biomedparse-mlx 0.1.1__tar.gz

biomedparse_mlx-0.1.1/.gitignore

@@ -0,0 +1,14 @@
+.venv/
+work/
+build/
+__pycache__/
+.pytest_cache/
+.hypothesis/
+.ruff_cache/
+dist/
+weights/
+outputs/
+*.ckpt
+*.safetensors
+*.npz
+.DS_Store

biomedparse_mlx-0.1.1/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

biomedparse_mlx-0.1.1/PKG-INFO

@@ -0,0 +1,131 @@
+Metadata-Version: 2.5
+Name: biomedparse-mlx
+Version: 0.1.1
+Summary: Native MLX inference for BioMedParse v2 on Apple Silicon
+Author: Joseph Sandoval, Alfredo Sandoval Jr.
+License-Expression: Apache-2.0 AND MIT AND BSD-3-Clause
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Classifier: Operating System :: MacOS :: MacOS X
+Requires-Python: <3.15,>=3.13
+Requires-Dist: medmlx-core==0.2.3
+Requires-Dist: nibabel<6,>=5.3
+Requires-Dist: numpy<3,>=2
+Requires-Dist: pillow<14,>=13
+Requires-Dist: pydicom<4,>=3
+Requires-Dist: scikit-image<1,>=0.25
+Requires-Dist: tokenizers<0.23,>=0.22
+Provides-Extra: assets
+Requires-Dist: huggingface-hub<2,>=1; extra == 'assets'
+Provides-Extra: conversion
+Requires-Dist: safetensors<1,>=0.6; extra == 'conversion'
+Requires-Dist: torch<3,>=2.6; extra == 'conversion'
+Provides-Extra: dev
+Requires-Dist: hypothesis<7,>=6.140; extra == 'dev'
+Requires-Dist: pyright==1.1.414; extra == 'dev'
+Requires-Dist: pytest<10,>=8.4; extra == 'dev'
+Requires-Dist: ruff<1,>=0.13; extra == 'dev'
+Provides-Extra: oracle
+Requires-Dist: fvcore>=0.1.5; extra == 'oracle'
+Requires-Dist: hydra-core<2,>=1.3; extra == 'oracle'
+Requires-Dist: safetensors<1,>=0.6; extra == 'oracle'
+Requires-Dist: simpleitk<3,>=2.4; extra == 'oracle'
+Requires-Dist: timm<2,>=1; extra == 'oracle'
+Requires-Dist: torch<3,>=2.6; extra == 'oracle'
+Requires-Dist: transformers<6,>=5; extra == 'oracle'
+Description-Content-Type: text/markdown
+
+# biomedparse-mlx
+
+Native MLX port of [Microsoft BioMedParse v2](https://github.com/microsoft/BiomedParse/tree/v2)
+for Apple Silicon. Segment medical images from text prompts, locally on Mac.
+
+- Text-guided 3D segmentation with multiple prompts and labels
+- Raw NIfTI and DICOM windowing, with geometry-preserving NIfTI mask output
+- Float32 model execution on Metal; PyTorch is used for conversion and oracle tests
+- A 2D image path with overlapping prompt masks; dedicated 2D weights remain unqualified
+
+Part of [MedMLX](https://github.com/MedMLX).
+[Technical notes](https://github.com/MedMLX/biomedparse-mlx/blob/main/docs/technical.md) · [Usage](https://github.com/MedMLX/biomedparse-mlx/blob/main/docs/usage.md)
+
+[Quick start](#quick-start) · [Input and output](#input-and-output) · [Technical details](#technical-details) · [License](#license)
+
+## Requirements
+
+Apple Silicon Mac with Metal, Python 3.13 or 3.14 and [uv](https://docs.astral.sh/uv/).
+The released checkpoint requires access to the gated Microsoft model on Hugging Face.
+
+## Quick start
+
+Prepare the locked checkout and local checkpoint assets:
+
+```bash
+gh repo clone MedMLX/biomedparse-mlx
+cd biomedparse-mlx
+make env
+MACOSX_DEPLOYMENT_TARGET=27.0 uv sync --locked --extra dev --extra oracle --extra conversion --extra assets
+
+uv run --locked --no-sync hf download microsoft/BiomedParse biomedparse_v2.ckpt \
