Resolve "Update modelangelo and dynamight process names for Relion compatibility"
updated with a @colinpalmer's suggestions
Added features so jobs can have more flexible categories in the Doppio GUI and play well with the relion process names.
A job's category is still determined by taking the 2nd term in its PROCESS_NAME. IE refmac.atomic_model_refine but jobs also now have CATEGORY_LABEL which can be used to override this.
All PipelinerJob subclasses now have a self.category attr.get_category_label() method. If CATEGORY_LABEL is empty it uses the 2nd term from PROCESS_NAME as before. Either way it then checks the resulting category against a list of approved category names in pipeliner.data_structure which will hopefully help prevent issues with duplicated categories with slightly different names, misspellings and etc..
get_category_label() returns the categories already formatted as doppio would with spaces and capitalisation. This processing of the category names will be removed from doppio.
Also took the opportunity to clean up some of the category names to make them more descriptive as we're no longer limited by the relion process names. Any suggestions are welcome, I added everyone as reviewers so you can take a look at the categories.
Requires small changes in Doppio which are in a separate MR https://gitlab.com/ccpem/doppio/-/merge_requests/356.
| Job | Category |
|---|---|
| acedrg.create_ligand | Create Ligand |
| ccpem_utils.map_utilities.crop_pad_mask_map | Map Utilities |
| checkmysequence.atomic_model_validation | Atomic Model Validation |
| cinderella.select.class_averages | Automated Class Selection |
| cinderella.select.class_averages.train | Automated Class Selection |
| confidencemap.map_analysis | Map Analysis |
| cryoef.map_analysis | Map Analysis |
| cryolo.autopick | Automated Particle Picking |
| doublehelix.atomic_model_utilities.assign_sequence | Atomic Model Utilities |
| dynamight | Continuous Heterogeneity |
| em_placement.atomic_model_fit | Atomic Model Fit |
| emda.map_utilities.create_mask | Map Utilities |
| emdb_validation_analysis.map_model_validation | Map Model Validation |
| emplace_local.atomic_model_fit | Atomic Model Fit |
| findmysequence.atomic_model_utilities.assign_sequence | Atomic Model Utilities |
| flex_em.atomic_model_refine | Atomic Model Refine |
| gemmi.atomic_model_utilities.model_to_map | Atomic Model Utilities |
| gemmi.atomic_model_utilities.process_model | Atomic Model Utilities |
| icebreaker.micrograph_analysis.enhancecontrast | Micrograph Analysis |
| icebreaker.micrograph_analysis.micrographs | Micrograph Analysis |
| icebreaker.micrograph_analysis.particles | Micrograph Analysis |
| icebreaker.micrograph_analysis.summary | Micrograph Analysis |
| lafter.postprocess.local_denoising | Map Postprocessing |
| locscale.postprocess.local_sharpening | Map Postprocessing |
| modelangelo | Atomic Model Build |
| modelcraft.atomic_model_build | Atomic Model Build |
| molprobity.atomic_model_validation.geometry | Atomic Model Validation |
| molrep.atomic_model_fit | Atomic Model Fit |
| parakeet.simulate | Simulate |
| pipeliner.atomic_model_validation | Atomic Model Validation |
| pipeliner.deposition.empiar | Deposition |
| pipeliner.fetch.alphafold | Fetch |
| pipeliner.fetch.emdb | Fetch |
| pipeliner.fetch.pdb | Fetch |
| pipeliner.fetch.sequence | Fetch |
| pipeliner.image_analysis.average_particle_ps | Image Analysis |
| pipeliner.select.autoselect3d | Automated Class Selection |
| pipeliner.select.random_sample | Subset Selection |
| pipeliner.workflow.import_external | Workflow |
| process_predicted_model.atomic_model_utilities | Atomic Model Utilities |
| proshade.map_analysis.symmetry | Map Analysis |
| proshade.map_utilities.overlay | Map Utilities |
| refmac_servalcat.atomic_model_refine | Atomic Model Refine |
| relion.autopick.log | Automated Particle Picking |
| relion.autopick.log.helical | Automated Particle Picking |
| relion.autopick.ref2d | Automated Particle Picking |
| relion.autopick.ref2d.helical | Automated Particle Picking |
| relion.autopick.ref3d | Automated Particle Picking |
| relion.autopick.ref3d.helical | Automated Particle Picking |
| relion.autopick.topaz.pick | Automated Particle Picking |
| relion.autopick.topaz.pick.helical | Automated Particle Picking |
| relion.autopick.topaz.train | Automated Particle Picking |
| relion.autopick.topaz.train.helical | Automated Particle Picking |
| relion.class2d.em | 2D Classification |
| relion.class2d.em.helical | 2D Classification |
| relion.class2d.vdam | 2D Classification |
| relion.class2d.vdam.helical | 2D Classification |
| relion.class3d | 3D Classification |
| relion.class3d.helical | 3D Classification |
| relion.class3d.helical.multiref | 3D Classification |
| relion.class3d.multiref | 3D Classification |
| relion.ctffind.ctffind4 | CTF Determination |
| relion.ctffind.gctf | CTF Determination |
| relion.ctfrefine | CTF Refinement |
| relion.ctfrefine.anisomag | CTF Refinement |
| relion.external | External |
| relion.extract | Extract Particles |
| relion.extract.helical | Extract Particles |
| relion.import | Import |
| relion.import.coordinates | Import |
| relion.import.movies | Import |
| relion.initialmodel | Initial Model Generation |
| relion.joinstar.micrographs | Join Star Files |
| relion.joinstar.movies | Join Star Files |
| relion.joinstar.particles | Join Star Files |
| relion.localres.own | Local Resolution Determination |
| relion.localres.resmap | Local Resolution Determination |
| relion.manualpick | Manual Particle Picking |
| relion.manualpick.helical | Manual Particle Picking |
| relion.map_utilities.align_symmetry | Map Utilities |
| relion.map_utilities.apply_bfactor | Map Utilities |
| relion.map_utilities.apply_symmetry | Map Utilities |
| relion.map_utilities.filter_map | Map Utilities |
| relion.map_utilities.flip_handedness | Map Utilities |
| relion.map_utilities.rebox_rescale_map | Map Utilities |
| relion.maskcreate | Mask Creation |
| relion.motioncorr.motioncor2 | Motion Correction |
| relion.motioncorr.own | Motion Correction |
| relion.multibody.flexanalysis | Multi-body Refinement |
| relion.multibody.refine | Multi-body Refinement |
| relion.polish | Particle Polishing |
| relion.polish.train | Particle Polishing |
| relion.postprocess | Map Postprocessing |
| relion.reconstruct | Reconstruct |
| relion.refine3d | 3D Refinement |
| relion.refine3d.helical | 3D Refinement |
| relion.reproject | Reproject |
| relion.select.class2dauto | Automated Class Selection |
| relion.select.discard | Subset Selection |
| relion.select.interactive | Subset Selection |
| relion.select.onvalue | Subset Selection |
| relion.select.removeduplicates | Subset Selection |
| relion.select.split | Subset Selection |
| relion.subtract | Particle Subtraction |
| relion.subtract.revert | Particle Subtraction |
| repic.autopick.consensus | Automated Particle Picking |
| servalcat.difference_map | Difference Map |
| servalcat.map_utilities.trim | Map Utilities |
| slice.atomic_model_split | Atomic Model Split |
| tempy_reff.atomic_model_refine | Atomic Model Refine |
Closes #422 (closed)