autoimmune 0.0.1__tar.gz

autoimmune-0.0.1/.github/workflows/ci.yaml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install ruff
+      - run: ruff check src/ tests/
+      - run: ruff format --check src/ tests/
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: pip install -e ".[dev]"
+      - run: pytest --tb=short -q
+
+  typecheck:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install -e ".[dev]"
+      - run: mypy src/

autoimmune-0.0.1/.github/workflows/python-publish.yaml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  id-token: write
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install build
+      - run: python -m build
+      - uses: pypa/gh-action-pypi-publish@release/v1

autoimmune-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# 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
+.envrc
+.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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# macOS
+.DS_Store

autoimmune-0.0.1/.python-version

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+3.11

autoimmune-0.0.1/AGENTS.md

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+# Agent Instructions for autoimmune
+
+## Architecture
+
+This is a Python package using a `src/` layout with `hatchling` as the build backend.
+Source code lives in `src/autoimmune/`, tests in `tests/`.
+
+## Code Style
+
+- Python 3.11+. Use modern typing syntax (`X | Y`, `type` aliases, `Self`).
+- All tools configured in `pyproject.toml` — no separate config files.
+- Ruff for linting and formatting. Run `ruff check` and `ruff format` before committing.
+- Type hints required on all public function signatures.
+- Google-style docstrings on public classes and functions.
+
+## Testing
+
+- Use pytest. Test files mirror source layout: `src/autoimmune/foo.py` -> `tests/test_foo.py`.
+- Run `pytest` to verify changes. All tests must pass before committing.
+- Mark slow tests with `@pytest.mark.slow`.
+
+## What Not To Do
+
+- Do not add `setup.py`, `setup.cfg`, or `requirements.txt`.
+- Do not use `print()` in library code — use `logging`.
+- Do not commit generated files, model weights, or large data.
+- Do not add `# type: ignore` without a specific error code and justification.
+- Do not use bare `except:` clauses.

autoimmune-0.0.1/CLAUDE.md

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+# autoimmune
+
+## Quick Reference
+
+```bash
+# Install (editable, with dev extras)
+pip install -e ".[dev]"
+
+# Run tests
+pytest
+
+# Lint & format
+ruff check src/ tests/
+ruff format src/ tests/
+
+# Type check
+mypy src/
+```
+
+## Project Structure
+
+```
+autoimmune/
+├── src/
+│   └── autoimmune/       # importable package
+├── tests/                # pytest tests mirror src/ layout
+├── pyproject.toml        # single source of truth for config
+└── CLAUDE.md             # this file
+```
+
+## Conventions
+
+- **Python 3.11+** with modern syntax (`match`, `X | Y` unions, `type` aliases).
+- **src layout** — always import from `autoimmune`, never relative to the repo root.
+- **Ruff** for linting and formatting. All config in `pyproject.toml`.
+- **pytest** for testing. Mark slow tests with `@pytest.mark.slow`.
+- Type hints on all public function signatures.
+- Google-style docstrings on public APIs.
+- Max line length: 100 characters.

autoimmune-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Bryan Briney
+
+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.

autoimmune-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: autoimmune
+Version: 0.0.1
+Summary: Autoimmune
+Project-URL: Homepage, https://github.com/briney/autoimmune
+Project-URL: Repository, https://github.com/briney/autoimmune
+Project-URL: Issues, https://github.com/briney/autoimmune/issues
+Author-email: Bryan Briney <briney@scripps.edu>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Provides-Extra: dev
+Requires-Dist: mypy>=1.10; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.4; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# autoimmune
+
+## Installation
+
+```bash
+pip install autoimmune
+```
+
+### Development
+
+```bash
+git clone https://github.com/briney/autoimmune.git
+cd autoimmune
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+```
+
+## Testing
+
+```bash
+pytest
+```

autoimmune-0.0.1/README.md

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+# autoimmune
+
+## Installation
+
+```bash
+pip install autoimmune
+```
+
+### Development
+
+```bash
+git clone https://github.com/briney/autoimmune.git
+cd autoimmune
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+```
+
+## Testing
+
+```bash
+pytest
+```

autoimmune-0.0.1/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "autoimmune"
+version = "0.0.1"
+description = "Autoimmune"
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.11"
+authors = [{ name = "Bryan Briney", email = "briney@scripps.edu" }]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = []
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "pytest-cov>=5.0",
+    "ruff>=0.4",
+    "mypy>=1.10",
+]
+
+[project.urls]
+Homepage = "https://github.com/briney/autoimmune"
+Repository = "https://github.com/briney/autoimmune"
+Issues = "https://github.com/briney/autoimmune/issues"
+
+# -- Ruff ------------------------------------------------------------------
+
+[tool.ruff]
+line-length = 100
+target-version = "py311"
+
+[tool.ruff.lint]
+select = [
+    "E",   # pycodestyle errors
+    "W",   # pycodestyle warnings
+    "F",   # pyflakes
+    "I",   # isort
+    "N",   # pep8-naming
+    "UP",  # pyupgrade
+    "B",   # flake8-bugbear
+    "SIM", # flake8-simplify
+    "TCH", # flake8-type-checking
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["autoimmune"]
+
+# -- Pytest -----------------------------------------------------------------
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+]
+
+# -- Mypy -------------------------------------------------------------------
+
+[tool.mypy]
+python_version = "3.11"
+strict = true
+warn_return_any = true
+warn_unused_configs = true

autoimmune-0.0.1/src/autoimmune/__init__.py

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+"""autoimmune."""
+
+__version__ = "0.0.1"

autoimmune-0.0.1/tests/test_placeholder.py

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+from __future__ import annotations
+
+import autoimmune
+
+
+def test_version():
+    assert autoimmune.__version__ == "0.0.1"