Feature/coverage next 20260519

[ChrisChilders-USDA]

Expand test coverage, enforce artifact hygiene, update handoff

Summary

• Expanded test coverage in gff3.py, replace_OGS.py, gff3_sort.py, gff3_ID_generator.py
• Added/updated tests for parser edge cases, error paths, and ID generation
• Enforced artifact hygiene (no out_user_defined.fa, tests/init.py cleanup)
• All tests passing, coverage up to 69% (gff3.py 60%, replace_OGS.py 62%, gff3_sort.py 68%, gff3_ID_generator.py 82%)
• Created and populated docs/HANDOFF.md for seamless handoff/resume

Reviewers

• @ChrisChilders-USDA
• @github-copilot

Assisted-by

• Assisted-by: GitHub Copilot (GPT-5.4)

[codecov]

Codecov Report

❌ Patch coverage is 75.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 69.16%. Comparing base (e2e6bbd) to head (ebd7b9e).
⚠️ Report is 5 commits behind head on master.

Files with missing lines	Patch %	Lines
gff3tool/bin/gff3_to_fasta.py	75.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #146       +/-   ##
===========================================
+ Coverage   54.86%   69.16%   +14.30%     
===========================================
  Files          28       28               
  Lines        5313     5313               
===========================================
+ Hits         2915     3675      +760     
+ Misses       2398     1638      -760     

Files with missing lines	Coverage Δ
gff3tool/bin/gff3_to_fasta.py	51.96% <75.00%> (+8.54%)	⬆️

... and 6 files with indirect coverage changes

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[Copilot]

Pull request overview

This PR primarily expands unit-test coverage across core parsing/QC and CLI entrypoints, while also adjusting gff3_to_fasta argument-validation order to reduce unintended output artifacts during invalid invocations. It also adds a handoff document and a small test-run cleanup step.

Changes:

• Add/expand unit tests for parser edge cases, intra-model QC checks, replace logic, sorting behavior, and ID generation.
• Update gff3_to_fasta.main() to validate user_defined arguments before opening the output file.
• Add a handoff markdown file and extend tests.sh to remove a couple of local-run artifacts.

Reviewed changes

Copilot reviewed 10 out of 11 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
gff3tool/bin/gff3_to_fasta.py	Reorders validation vs. output-file creation to avoid creating output on invalid user_defined args.
tests/unit/test_gff3_to_fasta_cli.py	Adds coverage for CLI error paths and output formatting (pep/user_defined).
tests/unit/test_gff3_core.py	Adds parser/directive/reference/phase/IO edge-case coverage.
tests/unit/test_intra_model_engine.py	Adds coverage for intra-model QC error paths (redundant length, pseudo child type, distinct isoforms, internal stops).
tests/unit/test_replace_OGS.py	Adds tests for UTR generation and replacer behaviors; extends FakeGff test harness.
tests/unit/test_gff3_sort_functions.py	Adds coverage for PositionSort/StrandSort/TypeSort edge behavior.
tests/unit/test_gff3_sort_main.py	New tests covering gff3_sort.main() paths (sorting order, isoform sort, omitted lines, embedded FASTA).
tests/unit/test_gff3_id_generator.py	Adds coverage for main() exit conditions and UUID/non-UUID ID generation behavior.
tests/unit/test_gff3_fix_engine.py	Extends FakeGff surface and adds fix-engine behavior tests (boundary/remove/delete/pseudogene/components).
tests.sh	Adds post-run cleanup of a couple of local-run artifacts.
handoff/HANDOFF.md	Adds a session handoff document describing coverage work and next steps.

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[Copilot]

Updated in commit 2099a7b: HANDOFF.md is now located at docs/HANDOFF.md so the location matches the PR references.

[Copilot]

Pull request overview

Copilot reviewed 10 out of 11 changed files in this pull request and generated 2 comments.

[MonicaPoelchau-USDA]

I tested this branch on a separate test dataset - look good.