Scipion-em-xmipp

- New protocols
- movie_alignment_consensus: protocol for the comparison of two global alignments
- PCA classification: 2D Classification method that can works in streaming and in static

- Protocols updated
- deep_center: Deep center calculates an approximate center for the particles.
- validate_fscq: Added cif support
- reconstruct_fourier: Enable reconstructing with halves in the reconstruct fourier
- simulate_ctf: Simulate CTF can add noise before and after CTF.
- extract_particles: Local average added
- compare_reprojections: Downsampling option,autodown sampling, allows input 2D in several formats, allows input 3D in several formats, ranking option available, extraction option available
- cl2d: ensuring a save classes creating and adding possible output
- Protocols fixed
- resolution_deepres:now works with queue system
- ProcessVolumes: Fix header for resize voxels
- resolution_bfactor:Fix local resolution to local bfactor
- resolution_bfactor: create output for res bfac
- extract_particles: Bug fix in the downsampling factor of extract particles
- core_analysis: define correctly the particles pointer to have indirect pointer
- tilt_analysis: estimate automatically the window size new option
- movie_doseanalysis: update correctly the outputSet
- extract_particles: Check if resizing is enabled
- particle_pick_remove_duplicates: Remove duplicates coordinates
- Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols))
- deep_denoissing
- metaprotocol_create_subset
- metaprotocol_golden_highres
- solid_angle
- split_volume
- More scipio-em-xmipp
- Solve Sonar Cloud reported bugs
- Flexible import of pyQT on chimera script
- Removing tkAgg matplotlib requirement in viewer_structure_map
- DLTK installation bug local variable and Fix use gpu
- updated scikit-learn version

- New protocols
- Volume local adjustment
- Protocols updated
- convert_pdb: Allowed conversion natively from CIFs
- particle_pick_automatic: The model can now be given by a directory
- volume_local_adjust: Save occupancy volume
- extract_particles: Added two different cases for downsampling, by dimensions and by sampling rate
- Protocols fixed
- movie_resize: Fixed movie resize output size
- movie_gain: Fix update output step by using a generic one from scipion
- tilt_analysis: Fixes in the generated tilt images and in updating correctly the output sets
- ctf_consensus: Fix the dependencies of the step
- preprocess_micrographs: Fixed output size in preprocess micrographs
- deep_center_assignment: Fixed deep center calls
- extract_particles_movies: Get coords correctly
- particle_pick_consensus: Fix MicsPointer
- trigger_data: fix updateOutput and close correclty the output set
- Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols))
- classification_gpuCorr
- classification_gpuCorr_full
- classification_gpuCorr_semi
- More scipio-em-xmipp
- Updated Nvidia driver required version

- New protocols
- Movie Dose analysis
- deep_center
- deep_global_assignment
- deep_center_predict
- deep_global_assignment_predict
- Protocols updated
- consensus_classes (Efficient p-value calculation, updated intersection merging process, generalized protocol for other set of classes)
- Movie Gain: changed _stepsCheckSecs and fixed inputMovies calling, np.asscalar discontinued in numpy 1.16
- convert_pdb: dont allow set size if template volume, to convert a set of pdbs to volumes, generates an mrc file
- CTF_consensus: add 4 threads by default
- process: Better instantiation of Scipion subclasses
- create_mask3d: Addding a validate in 3dmask, add :mrc to input filename
- consensus_local_ctf: save defocus in proper fields, compute consensus for local defocus U and V separately, add consensus angle
- align_volume: Included the label in the volumes
- crop_resize: Add mask as input. Mask resize is now possible
- subtract_projection: change pad validation error for warning, parallelized
- Protocols fixed
- Tilt analysis: Close correctly the output sets once finished
- Deep micrograph cleaner: fix two bugs that occured during streaming implementation bug
- volume_adjust_sub: fix with :mrc
- Picking consensus: define correctly the possibleOutputs bug
- Center particles: streaming bug when definining the outputs bug
- volume_subtraction: bug fixed in filename
- compare_reprojections: fix update subtract projection output
- deep_micrograph_screen: Bug fix that prevents using small GPUs
- consensus_classes:Fixed manual output generation
- Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols))
- apply_deformation_zernike3d
- classify_kmeans2d
- kmeans_clustering
- particle_boxSize
- rotational_spectra
- split_volume_hierarchical_cluster
- Viewers
- viewer_resolution_fs: fixing 0.1 threshold not found
- viewer_projmatch, viewer_metaprotocol_golden_highres: Fixing viewers, change removed ChimeraClientView to ChimeraView
- monores_viewer: fix histogram
- viewer_structure_map: Change the label for each volume

- New protocol status: beta, new, production and updated. Will appear in the left pannel of Scipion
- Protocol subtract_projection: user experience improvements, no final mask by default, apply ciruclar mask in adjustment image to avoid edge artifacts, validate same sampling rate with tolerance in third decimal
- Protocol convert_pdb: Allowed to save centered PDB used for conversion.
- Protocol align_volume_and_particles: add alingment validation
- Protocol FlexAlign: updating protocol to reflect changes in the executable, fixed test, removing unused protocol (Movie average)
- Protocol align_volume_and_particles:Align volume and particles adapted to tomography and works in the absence of tomo plugin.
- Protocol volume_consensus: validate same sampling rate with tolerance in third decimal
- Protocols deprecated (for more details visit the [wiki](https://github.com/I2PC/xmipp/wiki/Deprecating-programs)): protocol_deep _align, reconstruct_heterogeneous, protocol_metaprotocol_create_output, protocol_metaprotocol_discrete_heterogeneity_scheduler

- Align volume and particles works in the absence of tomo plugin.

- Align volume and particles adapted to tomography. Defines possible outputs. Optimized. Test more exhaustive for matrices