test: add unit tests for Variant, ReferenceMapping, Haplotype, and _parse_pop_freqs

[ameynert]

Extends test_remap_divref.py with direct tests for the model methods and private helper that were previously only exercised indirectly via reference_mapping():

• Variant.render(): SNP, insertion, deletion
• Haplotype.parsed_variants(): single variant, multiple variants, caching (second call returns same list object)
• Haplotype.contig(): returns chromosome of first variant
• ReferenceMapping.variants_involved_str(): empty, single, multiple
• _parse_pop_freqs(): all floats, mixed nulls, single null

Summary by CodeRabbit

Tests

• Expanded test coverage for variant parsing, formatting, and helper functions
• Added tests for variant rendering formats, haplotype parsing with caching verification, population frequency parsing, and error handling for malformed input

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

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Reviewing files that changed from the base of the PR and between 0a3aef2 and 32993fe.

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• divref/tests/tools/test_remap_divref.py

🚧 Files skipped from review as they are similar to previous changes (1)

• divref/tests/tools/test_remap_divref.py

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📝 Walkthrough

Walkthrough

This pull request adds comprehensive unit tests for the remap_divref module, covering functionality for variant rendering, haplotype parsing, reference mapping operations, and population frequency parsing. The test module docstring was updated and new test cases were added with appropriate imports.

Changes

Cohort / File(s)	Summary
Test Module Updates divref/tests/tools/test_remap_divref.py	Updated module docstring to reflect remap_divref coverage; added imports for pytest, Variant, and _parse_pop_freqs; added six unit test functions covering variant rendering, haplotype variant parsing and caching, contig extraction, reference mapping string formatting, population frequency parsing, and error handling for malformed variant input.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• feat: add remap_divref tool #12: Introduces the remap_divref tool with Variant, Haplotype, ReferenceMapping, and _parse_pop_freqs implementations that are directly tested by the new unit tests in this PR.

Poem

🐰 Whiskers twitch with testing pride,
Methods now have tests inside,
Variants parse and frequencies flow,
Coverage blooms—our code's aglow! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 5.56% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and specifically describes the main change: adding unit tests for four key components (Variant, ReferenceMapping, Haplotype, _parse_pop_freqs), which directly matches the changeset that adds comprehensive test coverage for these entities.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch am_15_test_remap_divref_models

---

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[coderabbitai]

🧹 Nitpick comments (1)

divref/tests/tools/test_remap_divref.py (1)

191-217: Add one explicit error-path test for parsing/contig edge inputs.

This block has strong happy-path coverage, but it should also lock behavior for malformed or empty variant strings (e.g., invalid delimiter count), especially since contig() depends on parsed output indexing.

🧪 Suggested test additions

+import pytest
+
+def test_parsed_variants_malformed_variant_raises() -> None:
+    hap = create_haplotype(variants="chr1:100:A", n_variants=1)
+    with pytest.raises(ValueError):
+        hap.parsed_variants()
+
+
+def test_contig_with_malformed_variant_raises() -> None:
+    hap = create_haplotype(variants="chr1:100:A", n_variants=1)
+    with pytest.raises(ValueError):
+        hap.contig()

As per coding guidelines, "**/*.py: New public functions require at least one happy-path test + one error case; bug fixes should include regression test".

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@divref/tests/tools/test_remap_divref.py` around lines 191 - 217, Add a
failing-input unit test that verifies parsing and contig() handle malformed or
empty variant strings: use create_haplotype with variants="" and with a
malformed entry like "chr1:100:A" (wrong delimiter count) and assert
parsed_variants() raises the expected exception or returns an empty list (match
project behavior), and that contig() either raises the same error or returns
None/empty string accordingly; reference the parsed_variants() and contig()
methods to locate the parsing logic and ensure the test asserts the explicit
error-path contract expected by the codebase.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@divref/tests/tools/test_remap_divref.py`:
- Around line 191-217: Add a failing-input unit test that verifies parsing and
contig() handle malformed or empty variant strings: use create_haplotype with
variants="" and with a malformed entry like "chr1:100:A" (wrong delimiter count)
and assert parsed_variants() raises the expected exception or returns an empty
list (match project behavior), and that contig() either raises the same error or
returns None/empty string accordingly; reference the parsed_variants() and
contig() methods to locate the parsing logic and ensure the test asserts the
explicit error-path contract expected by the codebase.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

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Run ID: d97de64f-d5ec-4df6-b55f-f88044aff736

📥 Commits

Reviewing files that changed from the base of the PR and between 57fd3ea and 0a3aef2.

📒 Files selected for processing (1)

• divref/tests/tools/test_remap_divref.py