ossify 0.0.1__tar.gz

ossify-0.0.1/.bmv-post-commit.sh

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+#!/bin/bash
+git push --tags

ossify-0.0.1/.claude/settings.local.json

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+{
+  "permissions": {
+    "allow": [
+      "Read(//Users/caseysm/Work/Code/morphsync/src/morphsync/**)",
+      "Bash(poe test:*)",
+      "Bash(python test_synapse_bug.py:*)",
+      "Bash(uv run pytest:*)",
+      "Bash(uv run mkdocs build:*)",
+      "Bash(uv run:*)"
+    ],
+    "deny": [],
+    "ask": []
+  }
+}

ossify-0.0.1/.github/workflows/mkdocs_publish.yml

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+name: mkdocs 
+on:
+  push:
+    branches:
+      - master 
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: pip install mkdocs-material mkdocstrings[python]
+      - run: mkdocs gh-deploy --force

ossify-0.0.1/.github/workflows/python-package.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: Python test and lint
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+    name: python
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v2
+        with:
+          version: "0.5.2"
+      - name: Install project and dependencies
+        run: uv sync --python ${{ matrix.python-version }}
+      - name: Run tests
+        run: uv run pytest tests
+      - name: Lint with ruff
+        run: uv run ruff check src/*

ossify-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+scratch.ipynb
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/
+
+.DS_Store
+test-reports/
+var/
+.vscode
+*.orig
+*.sublime-workspace
+

ossify-0.0.1/.polyscope.ini

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+{
+    "uiScale": 1.0,
+    "windowHeight": 1023,
+    "windowPosX": 20,
+    "windowPosY": 72,
+    "windowWidth": 1601
+}

ossify-0.0.1/.pre-commit-config.yaml

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+files: src|tests
+
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.11.2
+  hooks:
+    # Run the linter.
+    - id: ruff 
+      types_or: [ python, pyi]
+    - id: ruff
+      args: ["--select", "I", "--fix"]
+    - id: ruff-format
+      types_or: [ python, pyi]

