == 'segment'
+Requires-Dist: mlx-segment-ct==0.3.0; extra == 'segment'
+Requires-Dist: nnunet-mlx==0.5.2; extra == 'segment'
+Requires-Dist: sam3-mlx[video]==0.1.5; extra == 'segment'
+Requires-Dist: segresnet-mlx==0.2.2; extra == 'segment'
+Requires-Dist: swin-unetr-mlx==0.2.2; extra == 'segment'
+Requires-Dist: synthseg-mlx==0.2.2; extra == 'segment'
+Requires-Dist: totalsegmentator-mlx==0.1.2.post1; extra == 'segment'
+Requires-Dist: unest-mlx==0.2.3; extra == 'segment'
+Provides-Extra: setup
+Requires-Dist: huggingface-hub<2,>=0.34; extra == 'setup'
+Requires-Dist: uv<1,>=0.8; extra == 'setup'
+Provides-Extra: vision
+Requires-Dist: lung-nodule-mlx==0.2.2; extra == 'vision'
+Requires-Dist: mlxradiomics[io]==0.1.0.dev4; extra == 'vision'
+Requires-Dist: radimagenet-mlx==0.2.2; extra == 'vision'
+Description-Content-Type: text/markdown
+
+# MedMLX
+
+## Model setup for applications
+
+Install the `setup` extra to use `medmlx setup MODEL --progress`. It reuses
+explicitly supplied model directories, the MedMLX asset cache, or the Hub cache,
+then downloads missing native files and retains publisher notices. It returns
+the runner arguments for the application to remember. Downloads can be resumed
+by running setup again; `--plan` only describes the operation.
+
+`medmlx.list_setup_plans()`, `setup_plan(model_id)`, and
+`setup_model(model_id, existing_paths=..., progress=...)` expose the same actions
+to Python clients. The default asset cache search is `~/.cache/medmlx` (override
+with `MEDMLX_ASSET_CACHE`); downloads use the normal Hugging Face cache. Setup
+supports published VISTA3D CT, Reason-CT, FleXray flagship, and named BraTS bundles,
+plus the radiomics runtime. Other checkpoints require their provider's setup.
+Runtime installation uses this release's family pins. Frozen applications must
+already bundle the runtime; setup can still download their model files. An
+already installed runtime is detected by package metadata and is not checked
+against the family pin or imported by that check.
+Setup checks required files and available provider admission contracts. Model
+execution retains responsibility for tensor compatibility and input validation.
+
+One Python API, command line and MCP server for native medical imaging on Apple Silicon.
+Run TotalSegmentator, nnU-Net, MedSAM2, SynthSeg and more through their independent MLX runtimes.
+
+[Models](https://github.com/MedMLX) · [Docs](https://github.com/MedMLX/medmlx/blob/main/docs/declaring-models.md) · [Website](https://medmlx.org)
+
+![Outputs across CT, PET/CT, radiographs, endoscopy and MRI](https://raw.githubusercontent.com/MedMLX/medmlx/main/docs/gallery.jpg)
+
+**Apple Silicon · Metal · Python 3.13** · [uv](https://docs.astral.sh/uv/)
+
+## Install
+
+Install all model families with MCP and model setup support:
+
+```sh
+uv venv --python 3.13
+source .venv/bin/activate
+uv pip install "medmlx[all,mcp,setup]"
+medmlx models
+```
+
+Choose `segment`, `generate` or `vision` instead of `all` for a smaller install.
+The segment extra includes SAM3 image/video support; generate includes NV-Reason-CT
+and the weight-free FDG PET adapter. Model weights have their own download and access
+requirements. Provisional `medgemma` and `lingshu` adapters use an explicitly selected
+separate MedVLM environment; real-checkpoint inference through these bridges is
+unqualified. The MedVLM runtime is not bundled because its MLX and Transformers
+requirements conflict with the unified environment. See the
+[bridge setup and limits](https://github.com/MedMLX/medmlx/blob/main/docs/medvlm-bridge.md) and
+[dependency compatibility notes](https://github.com/MedMLX/medmlx/blob/main/docs/release-notes.md).
