fix: subtyping_report.py edge cases

[peterk87]

This PR fixes #134

• fix: subtyping_report.py edge cases when HA/NA segments are absent or IAV contamination skews genus detection ([BUG]: Edge cases affecting the suptyping_report.py #134)
• test: add nf-test for subtyping_report.nf covering missing HA/NA segments and IBV/IAV contamination ([BUG]: Edge cases affecting the suptyping_report.py #134)
• dev: add pytest job to CI (via uv) and tests/requirements.txt for bin script unit tests

[Copilot]

Pull request overview

This PR addresses reported edge cases in bin/subtyping_report.py around missing HA/NA segments and improves robustness against IAV contamination skewing genus detection, while adding automated coverage via nf-test and pytest and wiring those tests into CI.

Changes:

• Update subtyping_report.py to (a) always populate H/N result columns even when segments are missing and (b) determine genus via segment-level voting to reduce contamination bias.
• Add nf-test coverage for missing HA/NA segments and IBV-with-IAV-contamination scenarios; add pytest unit tests for key helper logic.
• Add a pytest job to CI (via uv) and expand .gitignore to cover common Nextflow, nf-test, and Python artifacts.

Reviewed changes

Copilot reviewed 10 out of 14 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
bin/subtyping_report.py	Implements genus voting changes and missing-segment handling; refactors typing annotations and result table column handling.
tests/bin/test_subtyping_report.py	Adds unit tests for genus voting, missing-segment behavior, and result column reindexing.
tests/modules/local/subtyping_report.nf.test	Adds nf-test coverage for HA/NA missing inputs and contamination scenario.
tests/modules/local/subtyping_report.nf.test.snap	Stores nf-test snapshots for the added module tests.
tests/nextflow.config	Ensures bin/ is on PATH for SUBTYPING_REPORT during nf-test runs.
tests/requirements.txt	Adds a dedicated dependency set for running pytest against bin scripts.
tests/data/subtyping_report/flu_metadata.csv	Provides metadata fixtures for nf-test scenarios.
tests/data/subtyping_report/blastn_results/*	Provides BLAST fixtures for missing-segment and contamination scenarios.
tests/data/subtyping_report/vadr_outdirs/.gitkeep	Placeholder to stage an empty VADR directory in tests.
.github/workflows/ci.yml	Adds a pytest job and updates caches/artifact actions; updates Nextflow matrix latest version.
.github/workflows/linting.yml	Updates GitHub Actions versions used by markdown linting.
.gitignore	Expands ignores for Nextflow/nf-test/Python/IDE outputs while keeping tests/data/ tracked.
CHANGELOG.md	Adds an Unreleased entry describing the bugfixes and new tests/CI updates.

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