teddympnn 0.0.1__tar.gz

teddympnn-0.0.1/.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

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

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+name: CI
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Lint
+        run: ruff check src/ tests/
+
+      - name: Format check
+        run: ruff format --check src/ tests/
+
+      - name: Type check
+        run: mypy src/
+
+      - name: Test
+        run: pytest

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

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+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  pypi-publish:
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install build tooling (PEP 517)
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build
+
+      - name: Build distributions
+        run: python -m build
+
+      - name: List built artifacts (size)
+        run: ls -lh dist/
+
+      - name: Validate metadata (optional)
+        run: |
+          python -m pip install twine
+          twine check dist/*
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

teddympnn-0.0.1/.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
+
+# 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
+
+# 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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# 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
+
+# macOS
+.DS_Store

teddympnn-0.0.1/.python-version

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+3.11

teddympnn-0.0.1/AGENTS.md

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+# Agent Instructions
+
+General instructions for AI coding agents working on this project.
+Not specific to any single agent or tool.
+
+## Project Overview
+
+teddyMPNN is a message passing neural network for protein-protein interfaces.
+
+## Architecture
+
+<!-- Describe the main modules/components, their responsibilities, and how they interact.
+     Include data flow if relevant. -->
+
+TODO: Fill in as the project develops.
+
+## Development Workflow
+
+- Install: `pip install -e ".[dev]"`
+- Test: `pytest`
+- Lint: `ruff check src/ tests/`
+- Format: `ruff format src/ tests/`
+- Type check: `mypy src/`
+
+Always run tests and lint before considering work complete.
+
+## Conventions
+
+- **Formatting**: Ruff handles this. Do not manually adjust formatting.
+- **Imports**: Sorted by ruff (isort rules). Do not manually reorder.
+- **Types**: All function signatures must have type annotations. Use modern syntax (`X | None` not `Optional[X]`).
+- **Docstrings**: Google style. Required on all public functions, classes, and modules.
+- **Tests**: Every new function or class should have corresponding tests. Use `pytest` fixtures, not `setUp`/`tearDown`.
+- **Error handling**: Prefer specific exceptions over bare `except`. Define custom exceptions in a `exceptions.py` module if the project needs them.
+- **Naming**: snake_case for functions/variables, PascalCase for classes, UPPER_SNAKE for constants.
+
+## What Not to Do
+
+- Do not add dependencies without explicit approval. Prefer the standard library when reasonable.
+- Do not create separate config files (`.flake8`, `pytest.ini`, `mypy.ini`, etc.). All tool config lives in `pyproject.toml`.
+- Do not use `setup.py`, `setup.cfg`, or `requirements.txt`.
+- Do not modify CI configuration without explicit approval.
+- Do not add `# type: ignore` without a comment explaining why.
+- Do not write tests that depend on external services or network access without mocking.
+
+## Sensitive Areas
+
+<!-- List files, modules, or patterns that need extra care — e.g., security-critical code,
+     performance-sensitive paths, or tricky algorithms. Agents should be extra cautious
+     modifying these and should flag changes for human review. -->
+
+TODO: Fill in as the project develops.

teddympnn-0.0.1/CLAUDE.md

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+# teddyMPNN
+
+A message passing neural network for protein-protein interfaces.
+
+## Quick Reference
+
+```bash
+# Install (editable, with dev dependencies)
+pip install -e ".[dev]"
+
+# Run tests
+pytest
+
+# Lint and format
+ruff check src/ tests/
+ruff format src/ tests/
+
+# Type check
+mypy src/
+
+# CLI
+python -m teddympnn --help
+```
+
+## Project Structure
+
+```
+src/teddympnn/     # Main package code
+tests/             # Test suite (mirrors src structure)
+```
+
+## Code Conventions
+
+- Python 3.11+ — use modern syntax (type unions with `|`, `match` statements, etc.)
+- All public functions and classes need docstrings (Google style)
+- Type hints on all function signatures
+- Tests go in `tests/` mirroring the src structure: `src/foo/bar.py` → `tests/test_bar.py`
+- Ruff handles formatting and linting — don't override its defaults beyond pyproject.toml config
+
+## Before Committing
+
+1. `ruff check --fix src/ tests/` — auto-fix lint issues
+2. `ruff format src/ tests/` — format code
+3. `pytest` — all tests pass
+4. Write a meaningful commit message: `<component>: <what changed and why>`
+
+## Architecture
+
+<!-- Update this section as the project develops. Describe the main components,
+     how data flows, and any non-obvious design decisions. -->
+
+TODO: Fill in as the project takes shape.

teddympnn-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.

teddympnn-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: teddympnn
+Version: 0.0.1
+Summary: A message passing neural network for protein-protein interfaces
+Project-URL: Repository, https://github.com/briney/teddympnn
+Author-email: Bryan Briney <briney@scripps.edu>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.11
+Requires-Dist: typer>=0.9
+Provides-Extra: dev
+Requires-Dist: mypy>=1.0; extra == 'dev'
+Requires-Dist: pre-commit>=3.0; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: ruff>=0.4; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# teddyMPNN
+
+A message passing neural network for protein-protein interfaces.
+
+## Installation
+
+```bash
+pip install teddympnn
+```
+
+For development:
+
+```bash
+git clone https://github.com/briney/teddympnn.git
+cd teddympnn
+pip install -e ".[dev]"
+```
+
+## Usage
+
+```bash
+python -m teddympnn --help
+```
+

teddympnn-0.0.1/README.md

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+# teddyMPNN
+
+A message passing neural network for protein-protein interfaces.
+
+## Installation
+
+```bash
+pip install teddympnn
+```
+
+For development:
+
+```bash
+git clone https://github.com/briney/teddympnn.git
+cd teddympnn
+pip install -e ".[dev]"
+```
+
+## Usage
+
+```bash
+python -m teddympnn --help
+```
+