Scipion-em-xmipp

- Protocol_cl2d_align: The input can now be a set of averages or a set of 2D classes
- Protocol_local_ctf: Default value are now changed for maxDefocusChange
- Protocol_apply_zernike3d: Now accepts either a Volume or SetOfVolumes and applies the coefficients in a loop in the deform step
- Protocol_postProcessing_deepPostProcessing: Managed GPU memory to avoid errors
- Protocol_resolution_deepres: Mandatory mask
- Protocol center particles and Gl2d (all options): Fix streaming
- Protocol_create_3d_mask: Allows volume Null=True
- Protocol_reconstruct_fourier: Set pixel size
- GL2D static: Bug fixing
- Protocol_trigger_data: Bug fixing
- Protocol_crop_resize: Set sampling rate of mrc files when cropping resizing volumes or particles
- subtract_projection: New protocol for boosting particles. Add protocol to wizard XmippParticleMaskRadiusWizard as now the protocol uses it

- **New tests:** deep_hand, pick_noise, screen_deep_learning, resolution_B_factor
- Fixed TestHighres test

- rotate_volume: New protocol
- subtract_projection: New implementation based on adjustment by regression instead of POCS and improved performance
- local_ctf: Add new sameDefocus option + formatting
- compare_reprojections & protocol_align_volume: Fast Fourier by default
- crop_resize: Allows input pointers
- resolution_deepres: Resize output to original size
- denoise_particles: Added setOfAverages as input option
- process: Change output from stk (spider) to mrcs (mrc)
- trigger_data: Bug fixed
- screen_deeplearning: Added descriptive help
- center_particles: Added summary info
- align_volume_and_particles: Summary error fixed
- cl2d: Summary errors solved
- New tests: test_protocol_reconstruct_fourier, test_protocols_local_defocus, test_protocols_local_defocus, TestXmippAlignVolumeAndParticles, TestXmippRotateVolume
- Improved tests: test_protocols_deepVolPostprocessing, test_protocols_xmipp_3d, Test ProjSubtracion
- Excluded tests: test_protocols_zernike3d, test_protocols_metaprotocol_heterogeneity

- protocol_core_analysis: New protocol
- protocol_compare_angles: Bug fix in compare angles under some conditions
- protocol_center_particles: protocol simplified (removed setofCoordinates as output)
- protocol_CTF_consensus: concurrency error fixed
- protocol_convert_pdb: remove size if deactivated
- protocol_resolution_deepres: binary masked not stored in Extra folder and avoiding memory problems on GPUs
- protocol_add_noise: fixes
- protocol_compare_reprojections: improve computation of residuals + tests + fix + formatting
- protocol_screen_deepConsensus: multiple fixes in batch processing, trainging and streaming mode
- protocol_shift_particles: apply transform is now optional

- Visit changeLog.md of xmipp

- CUDA-11 support
- New protocol: Deep align
- ChimeraX support
- Improvements of streaming process
- Several performance optimizations
- Build time optimization
- Multiple bug fixes
- Improved documentation

- New Protocol: MicrographCleaner is a new algorithm that removes coordinates picked from carbon edges, aggregations, ice crystals and other contaminations
- New functionality: The protocol compare reprojections can now compute the residuals after alignment
- New protocol: Split frames divide input movies into odd and even movies so that they can be processed independently
- New protocol: Continuous heterogeneity analysis using spherical harmonics (not ready to be used)
- Bug fixing when some micrograph has no coordinates in the consensus-picking.
- New functionalities: Different architectures and training modes
- Normal Mode Analysis protocols have been moved to the plugin ContinuousFlex
- Fixing MPI version of the Fourier Reconstruction
- New protocol: local CTF integration and consensus protocol for local ctf (also the viewers)
- Local CTF analysis tools: Not yet ready for general public
- New functionallity: Introducing the posibility of automatic estimation of the gain orientation.
- Bugs fixings regarding stability on streaming processing
- Support of heterogeneous movie sets
- New protocol: Clustering of subtomogram coordinates into connected components that can be processed independently
- New Protocol: Removing duplicated coordinates
- New protocol: Subtomograms can be projected in several ways to 2D images so that 2D clustering tools can be used
- New protocol: Regions of Interest can be defined in tomograms (e.g., membranes)
- Bug fixing in mask3d protocol
- Bug fix: in helical search symmetry protocol
- Enhanced precision of the FlexAlign program
- Now, deepLearningToolkit is under its own conda environment
- Multiple protocols accelerated using GPU
- New functionality: Xmipp CTF estimation can now take a previous defocus and do not change it
- New functionallity: CTF-consensus is able to take the primary main values or an average of the two.
- New functionallity: CTF-consensus is able to append metadata from the secondary input
- New functionality: Xmipp Highres can now work with non-phase flipped images
- New functionality: Xmipp Preprocess particles can now phase flip the images
- New protocol: Tool to evaluate the quality of a map-model fitting
- Allowing multi-GPU processing using FlexAlign
- Improvement in monores and localdeblur
- Randomize phases also available for images
- Change the plugin to the new Scipion structure
- Migrating the code to python3