Testing Refactor

[lispandfound]

This PR does three things that couldn't easily be separated:

1. Moves from Jenkins to GitHub Actions for our standard PR workflow.
2. Migrates tests out of the qcore package into the tests folder
3. Adds a bunch more tests to improve coverage for the functions that weren't previously deleted.

As part of (1) and (2), the PR moved to a pyproject.toml based setup for everything and deleted the requirements.txt

Note

The high line count is because I added a uv.lock file to get the GitHub Actions to reliably reproduce.

Note

Coverage check fails for now because of numba functions. This is addressed in #365 and #366

[gemini-code-assist]

Summary of Changes

Hello @lispandfound, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request represents a substantial refactoring effort aimed at modernizing the project's development and testing infrastructure. By migrating to GitHub Actions and a pyproject.toml setup, the project benefits from improved automation, clearer dependency management, and a more organized test suite. The addition of numerous new tests further enhances the robustness and maintainability of the codebase, ensuring higher quality and more reliable future development.

Highlights

• CI/CD Migration: The project has transitioned its standard Pull Request workflow from Jenkins to GitHub Actions, streamlining the continuous integration and delivery process.
• Test Infrastructure Refactor: All tests have been migrated out of the qcore package and into a dedicated tests folder, improving project structure and test discoverability.
• Dependency Management Update: The project now uses a pyproject.toml based setup for dependency management, replacing the requirements.txt file and providing a more modern and standardized approach.
• Increased Test Coverage: A significant number of new tests have been added across various modules to improve overall code coverage and ensure the reliability of existing functionalities.

Ignored Files

• Ignored by pattern: .github/workflows/** (5)
  • .github/workflows/deptry.yml
  • .github/workflows/git-extension.yml
  • .github/workflows/publish-PyPi.yml
  • .github/workflows/pytest.yml
  • .github/workflows/ruff.yml

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[gemini-code-assist]

Code Review

This pull request introduces a significant and valuable refactoring of the project. The migration from Jenkins to GitHub Actions, the move to a pyproject.toml-based setup, and the relocation and expansion of tests are all excellent steps towards modernizing the repository and improving its maintainability. The new tests are comprehensive, using property-based testing and covering many edge cases, which greatly increases confidence in the code's correctness and robustness. Overall, this is a high-quality contribution. I have one point of clarification regarding the packaged data.

[lispandfound]

Coverage is improved in type checking PR which adds some coverage exclusions for the numba functions that are causing low test coverage.

[Copilot]

Pull request overview

This PR performs a major infrastructure refactoring by migrating from Jenkins to GitHub Actions for CI/CD, reorganizing the test suite from qcore/test/ to a top-level tests/ directory, and modernizing the build configuration to use pyproject.toml instead of requirements.txt. The changes also include significant test coverage improvements by adding new test cases for previously untested or under-tested functionality.

Key Changes:

• Migrated CI/CD from Jenkins to GitHub Actions with workflows for pytest, ruff, and deptry
• Moved all tests from qcore/test/ to tests/ directory following pytest conventions
• Converted dependency management from requirements.txt to pyproject.toml with explicit dependencies
• Added extensive test coverage for functions in utils, timeseries, siteamp, simulation_structure, shared, point_in_polygon, nhm, geo, coordinates, CLI, and archive_structure modules

Reviewed changes

Copilot reviewed 24 out of 54 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_xyts.py	Added type assertions and invalid file handling test
tests/test_utils.py	New test file for YAML loading functionality
tests/test_timeseries.py	Added comprehensive tests for text output, error handling, and edge cases
tests/test_src_site_dist.py	New comprehensive test suite for distance calculations
tests/test_siteamp.py	Added return type annotations and input validation tests
tests/test_simulation_structure.py	New test suite for simulation structure path utilities
tests/test_shared.py	New test suite for station and corner parsing utilities
tests/test_point_in_polygon.py	New test suite for polygon containment checks
tests/test_nhm.py	New comprehensive test suite for NHM fault operations
tests/test_grid.py	Added return type annotations and type assertion tests
tests/test_geo.py	New comprehensive test suite for geographic calculations
tests/test_coordinates.py	Code formatting improvements and consistency fixes
tests/test_cli.py	Enhanced CLI testing with additional edge cases
tests/test_archive_structure.py	New test suite for archive path utilities
pyproject.toml	Migrated from requirements.txt with explicit dependencies and version constraints
.github/workflows/*.yml	New GitHub Actions workflows for pytest, ruff, deptry checks
requirements.txt	Deleted in favor of pyproject.toml
Jenkinsfile	Deleted as part of migration to GitHub Actions
qcore/test/*	All test files removed as tests migrated to top-level tests/ directory

Comments suppressed due to low confidence (2)

tests/test_timeseries.py:951

• Missing import for tempfile module. The code uses tempfile.TemporaryFile but doesn't import tempfile at the top of the file.
  tests/test_coordinates.py:92
• Variable geod is not used.

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