brainmint 0.1.0__tar.gz

brainmint-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: ["dev", "main"]
+  pull_request:
+    branches: ["main"]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  import-no-deps:
+    name: Import without dependencies
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Install package without dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --no-deps -e .
+
+      - name: Check lightweight root import
+        run: python -c "import brainmint; print(brainmint.__version__)"
+
+  package-tests:
+    name: Package tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    timeout-minutes: 25
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[dev]"
+
+      - name: Check installed package metadata
+        run: python -m pip check
+
+      - name: Compile package and tests
+        run: python -m compileall -q brainmint tests
+
+      - name: Run tests
+        run: python -m pytest
+
+  lint:
+    name: Lint package-safe surface
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Install lint tools
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install "ruff>=0.6"
+
+      - name: Run Ruff
+        run: |
+          ruff check .
+
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Build package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build twine
+          python -m build
+          python -m twine check dist/*

brainmint-0.1.0/.github/workflows/release.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/brainmint
+
+    permissions:
+      id-token: write
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build
+        run: |
+          python -m pip install --upgrade pip build twine
+          python -m build
+          twine check dist/*
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

brainmint-0.1.0/.github/workflows/testpypi.yml

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+name: Publish to TestPyPI
+
+on:
+  workflow_dispatch:
+  push:
+    branches: ["dev"]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/brainmint
+    permissions:
+      id-token: write
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build
+        run: |
+          python -m pip install --upgrade pip build twine
+          python -m build
+          twine check dist/*
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true

brainmint-0.1.0/.gitignore

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+# Byte-compiled / optimized / extension files
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+*.dll
+
+# Build and packaging
+build/
+dist/
+*.egg-info/
+.eggs/
+wheels/
+MANIFEST
+brainmint/_version.py
+
+# Test, lint, type, and coverage artifacts
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.pyre/
+.pytype/
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+.tox/
+.nox/
+
+# Environments and local package managers
+.env
+.envrc
+.venv/
+venv/
+env/
+ENV/
+__pypackages__/
+.pdm-python
+.pdm-build/
+.pixi/
+
+# Editors and OS files
+.vscode/
+.idea/
+*.code-workspace
+.DS_Store
+Thumbs.db
+Desktop.ini
+*~
+.nfs*
+
+# Logs and job artifacts
+*.log
+*.out
+*.err
+slurm-*.out
+slurm-*.err
+job-*.out
+job-*.err
+*.sbatch
+*.slurm
+*.sl
+
+# Notebooks and local scratch
+.ipynb_checkpoints/
+scratch/
+tmp/
+*.tmp
+
+# BrainMint research artifacts that do not belong in the package repo
+/data/
+/models/
+/checkpoints/
+/outputs/
+/out/
+/_out*/
+/wandb/
+/lightning_logs/
+/nobackup_ds/
+/z_temp_data/
+/external/repos/
+/repos/
+*.ckpt
+*.pt
+*.pth
+*.nii
+*.nii.gz
+
+# Publishing credentials
+.pypirc

brainmint-0.1.0/CHANGELOG.md

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+# Changelog
+
+<!-- ## [Unreleased]
+
+### Added
+
+### Changed
+
+### Fixed -->
+
+## [0.1.0] - 2026-06-06
+
+### Added
+
+* Initial public release of **BrainMint**.
+* Added the standalone `brainmint` Python package.
+* Added package metadata, version handling, typed-package marker, tests, and CI/publishing workflows.
+
+<!-- [Unreleased]: https://github.com/yasinzaii/brainmint/compare/v0.1.0...HEAD -->
+[0.1.0]: https://github.com/yasinzaii/brainmint/releases/tag/v0.1.0

brainmint-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Muhammad Nabi Yasinzai
+
+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.