+  --revision e473e5b2b1a3f44649734afd3dc7cf1770aaa9e2 --local-dir weights/source
+uv run --locked --no-sync hf download openai/clip-vit-base-patch32 tokenizer.json \
+  --revision 3d74acf9a28c67741b2f4f2ea7635f0aaf6f0268 --local-dir weights
+
+uv run --locked --no-sync biomedparse-mlx convert \
+  --source weights/source/biomedparse_v2.ckpt --output weights/biomedparse-v2.npz
+```
+
+The source checkpoint is about 4.46 GB. Conversion writes a float32 tensor bundle
+and a versioned receipt. Inference uses local assets without implicit downloads.
+
+Segment a preprocessed volume:
+
+```bash
+uv run --locked --no-sync biomedparse-mlx segment \
+  --image scan.npy --weights weights/biomedparse-v2.npz --tokenizer weights/tokenizer.json \
+  --prompt 'Visualization of the liver in abdominal CT imaging' --label 6 \
+  --output-dir outputs/liver --slice-batch-size 2 --seed 7
+```
+
+Repeat `--prompt` and `--label` for multiple structures. Existing outputs require
+`--overwrite`. Python usage, raw-image windowing, instance segmentation and the
+`segment-2d` command are described in [docs/usage.md](https://github.com/MedMLX/biomedparse-mlx/blob/main/docs/usage.md).
+The model is discoverable by [medmlx](https://github.com/MedMLX/medmlx) as `biomedparse-v2`.
+
+## Input and output
+
+Volumes are preprocessed numeric `.npy` arrays or `.npz` files containing `imgs`
+in the upstream 0..255 intensity range. Raw NIfTI volumes and DICOM slices require
+explicit `--modality` and, for CT, `--ct-site` windowing options. Volume slicing
+follows upstream's fixed shape heuristic.
+
+The volume path writes `segmentation.npz` with uint16 labels on the original array
+grid, prompt-by-slice existence probabilities, and `run.json`. NIfTI inputs also
+produce `segmentation.nii.gz` on the source affine. The 2D path returns separate,
+potentially overlapping masks and probabilities per prompt.
+
+## Technical details
+
+The native graph follows the pinned BioMedParse v2 architecture and checkpoint
+contract. Controlled oracle comparisons replay upstream attention masks; matching
+integer seeds alone does not align Torch and MLX sampling. Recorded qualification
+covers bounded synthetic and AMOS cases. Dedicated 2D weights, broader task
+accuracy and clinical performance remain unqualified.
+
+Architecture, numerical tolerances, development checks and recorded measurements
+are in [docs/technical.md](https://github.com/MedMLX/biomedparse-mlx/blob/main/docs/technical.md).
+
+## Intended use
+
+Intended for research and education, not clinical diagnosis or treatment decisions.
+Outputs require human review.
+
+## License
+
+Original contributions: Apache-2.0; see [LICENSE](https://github.com/MedMLX/biomedparse-mlx/blob/main/LICENSE). Upstream MIT/BSD notices and full
+license texts are retained in [THIRD_PARTY_NOTICES.md](https://github.com/MedMLX/biomedparse-mlx/blob/main/THIRD_PARTY_NOTICES.md).
+Model weights have separate publisher terms: Microsoft's model card declares
+CC-BY-NC-SA-4.0. Weights, tokenizers, datasets and masks are excluded from Git.
+
+## Implementation mapping
+
+[Central implementation map](https://github.com/MedMLX/Med-MLX/blob/main/implementation-maps/biomedparse-mlx.json) records upstream-to-native changes, source references and qualification scope.

