Initial commit

.github/workflows/autoformat.yml

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+name: autoformat
+
+on:
+  issue_comment:
+    types: [created, edited]
+jobs:
+  run_autoformat:
+    uses: BrainLesion/BrainLes/.github/workflows/autoformat.yml@main
+    secrets: inherit

.github/workflows/pr-lint.yml

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+name: lint
+
+on:
+  pull_request:
+    branches:
+      - main
+jobs:
+  run_lint:
+    uses: BrainLesion/BrainLes/.github/workflows/pr_lint.yml@main
+    secrets: inherit

.github/workflows/release.yml

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+name: release
+
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+
+jobs:
+  publish:
+    name: Publish to test PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          pip install build
+          pip install twine
+      - name: Build package
+        run: python -m build
+      - name: Upload to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          twine upload dist/*.whl

.github/workflows/tests.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: tests
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest] #, windows-latest, macos-latest] # Extend to your needs
+        python-version: ["3.9", "3.10", "3.11", "3.12"] # Extend to your needs
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip" # caching pip dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry
+          python -m poetry install
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          python -m poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          python -m poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      # TODO adapt package_name to the name of your package
+      - name: Test with pytest
+        run: |
+          python -m poetry run pytest --cov package_name
+      # Add the following block to upload coverage to Codecov, requires a CODECOV_TOKEN secret to be set in the repository
+      # - name: Upload results to Codecov
+      #   # Only upload to Codecov after a merge to the main branch
+      #   if: github.ref == 'refs/heads/main' && github.event_name == 'push'
+      #   uses: codecov/codecov-action@v4
+      #   with:
+      #     token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.readthedocs.yaml

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+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      # VIRTUAL_ENV needs to be set manually for now.
+      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+
+sphinx:
+  configuration: docs/source/conf.py

CONTRIBUTING.md

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+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+# Contributing
+
+First off, thanks for taking the time to contribute! 🎉
+
+
+## Contribute Code 
+Fork the repository, clone it and implement your contribution.
+
+**Setup:**
+- We use [poetry](https://python-poetry.org/), make sure it is installed: `pip install poetry`
+- Install dependencies by running: `poetry install`
+
+**Requirements:**
+- Our project follows the [black code style](https://github.com/psf/black). Make sure your code is formatted accordingly.
+- Please add _meaningful_ docstring for your functions and annotate types
+- Please add _meaningful_ tests for your contribution in `/tests` and make sure _all_ tests are passing by running `python -m pytest`
+
+
+
+Once done, create a Pull Request to integrate the code into our project!

README.md

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+# PACKAGE_NAME
+
+[![Python Versions](https://img.shields.io/pypi/pyversions/PACKAGE_NAME)](https://pypi.org/project/PACKAGE_NAME/)
+[![Stable Version](https://img.shields.io/pypi/v/PACKAGE_NAME?label=stable)](https://pypi.python.org/pypi/PACKAGE_NAME/)
+[![Documentation Status](https://readthedocs.org/projects/PACKAGE_NAME/badge/?version=latest)](http://PACKAGE_NAME.readthedocs.io/?badge=latest)
+[![tests](https://github.com/BrainLesion/PACKAGE_NAME/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/PACKAGE_NAME/actions/workflows/tests.yml)
+[![codecov](https://codecov.io/gh/BrainLesion/PACKAGE_NAME/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/PACKAGE_NAME)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+
+Description 
+## Features
+
+
+## Installation
+
+With a Python 3.8+ environment, you can install `PACKAGE_NAME` directly from [PyPI](https://pypi.org/project/brats/):
+
+```bash
+pip install PACKAGE_NAME
+```
+
+
+## Use Cases and Tutorials
+
+A minimal example to create a segmentation could look like this:
+
+```python
+    # example
+```
+
+<!-- For more examples and details please refer to our extensive Notebook tutorials here [NBViewer](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/PACKAGE_NAME/tutorial.ipynb) ([GitHub](https://github.com/BrainLesion/tutorials/blob/main/PACKAGE_NAME/tutorial.ipynb)). For the best experience open the notebook in Colab. -->
+
+
+## Citation
+
+If you use PACKAGE_NAME in your research, please cite it to support the development!
+
+```
+TODO: citation will be added asap
+```
+
+## Contributing
+
+We welcome all kinds of contributions from the community!
+
+### Reporting Bugs, Feature Requests and Questions
+
+Please open a new issue [here](https://github.com/BrainLesion/PACKAGE_NAME/issues).
+
+### Code contributions
+
+Nice to have you on board! Please have a look at our [CONTRIBUTING.md](CONTRIBUTING.md) file.

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)