pycat-napari 1.0.0__tar.gz

pycat_napari-1.0.0/.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
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+# Django stuff:
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+# 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
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+#Pipfile.lock
+
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+#   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
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+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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+.env
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+/site
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+.mypy_cache/
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pycat_napari-1.0.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: false
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+    - requirements: docs/requirements.txt
+
+formats:
+  - pdf
+  - epub

pycat_napari-1.0.0/CHANGELOG.md

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+# Changelog
+All notable changes to PyCAT-Napari will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.0.0] - 2024-11-22
+### Added
+- Initial public release of PyCAT-Napari
+- Complete GUI interface built on Napari viewer
+- Core functionalities for biomolecular condensate analysis:
+  * Image processing and analysis tools
+  * Fluorescence image analysis capabilities
+  * Condensate feature detection and measurement
+  * Data visualization tools
+  * Colocalization and Correlation analyses 
+- Command-line interface via `run-pycat` command
+- Python API for programmatic access to analysis tools
+- Support for multiple imaging file formats
+- Integration with popular scientific Python libraries
+- Platform support for Windows, macOS (including Apple Silicon), and Linux
+- Comprehensive error handling and user feedback
+- Basic documentation and usage examples
+
+### Dependencies
+- Compatible with Python 3.9+
+- Core dependencies include:
+  * napari
+  * numpy
+  * opencv-python-headless
+  * scikit-image
+  * scipy
+  * torch
+  * And other scientific computing libraries
+
+### Fixed
+- (List any bug fixes here)
+
+### Changed
+- (List any changes to existing features here)
+
+### Deprecated
+- (List any features that are deprecated and will be removed in future releases here)
+
+[1.0.0]: https://github.com/BanerjeeLab-repertoire/pycat-napari/releases/tag/v1.0.0

pycat_napari-1.0.0/CONTRIBUTING.md

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+# Contributing to PyCAT-Napari
+
+We appreciate your interest in contributing to PyCAT-Napari! This document provides guidelines and information about contributing to this project. The best tools are ones built by the community so it is my hope that PyCAT will be a valuable resource and that it will help to advance our understanding of the complex biological processes that underlie the formation and function of biomolecular condensates. I hope it is useful to the community and that others will contribute to its development.
+
+## Table of Contents
+- [Code of Conduct](#code-of-conduct)
+- [Getting Started](#getting-started)
+- [Development Setup](#development-setup)
+- [Making Contributions](#making-contributions)
+- [Branch Naming Conventions](#branch-naming-conventions)
+- [Commit Message Guidelines](#commit-message-guidelines)
+- [Pull Request Guidelines](#pull-request-guidelines)
+- [Code Review Process](#code-review-process)
+- [Style Guidelines](#style-guidelines)
+- [Testing](#testing)
+- [Submitting Changes](#submitting-changes)
+
+## Code of Conduct
+By participating in this project, you agree to maintain a respectful and constructive environment for all contributors. Please report any unacceptable behavior to the project maintainers.
+
+## Getting Started
+1. Fork the repository
+2. Clone your fork locally
+3. Create a virtual environment and install dependencies
+
+```bash
+git clone https://github.com/BanerjeeLab-repertoire/pycat-napari.git
+cd pycat-napari
+python -m venv venv
+source venv/bin/activate  # On Windows: venv\Scripts\activate
+pip install -e ".[dev]"
+```
+
+## Development Setup
+The project uses a src-layout and requires several development dependencies:
+
+```bash
+# Install development dependencies
+pip install -e ".[dev]"
+
+# Install test dependencies
+pip install -e ".[test]"
+```
+
+## Making Contributions
+1. Create a new branch for your feature or fix:
+   ```bash
+   git checkout -b feature-name
+   ```
+2. Make your changes
+3. Write or update tests as needed
+4. Run the test suite
+5. Push your changes and create a pull request
+
+## Branch Naming Conventions
+- `feature/your-feature-name` for new features
+- `bugfix/your-bugfix-name` for bug fixes
+- `hotfix/your-hotfix-name` for hotfixes
+
+## Commit Message Guidelines
+- Use the present tense ("Add feature" not "Added feature")
+- Use the imperative mood ("Move cursor to..." not "Moves cursor to...")
+- Limit the first line to 72 characters or less
+- Reference issues and pull requests liberally
+
+## Pull Request Guidelines
+- Provide a clear description of what the pull request does
+- Reference any related issues or pull requests
+- Include screenshots or gifs if the changes affect the UI
+- Ensure all tests pass before submitting
+
+## Code Review Process
+- All submissions, including submissions by project members, require review
+- Be respectful and constructive in your feedback
+- Provide context for suggested changes
+
+## Style Guidelines
+- Follow PEP 8 style guidelines
+- Use meaningful variable and function names
+- Document new functions and classes using docstrings
+- Keep functions focused and concise
+- Add comments for complex logic
+
+## Testing
+- Add tests for new features
+- Ensure all tests pass before submitting:
+  ```bash
+  pytest tests/
+  ```
+- Maintain or improve test coverage
+
+## Submitting Changes
+1. Update the CHANGELOG.md with your changes
+2. Ensure your code is properly formatted
+3. Push your changes to your fork
+4. Create a Pull Request with a clear description:
+   - What changes were made
+   - Why the changes were made
+   - Any special notes for reviewers
+
+## Questions or Problems?
+- Open an issue for bugs or feature requests at: https://github.com/BanerjeeLab-repertoire/pycat-napari/issues
+- Contact the maintainers for other questions
+
+Thank you for contributing to PyCAT-Napari!

pycat_napari-1.0.0/LICENSE

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+License
+-------
+
+BSD 3-Clause License
+
+Copyright (c) 2024, Christian Neureuter, Banerjee Lab, State University of New York at Buffalo
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the 
+following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following 
+disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following 
+disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the University at Buffalo, the author, nor the names of its contributors may be used to endorse 
+or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, 
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE 
+USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+Third-Party Software Notice
+---------------------------
+This project includes third-party software components licensed under various open-source licenses. For more information 
+regarding these licenses, please refer to the THIRD_PARTY_LICENSES.txt file located in the root directory of this project.

pycat_napari-1.0.0/MANIFEST.in

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+# Inlcude the PyCAT logo for app icon
+include src/pycat/icons/*.png
+
+# Include license and project info
+include LICENSE
+include README.md
+include CHANGELOG.md
+include CONTRIBUTING.md
+include THIRD_PARTY_LICENSES.txt
+include pyproject.toml
+
+# Include package data
+recursive-include src/pycat/icons/*.png
+
+# Include test files
+recursive-include tests *.py
+
+# Include configuration files
+recursive-include config *.txt
+recursive-include config *.yml
+recursive-include config *.yaml
+
+# Include Jupyter Notebooks
+recursive-include notebooks *.ipynb
+
+# Include YAML files in the root directory
+include *.yaml
+
+# Documentation
+recursive-include docs *.md
+recursive-include docs *.rst
+recursive-include docs *.txt
+
+# Exclude development files
+global-exclude *.py[cod] __pycache__
+global-exclude *.so *.dylib *.dll
+global-exclude .git*
+global-exclude .DS_Store
+global-exclude *.swp *.swo
+global-exclude .vscode/
+global-exclude venv/
+global-exclude .env
+global-exclude .mypy_cache/
+global-exclude .pytest_cache/
+global-exclude .ipynb_checkpoints/