Feat (Logging) - Add optional rotating file logging

[WACHIFOO]

Summary

Adds an optional, additive logging system to the controller software. It mirrors
everything the app already prints to the terminal (status messages and tracebacks)
into a rotating log file, without changing the existing terminal behaviour and
without modifying any of the existing print() calls.

Motivation

The controller currently has no logging — status and errors are only written to the
terminal. That terminal is invisible in the two most common deployments:

• the packaged single-click executable, and
• a Raspberry Pi launched from a desktop icon.

So when a pump misbehaves or the serial connection to the Arduino fails, there is no
persistent record to diagnose the problem or attach to a bug report. This is exactly
the kind of failure users hit in a wet-lab setup.

What this PR does

• Adds SOFTWARE/poseidon_logging.py, a small self-contained module.
• main() calls setup_logging() once at startup (a 2-line change in
  poseidon_main.py; no existing print() is touched).
• Writes to logs/poseidon.log (rotating, ~1 MB × 3 backups) with timestamps, level
  and thread name.
• On by default, disabled with the environment variable POSEIDON_LOG=0.
• Documents the feature in the README and ignores logs/ and *.log.

Design notes

• Additive / non-invasive: sys.stdout and sys.stderr are wrapped so the existing
  print() calls and tracebacks are captured transparently. The console output is
  unchanged (plain text, no prefixes; stdout→stdout, stderr→stderr).
• Safe fallbacks: if the log file can't be created (e.g. a read-only folder) or there
  is no console (frozen .exe), it degrades gracefully and the app behaves exactly as
  before.
• Thread-safe: the app is multithreaded (QThread); each thread buffers its own
  lines, and a re-entrancy guard prevents a failing log handler from recursing.
• No new dependencies — standard library only.

Example

The same status/errors you see in the terminal, now also captured with context:

​ 2026-06-07 07:28:12,986 INFO [MainThread] RUN command sent. 2026-06-07 07:28:12,990 ERROR [PumpWorker] Traceback (most recent call last): 2026-06-07 07:28:12,991 ERROR [PumpWorker] ... 2026-06-07 07:28:12,992 ERROR [PumpWorker] OSError: could not open serial port 'COM3' ​

Testing

Pure-Python module, no hardware/PyQt/serial needed. From the SOFTWARE/ folder:

​ python -m unittest test_poseidon_logging ​

17 tests cover: the POSEIDON_LOG off switch, file capture of stdout and stderr
tracebacks, line buffering and blank-line preservation, idempotent setup, the
no-console (frozen exe) fallback, the file-creation failure fallback, thread-safe
concurrent writes, stdout/stderr console separation, the file-like interface, and the
re-entrancy guard.

Testing notes

I don't have the pump/microscope hardware, so I haven't run this on a physical
device. The change is additive and doesn't touch the pump, serial, or GUI logic —
it only adds a log file and wraps stdout/stderr — so runtime behaviour should be
unaffected. I verified the logging module with the unit tests above and a standalone
script reproducing the app's real output patterns (status prints, a worker-thread
traceback, concurrent output). A maintainer with hardware may want a quick smoke test
to confirm startup is unaffected.

Backwards compatibility

Fully backwards compatible. With POSEIDON_LOG=0 the behaviour is identical to before;
with logging on, the terminal output is unchanged and only a log file is added.

Files changed

File	Change
SOFTWARE/poseidon_logging.py	new module
SOFTWARE/test_poseidon_logging.py	new tests
SOFTWARE/poseidon_main.py	+2 lines (import + setup_logging() call)
README.MD	new "Logging" section
.gitignore	ignore logs/ and *.log

Checklist

• Additive — no existing print() modified
• No new dependencies (stdlib only)
• On by default, opt-out via POSEIDON_LOG=0
• Tests added and passing (python -m unittest test_poseidon_logging)
• README updated
• Minimal diff to existing files

Happy to adjust scope or close this if it doesn't fit the project's direction.❤️