refactor(clip): use ClippingMode enum instead of String for --clipping-mode

[nh13]

Summary

• Derive clap::ValueEnum on the existing ClippingMode enum so that clap validates the --clipping-mode argument at parse time instead of at runtime
• Remove two manual match self.clipping_mode.as_str() blocks in clip.rs (one in execute(), one in the pipeline closure)
• Change clipping_mode field type from String to ClippingMode in the Clip CLI struct
• Add Display impl on ClippingMode for the info log line
• Remove the now-unnecessary test_clip_execute_invalid_clipping_mode test (invalid values are rejected by clap at parse time)

Test plan

• cargo ci-fmt passes
• cargo ci-lint passes
• cargo nextest run --no-fail-fast — 1734 tests pass, 7 skipped
• Verify fgumi clip --help shows the valid values for --clipping-mode
• Verify fgumi clip --clipping-mode invalid ... is rejected by clap with a helpful error

[codecov]

Codecov Report

❌ Patch coverage is 98.11321% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 88.06%. Comparing base (f13e78b) to head (850b2ad).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/commands/clip.rs	98.11%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #218      +/-   ##
==========================================
- Coverage   88.07%   88.06%   -0.02%     
==========================================
  Files         113      113              
  Lines       52863    52816      -47     
==========================================
- Hits        46561    46511      -50     
- Misses       6302     6305       +3     

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[coderabbitai]

📝 Walkthrough

Walkthrough

The changes add clap v4 as a dependency and refactor clipping mode handling from string-based to enum-based. The ClippingMode enum now derives clap::ValueEnum, implements Display, and includes a custom CLI value name mapping for SoftWithMask. The Clip command struct's clipping_mode field transitions from String to ClippingMode, replacing string validation and parsing logic with direct enum usage. Tests are updated to use enum variants instead of string literals, and invalid mode tests are removed.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly and concisely describes the main refactor: moving from String to ClippingMode enum for the --clipping-mode argument.
Description check	✅ Passed	Description is directly relevant, detailing the specific changes made, rationale, and test plan for the clipping mode enum refactor.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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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 nh/refactor-clipping-mode-enum

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[coderabbitai]

🧹 Nitpick comments (1)

src/commands/clip.rs (1)

1081-1108: Parameterize the enum-mode test with rstest.

This test currently checks one case and is a good fit for rstest cases over all variants.

♻️ Suggested refactor

-    #[test]
-    fn test_clipping_mode_enum_values() {
-        // Test that clipping_mode enum variants are set properly
-        let soft = Clip {
+    #[rstest]
+    #[case(ClippingMode::Soft)]
+    #[case(ClippingMode::SoftWithMask)]
+    #[case(ClippingMode::Hard)]
+    fn test_clipping_mode_enum_values(#[case] mode: ClippingMode) {
+        let clip = Clip {
             io: BamIoOptions {
                 input: PathBuf::from("input.bam"),
                 output: PathBuf::from("output.bam"),
             },
             reference: PathBuf::from("reference.fa"),
-            clipping_mode: ClippingMode::Soft,
+            clipping_mode: mode,
             clip_overlapping_reads: true,
             clip_extending_past_mate: false,
@@
             scheduler_opts: SchedulerOptions::default(),
             queue_memory: QueueMemoryOptions::default(),
         };
 
-        assert_eq!(soft.clipping_mode, ClippingMode::Soft);
+        assert_eq!(clip.clipping_mode, mode);
     }

As per coding guidelines "**/*.rs: Use rstest for parameterized tests".

🤖 Prompt for AI Agents

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

In `@src/commands/clip.rs` around lines 1081 - 1108, Replace the single-case
test_clipping_mode_enum_values with an rstest-parameterized test: add the
#[rstest] attribute (and import rstest::rstest) and change the function
signature to accept a clipping_mode: ClippingMode parameter with a #[case(...)]
for each ClippingMode variant; inside the test construct the Clip using that
clipping_mode (same construction as before) and assert_eq!(clipping_mode,
clip.clipping_mode). Keep the test name (test_clipping_mode_enum_values) and
reference the Clip struct and ClippingMode enum so the IDE can locate the code.

🤖 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/clip.rs`:
- Around line 1081-1108: Replace the single-case test_clipping_mode_enum_values
with an rstest-parameterized test: add the #[rstest] attribute (and import
rstest::rstest) and change the function signature to accept a clipping_mode:
ClippingMode parameter with a #[case(...)] for each ClippingMode variant; inside
the test construct the Clip using that clipping_mode (same construction as
before) and assert_eq!(clipping_mode, clip.clipping_mode). Keep the test name
(test_clipping_mode_enum_values) and reference the Clip struct and ClippingMode
enum so the IDE can locate the code.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: eecbaf1d-a2b4-4854-932b-02fd7e34f098

📥 Commits

Reviewing files that changed from the base of the PR and between f13e78b and 850b2ad.

⛔ Files ignored due to path filters (1)

• Cargo.lock is excluded by !**/*.lock

📒 Files selected for processing (3)

• crates/fgumi-sam/Cargo.toml
• crates/fgumi-sam/src/clipper.rs
• src/commands/clip.rs