Add CLI for running TurtleMD

[andersle]

This PR will add a CLI so that we can run TurtleMD from input files.

• Add CLI methods
• Add support for creating simulations from input files
• Add support for reading/writing input files
• Add support for reading/writing trajectories
• Add support for writing to screen/log during a CLI-run simulation

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
turtlemd
__init__.py	2	0	100%
bin.py	20	17	15%	10–53
integrators.py	171	163	5%	14–353
random.py	4	1	75%	13
units.py	28	23	18%	10–104
version.py	2	0	100%
turtlemd/inout
__init__.py	2	0	100%
common.py	64	51	20%	41–55, 76–84, 110–150, 171–175, 190–195
settings.py	104	95	9%	14–211
xyz.py	77	57	26%	22–23, 39–71, 84–102, 120–133
turtlemd/potentials
__init__.py	3	1	67%	5
lennardjones.py	178	149	16%	76–85, 94–116, 127–143, 155–183, 196–224, 237–273, 279, 288, 294, 314–362, 438–461
potential.py	31	12	61%	31–33, 37–41, 59–61, 65–68
well.py	94	90	4%	22–286
turtlemd/simulation
__init__.py	2	2	0%	2–4
mdsimulation.py	48	48	0%	2–90
stopping.py	23	23	0%	2–49
turtlemd/system
__init__.py	4	1	75%	6
box.py	155	113	27%	18–34, 49–51, 73–89, 131–158, 162, 206–230, 243–254, 267–269, 286–297, 309, 313–318, 331–340, 353–368, 372–382, 394–403, 407–411
particles.py	108	79	27%	34–35, 39–48, 69–88, 96–106, 110, 114–127, 140–142, 147, 158–163, 173–178, 202–209, 229–233, 267–276
system.py	83	78	6%	21–147
turtlemd/tools
__init__.py	2	0	100%
tools.py	22	18	18%	59–78
TOTAL	1227	1021	17%

Coverage summary (Python 3.12.2)

Tests	Skipped	Failures	Errors	Time
10	0 💤	0 ❌	10 🔥	1.420s ⏱️