+
+## Run a model
+
+```sh
+medmlx describe totalsegmentator
+medmlx readiness totalsegmentator --arguments arguments.json --root /path/to/work
+medmlx checkpoints --model-id nnunet
+medmlx run totalsegmentator --arguments arguments.json --root /path/to/work
+```
+
+`describe` includes the provider's full instructions and argument descriptions,
+including documented units and ranges. Descriptions reproduce provider documentation;
+they do not establish validated constraints or numerical qualification. Relative
+paths resolve against `--root`.
+Readiness preserves `ready` as a boolean for imports/provider checks and Metal;
+`runtime_ready` makes that same limited meaning explicit. Neither validates run
+inputs or weights. The separate `run_ready` is `false` for a known blocker and
+`null` while input/checkpoint contents remain unverified; this check never returns
+`run_ready=true`. Passing arguments checks names, required arguments and local
+input/weight path existence, without running inference or creating outputs.
+
+`checkpoints` lists five source references, including catalog-only liver and AutoPET
+entries for the general nnU-Net provider. It neither stages assets nor qualifies a
+checkpoint. The same action is available as `list_checkpoints` in Python and MCP.
+
+```python
+import json
+from pathlib import Path
+import medmlx
+
+arguments = json.loads(Path("arguments.json").read_text())
+result = medmlx.run("totalsegmentator", arguments=arguments, root="/path/to/work")
+```
+
+For an MCP client, use `medmlx serve --root /path/to/work` as its stdio command.
+Jobs belong to that server session; disconnecting cancels workers and their child
+processes. Client registration and persistent filesystem access are configured by
+that client, not changed by this package. Some providers fetch default assets when
+paths are omitted; supply explicit local checkpoints for offline execution.
+See the [MCP guide](https://github.com/MedMLX/medmlx/blob/main/docs/mcp.md) for client setup, tools, and a complete job workflow.
+For checkpoint conversion and development, see [conversion](https://github.com/MedMLX/medmlx/blob/main/conversion/README.md) and [core](https://github.com/MedMLX/medmlx/blob/main/packages/core/docs/technical.md).
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/medmlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/medmlx/blob/main/THIRD_PARTY_NOTICES.md).
+Runtimes and model weights retain their own terms.
+
+For research and education. Outputs require human review.

medmlx-0.3.2/README.md

@@ -0,0 +1,100 @@
+# MedMLX
+
+## Model setup for applications
+
+Install the `setup` extra to use `medmlx setup MODEL --progress`. It reuses
+explicitly supplied model directories, the MedMLX asset cache, or the Hub cache,
+then downloads missing native files and retains publisher notices. It returns
+the runner arguments for the application to remember. Downloads can be resumed
+by running setup again; `--plan` only describes the operation.
+
+`medmlx.list_setup_plans()`, `setup_plan(model_id)`, and
+`setup_model(model_id, existing_paths=..., progress=...)` expose the same actions
+to Python clients. The default asset cache search is `~/.cache/medmlx` (override
+with `MEDMLX_ASSET_CACHE`); downloads use the normal Hugging Face cache. Setup
+supports published VISTA3D CT, Reason-CT, FleXray flagship, and named BraTS bundles,
+plus the radiomics runtime. Other checkpoints require their provider's setup.
+Runtime installation uses this release's family pins. Frozen applications must
+already bundle the runtime; setup can still download their model files. An
+already installed runtime is detected by package metadata and is not checked
+against the family pin or imported by that check.
+Setup checks required files and available provider admission contracts. Model
+execution retains responsibility for tensor compatibility and input validation.
+
+One Python API, command line and MCP server for native medical imaging on Apple Silicon.
+Run TotalSegmentator, nnU-Net, MedSAM2, SynthSeg and more through their independent MLX runtimes.
+
+[Models](https://github.com/MedMLX) · [Docs](https://github.com/MedMLX/medmlx/blob/main/docs/declaring-models.md) · [Website](https://medmlx.org)
+
+![Outputs across CT, PET/CT, radiographs, endoscopy and MRI](https://raw.githubusercontent.com/MedMLX/medmlx/main/docs/gallery.jpg)
+
+**Apple Silicon · Metal · Python 3.13** · [uv](https://docs.astral.sh/uv/)
+
+## Install
+
+Install all model families with MCP and model setup support:
+
+```sh
+uv venv --python 3.13
+source .venv/bin/activate
+uv pip install "medmlx[all,mcp,setup]"
+medmlx models
+```
+
+Choose `segment`, `generate` or `vision` instead of `all` for a smaller install.
