Fix the outputs to stdout/stderr

[max-models]

• Added a hack to move the tqdm output to stdout instead of stderr
  • https://stackoverflow.com/questions/75580592/why-is-tqdm-output-directed-to-sys-stderr-and-not-to-sys-stdout
  • Redirect both sys.stdout and sys.stderr tqdm/tqdm#422
• Added a stdout handler which uses a BelowWarningFilter

DEBUG/INFO go to stdout, WARNING and above to stderr; records that pass the logger level are also written to the log file.

This means the levels for the different loggers are no longer the same, and these lines were therefore removed:

for handler in logger.handlers:
        handler.setLevel(level)

[Copilot]

Pull request overview

This PR adjusts runtime output streams to better separate “normal” output from errors in batch/cluster environments by moving tqdm progress bars (and low-severity logs) away from stderr.

Changes:

• Added a struphy.utils.progress shim that configures tqdm to write to sys.stdout by default.
• Updated multiple modules to import tqdm from struphy.utils.progress instead of directly from tqdm.
• Updated struphy logger configuration to route DEBUG/INFO to stdout and WARNING+ to stderr, and to log more verbosely to struphy.log.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/struphy/utils/progress.py	Introduces a stdout-targeting tqdm wrapper for consistent progress bar output.
src/struphy/simulation/sim.py	Switches to the new tqdm wrapper and reformats progress bar construction.
src/struphy/post_processing/post_processing_tools.py	Uses the new stdout tqdm import path.
src/struphy/post_processing/orbits/orbits_tools.py	Uses the new stdout tqdm import path.
src/struphy/diagnostics/diagn_tools.py	Uses the new stdout tqdm import path.
src/struphy/init.py	Adds stdout/stderr split logging handlers and adjusts file handler verbosity.

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[max-models]

There are still a few messages that appear in the .err files, such as

Starting run for model Maxwell on 1 ranks ...
WARNING: Class "BasisProjectionOperators" called with degree=(1, 1, 1) (interpolation of piece-wise constants should be avoided).
Struphy run finished.

edit: moved these to logger.info in bd67126