Fix TypeError in check_files SPC level-of-theory validation

[bobbypaton]

Fixes #111

Problem

Combining --check with --spc <suffix> crashed:

File "goodvibes/validation.py", line 330, in check_files
    l_o_t_spc = [level_of_theory(name) for name in names_spc]
TypeError: 'list' object is not callable

check_files() takes level_of_theory as a list of per-file strings, but the SPC-validation branch still contained a call from before the refactor, when io.level_of_theory (a file parser) was imported at module level. The list parameter shadowed the function name. Not Windows-specific — reproduces on any platform.

Fix

• Import the parser as read_level_of_theory (aliased so the parameter no longer shadows it) and use it to read each SPC file's level of theory — the correct behavior, since the parameter only holds the freq-level strings.
• On the mismatch path, pass names_spc (the SPC filenames) to print_check_fails instead of the parent filenames, so groups are attributed correctly when an SPC file is missing.

Testing

• Reproduced the crash with goodvibes ethane.out --spc TZ --check; after the fix the run completes and reports Using B3LYP/6-311G(d,p) in all the single-point corrections (the TZ single-point level, distinct from the B3LYP/6-31G(d) freq level).
• Added regression test test_check_files_spc_reads_spc_level_of_theory.
• Full suite: 2512 passed; ruff clean.

Summary by CodeRabbit

• Bug Fixes
  • Corrected single-point correction validation so the level of theory is derived from the single-point (SPC) data files.
  • Improved mismatch reporting to reference the relevant SPC files when discrepancies are detected.
  • When SPC files are missing, the validation now logs a caution instead of failing the “levels of theory” check.
• Tests
  • Added regression coverage for SPC level-of-theory reading and for missing-SPC handling.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

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📒 Files selected for processing (2)

• goodvibes/validation.py
• tests/test_validation.py

🚧 Files skipped from review as they are similar to previous changes (2)

• tests/test_validation.py
• goodvibes/validation.py

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📝 Walkthrough

Walkthrough

goodvibes/validation.py now re-reads SPC level-of-theory values from the SPC files themselves during check_files, uses SPC filenames in mismatch reporting, and logs a caution when SPC files are missing. tests/test_validation.py adds regression coverage for both the SPC-derived level-of-theory message and the missing-file path.

Changes

SPC level-of-theory validation fix

Layer / File(s)	Summary
SPC level-of-theory re-read and reporting fix goodvibes/validation.py	Imports read_level_of_theory alias and uses it to recompute SPC level-of-theory per file instead of the passed-in parameter; reports mismatches using names_spc and logs a missing-file caution.
SPC validation regression tests tests/test_validation.py	Adds imports for ThermoOptions and datapath, plus tests covering the SPC-derived level-of-theory message and the missing SPC file caution path.

Estimated code review effort: 2 (Simple) | ~10 minutes

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly matches the main change: fixing the SPC validation TypeError in check_files.
Linked Issues check	✅ Passed	The fix addresses #111 by stopping check_files from calling a list as a function during --check with --spc, and regression tests cover the crash path.
Out of Scope Changes check	✅ Passed	The changes stay focused on SPC validation and its regression tests, with no unrelated functionality added.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

✨ Finishing Touches

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• Commit unit tests in branch fix/check-spc-lot

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

goodvibes/validation.py (1)

355-360: 🚀 Performance & Scalability | 🔵 Trivial | ⚡ Quick win

Avoid reading each SPC file twice. level_of_theory(name) and parse_qcdata(name) both reopen the same SPC file; if SPC validation needs both the level and geometry, surface the level of theory from parse_qcdata (or combine the two parsers) so each file is read once.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@goodvibes/validation.py` around lines 355 - 360, The SPC duplicate-check loop
currently reads each file twice via level_of_theory(name) and
parse_qcdata(name), so update the validation flow to reuse a single parse per
file. Adjust parse_qcdata or its caller in the SPC handling path to return the
level of theory alongside cartesians, then have the logic that builds
geom_duplic_list_spc consume that combined result instead of reopening each SPC
file.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@goodvibes/validation.py`:
- Around line 330-336: Guard the SPC level-of-theory check in validation logic
so it only reports success when the SPC file list is complete and non-empty. In
the `l_o_t_spc` / `all_same` branch, add the same kind of length check used by
the geometry block before accessing `l_o_t_spc[0]`, and route empty or partial
`names_spc` cases to `print_check_fails` instead of logging the blanket success
message. This should be fixed in the SPC-reading section that uses
`read_level_of_theory`, `all_same`, and `print_check_fails`.

---

Nitpick comments:
In `@goodvibes/validation.py`:
- Around line 355-360: The SPC duplicate-check loop currently reads each file
twice via level_of_theory(name) and parse_qcdata(name), so update the validation
flow to reuse a single parse per file. Adjust parse_qcdata or its caller in the
SPC handling path to return the level of theory alongside cartesians, then have
the logic that builds geom_duplic_list_spc consume that combined result instead
of reopening each SPC file.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

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Configuration used: defaults

Review profile: CHILL

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Run ID: 3af0d489-fce8-487a-baf9-68650ba0a158

📥 Commits

Reviewing files that changed from the base of the PR and between a693b3c and 4c9b9d3.

📒 Files selected for processing (2)

• goodvibes/validation.py
• tests/test_validation.py

[bobbypaton]

fixed per suggestion from coderabbit