Tidy some docstrings

[hyanwong]

And remove extraneous timedelta param

Summary by CodeRabbit

• Documentation

  • Added a call to action for contributions by providing a link to the GitHub repository.
  • Enhanced method documentation in the Graph class for better clarity.

• Refactor

  • Updated methods in Graph and Tables classes to include parameter and return type annotations.
  • Removed the timedelta parameter from the from_tree_sequence method and adjusted related logic.

• Tests

  • Modified the test case to handle time changes differently, improving test coverage and accuracy.

[coderabbitai]

Walkthrough

The recent changes enhance documentation and type annotations across several files, improving code clarity and maintainability. In giglib/graph.py, parameter descriptions and return types were added. In giglib/tables.py, docstrings and type annotations were updated, and a parameter was removed. The test file tests/test_tables.py was updated to match these modifications. Additionally, a call to action for contributions was included in the documentation.

Changes

Files	Change Summary
docs/index.md	Added a call to action for contribution by providing a link to the GitHub repository.
giglib/graph.py	Added parameter descriptions and return types for methods to_tree_sequence, decapitate, and sample_resolve in the Graph class.
giglib/tables.py	Clarified copy method docstring, added type annotations, and removed timedelta parameter from from_tree_sequence method.
tests/test_tables.py	Modified test_simple_from_tree_sequence_with_timedelta to adjust for the removal of the timedelta parameter.

Poem

In the code where graphs do weave,
 > Types and docs now interleave,
 > From tables' time to tests' embrace,
 > Clarity and rhyme replace the chase.
 > Contributions call, come one, come all,
 > To improve the code, both big and small!

---

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[coderabbitai]

Actionable comments posted: 0

Outside diff range, codebase verification and nitpick comments (1)

docs/index.md (1)

26-26: Convert bare URL to markdown link.

Bare URLs should be converted to markdown links to enhance readability and compliance with Markdownlint rules.

- Please visit https://github.com/hyanwong/giglib to contribute to development.
+ Please visit [the project's GitHub repository](https://github.com/hyanwong/giglib) to contribute to development.

Tools

Markdownlint

26-26: null
Bare URL used

(MD034, no-bare-urls)

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 605e88c and c41bf23.

Files selected for processing (4)

• docs/index.md (1 hunks)
• giglib/graph.py (3 hunks)
• giglib/tables.py (6 hunks)
• tests/test_tables.py (1 hunks)

Files skipped from review due to trivial changes (1)

• giglib/graph.py

Additional context used

Markdownlint

docs/index.md

26-26: null
Bare URL used

(MD034, no-bare-urls)

Additional comments not posted (7)

tests/test_tables.py (1)

34-35: LGTM! Changes are correctly implemented.

The test function test_simple_from_tree_sequence_with_timedelta has been correctly updated to remove the timedelta parameter from the from_tree_sequence method call and introduce the change_times method call to manage the timedelta parameter.

giglib/tables.py (6)

1139-1143: Docstring and type annotation update in Tables.copy method approved.

The updated docstring and the addition of the return type annotation improve the clarity and documentation of the method.

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1244-1246: Docstring and type annotation update in Tables.graph method approved.

The updated docstring and the addition of the return type annotation improve the clarity and documentation of the method.

---

1256-1257: Docstring and type annotation update in Tables.sample_ids property approved.

The updated docstring and the addition of the return type annotation improve the clarity and documentation of the property.

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1273-1278: Docstring and type annotation update in Tables.decapitate method approved.

The updated docstring and the addition of the return type annotation improve the clarity and documentation of the method.

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1311-1319: Docstring and type annotation update in Tables.from_tree_sequence method approved.

The updated docstring and the addition of the return type annotation improve the clarity and documentation of the method. The removal of the timedelta parameter simplifies the method signature.

---

1139-1143: Docstring and type annotation update in Tables.copy method approved.

The updated docstring and the addition of the return type annotation improve the clarity and documentation of the method.