biomedparse_mlx-0.1.1/README.md

@@ -0,0 +1,94 @@
+# biomedparse-mlx
+
+Native MLX port of [Microsoft BioMedParse v2](https://github.com/microsoft/BiomedParse/tree/v2)
+for Apple Silicon. Segment medical images from text prompts, locally on Mac.
+
+- Text-guided 3D segmentation with multiple prompts and labels
+- Raw NIfTI and DICOM windowing, with geometry-preserving NIfTI mask output
+- Float32 model execution on Metal; PyTorch is used for conversion and oracle tests
+- A 2D image path with overlapping prompt masks; dedicated 2D weights remain unqualified
+
+Part of [MedMLX](https://github.com/MedMLX).
+[Technical notes](https://github.com/MedMLX/biomedparse-mlx/blob/main/docs/technical.md) · [Usage](https://github.com/MedMLX/biomedparse-mlx/blob/main/docs/usage.md)
+
+[Quick start](#quick-start) · [Input and output](#input-and-output) · [Technical details](#technical-details) · [License](#license)
+
+## Requirements
+
+Apple Silicon Mac with Metal, Python 3.13 or 3.14 and [uv](https://docs.astral.sh/uv/).
+The released checkpoint requires access to the gated Microsoft model on Hugging Face.
+
+## Quick start
+
+Prepare the locked checkout and local checkpoint assets:
+
+```bash
+gh repo clone MedMLX/biomedparse-mlx
+cd biomedparse-mlx
+make env
+MACOSX_DEPLOYMENT_TARGET=27.0 uv sync --locked --extra dev --extra oracle --extra conversion --extra assets
+
+uv run --locked --no-sync hf download microsoft/BiomedParse biomedparse_v2.ckpt \
+  --revision e473e5b2b1a3f44649734afd3dc7cf1770aaa9e2 --local-dir weights/source
+uv run --locked --no-sync hf download openai/clip-vit-base-patch32 tokenizer.json \
+  --revision 3d74acf9a28c67741b2f4f2ea7635f0aaf6f0268 --local-dir weights
+
+uv run --locked --no-sync biomedparse-mlx convert \
+  --source weights/source/biomedparse_v2.ckpt --output weights/biomedparse-v2.npz
+```
+
+The source checkpoint is about 4.46 GB. Conversion writes a float32 tensor bundle
+and a versioned receipt. Inference uses local assets without implicit downloads.
+
+Segment a preprocessed volume:
+
+```bash
+uv run --locked --no-sync biomedparse-mlx segment \
+  --image scan.npy --weights weights/biomedparse-v2.npz --tokenizer weights/tokenizer.json \
+  --prompt 'Visualization of the liver in abdominal CT imaging' --label 6 \
+  --output-dir outputs/liver --slice-batch-size 2 --seed 7
+```
+
+Repeat `--prompt` and `--label` for multiple structures. Existing outputs require
+`--overwrite`. Python usage, raw-image windowing, instance segmentation and the
+`segment-2d` command are described in [docs/usage.md](https://github.com/MedMLX/biomedparse-mlx/blob/main/docs/usage.md).
+The model is discoverable by [medmlx](https://github.com/MedMLX/medmlx) as `biomedparse-v2`.
+
+## Input and output
+
+Volumes are preprocessed numeric `.npy` arrays or `.npz` files containing `imgs`
+in the upstream 0..255 intensity range. Raw NIfTI volumes and DICOM slices require
+explicit `--modality` and, for CT, `--ct-site` windowing options. Volume slicing
+follows upstream's fixed shape heuristic.
+
+The volume path writes `segmentation.npz` with uint16 labels on the original array
+grid, prompt-by-slice existence probabilities, and `run.json`. NIfTI inputs also
+produce `segmentation.nii.gz` on the source affine. The 2D path returns separate,
+potentially overlapping masks and probabilities per prompt.
+
+## Technical details
+
+The native graph follows the pinned BioMedParse v2 architecture and checkpoint
+contract. Controlled oracle comparisons replay upstream attention masks; matching
+integer seeds alone does not align Torch and MLX sampling. Recorded qualification
+covers bounded synthetic and AMOS cases. Dedicated 2D weights, broader task
+accuracy and clinical performance remain unqualified.
+
+Architecture, numerical tolerances, development checks and recorded measurements
+are in [docs/technical.md](https://github.com/MedMLX/biomedparse-mlx/blob/main/docs/technical.md).
+
+## Intended use
+
+Intended for research and education, not clinical diagnosis or treatment decisions.
+Outputs require human review.
+
+## License
+
+Original contributions: Apache-2.0; see [LICENSE](https://github.com/MedMLX/biomedparse-mlx/blob/main/LICENSE). Upstream MIT/BSD notices and full
+license texts are retained in [THIRD_PARTY_NOTICES.md](https://github.com/MedMLX/biomedparse-mlx/blob/main/THIRD_PARTY_NOTICES.md).
+Model weights have separate publisher terms: Microsoft's model card declares
+CC-BY-NC-SA-4.0. Weights, tokenizers, datasets and masks are excluded from Git.
+
+## Implementation mapping
+
+[Central implementation map](https://github.com/MedMLX/Med-MLX/blob/main/implementation-maps/biomedparse-mlx.json) records upstream-to-native changes, source references and qualification scope.

