Modernise repository to open-source standards

.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Report a bug in ptool
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: "Thanks for taking the time to report a bug!"
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: A clear description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to reproduce
+      description: Minimal steps to reproduce the behaviour.
+      placeholder: |
+        1. Run `ptool checksums ...`
+        2. Then run `ptool compare ...`
+        3. See error
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behaviour
+      description: What you expected to happen.
+    validations:
+      required: true
+
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: Output of `ptool --version` and `python --version`.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature Request
+description: Suggest a new feature or improvement
+labels: ["enhancement"]
+body:
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem
+      description: What problem does this feature solve?
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Proposed solution
+      description: Describe the solution you'd like.
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+      description: Any alternative approaches you've thought about.

.github/PULL_REQUEST_TEMPLATE.md

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+## Summary
+
+<!-- Describe what this PR does and why. -->
+
+## Changes
+
+- 
+
+## Test plan
+
+- [ ] Tests added or updated
+- [ ] `pytest tests/ -v` passes locally
+
+## Related issues
+
+<!-- Closes #... -->

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    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: pip install -e ".[dev]"
+
+      - name: Run tests
+        run: pytest tests/ -v

.gitignore

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-__pycache__
-ptool.egg-info
+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+*.egg
+dist/
+build/
+
+# Virtual environments
+.venv/
+.env/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+
+# Editor
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# HPC
 slurm-*.out
+
+# OS
+.DS_Store

CHANGELOG.md

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+# Changelog
+
+All notable changes to this project 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).
+
+## [Unreleased]
+
+### Added
+- Configurable checksum types: `imohash-64k` (default), `xxhash`, `md5`
+- `--checksum-type` option on `ptool checksums` command
+- Guard in `compare` and `summary` against mixing CSVs with different checksum types
+- Test suite covering checksum type correctness and false-negative behaviour
+- `pyproject.toml` replacing legacy `setup.py`
+- `CONTRIBUTING.md`, `CODE_OF_CONDUCT.md`, `SECURITY.md`, `CHANGELOG.md`
+- GitHub Actions CI workflow
+- GitHub issue and PR templates
+
+### Fixed
+- Invalid `str[pyarrow]` dtype string in `read_csv` (now `string[pyarrow]`), which caused a `TypeError` on pandas 2.x
+- Incorrect `license = "MIT"` metadata — corrected to GPL-3.0 to match the `LICENSE` file
+- Invalid PyPI classifier `Development Status :: 0.2.2` — corrected to `Development Status :: 4 - Beta`
+- Wrong `url` in package metadata (pointed to GitLab) — updated to GitHub
+
+### Changed
+- imohash sample size upgraded from 16 KB to 64 KB to reduce false-negative risk
+
+## [0.2.2] - 2024-01-01
+
+### Added
+- `sync_options`: support for additional sync configuration options
+
+## [0.2.1] - 2024-01-01
+
+### Fixed
+- Truncated prefix handling in checksum paths
+
+## [0.2.0] - 2024-01-01
+
+### Added
+- Initial public release with `checksums`, `compare`, `summary`, and `prepare-rsync` commands

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior:
+
+* The use of sexualized language or imagery, and sexual attention or advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at **pavan.siligam@gmail.com**. All complaints will be reviewed and investigated promptly and fairly.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 2.1.

CONTRIBUTING.md

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+# Contributing to ptool
+
+Thank you for considering contributing to ptool! This document describes how to get started.
+
+## Development setup
+
+1. Fork the repository and clone your fork:
+
+   ```shell
+   git clone https://github.com/<your-username>/pool_tool.git
+   cd pool_tool
+   ```
+
+2. Create the conda environment and install the package in editable mode:
+
+   ```shell
+   conda env create -f environment.yaml
+   conda activate ptool
+   pip install -e ".[dev]"
+   ```
+
+3. Verify the setup by running the test suite:
+
+   ```shell
+   pytest tests/ -v
+   ```
+
+## Workflow
+
+- Create a feature branch from `main`:
+
+  ```shell
+  git checkout -b my-feature
+  ```
+
+- Make your changes, add tests, and ensure all tests pass before opening a PR.
+- Write clear, descriptive commit messages.
+- Open a pull request against `main` and fill in the PR template.
+
+## Running tests
+
+```shell
+pytest tests/ -v
+```
+
+## Reporting bugs
+
+Please use the [bug report template](https://github.com/esm-tools/pool_tool/issues/new?template=bug_report.yml) when filing issues.
+
+## Code of conduct
+
+This project follows the [Contributor Covenant Code of Conduct](CODE_OF_CONDUCT.md). By participating you agree to abide by its terms.