refactor: replace all unwrap() calls in src/commands/ with expect()

[nh13]

Summary

• Audit and replace all 527 unwrap() calls across 27 files in src/commands/
• Production code (22 calls): converted to expect() with invariant-documenting messages explaining why the unwrap is safe
• Test code (505 calls): converted to expect() with context-specific failure messages for better diagnostics
• Zero unwrap() calls remain in src/commands/

Test plan

• cargo ci-test — all 2,213 tests pass
• cargo ci-fmt — formatting clean
• cargo ci-lint — no warnings

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 9c80e7cd-4b06-4618-81bd-493b275da753

📥 Commits

Reviewing files that changed from the base of the PR and between 9abaf50 and a2ac65f.

📒 Files selected for processing (27)

• src/commands/clip.rs
• src/commands/codec.rs
• src/commands/common.rs
• src/commands/compare/bams.rs
• src/commands/compare/raw_compare.rs
• src/commands/consensus_runner.rs
• src/commands/correct.rs
• src/commands/dedup.rs
• src/commands/downsample.rs
• src/commands/duplex.rs
• src/commands/duplex_metrics.rs
• src/commands/extract.rs
• src/commands/fastq.rs
• src/commands/filter.rs
• src/commands/group.rs
• src/commands/merge.rs
• src/commands/review.rs
• src/commands/shared_metrics.rs
• src/commands/simplex.rs
• src/commands/simplex_metrics.rs
• src/commands/simulate/common.rs
• src/commands/simulate/correct_reads.rs
• src/commands/simulate/fastq_reads.rs
• src/commands/simulate/grouped_reads.rs
• src/commands/simulate/mapped_reads.rs
• src/commands/sort.rs
• src/commands/zipper.rs

📝 Walkthrough

Walkthrough

This pull request systematically replaces .unwrap() calls with .expect(...) calls across numerous test files and a few production code paths. The changes affect approximately 25 files, adding explicit failure messages to result extraction operations on optional values, temporary file creation, BAM/FASTA file I/O, header construction, and tag parsing. No public API signatures or functional behavior are modified—only error handling and panic messaging are enhanced to aid debugging when tests fail or unexpected None values are encountered.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: a refactoring that replaces all unwrap() calls in src/commands/ with expect().
Description check	✅ Passed	The description is directly related to the changeset, clearly summarizing the scope (527 calls across 27 files), breakdown (22 production, 505 test), and verification (all tests pass).
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch nh/unwrap-audit-commands

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[codecov]

Codecov Report

❌ Patch coverage is 99.63325% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.94%. Comparing base (0ee001f) to head (a2ac65f).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/commands/downsample.rs	90.47%	2 Missing ⚠️
src/commands/simulate/mapped_reads.rs	85.71%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #224      +/-   ##
==========================================
+ Coverage   88.88%   88.94%   +0.05%     
==========================================
  Files         113      113              
  Lines       53521    53807     +286     
==========================================
+ Hits        47574    47856     +282     
- Misses       5947     5951       +4     

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[nh13]

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[coderabbitai]

🧹 Nitpick comments (1)

src/commands/simulate/common.rs (1)

655-657: Message overstates what this test validates.

Line 655 only tests "lognormal" lowercase, but the expect text says case-insensitive acceptance. Either adjust the message to lowercase-specific behavior or add an uppercase case in this test.

Suggested minimal fix

-            .expect("case-insensitive distribution name should be accepted");
+            .expect("lowercase distribution name should be accepted");

🤖 Prompt for AI Agents

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

In `@src/commands/simulate/common.rs` around lines 655 - 657, The test message
overclaims case-insensitivity for to_family_size_distribution(): either change
the expect() text to only refer to the lowercase input (e.g., "lowercase
distribution name should be accepted") or add an explicit uppercase test by
creating an args_upper (e.g., with "LogNormal" or "LOGNORMAL") and calling
to_family_size_distribution() on it and expecting success; update the
assertion(s) around args_lower and/or add the args_upper assertion so the test
name accurately matches the behavior of to_family_size_distribution().

🤖 Prompt for all review comments with AI agents

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

Nitpick comments:
In `@src/commands/simulate/common.rs`:
- Around line 655-657: The test message overclaims case-insensitivity for
to_family_size_distribution(): either change the expect() text to only refer to
the lowercase input (e.g., "lowercase distribution name should be accepted") or
add an explicit uppercase test by creating an args_upper (e.g., with "LogNormal"
or "LOGNORMAL") and calling to_family_size_distribution() on it and expecting
success; update the assertion(s) around args_lower and/or add the args_upper
assertion so the test name accurately matches the behavior of
to_family_size_distribution().

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 16513140-0445-45c4-b033-9e75eaf1ecd0

📥 Commits

Reviewing files that changed from the base of the PR and between ea6e3fc and 9abaf50.

📒 Files selected for processing (27)

• src/commands/clip.rs
• src/commands/codec.rs
• src/commands/common.rs
• src/commands/compare/bams.rs
• src/commands/compare/raw_compare.rs
• src/commands/consensus_runner.rs
• src/commands/correct.rs
• src/commands/dedup.rs
• src/commands/downsample.rs
• src/commands/duplex.rs
• src/commands/duplex_metrics.rs
• src/commands/extract.rs
• src/commands/fastq.rs
• src/commands/filter.rs
• src/commands/group.rs
• src/commands/merge.rs
• src/commands/review.rs
• src/commands/shared_metrics.rs
• src/commands/simplex.rs
• src/commands/simplex_metrics.rs
• src/commands/simulate/common.rs
• src/commands/simulate/correct_reads.rs
• src/commands/simulate/fastq_reads.rs
• src/commands/simulate/grouped_reads.rs
• src/commands/simulate/mapped_reads.rs
• src/commands/sort.rs
• src/commands/zipper.rs