Schedule PymatgenTest for migration from unittest to pytest

[DanielYang59]

Summary

• Avoid catching all warnings, add a message filter, and clean up assert no warning tests with warnings filter

Schedule PymatgenTest for migration after a grace period

• We cannot migrate PymatgenTest directly as it's public and quite some external code use PymatgenTest, added a grace period until 2026-01-01 and let downstream code finish their migration first (get rid of some unittest-specific functions), as pytest is not compatible with some unittest functions
• OR, do we want to deprecated PymatgenTest with a more general MatSciTest (or some other name) as it's intended to be used by other packages?
• Issue migration warning, and test methods specific to TestCase such that we know potential side effect, also provide a migration guide (not really our job, but at least provide links to some resources), ruff does have rules (for example PT009) but we cannot trust this as not every project enables ruff

---

Super brief migration guide

• Setup/teardown methods (setUp, setUpClass, tearDown, tearDownClass):
  1. Recommended by pytest: Use fixtures
     OR
  2. Use pytest's xUnit-style setup/teardown: [setup/teardown]_[class/method/function].
• Assertion methods (assertTrue, assertFalse, assertEqual, etc.): Replace with direct Python assert statements.

[DanielYang59]

This test is failing as RuntimeError with a different message is raised:

>       with pytest.raises(RuntimeError, match="mcsqs exited before timeout reached"):
E       AssertionError: Regex pattern did not match.
E        Regex: 'mcsqs exited before timeout reached'
E        Input: 'mcsqs did not generate output files, is search_time sufficient or are number of instances too high?'

But looks like both exceptions are very similar (all pointing to timeout) so I would just change the error message here:

pymatgen/src/pymatgen/command_line/mcsqs_caller.py

Lines 136 to 160 in 31f1e1f

	try:
	for process in mcsqs_find_sqs_processes:
	process.communicate(timeout=search_time * 60)
	if instances and instances > 1:
	process = Popen(["mcsqs", "-best"])
	process.communicate()
	if os.path.isfile("bestsqs.out") and os.path.isfile("bestcorr.out"):
	return _parse_sqs_path(".")
	raise RuntimeError("mcsqs exited before timeout reached")
	except TimeoutExpired:
	for process in mcsqs_find_sqs_processes:
	process.kill()
	process.communicate()
	# Find the best sqs structures
	if instances and instances > 1:
	if not os.path.isfile("bestcorr1.out"):
	raise RuntimeError(
	"mcsqs did not generate output files, "
	"is search_time sufficient or are number of instances too high?"
	)

[DanielYang59]

I would reopen this after #4212 is reviewed/merged as I opened too many PRs for me to track