Raise exceptions directly instead of logging-and-raising

[galjos]

Replaces the package's log-and-raise control-flow pattern with explicit raise, removing a real footgun.

Problem

40 call sites did self.logger.error("msg", exception=TSValueError), where the custom logger raises the exception as a side effect of logging. That:

• reads as logging when it is actually control flow;
• depends on which package last won logging.setLoggerClass (PQAnalysis's CustomLogger also raises on .error, so the behaviour is non-obvious);
• hides the control flow from pylint — every such function looked like it could fall through (13 inconsistent-return-statements).

I hit this twice while building screening (had to log failures at warning, and a %-format crash).

Change

• self.logger.error("msg", exception=ExcType) -> raise ExcType("msg") across api.py, system.py, thermo.py, atoms.py, inputFileReader.py (40 sites, net -121 lines).
• Exception types and messages are unchanged, so every pytest.raises(..., match=...) / assert str(e.value) == ... still holds.
• except: lookups now raise ... from None (no misleading chain).
• Fixes a latent bug in dimensionality(): a 0D branch constructed a ValueError without raising it (silently returned None); it now raises.

Result

• Clears inconsistent-return-statements (13 -> 0), plus the no-else-raise/raise-missing-from the change would otherwise introduce.
• pylint 8.79 -> 8.93; full suite 159 passed, 0 skipped (with the DFTB+ binaries).

Note

This removes ThermoScreening's dependence on log-and-raise. The underlying logger machinery (the exception= param in custom_logging.py) is left in place but now unused by the package; screening.py still logs failures at warning because the active logger still raises on .error. Fully untangling the dual CustomLogger is a separate, larger change.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.93%. Comparing base (eacd9ea) to head (8de892b).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #58      +/-   ##
==========================================
+ Coverage   95.25%   95.93%   +0.68%     
==========================================
  Files          22       22              
  Lines        1286     1280       -6     
==========================================
+ Hits         1225     1228       +3     
+ Misses         61       52       -9     

Flag	Coverage Δ
unittests	95.93% <100.00%> (+0.68%)	⬆️

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