Relion5 input

[McHaillet]

Closes #190

@Phaips @rdrighetto also adding you here, in case you have ideas about the implementation for this.

I made a PR to tackle the RELION5 metadata input. I tested it on a RELION5 project I made from the frames of the tutorial. As it is now, it runs and gives expected results. It does make the input quite easy as the job can be started like this and all 3D-CTF data is fetched from the relion metadata:

pytom_match_template.py -t Templates/80S_14A.mrc -m Templates/mask.mrc -v Tomograms/job006/tomograms/rec_tomo200528_102.mrc --particle-diameter 300 --relion5-tomograms-star Tomograms/job006/tomograms.star -d TemplateMatching/ -g 0

If one would want to loop over all the tomograms in the RELION directory you could do something like this in bash:

for tomo in Tomograms/job006/tomograms/*.mrc; do pytom_match_template.py -t Templates/80S_14A.mrc -m Templates/mask.mrc -v "$tomo" --particle-diameter 300 --relion5-tomograms-star Tomograms/job006/tomograms.star -d TemplateMatching/ -g 0; done

This PR is still a draft because I need to add unit tests and tackle the defocus handedness parameter from RELION. I am not sure if it actually applies a flip to the images.

It also made me aware that the code could be improved using some sort of TiltSeries struct internally that associates all the tilt angles, CTF and dose. But, better left for later to not convolute this.

[github-actions]

File	Coverage		Missing
All files	89%	✅
src/pytom_tm/correlation.py	85%	❌	97-98 130
src/pytom_tm/entry_points.py	80%	❌	30 115-132 237-282 387-406 559-579 1092-1103
src/pytom_tm/extract.py	97%	✅	264-269
src/pytom_tm/io.py	84%	❌	20 40 56 72 85 104-110 127-131 138 144 181 186 233-235 305 451-459 484
src/pytom_tm/mask.py	80%	❌	75 93 103-104
src/pytom_tm/parallel.py	89%	✅	14-15 93 104-105 111 176
src/pytom_tm/plotting.py	16%	❌	19-21 24-31 35-43 47-50 53-69 72-73 76-77 97-102 118-126 132-149 164-172 176-193 197-205 209-216 222 228 233 247-397
src/pytom_tm/tmjob.py	98%	✅	371-372 388 482 610 659
src/pytom_tm/utils.py	78%	❌	18-20
src/pytom_tm/weights.py	96%	✅	58 313-317 324 534 539 544

Minimum allowed coverage is 88%

Generated by 🐒 cobertura-action against c9ffc02

[McHaillet]

I added unittests and fixed reading of the tomogram handedness. It's ready for review 👍

Also just added version number update to 0.8.0

[sroet]

1 missing test, couple other issues/corner cases. LGTM otherwise

[sroet]

Thanks for the fixes, LGTM