[Copilot]

IO failures (e.g., missing file/invalid path) were surfaced without consistently identifying which path failed, making troubleshooting harder. This change makes file-path context explicit across core read/write IO flows.

• Scope: path-aware IO errors

  • Added explicit map_err handling in src/io/mod.rs so Error::Io messages include the affected path for:
    • FASTA read (Reader::from_file)
    • FASTA write/create (Writer::to_file, write_record)
    • Newick read (fs::read_to_string)
    • Newick write/create (File::create, write_all)

• Behavioral coverage

  • Updated IO tests to assert path inclusion in error messages for missing/bad-path cases.
  • Added nonexistent Newick-read coverage mirroring FASTA missing-file behavior.

let newick = fs::read_to_string(&path).map_err(|err| {
    Error::Io(format!(
        "failed to read newick file {}: {err}",
        path.as_ref().display()
    ))
})?;

• Fixes Add file paths to io errors #169

[codecov]

Codecov Report

❌ Patch coverage is 90.00000% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.90%. Comparing base (527040d) to head (37132c4).
⚠️ Report is 44 commits behind head on develop.

Files with missing lines	Patch %	Lines
phyne/src/io/mod.rs	90.00%	3 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #207      +/-   ##
===========================================
+ Coverage    96.32%   96.90%   +0.58%     
===========================================
  Files           32       53      +21     
  Lines         4355     6564    +2209     
===========================================
+ Hits          4195     6361    +2166     
- Misses         160      203      +43     

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[github-actions]

Test Results

1 175 tests  +1   1 174 ✅ +1   29m 31s ⏱️ + 14m 42s
    5 suites ±0       1 💤 ±0 
    1 files   ±0       0 ❌ ±0 

Results for commit 37132c4. ± Comparison against base commit f76a766.

This pull request removes 3 and adds 4 tests. Note that renamed tests count towards both.

src/io/mod.rs - io ‑ read_newick_from_file (line 136)
src/io/mod.rs - io ‑ write_newick_to_file (line 160)
src/io/mod.rs - io ‑ write_sequences_to_file (line 88)

io::tests ‑ reading_nonexistent_newick
src/io/mod.rs - io ‑ read_newick_from_file (line 133)
src/io/mod.rs - io ‑ write_newick_to_file (line 159)
src/io/mod.rs - io ‑ write_sequences_to_file (line 81)

♻️ This comment has been updated with latest results.