Fix s_create_directory called with /* wildcard creating junk directory

[sbryngelson]

User description

Summary

• Fix s_read_serial_ic_data_files in m_start_up.fpp calling s_create_directory with a /* suffix, which creates a literal directory named * instead of cleaning the output directory.

Bug Details

The code at line 508 calls:

call s_create_directory(trim(proc_rank_dir)//'/*')

The comment above says "cleaned out to make room for new pre-process data", but s_create_directory runs mkdir -p "path/*", which creates a directory literally named * inside proc_rank_dir. The intent was to remove old files to make room for new data.

The old data files happen to get overwritten by subsequent writes, so this doesn't cause crashes, but it leaves a junk * directory behind and doesn't actually clean old files that may no longer be relevant.

Fix

Replace the s_create_directory(path/*) call with s_delete_directory(path) to actually remove the old directory contents. The subsequent s_create_directory(path/0) uses mkdir -p so it recreates both the parent and the /0 subdirectory.

Test plan

• Serial pre-process restart (old_ic) cases still work
• No * directory created in process rank directories

🤖 Generated with Claude Code

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CodeAnt-AI Description

Fix creation of a literal '*' directory when preparing per-rank pre-process folders

What Changed

• Removed the call that created a path ending with '/*' and replaced it with a call that deletes the existing rank directory before recreating the time-step subfolder
• The code now removes previous pre-process files instead of creating a literal '*' directory and then recreates the '/0' subdirectory for new data

Impact

✅ No leftover '*' directories in per-rank folders
✅ Old pre-process files are removed before new data is written
✅ More predictable serial pre-process restart behavior

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Summary by CodeRabbit

Release Notes

• Chores
  • Improved directory cleanup during initialization process to ensure consistent system state before starting operations.

Fixes #1220

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📝 Walkthrough

Walkthrough

Modified directory cleanup logic in the serial initial conditions data file reading function. Instead of deleting only directory contents, the entire proc_rank_dir directory is now removed before being recreated.

Changes

Cohort / File(s)	Summary
Directory Cleanup Logic src/pre_process/m_start_up.fpp	Changed post-data-read cleanup from deleting directory contents (trim(proc_rank_dir)//'/*') to deleting the entire directory (trim(proc_rank_dir)) before recreating the per-rank directory structure.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Poem

🐰 A directory's fate, now complete and whole,
Where once we trimmed the edges with care,
Now we clear the slate, reset the role,
Delete and rebuild, with methodical flair! ✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main bug fix: replacing a problematic s_create_directory call with /* wildcard that creates a junk '*' directory.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description check	✅ Passed	The pull request description provides clear context: it identifies the bug with s_create_directory being called with a /* suffix, explains the root cause (creating a literal * directory), describes the intended behavior, and provides the fix with a clear test plan. All key sections from the template are addressed.

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[codeant-ai]

Nitpicks 🔍

🔒 No security issues identified

⚡ Recommended areas for review Safety / accidental deletion risk Calling a delete routine on a computed path could accidentally remove the wrong directory if the path is empty, malformed, or outside the expected case directory. There is no guard in the new call to prevent accidental deletion of top-level or unrelated dirs. Assumed s_delete_directory semantics The fix assumes s_delete_directory removes the directory contents (or the whole dir) safely and that subsequent s_create_directory(trim(proc_rank_dir)//'/0') will recreate required parents. Confirm s_delete_directory behavior (recursive removal vs. removing only contents) to ensure the sequence produces the intended layout and does not leave a partially deleted state. Inconsistent wildcard usage The PR replaces a call that created a literal '' directory by calling s_delete_directory(trim(proc_rank_dir)) in s_read_serial_ic_data_files. However elsewhere the code still calls s_delete_directory(trim(proc_rank_dir)//'/') (in s_read_serial_grid_data_files). This inconsistency can leave the original problem present in other code paths or lead to different deletion semantics depending on how s_delete_directory is implemented.

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[Copilot]

Pull request overview

Fixes serial pre-process restart cleanup by removing an incorrect /* suffix that caused creation of a literal * directory instead of clearing old process-rank output.

Changes:

• Replace s_create_directory(proc_rank_dir//'/*') with s_delete_directory(proc_rank_dir) to properly remove prior output.
• Keep subsequent directory creation via s_create_directory(proc_rank_dir//'/0'), which recreates the expected folder structure.

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

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

Inline comments:
In `@src/pre_process/m_start_up.fpp`:
- Around line 508-509: s_read_serial_grid_data_files currently calls
s_delete_directory(trim(proc_rank_dir)//'/*'), which fails to expand the glob
because s_delete_directory wraps the path in quotes; change that call to
s_delete_directory(trim(proc_rank_dir)) to match the fix at the other call site
and ensure the entire per-rank directory is removed before recreating the /0
subdirectory via s_create_directory. Ensure you update the invocation inside
s_read_serial_grid_data_files (the proc_rank_dir argument) and keep the existing
s_delete_directory/s_create_directory implementations unchanged.

[codecov]

Codecov Report

❌ Patch coverage is 0% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 44.05%. Comparing base (84c46e0) to head (55bda76).

Files with missing lines	Patch %	Lines
src/pre_process/m_start_up.fpp	0.00%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1214   +/-   ##
=======================================
  Coverage   44.05%   44.05%           
=======================================
  Files          70       70           
  Lines       20498    20498           
  Branches     1990     1990           
=======================================
  Hits         9030     9030           
  Misses      10329    10329           
  Partials     1139     1139           

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