biomedparse_mlx-0.1.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,144 @@
+# Third-party notices
+
+MedMLX-authored additions are licensed under [Apache-2.0](LICENSE).
+The upstream attribution and license notices are retained below.
+
+biomedparse-mlx
+
+This package adapts the inference architecture and preprocessing of Microsoft's
+BioMedParse v2, revision f571d5ccaa4f8c0479bb89e390a7ef0dfc0736f4,
+https://github.com/microsoft/BiomedParse, licensed under Apache-2.0.
+The implementation was changed to use native MLX, channel-last tensors, local
+tokenizer assets, strict loading, and typed inference actions.
+
+FocalNet: Copyright (c) 2022 Microsoft; written by Jianwei Yang.
+X-Decoder language encoder: Copyright (c) 2022 Microsoft; written by Xueyan Zou.
+These portions carry MIT notices; full terms are retained below.
+
+Transformer/FPN, attention layers, and sine positional encoding retain upstream
+copyright (c) Facebook, Inc. and its affiliates (Meta). The BioMedParse source
+distributes these adaptations under its root Apache-2.0 license.
+
+Interpolation formulas follow PyTorch's UpSample.h and UpSampleKernel.cpp;
+PyTorch BSD terms are retained in THIRD_PARTY_NOTICES.md.
+
+Pretrained weights are separate assets. The Microsoft Hugging Face model card
+declares CC-BY-NC-SA-4.0; no checkpoint, tokenizer, dataset, or converted weights
+are distributed in this repository. Cite BioMedParse, BoltzFormer, and the
+CVPR 2025 Text-guided 3D Segmentation Challenge as requested by upstream.
+
+Dependencies declared in [pyproject.toml](pyproject.toml) are installed separately
+and retain their respective licenses.
+
+
+## Full license: FocalNet-MIT.txt
+
+    MIT License
+
+    Copyright (c) Microsoft Corporation.
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+
+    The above copyright notice and this permission notice shall be included in all
+    copies or substantial portions of the Software.
+
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+    SOFTWARE
+
+
+## Full license: PyTorch-BSD.txt
+
+From PyTorch:
+
+Copyright (c) 2016-     Facebook, Inc            (Adam Paszke)
+Copyright (c) 2014-     Facebook, Inc            (Soumith Chintala)
+Copyright (c) 2011-2014 Idiap Research Institute (Ronan Collobert)
+Copyright (c) 2012-2014 Deepmind Technologies    (Koray Kavukcuoglu)
+Copyright (c) 2011-2012 NEC Laboratories America (Koray Kavukcuoglu)
+Copyright (c) 2011-2013 NYU                      (Clement Farabet)
+Copyright (c) 2006-2010 NEC Laboratories America (Ronan Collobert, Leon Bottou, Iain Melvin, Jason Weston)
+Copyright (c) 2006      Idiap Research Institute (Samy Bengio)
+Copyright (c) 2001-2004 Idiap Research Institute (Ronan Collobert, Samy Bengio, Johnny Mariethoz)
+
+From Caffe2:
+
+Copyright (c) 2016-present, Facebook Inc. All rights reserved.
+
+All contributions by Facebook:
+Copyright (c) 2016 Facebook Inc.
+
+All contributions by Google:
+Copyright (c) 2015 Google Inc.
+All rights reserved.
+
+All contributions by Yangqing Jia:
+Copyright (c) 2015 Yangqing Jia
+All rights reserved.
+
+All contributions by Kakao Brain:
+Copyright 2019-2020 Kakao Brain
+
+All contributions by Cruise LLC:
+Copyright (c) 2022 Cruise LLC.
+All rights reserved.
+
+All contributions by Tri Dao:
+Copyright (c) 2024 Tri Dao.
+All rights reserved.
+
+All contributions by Arm:
+Copyright (c) 2021, 2023-2025 Arm Limited and/or its affiliates
+
+All contributions from Caffe:
+Copyright(c) 2013, 2014, 2015, the respective contributors
+All rights reserved.
+
+All other contributions:
+Copyright(c) 2015, 2016 the respective contributors
+All rights reserved.
+
+Caffe2 uses a copyright model similar to Caffe: each contributor holds
+copyright over their contributions to Caffe2. The project versioning records
+all such contribution and copyright details. If a contributor wants to further
+mark their specific copyright on a particular contribution, they should
+indicate their copyright solely in the commit message of the change when it is
+committed.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution.
+
+3. Neither the names of Facebook, Deepmind Technologies, NYU, NEC Laboratories America
+   and IDIAP Research Institute nor the names of its contributors may be
+   used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

