Restore gff3 chromosome name aliasing (2.1.2)

[YalanBi]

Summary

Closes #36: _read_gff_file no longer resolved chromosome name aliases (e.g. RefSeq accessions like NC_000001.11 vs a plain 1/chr1 genome FASTA) since the tabix-based get_gff_chrom_dict helper was removed to fix #28. Genes on such files were silently dropped with no warning when filtering against the genome's chromosome names.

Restored by recognizing region-type feature lines with a chromosome attribute during the same single sequential pass already used for parsing. No tabix/index requirement reintroduced, no second pass added.

CI: bumped every GitHub Action across all 5 workflows to their current major version (checkout v4->v7, setup-python v5->v7, dependency-review-action v4->v5.0.0, codeql-action v3->v4), and added build-check.yml (python -m build + twine check on PRs). No CHANGELOG/version bump for this part -- CI-only, no effect on the installed package.

Test plan

• Full pytest suite passes (22 passed), including a new regression test with a minimal RefSeq-style fixture
• Verified the new test reproduces the original silent-drop bug against the pre-fix code
• Verified via a fresh independent clone of the pushed branch
• Confirmed no conflict with Trouble while working with .csi indexes #28 (no tabix/.tbi reintroduced) or GFF/GTF import reads the file twice for the progress bar #37 (still single-pass)
• flake8/black clean
• python -m build + twine check dist/* pass at 2.1.2
• Validated all workflow YAML files parse correctly after the action bumps
• CI green across the full matrix (watch after pushing)

[github-actions]

Dependency Review

The following issues were found:

• ✅ 0 vulnerable package(s)
• ✅ 0 package(s) with incompatible licenses
• ✅ 0 package(s) with invalid SPDX license definitions
• ⚠️ 3 package(s) with unknown licenses.

See the Details below.

License Issues

.github/workflows/lint.yml

Package	Version	License	Issue Type
actions/checkout	7.*.*	Null	Unknown License

.github/workflows/tests.yml

Package	Version	License	Issue Type
actions/checkout	7.*.*	Null	Unknown License
actions/setup-python	7.*.*	Null	Unknown License

OpenSSF Scorecard

Package	Version	Score	Details
actions/actions/checkout	7.*.*	🟢 6.9	Details Check Score Reason Binary-Artifacts 🟢 10 no binaries found in the repo Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 24 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Fuzzing ⚠️ 0 project is not fuzzed Packaging ⚠️ -1 packaging workflow not detected License 🟢 10 license file detected Pinned-Dependencies 🟢 3 dependency not pinned by hash detected -- score normalized to 3 Signed-Releases ⚠️ -1 no releases found Security-Policy 🟢 9 security policy file detected SAST 🟢 10 SAST tool is run on all commits Branch-Protection 🟢 5 branch protection is not maximal on development and all release branches
actions/actions/checkout	7.*.*	🟢 6.9	Details Check Score Reason Binary-Artifacts 🟢 10 no binaries found in the repo Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 24 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Fuzzing ⚠️ 0 project is not fuzzed Packaging ⚠️ -1 packaging workflow not detected License 🟢 10 license file detected Pinned-Dependencies 🟢 3 dependency not pinned by hash detected -- score normalized to 3 Signed-Releases ⚠️ -1 no releases found Security-Policy 🟢 9 security policy file detected SAST 🟢 10 SAST tool is run on all commits Branch-Protection 🟢 5 branch protection is not maximal on development and all release branches
actions/actions/setup-python	7.*.*	🟢 6.6	Details Check Score Reason Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 17 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Binary-Artifacts 🟢 10 no binaries found in the repo Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Packaging ⚠️ -1 packaging workflow not detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Pinned-Dependencies 🟢 7 dependency not pinned by hash detected -- score normalized to 7 License 🟢 10 license file detected Fuzzing ⚠️ 0 project is not fuzzed Signed-Releases ⚠️ -1 no releases found Security-Policy 🟢 9 security policy file detected Branch-Protection ⚠️ 0 branch protection not enabled on development/release branches SAST 🟢 9 SAST tool is not run on all commits -- score normalized to 9

Scanned Files

• .github/workflows/lint.yml
• .github/workflows/tests.yml