Testing Refactor by lispandfound · Pull Request #363 · ucgmsim/qcore

lispandfound · 2026-01-07T20:54:30Z

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

Moves from Jenkins to GitHub Actions for our standard PR workflow.
Migrates tests out of the qcore package into the tests folder
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

* Initial plan * Add test coverage for explicit raise statements Co-authored-by: lispandfound <12835929+lispandfound@users.noreply.github.com> * Add comprehensive test coverage for geo module Co-authored-by: lispandfound <12835929+lispandfound@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: lispandfound <12835929+lispandfound@users.noreply.github.com>

* Initial plan * Add basic tests for omitted modules Co-authored-by: lispandfound <12835929+lispandfound@users.noreply.github.com> * fix: fix ruff and type-checking --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: lispandfound <12835929+lispandfound@users.noreply.github.com> Co-authored-by: Jake Faulkner <jake.faulkner@canterbury.ac.nz>

…ecking

gemini-code-assist · 2026-01-07T20:55:03Z

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

Using Gemini Code Assist

The full guide for Gemini Code Assist can be found on our documentation page, here are some quick tips.

Invoking Gemini

You can request assistance from Gemini at any point by creating a comment using either /gemini <command> or @gemini-code-assist <command>. Below is a summary of the supported commands on the current page.

Feature	Command	Description
Code Review	`/gemini review`	Performs a code review for the current pull request in its current state.
Pull Request Summary	`/gemini summary`	Provides a summary of the current pull request in its current state.
Comment	@gemini-code-assist	Responds in comments when explicitly tagged, both in pull request comments and review comments.
Help	`/gemini help`	Displays a list of available commands.

Customization

To customize Gemini Code Assist for GitHub experience, repository maintainers can create a configuration file and/or provide a custom code review style guide (such as PEP-8 for Python) by creating and adding files to a .gemini/ folder in the base of the repository. Detailed instructions can be found here.

Limitations & Feedback

Gemini Code Assist may make mistakes. Please leave feedback on any instances where its feedback is incorrect or counter productive. You can react with 👍 and 👎 on @gemini-code-assist comments. If you're interested in giving your feedback about your experience with Gemini Code Assist for Github and other Google products, sign up here.

You can also get AI-powered code generation, chat, as well as code reviews directly in the IDE at no cost with the Gemini Code Assist IDE Extension.

Review the Privacy Notices, Generative AI Prohibited Use Policy, Terms of Service, and learn how to configure Gemini Code Assist in GitHub here. Gemini can make mistakes, so double check it and use code with caution. ↩

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.

pyproject.toml

lispandfound · 2026-01-07T21:23:28Z

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.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

tests/test_shared.py

tests/test_utils.py

This reverts commit 22fecb6.

lispandfound and others added 30 commits November 12, 2025 16:44

refactor: align standards with the rest of the codebase

9170d4b

fix: swap git extension workflow

1ab2830

fix: target branches correctly

8e5076b

fix: remove GMT installation

2ac1f00

fix: use python 3.13

716c604

fix: add coverage extension to pytest

73d83ba

fix: use python 3.13 for deptry

3db0a8d

fix: make deptry happy

d4c24f2

fix: types should target master

225e7cc

fix: satisfy ty checks

66e1cc6

tests: improve test coverage for cli + coordinates

ddf4278

fix: better python gitignore

b9c06a8

ci: disable coverage for a bunch of modules

dfc7fd8

trigger ci

9a6c2a2

tests(distributions): add distribution testing

027d15e

docs(distributions): improve typing and docstrings

ab985eb

fix: add test coverage for NZGMDB function

72b4b5c

tests(distributions): add missing distributions tests

8f82186

refactor(timeseries): remove unused function

052836c

tests(geo): fix tests for geo module

20be0d9

fix(test_geo): be a little more relaxed with floating point comparisons

a3ede1c

ci: add coverage checks for the remaining modules

78f7682

Merge branch 'type_checking' of github.com:ucgmsim/qcore into type_ch…

e6427b8

…ecking

docs: appease numpydoc

400d5b9

fix: add basic check for load_nhm

0a43886

fix: coverage exclude numba functions

5de292b

fix: type check fixes

33581b7

ci: remove unused filelock dependency

6718b2b

lispandfound added 5 commits January 8, 2026 09:29

Pull out testing changes

b49bcf1

Merge branch 'remove_old_functions' into testing_infra_refactor

a360aa4

fix(simulation_structure): add get_runs_dir back

b22be00

Merge branch 'remove_old_functions' into testing_infra_refactor

0c942e0

ci: simplify pytest and deptry jobs

f94e661

ci: add uv.lock for reproducible CI builds

f7e40b2

gemini-code-assist bot reviewed Jan 7, 2026

View reviewed changes

pyproject.toml Outdated Show resolved Hide resolved

lispandfound added 8 commits January 8, 2026 09:56

build: add MANIFEST.in to exclude tests, .github, wiki, and uv.lock

1915827

tests: remove broken distributions test

3dd1038

fix: revert test_coordinates to remove_old_functions

8fb33b7

fix: revert test_geo.py to remove_old_functions

6996c49

tests: remove broken tests

c56e4d9

fix: fix pyproject warnings

d628997

refactor: remove config and registry

bc53ed6

Merge branch 'remove_old_functions' into testing_infra_refactor

be54ea3

lispandfound requested a review from Copilot January 7, 2026 21:20

Copilot started reviewing on behalf of lispandfound January 7, 2026 21:20 View session

ci: remove ruff action for now

6ae2088

Copilot AI reviewed Jan 7, 2026

View reviewed changes

tests/test_shared.py Show resolved Hide resolved

tests/test_utils.py Show resolved Hide resolved

lispandfound added 2 commits January 8, 2026 14:08

tests: add missing test files

22fecb6

Revert "tests: add missing test files"

38ae553

This reverts commit 22fecb6.

lispandfound changed the base branch from remove_old_functions to master January 13, 2026 23:02

Merge branch 'master' into testing_infra_refactor

1e719ca

lispandfound requested review from AndrewRidden-Harper, claudio525, joelridden and sungeunbae January 20, 2026 03:38

joelridden approved these changes Jan 20, 2026

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Testing Refactor#363

Testing Refactor#363
lispandfound wants to merge 78 commits intomasterfrom
testing_infra_refactor

lispandfound commented Jan 7, 2026 •

edited

Loading

Uh oh!

gemini-code-assist bot commented Jan 7, 2026

Uh oh!

gemini-code-assist bot left a comment

Uh oh!

Uh oh!

lispandfound commented Jan 7, 2026

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

lispandfound commented Jan 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

gemini-code-assist bot commented Jan 7, 2026

Summary of Changes

Highlights

Footnotes

Uh oh!

gemini-code-assist bot left a comment

Choose a reason for hiding this comment

Code Review

Uh oh!

Uh oh!

lispandfound commented Jan 7, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

lispandfound commented Jan 7, 2026 •

edited

Loading