Phase plate ctf and argparse grouping

[McHaillet]

In this PR I added the following:

• grouping of argparse parameters for pytom_match_template.py to make the help more readable!
• a phase shift parameter for CTF curves, with allows users to model a phase plate. Phase shift calculation follows standard conventions.

For the phase shift parameter I had to make job reading backwards compatible, so I added another version based check.

Closes #150 and closes #76

[github-actions]

File	Coverage		Missing
All files	80%	✅
src/pytom_tm/angles.py	94%	✅	44
src/pytom_tm/correlation.py	85%	✅	94-95 126
src/pytom_tm/entry_points.py	70%	❌	27 104-121 290-350 439-454 551-566 814-882 923-934
src/pytom_tm/extract.py	73%	❌	107-118 170-176 202-205 277-295
src/pytom_tm/io.py	48%	❌	15-19 25-28 34-37 43-46 52-55 62-66 74-87 93-100 107-114 129-131 184 218-219 261-263 279 295 312-321 341-346
src/pytom_tm/mask.py	80%	✅	70 85 94-95
src/pytom_tm/matching.py	95%	✅	186-196 340
src/pytom_tm/parallel.py	84%	✅	14-15 81-87 95-97 104 109 148
src/pytom_tm/plotting.py	16%	❌	20-22 25-32 36-44 48-51 54-70 73-74 77-78 98-103 119-127 133-150 165-173 177-194 198-206 210-217 223 229 234 248-398
src/pytom_tm/template.py	57%	❌	57-58 67 76-87 92-97 107-112 114
src/pytom_tm/tmjob.py	96%	✅	177-178 190 196-198 201 334 374
src/pytom_tm/utils.py	78%	❌	16-18
src/pytom_tm/weights.py	96%	✅	61 292-293 300 480 483 486

Minimum allowed coverage is 79%

Generated by 🐒 cobertura-action against 400175d

[sroet]

1 missing test, 2 leftover imports, 1 style comment (feel free to ignore) and a question about the convention. LGTM otherwise

[sroet]

LGTM, thanks for fixing my comments.

Feel free to merge