Add GitHub native code coverage reporting

[Copilot]

Set up code coverage uploads to GitHub's Code Quality API via actions/upload-code-coverage@v1, so coverage results appear directly on pull requests.

Changes

• Coverage generation expanded to PRs — --cov flags now run on all ubuntu-latest matrix entries (not just main pushes), giving GitHub both a baseline and per-PR comparison
• Added actions/upload-code-coverage@v1 step (pinned to 82c7aee) uploading coverage.xml as code-coverage/pytest with language Python
• Added code-quality: write permission to test-code job
• Checkout uses PR head SHA (ref: ${{ github.event.pull_request.head.sha || github.sha }}) so coverage line numbers map correctly to diffs
• Fork PRs are skipped gracefully via the standard guard condition

Existing coverage badge generation and HTML artifact upload for main are unchanged.

Summary by Sourcery

Enable uploading Python test coverage reports to GitHub’s Code Quality API from CI.

CI:

• Expand pytest coverage collection to all ubuntu-latest matrix runs instead of only main pushes.
• Upload coverage.xml via actions/upload-code-coverage with appropriate label and language for GitHub-native coverage reporting.
• Add code-quality: write and contents: read permissions and check out the PR head SHA to align coverage with diffs.
• Skip coverage upload for forked pull requests to avoid permission issues.

[sourcery-ai]

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

Adds GitHub-native code coverage reporting for pytest runs by extending coverage generation to all ubuntu-latest matrix entries and uploading coverage.xml via actions/upload-code-coverage, with appropriate permissions and checkout ref adjustments so coverage maps correctly to PR diffs while preserving existing main-branch coverage artifacts and badges.

File-Level Changes

Change	Details	Files
Extend pytest coverage generation to all ubuntu-latest matrix runs instead of only main-branch pushes.	Modify just test command to always add --cov and coverage XML/HTML reports on ubuntu-latest matrix entries, regardless of branch. Retain non-coverage test execution behavior for non-ubuntu matrix operating systems.	.github/workflows/test.yml
Integrate GitHub Code Quality coverage uploads using actions/upload-code-coverage with appropriate conditions and metadata.	Add Upload code coverage to GitHub job step gated to ubuntu-latest matrix runs and non-fork PRs. Configure upload-code-coverage action with coverage.xml, language Python, and label code-coverage/pytest. Pin upload-code-coverage action to a specific commit hash for reproducibility.	.github/workflows/test.yml
Adjust workflow permissions and checkout ref so coverage data can be written to Code Quality and aligned with PR diffs.	Add contents: read and code-quality: write permissions to the test-code job. Update actions/checkout configuration to use the PR head SHA (or default github.sha) as the ref to align coverage with the diff being tested.	.github/workflows/test.yml
Preserve existing main-branch coverage badge generation and HTML artifact behavior.	Keep Generate coverage badge step conditioned on main branch and ubuntu-latest, still using coverage.xml for badge generation and HTML coverage output. Ensure new coverage upload step does not alter or bypass existing artifact and badge generation logic for main.	.github/workflows/test.yml

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[sourcery-ai]

Hey - I've reviewed your changes and they look great!

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[github-code-quality]

Code Coverage Overview

Languages: Python

Python / code-coverage/pytest

The overall coverage in the copilot/set-up-code-... branch is 90%. Coverage data for the main branch is not yet available.

Show a code coverage summary of the most covered files.

File	main	copilot/set-up-code-... f78a95d	+/-
utils.py	—	100%	—
cells/transmon.py	—	100%	—
tech.py	—	100%	—
models/waveguides.py	—	100%	—
models/qubit.py	—	100%	—
cells/waveguides.py	—	100%	—
cells/capacitor.py	—	99%	—
cells/unimon.py	—	98%	—
cells/resonator.py	—	97%	—
cells/inductor.py	—	93%	—

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_{Updated July 01, 2026 10:56 UTC
Code Coverage is in Public Preview. Learn more and provide us with your feedback.}

[nikosavola]

@copilot Please fix the pre-commit hooks for this PR

[Copilot]

@copilot Please fix the pre-commit hooks for this PR

Fixed in 2nd commit. The issues were:

1. actionlint didn't recognize the code-quality permission scope (too new). Moved the coverage upload into a dedicated upload-coverage job and added .github/actionlint.yaml with an ignore rule for that scope.
2. zizmor ref-version-mismatch warnings on actions/checkout (v6 → v6.0.2) and xu-cheng/latex-action (v4.0.0 → 4.1.0) — fixed the version comments across all affected workflows.

All pre-commit hooks now pass cleanly.