Fix pre-commit issues, replace ! syntax with subprocess.run

Tests/Data/HydroMechanics/SeabedResponse/Stationary_waves.py

Tests/Data/Mechanics/CooksMembrane/CooksMembraneBbar.py

...iscWithHole/Linear_Disc_with_hole_convergence_analysis.py

Tests/Data/Mechanics/Linear/SimpleMechanics.py

Tests/Data/Mechanics/PLLC/PLLC.py

Tests/Data/Notebooks/SimplePETSc.py

...ransport/DiffusionSorptionDecay/DiffusionSorptionDecay.py

...onentTransport/MultiLayerDiffusion/MultiLayerDiffusion.py

...tTransport/ReactiveTransport/CO2Injection/CO2Injection.md

...onentTransport/ReactiveTransport/DecayChain/DecayChain.py

...ransport/RadionuclidesMigration/RadionuclidesMigration.py

Tests/Data/Parabolic/LiquidFlow/AxiSymTheis/axisym_theis.py

.../BlockingConductingFracture/BlockingConductingFracture.py

...Data/Parabolic/ThermalTwoPhaseFlowPP/HeatPipe/heatpipe.py

Tests/Data/Parabolic/TwoPhaseFlowPrho/MoMaS/MoMaS.py

...opagating_jupyter_notebook/Kregime_Propagating_jupyter.py

...ata/PhaseField/PForthotropy_jupyter_notebook/sen_shear.py

Tests/Data/PhaseField/beam_jupyter_notebook/beam.py

...eField/kregime_jupyter_notebook/Kregime_Static_jupyter.py

...ta/PhaseField/surfing_jupyter_notebook/surfing_pyvista.py