Index refactor

[rjgildea]

1. Refactor basis vector search code into strategies in dials.algorithms.indexing.basis_vector_search.strategies
   • fft1d, fft3d, real_space_grid_search
   • take as input a list of reciprocal lattice vectors and return a list of candidate basis vectors
2. Refactor basis vector combination code into algorithms.indexing.basis_vector_search.combinations
   • Implemented as a sequence of iterators that can be chained together
   • candidate_orientation_matrices: finds suitable combinations of basis vectors in P1
   • filter_known_symmetry: filters output of previous to only accept those models that match known symmetry
   • filter_similar_orientations
3. Refactor assign_indices to a strategy pattern in dials.algorithms.indexing.assign_indices
   • assign_indices_global, assign_indices_local
4. Move non-primitive basis code to separate module dials.algorithms.indexing.non_primitive_basis with tests
5. New dials.algorithms.indexing.model_evaluation
   • Move/rename SolutionTrackers: ModelRankWeighted, ModelRankFilter
   • move run_one_refinement inner function to new ModelEvaluation class
6. Attempt to encapsulate handling of known symmetry into external class dials.algorithms.indexing.symmetry.SymmetryHandler, with tests
7. New dials.algorithms.indexing.lattice_search module
   • Single BasisVectorSearch inheriting from indexer_base to consolidate previous fft1d, fft3d and real_space_grid_search classes. Code that is specific to a basis vector search now lives in this class instead of indexer_base.
   • Add simple test for BasisVectorSearch class
8. Move basis vector optimisation code to new module dials.algorithms.indexing.basis_vector_search.optimise with tests
9. Replace scan_range parameter with image_range
10. Refactor command line script to a functional interface
    • add joint_indexing=False option to allow indexing multiple independent experiments in a single dials.index process
11. Some refactoring of indexer.index() method to minimise code duplication with stills_indexer

[ndevenish]

Checking with quality tools; there are some outright undefined variables; I checked the stills_indexer ones and these were moved out in this branch. The others might have existed anyway. This is obviously not covered by tests.

algorithms/indexing/model_evaluation.py:53:42: F821 undefined name 'difference_rotation_matrix_axis_angle'
algorithms/indexing/stills_indexer.py:118:20: F821 undefined name 'stills_indexer_fft3d'
algorithms/indexing/stills_indexer.py:120:20: F821 undefined name 'stills_indexer_fft1d'
algorithms/indexing/stills_indexer.py:122:20: F821 undefined name 'stills_indexer_real_space_grid_search'

Otherwise, there is a whole load of flake8 unused variables; I know not all these files have been completely rewritten but it'd be nice to get rid of the flake8 warnings; most of these are probably harmless, but I'm worried about cases where the variable should be used but isn't - is impossible for me to tell the difference...

algorithms/indexing/assign_indices.py:40:9: F841 local variable 'diffs' is assigned to but never used
algorithms/indexing/assign_indices.py:41:9: F841 local variable 'norms' is assigned to but never used
algorithms/indexing/assign_indices.py:42:9: F841 local variable 'hkl_ints' is assigned to but never used
algorithms/indexing/assign_indices.py:112:9: F841 local variable 'diffs' is assigned to but never used
algorithms/indexing/assign_indices.py:113:9: F841 local variable 'norms' is assigned to but never used
algorithms/indexing/assign_indices.py:114:9: F841 local variable 'hkl_ints' is assigned to but never used
algorithms/indexing/assign_indices.py:141:13: F841 local variable 'ref_sel' is assigned to but never used
algorithms/indexing/basis_vector_search/combinations.py:74:9: F841 local variable 'best_model' is assigned to but never used
algorithms/indexing/basis_vector_search/conftest.py:22:5: F841 local variable 'sg' is assigned to but never used
algorithms/indexing/basis_vector_search/strategies.py:267:9: F841 local variable 'sites_frac' is assigned to but never used
algorithms/indexing/basis_vector_search/strategies.py:282:9: F841 local variable 'orth' is assigned to but never used
algorithms/indexing/basis_vector_search/strategies.py:390:9: F841 local variable 'rlgrid' is assigned to but never used
algorithms/indexing/basis_vector_search/test_combinations.py:69:5: F841 local variable 'crystal_symmetry' is assigned to but never used
algorithms/indexing/indexer.py:831:17: F841 local variable 'isel' is assigned to but never used
algorithms/indexing/indexer.py:832:17: F841 local variable 'ref_panel' is assigned to but never used
algorithms/indexing/indexer.py:922:9: F841 local variable 'verbosity' is assigned to but never used
algorithms/indexing/model_evaluation.py:343:9: F841 local variable 'e' is assigned to but never used
algorithms/indexing/nearest_neighbor.py:96:9: F841 local variable 'centers' is assigned to but never used
algorithms/indexing/nearest_neighbor.py:138:9: F841 local variable 'fig' is assigned to but never used
algorithms/indexing/non_primitive_basis.py:30:9: F841 local variable 'cryst_orig' is assigned to but never used
algorithms/indexing/refinement.py:21:5: F841 local variable 'detector' is assigned to but never used
algorithms/indexing/stills_indexer.py:55:9: F841 local variable 'PX' is assigned to but never used
algorithms/indexing/stills_indexer.py:56:9: F841 local variable 'fig' is assigned to but never used
algorithms/indexing/stills_indexer.py:92:5: F841 local variable 'history' is assigned to but never used
algorithms/indexing/stills_indexer.py:590:21: F841 local variable 'crystal_model_nv0' is assigned to but never used
algorithms/indexing/stills_indexer.py:793:9: F841 local variable 'crystal_model_nv0' is assigned to but never used
algorithms/indexing/symmetry.py:161:5: F841 local variable 'supergroup' is assigned to but never used
algorithms/indexing/symmetry.py:163:5: F841 local variable 'triclinic_miller' is assigned to but never used
algorithms/indexing/symmetry.py:622:9: F841 local variable 'primitive_subsym' is assigned to but never used
algorithms/indexing/test_assign_indices.py:80:5: F841 local variable 'miller_set' is assigned to but never used
algorithms/indexing/test_index.py:52:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:120:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:151:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:226:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:263:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:300:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:337:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:372:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:403:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:438:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:476:9: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:515:13: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:563:5: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:607:5: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:633:5: F841 local variable 'result' is assigned to but never used
algorithms/indexing/test_index.py:777:5: F841 local variable 'experiments_list' is assigned to but never used
algorithms/indexing/test_lattice_search.py:58:5: F841 local variable 'indexed_reflections' is assigned to but never used
algorithms/indexing/test_lattice_search.py:99:5: F841 local variable 'indexed_reflections' is assigned to but never used
algorithms/indexing/test_max_cell.py:25:5: F841 local variable 'expts' is assigned to but never used
algorithms/indexing/test_symmetry.py:74:5: F841 local variable 'cs_new' is assigned to but never used
algorithms/indexing/test_symmetry.py:120:5: F841 local variable 'subgroups' is assigned to but never used

[rjgildea]

@ndevenish have addressed the flake8 issues highlighted above