brainmint-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: brainmint
+Version: 0.1.0
+Summary: Brain MRI synthesis, compression, modality translation, and evaluation toolkit.
+Author: Muhammad Nabi Yasinzai
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/yasinzaii/brainmint
+Project-URL: Repository, https://github.com/yasinzaii/brainmint
+Project-URL: Issues, https://github.com/yasinzaii/brainmint/issues
+Keywords: MRI,brain MRI,neuroimaging,medical imaging,diffusion models,synthetic data,modality translation,deep learning
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: einops>=0.7
+Requires-Dist: numpy>=1.24
+Requires-Dist: omegaconf>=2.3
+Requires-Dist: torch>=2.1
+Requires-Dist: monai>=1.3
+Requires-Dist: nibabel>=5.2
+Requires-Dist: hydra-core>=1.3
+Provides-Extra: external
+Requires-Dist: huggingface-hub>=0.20; extra == "external"
+Provides-Extra: io
+Requires-Dist: pillow>=10; extra == "io"
+Provides-Extra: medical
+Requires-Dist: scipy>=1.11; extra == "medical"
+Provides-Extra: metrics
+Requires-Dist: medmetric[monai]>=0.1.1; extra == "metrics"
+Requires-Dist: tqdm>=4.66; extra == "metrics"
+Provides-Extra: train
+Requires-Dist: pytorch-lightning>=2.2; extra == "train"
+Requires-Dist: tabulate>=0.9; extra == "train"
+Requires-Dist: tensorboard>=2.15; extra == "train"
+Requires-Dist: torchmetrics>=1.3; extra == "train"
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: pytest-cov>=5; extra == "dev"
+Requires-Dist: ruff>=0.5; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+Provides-Extra: all
+Requires-Dist: huggingface-hub>=0.20; extra == "all"
+Requires-Dist: medmetric[monai]>=0.1.1; extra == "all"
+Requires-Dist: pillow>=10; extra == "all"
+Requires-Dist: pytorch-lightning>=2.2; extra == "all"
+Requires-Dist: scipy>=1.11; extra == "all"
+Requires-Dist: tabulate>=0.9; extra == "all"
+Requires-Dist: tensorboard>=2.15; extra == "all"
+Requires-Dist: torchmetrics>=1.3; extra == "all"
+Requires-Dist: tqdm>=4.66; extra == "all"
+Dynamic: license-file
+
+# BrainMint
+
+BrainMint is a Python package for brain MRI synthesis, compression, modality translation, inference utilities, and evaluation support.
+
+This repository is the reusable package extracted from the original GenMRI study repository. It should contain library code, package-safe tests, and package documentation only. Study configs, private paths, datasets, checkpoints, generated outputs, and cloned external repositories should stay outside this repository.
+
+## Install
+
+Install the base package with pip:
+
+```bash
+pip install brainmint
+```
+
+Common optional installs:
+
+| Use case | Install command |
+| --- | --- |
+| Metrics and evaluation | `pip install "brainmint[metrics]"` |
+| Training utilities | `pip install "brainmint[train]"` |
+| Full runtime stack | `pip install "brainmint[all]"` |
+
+Smaller targeted extras are kept in `pyproject.toml` for dependency control, but the commands above are the ones most users should need.
+
+## External Repositories
+
+External model repositories are materialized outside the package tree. For research runs, set:
+
+```bash
+export BRAINMINT_EXTERNAL_ROOT=/path/to/external
+```
+
+or configure it in Python:
+
+```python
+import brainmint.external
+
+brainmint.external.set_external_repo_root("/path/to/external")
+```
+
+## Tests
+
+Default tests are package-safe and do not require study Hydra configs, GPU, checkpoints, network access, or cloned external repositories:
+
+```bash
+python -m pytest
+```
+
+Copied study-era tests are opt-in while BrainMint is being separated from the original study repository:
+
+```bash
+python -m pytest --run-study-config-tests
+```
+
+## License
+
+MIT. See `LICENSE`.

brainmint-0.1.0/README.md

@@ -0,0 +1,57 @@
+# BrainMint
+
+BrainMint is a Python package for brain MRI synthesis, compression, modality translation, inference utilities, and evaluation support.
+
+This repository is the reusable package extracted from the original GenMRI study repository. It should contain library code, package-safe tests, and package documentation only. Study configs, private paths, datasets, checkpoints, generated outputs, and cloned external repositories should stay outside this repository.
+
+## Install
+
+Install the base package with pip:
+
+```bash
+pip install brainmint
+```
+
+Common optional installs:
+
+| Use case | Install command |
+| --- | --- |
+| Metrics and evaluation | `pip install "brainmint[metrics]"` |
+| Training utilities | `pip install "brainmint[train]"` |
+| Full runtime stack | `pip install "brainmint[all]"` |
+
+Smaller targeted extras are kept in `pyproject.toml` for dependency control, but the commands above are the ones most users should need.
+
+## External Repositories
+
+External model repositories are materialized outside the package tree. For research runs, set:
+
+```bash
+export BRAINMINT_EXTERNAL_ROOT=/path/to/external
+```
+
+or configure it in Python:
+
+```python
+import brainmint.external
+
+brainmint.external.set_external_repo_root("/path/to/external")
+```
+
+## Tests
+
+Default tests are package-safe and do not require study Hydra configs, GPU, checkpoints, network access, or cloned external repositories:
+
+```bash
+python -m pytest
+```
+
+Copied study-era tests are opt-in while BrainMint is being separated from the original study repository:
+
+```bash
+python -m pytest --run-study-config-tests
+```
+
+## License
+
+MIT. See `LICENSE`.

brainmint-0.1.0/brainmint/__init__.py

@@ -0,0 +1,12 @@
+"""BrainMint models, integrations, and inference tools for medical image synthesis."""
+
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import version as _metadata_version
+
+try:
+    from ._version import __version__
+except (ImportError, ModuleNotFoundError):
+    try:
+        __version__ = _metadata_version("brainmint")
+    except PackageNotFoundError:
+        __version__ = "0.0.0"

brainmint-0.1.0/brainmint/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.1.0'
+__version_tuple__ = version_tuple = (0, 1, 0)
+
+__commit_id__ = commit_id = 'ge80ffa22a'