ossify-0.0.1/CLAUDE.md

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+# ossify Development Guide
+
+This guide documents the development workflow, testing strategies, and coding standards for ossify.
+
+## Development Environment
+
+### Package Management: UV + Poe
+
+This project uses **UV** for dependency management and **Poe** for task running instead of the system Python environment:
+
+```bash
+# Install dependencies (automatically creates virtual environment)
+uv sync
+
+# Run tasks via Poe (preferred over direct python commands)
+poe test          # Run tests with coverage
+poe doc-preview   # Preview documentation
+poe bump patch    # Bump version (patch/minor/major)
+poe drybump patch # Dry run version bump
+```
+
+### Key Commands
+
+From `pyproject.toml`:
+
+- **Testing**: `poe test` → `uv run pytest --cov=ossify tests`
+- **Documentation**: `poe doc-preview` → `uv run mkdocs serve`
+- **Version Management**: `poe bump patch/minor/major`
+- **Linting**: `uv run ruff check src/ tests/`
+
+## Python Version Requirements
+
+- **Minimum**: Python 3.10+ (leverages match statements and improved type annotations)
+- **Tested**: Python 3.10, 3.11, 3.12
+- **Compatibility**: Use `typing-extensions` for Python < 3.11 features
+
+## Type Hinting Standards
+
+### Required Practices
+
+- **All functions/methods** must have complete type annotations
+- **All class attributes** must have type hints (use `attrs` or `dataclasses` with type annotations).
+- **Import patterns**:
+  ```python
+  from typing import Optional, Union, Literal, Any, Dict, List, Tuple
+  from typing_extensions import Self  # For Python < 3.11
+  ```
+- **All python files**: Follow ruff guidelines for linting, imports, and code style.
+
+### Common Patterns
+
+## Testing Strategy
+
+### Dual-Level Testing Approach
+
+Always implement **both** high-level integration tests and low-level unit tests:
+
+#### High-Level Integration Tests
+Focus on real-world workflows and end-to-end functionality:
+
+#### Low-Level Unit Tests
+Focus on individual methods, edge cases, and error conditions:
+
+### Testing Guidelines
+
+- **Coverage Target**: Aim for >90% line coverage, >85% branch coverage
+- **Test Organization**: Mirror source structure in `tests/` directory
+- **Mocking Strategy**: Mock external dependencies (neuroglancer), test actual behavior for internal logic
+- **Parametrization**: Use `@pytest.mark.parametrize` for testing multiple inputs
+- **Fixtures**: Create reusable test data in `conftest.py`
+
+### Running Tests
+
+```bash
+# Full test suite with coverage
+poe test
+
+# Specific test file
+uv run pytest tests/EXAMPLE_TEST_FILE.py -v
+
+# Coverage report
+uv run pytest --cov=ossify --cov-report=html tests/
+```
+
+## Code Architecture Patterns
+
+## Common Development Workflows
+
+### Bug Fixes
+
+1. Write failing test first (TDD approach)
+2. Describe problem fully to determine whether the behavior is a bug, intentional, or based on unspecified assumptions.
+3. Implement minimal fix
+4. Ensure all tests pass
+5. Check type annotations are correct
+6. Run full test suite: `poe test`
+
+## Documentation Standards
+
+- **Docstrings**: Use Google/NumPy style docstrings
+- **Examples**: Include usage examples in docstrings
+- **Type Information**: Document parameter and return types in docstrings
+- **API Documentation**: Use mkdocs with mkdocstrings for auto-generation
+
+```python
+def add_points(
+    self, 
+    data: pd.DataFrame,
+    point_column: Union[str, List[str]],
+    segment_column: Optional[str] = None
+) -> Self:
+    """Add point annotations to the viewer state.
+    
+    Args:
+        data: DataFrame containing point data
+        point_column: Column name(s) for coordinates. Can be:
+            - Single string for prefix (e.g., 'pos' → ['pos_x', 'pos_y', 'pos_z'])  
+            - List of column names (e.g., ['x', 'y', 'z'])
+        segment_column: Optional column containing segment IDs
+        
+    Returns:
+        Self for method chaining
+        
+    Examples:
+        >>> vs = ViewerState()
+        >>> vs.add_points(df, point_column=['x', 'y', 'z'])
+        >>> vs.add_points(df, point_column='position')  # Uses position_x, position_y, position_z
+    """
+```
+
+## Pre-Commit Workflow
+
+Before committing changes:
+
+```bash
+# Run full test suite
+poe test
+
+# Run linting
+uv run ruff check src/ tests/
+
+# Check type annotations
+uv run mypy src/ --ignore-missing-imports  # if mypy is configured
+
+# Ensure documentation builds
+poe doc-preview
+```
+
+## Release Process
+
+```bash
+# Check what will be bumped
+poe drybump patch  # or minor/major
+
+# Bump version and create tag
+poe bump patch     # or minor/major
+```
+
+This automatically:
+- Updates version in `pyproject.toml` and `src/ossify/__init__.py`
+- Creates git commit and tag
+- Runs pre/post commit hooks including `uv sync`

ossify-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 Casey Schneider-Mizell
+
+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.

ossify-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: ossify
+Version: 0.0.1
+Summary: Mesh and skeleton analysis
+Author-email: Casey Schneider-Mizell <caseysm@gmail.com>
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.11
+Requires-Dist: caveclient>=7.6.0
+Requires-Dist: cloud-files>=5.8.0
+Requires-Dist: cloud-volume>=11.1.5
+Requires-Dist: matplotlib>=3.10.6
+Requires-Dist: morphsync==0.1.0
+Requires-Dist: numpy>=2.0.2
+Requires-Dist: orjson>=3.10.15
+Requires-Dist: scipy>=1.15
+Requires-Dist: trimesh[easy]>=4.6.2
+Provides-Extra: legacy
+Requires-Dist: h5py>=3.14.0; extra == 'legacy'
+Description-Content-Type: text/markdown
+
+Welcome to ossify!

ossify-0.0.1/README.md

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+Welcome to ossify!