Avoid shell=True when invoking PACKMOL

[rayair250-droid]

Summary

PACKMOL is currently launched through a shell with an interpolated temp path:

proc = Popen(
    f"{PACKMOL} < {packmol_inp.name}",
    stdin=PIPE, stdout=PIPE, stderr=PIPE,
    universal_newlines=True, shell=True,
)

Two problems:

1. Shell-injection anti-pattern — building a shell command line by interpolating a path into an f-string with shell=True.
2. Breaks on spaces / shell metacharacters — if the temp file path contains a space (e.g. TMPDIR under a user directory with spaces, common on macOS/Windows), the < redirection targets the wrong token and PACKMOL fails.

The shell was only being used for the < input redirection; stdin=PIPE was set but nothing was ever written to it.

Fix

Feed the input file directly as stdin and pass the executable as an argument list, dropping the shell. PACKMOL is a resolved absolute path from shutil.which("packmol"), so no shell word-splitting is needed.

with open(packmol_inp.name) as inp_file:
    proc = Popen(
        [PACKMOL],
        stdin=inp_file, stdout=PIPE, stderr=PIPE,
        universal_newlines=True,
    )
    out, err = proc.communicate()

Behavior is unchanged (PACKMOL reads its config from stdin exactly as before), and the call is now injection-safe and robust to paths with spaces.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.07%. Comparing base (51e6c9b) to head (8dfff46).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1347   +/-   ##
=======================================
  Coverage   86.07%   86.07%           
=======================================
  Files          52       52           
  Lines        4897     4898    +1     
=======================================
+ Hits         4215     4216    +1     
  Misses        682      682           

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