[alpae]

Step 1 of the bug list in #124: small fixes that don't change the inferred HOGs. One commit per issue.

#122: small internal bugs

• UnionFind: takes over the fixed version from zoo.
  • remove() of a set's root, or of an element that others still point to, no longer breaks find().
  • union() counts a shared root's weight only once.
  • The identical copy of the class in _utils_roothog.py is removed; it shadowed the import.
• Representative: Representative(rep, elements) copies rep's sets instead of extending them in place.
• HOG class:
  • find_representative() uses get_subelements() instead of the non-existent get_members().
  • A merged HOG without representatives raises a clear ValueError; the default argument was a typing object.
• batch_roothogs: rejects rootHOG files with the same name in different subfolders instead of letting them overwrite each other.
• Pairwise relations: an empty orthologGroup no longer crashes set.union().
• prepare_species_tree: returns the species leaf for a single-species rootHOG. Output is unchanged: such rootHOGs still produce no group.
• copy_tree: the dead feature-collecting loop is removed (its set.union() result was discarded), and the docstring now says what the newick copy keeps. The output is identical.

#118: input validation

• Input folders:
  • Hidden files are ignored, e.g. the ._<name> AppleDouble files of macOS archives or .DS_Store. check-input and parse_proteomes share list_proteome_files(), so both agree on what a proteome is.
  • Files without an extension no longer crash parse_proteomes.
  • Species names taken from hogmap files keep their dots.
  • An empty proteome is reported as invalid instead of raising ZeroDivisionError.
• Species tree:
  • Duplicate internal node names are reported.
  • Trees without internal nodes no longer raise UnboundLocalError.
  • Internal node names are replaced by internal_<n> if they are empty or shorter than 3 characters after removing special characters, or if they equal a leaf name. Generated names never clash with existing ones. The checked tree of testdata is unchanged.
  • An unreadable species tree exits with status 1 instead of 0.
• Splice files: single-line splice files are no longer ignored by check_splice.

#123: report without CompletenessScore

• The four report cells that plot CompletenessScore now check that the column exists.
• The options nf-test now disables all three scores and checks that report.html is still produced.

Tests

• The 18 strict xfails of these issues pass and their markers are removed; some characterisation tests are updated to the new behaviour.
• New tests:
  • UnionFind edge cases, including the union weight bug;
  • internal-node renaming edge cases;
  • exit status of an unreadable species tree;
  • a merged HOG without representatives.
• Locally:
  • fast pytest suite green: 339 passed, 11 skipped (fungi-30 golden tests, tool versions differ locally), 26 xfailed;
  • nf-tests/options.nf.test green.
• No golden snapshot changes.

Fixes #118
Fixes #122
Fixes #123

🤖 Generated with Claude Code

[Copilot]

🟡 Changes recommended

The node-name allocator can move an existing taxonomic label to a different clade, and hidden FASTA files remain eligible for downstream omamer processing.

2 open issues

• Exclude hidden FASTA files from the proteomes channel · New
• Generated names can overwrite labels on unvisited internal nodes · New

What changed in this PR

This PR addresses internal helper bugs, input-validation failures, and reporting without CompletenessScore, as part of the pre-ete4 migration cleanup. It is intended to preserve inferred HOGs and existing golden snapshots.

Changes:

• Fix UnionFind, representative handling, rootHOG batching, and tree/XML helper edge cases.
• Improve input filtering, species-tree validation, and error handling.
• Guard optional-score plots and expand regression coverage.

File	Description
tests/​test_unionfind.py	Cover removal, shared-root weights, and use of the shared implementation.
tests/​test_species_tree_prep.py	Verify single-species trees and failure exit codes.
tests/​test_roothog_io.py	Enable hidden-file and extension-handling regression tests.
tests/​test_report_contract.py	Enable checks for guarded completeness plots.
tests/​test_pairwise_relations.py	Enable empty-group regression coverage.
tests/​test_hog_class.py	Verify representative copying, lookup, and required arguments.
tests/​test_check_input.py	Expand input-validation and node-renaming coverage.
tests/​test_batch_roothogs.py	Require rejection of duplicate rootHOG filenames.
nf-tests/​options.nf.test	Check report generation with all scores disabled.
FastOMA/​zoo/​unionfind.py	Repair removal and avoid double-counting shared roots.
FastOMA/​zoo/​hog/​transform.py	Handle empty ortholog groups.
FastOMA/​fastoma_notebook_stat.ipynb	Guard four optional completeness-score plots.
FastOMA/​check_input.py	Improve file filtering, validation, and internal-node naming.
FastOMA/​batch_roothogs.py	Reject filename collisions before batching.
FastOMA/​_utils_subhog.py	Correct tree-read exit codes and single-species selection.
FastOMA/​_utils_roothog.py	Share proteome discovery and remove duplicate UnionFind code.
FastOMA/​_infer_subhog.py	Remove ineffective feature collection and clarify copy semantics.
FastOMA/​_hog_class.py	Fix representative copying, lookup, and constructor defaults.

_{Review effort: Balanced}

[Copilot]

🟢 Approval recommended

No active review issues are recorded for the input-validation, helper, and reporting fixes.

1 open issue

• Exclude hidden FASTA files from the proteomes channel

1 resolved since last review

• Generated names can overwrite labels on unvisited internal nodes

_{Review effort: Balanced}