feat: update typeline and support Python 3.13

[clintval]

Summary by CodeRabbit

• New Features
  • Added support and documentation for Python 3.13.
• Chores
  • Updated project configuration to the standardized format and reorganized metadata, dependencies, and tool settings.
  • Improved and clarified development workflow by updating continuous integration and build processes.
• Documentation
  • Updated badges and removed obsolete instructions for task runner plugins.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

This update introduces several changes across the project. The continuous integration workflows are updated to use Poetry 2.1.1 via the snok/install-poetry GitHub Action, and Python 3.13 is added to the test and build matrices. Documentation is revised to reflect these changes, including removal of manual plugin installation instructions and an updated Python version badge. The pyproject.toml file is migrated to the PEP 621 [project] format with updated metadata, dependencies, and tool configurations. Additionally, the BedReader and BedWriter classes are updated to inherit from TsvReader and TsvWriter respectively.

Changes

File(s)	Change Summary
.github/workflows/publish_bedspec.yml, .github/workflows/tests.yml	Updated Poetry installation to use snok/install-poetry@v1 GitHub Action with Poetry 2.1.1; removed manual installation steps; expanded Python matrix in tests to include 3.13; removed poethepoet installation in tests.
.github/workflows/wheels.yml	Added Python 3.13 to the build matrix for wheel building.
CONTRIBUTING.md	Removed instructions for manual installation of the poethepoet plugin and references to Poetry v2.0.0 plugin support.
README.md	Updated the supported Python versions badge to include Python 3.13.
bedspec/_reader.py	Changed import and base class for BedReader from TsvRecordReader to TsvReader.
bedspec/_writer.py	Changed import and base class for BedWriter from TsvRecordWriter to TsvWriter.
pyproject.toml	Migrated to [project] table format; updated metadata, dependencies, and URLs; reorganized dev dependencies; updated tool configurations for poe, mypy, pyright, and ruff; adjusted task runner flags and linting rules; set new project version (0.7.0).

Sequence Diagram(s)

sequenceDiagram
    participant Developer
    participant GitHub Actions
    participant Poetry Installer
    participant Test Runner

    Developer->>GitHub Actions: Push code / PR
    GitHub Actions->>Poetry Installer: Install Poetry 2.1.1 via snok/install-poetry@v1
    GitHub Actions->>GitHub Actions: Set up Python (3.10, 3.11, 3.12, 3.13)
    GitHub Actions->>GitHub Actions: Install dependencies
    GitHub Actions->>Test Runner: Run tests/build wheels
    Test Runner-->>GitHub Actions: Report results
    GitHub Actions-->>Developer: Display CI status

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Possibly related PRs

• clintval/bedspec#27: Changes the base classes for BedReader and BedWriter from TsvStructReader/Writer to TsvRecordReader/Writer, indicating both PRs update the same classes but with different base classes and method adjustments.

Poem

In the garden of code, a new path is paved,
Poetry blooms, and old plugins are waived.
Python 3.13 joins the warren’s delight,
Readers and writers hop to new heights.
Docs are refreshed, the badge shines anew—
A rabbit’s proud leap, for the whole coding crew!
🐇✨

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📥 Commits

Reviewing files that changed from the base of the PR and between 32fa692 and 4e62f9d.

⛔ Files ignored due to path filters (1)

• poetry.lock is excluded by !**/*.lock

📒 Files selected for processing (8)

• .github/workflows/publish_bedspec.yml (2 hunks)
• .github/workflows/tests.yml (2 hunks)
• .github/workflows/wheels.yml (1 hunks)
• CONTRIBUTING.md (0 hunks)
• README.md (1 hunks)
• bedspec/_reader.py (2 hunks)
• bedspec/_writer.py (1 hunks)
• pyproject.toml (8 hunks)

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