+The segment extra includes SAM3 image/video support; generate includes NV-Reason-CT
+and the weight-free FDG PET adapter. Model weights have their own download and access
+requirements. Provisional `medgemma` and `lingshu` adapters use an explicitly selected
+separate MedVLM environment; real-checkpoint inference through these bridges is
+unqualified. The MedVLM runtime is not bundled because its MLX and Transformers
+requirements conflict with the unified environment. See the
+[bridge setup and limits](https://github.com/MedMLX/medmlx/blob/main/docs/medvlm-bridge.md) and
+[dependency compatibility notes](https://github.com/MedMLX/medmlx/blob/main/docs/release-notes.md).
+
+## Run a model
+
+```sh
+medmlx describe totalsegmentator
+medmlx readiness totalsegmentator --arguments arguments.json --root /path/to/work
+medmlx checkpoints --model-id nnunet
+medmlx run totalsegmentator --arguments arguments.json --root /path/to/work
+```
+
+`describe` includes the provider's full instructions and argument descriptions,
+including documented units and ranges. Descriptions reproduce provider documentation;
+they do not establish validated constraints or numerical qualification. Relative
+paths resolve against `--root`.
+Readiness preserves `ready` as a boolean for imports/provider checks and Metal;
+`runtime_ready` makes that same limited meaning explicit. Neither validates run
+inputs or weights. The separate `run_ready` is `false` for a known blocker and
+`null` while input/checkpoint contents remain unverified; this check never returns
+`run_ready=true`. Passing arguments checks names, required arguments and local
+input/weight path existence, without running inference or creating outputs.
+
+`checkpoints` lists five source references, including catalog-only liver and AutoPET
+entries for the general nnU-Net provider. It neither stages assets nor qualifies a
+checkpoint. The same action is available as `list_checkpoints` in Python and MCP.
+
+```python
+import json
+from pathlib import Path
+import medmlx
+
+arguments = json.loads(Path("arguments.json").read_text())
+result = medmlx.run("totalsegmentator", arguments=arguments, root="/path/to/work")
+```
+
+For an MCP client, use `medmlx serve --root /path/to/work` as its stdio command.
+Jobs belong to that server session; disconnecting cancels workers and their child
+processes. Client registration and persistent filesystem access are configured by
+that client, not changed by this package. Some providers fetch default assets when
+paths are omitted; supply explicit local checkpoints for offline execution.
+See the [MCP guide](https://github.com/MedMLX/medmlx/blob/main/docs/mcp.md) for client setup, tools, and a complete job workflow.
+For checkpoint conversion and development, see [conversion](https://github.com/MedMLX/medmlx/blob/main/conversion/README.md) and [core](https://github.com/MedMLX/medmlx/blob/main/packages/core/docs/technical.md).
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/medmlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/medmlx/blob/main/THIRD_PARTY_NOTICES.md).
+Runtimes and model weights retain their own terms.
+
+For research and education. Outputs require human review.

medmlx-0.3.2/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,25 @@
+# Third-party notices
+
+MedMLX-authored API, CLI, MCP and tooling code is licensed under
+[Apache-2.0](LICENSE). Upstream portions retain their own attribution and terms.
+
+## MONAI-derived shared runtime
+
+The shared runtime in `packages/core` contains sliding-window algorithms derived
+from MONAI 1.6.0 and channel-last layer arithmetic translated from MONAI 1.4.0.
+Copyright (c) MONAI Consortium. Licensed under Apache-2.0; see the
+[core attribution and full MONAI license](packages/core/THIRD_PARTY_NOTICES.md).
+The native NumPy/MLX implementations and their restricted APIs are MedMLX
+modifications. The core is also distributed separately as `medmlx-core`.
+
+## Dependencies and model runtimes
+
+The frontend, core and conversion environments declare their dependencies in
+[pyproject.toml](pyproject.toml),
+[packages/core/pyproject.toml](packages/core/pyproject.toml) and
+[conversion/pyproject.toml](conversion/pyproject.toml). Installed dependencies
+retain their respective licenses.
+
+Model runtime repositories register independently through `medmlx.models`.
+Their code, checkpoints, tokenizer assets and datasets retain their original
+terms; installing a frontend extra does not relicense those materials.