biomedparse_mlx-0.1.1/pyproject.toml

@@ -0,0 +1,87 @@
+[build-system]
+requires = ["hatchling>=1.27"]
+build-backend = "hatchling.build"
+
+[project]
+name = "biomedparse-mlx"
+version = "0.1.1"
+description = "Native MLX inference for BioMedParse v2 on Apple Silicon"
+readme = "README.md"
+classifiers = ["Operating System :: MacOS :: MacOS X"]
+license = "Apache-2.0 AND MIT AND BSD-3-Clause"
+license-files = ["LICENSE", "THIRD_PARTY_NOTICES.md"]
+authors = [{ name = "Joseph Sandoval" }, { name = "Alfredo Sandoval Jr." }]
+requires-python = ">=3.13,<3.15"
+dependencies = [
+  "medmlx-core==0.2.3",
+  "numpy>=2,<3",
+  "tokenizers>=0.22,<0.23",
+  "nibabel>=5.3,<6",
+  "pillow>=13,<14",
+  "pydicom>=3,<4",
+  "scikit-image>=0.25,<1",
+]
+
+[project.scripts]
+biomedparse-mlx = "biomedparse_mlx.cli:main"
+
+[project.entry-points."medmlx.models"]
+biomedparse-v2 = "biomedparse_mlx.medmlx:MODEL"
+
+[project.optional-dependencies]
+conversion = ["torch>=2.6,<3", "safetensors>=0.6,<1"]
+assets = ["huggingface-hub>=1,<2"]
+dev = ["pyright==1.1.414", "ruff>=0.13,<1", "pytest>=8.4,<10", "hypothesis>=6.140,<7"]
+oracle = ["torch>=2.6,<3", "timm>=1,<2", "fvcore>=0.1.5", "hydra-core>=1.3,<2", "safetensors>=0.6,<1", "transformers>=5,<6", "simpleitk>=2.4,<3"]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/biomedparse_mlx"]
+
+
+[tool.uv]
+constraint-dependencies = ["setuptools>=84.1.0", "filelock>=4.2.1", ]
+environments = ["sys_platform == 'darwin' and platform_machine == 'arm64'"]
+
+[tool.ruff]
+target-version = "py313"
+line-length = 100
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "UP", "B", "SIM", "RUF", "ANN401", "TID251", "TID252"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--strict-config --strict-markers"
+markers = ["metal: evaluated native MLX execution", "oracle: upstream PyTorch comparison"]
+
+[tool.pyright]
+include = ["src", "tests", "typings"]
+stubPath = "typings"
+extraPaths = ["src"]
+pythonVersion = "3.13"
+typeCheckingMode = "strict"
+enableTypeIgnoreComments = false
+reportUnnecessaryTypeIgnoreComment = "error"
+
+[tool.ruff.lint.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
+"typing.Any" = { msg = "Use a precise type or protocol." }
+"typing_extensions.Any" = { msg = "Use a precise type or protocol." }
+
+[tool.uv.sources]
+medmlx-core = { git = "https://github.com/MedMLX/medmlx.git", rev = "e765f0a94aa31e8dfcdc599e4a4206eaca84f8b0", subdirectory = "packages/core" }
+
+[tool.hatch.build.targets.sdist]
+exclude = ["AGENTS.md", "CLAUDE.md", ".claude", ".codex", ".cursor"]
+only-include = [
+  "src/biomedparse_mlx",
+  "pyproject.toml",
+  "README.md",
+  "LICENSE",
+  "THIRD_PARTY_NOTICES.md",
+]