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6 months ago Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:
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0e2f5e2) 92.39% compared to head (e6d9fa9) 92.39%. Report is 3 commits behind head on main.
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```diff @@ Coverage Diff @@ ## main #236 +/- ## ======================================= Coverage 92.39% 92.39% ======================================= Files 37 37 Lines 2434 2434 ======================================= Hits 2249 2249 Misses 185 185 ``` | [Flag](https://app.codecov.io/gh/rs-station/reciprocalspaceship/pull/236/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=rs-station) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/rs-station/reciprocalspaceship/pull/236/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=rs-station) | `92.39% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=rs-station#carryforward-flags-in-the-pull-request-comment) to find out more.:umbrella: View full report in Codecov by Sentry.
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This PR contains the following updates:
>=0.5.5, <=0.6.3->>=0.5.5, <=0.6.4Release Notes
project-gemmi/gemmi (gemmi)
### [`v0.6.4`](https://togithub.com/project-gemmi/gemmi/releases/tag/v0.6.4): 0.6.4 [Compare Source](https://togithub.com/project-gemmi/gemmi/compare/v0.6.3...v0.6.4) Library - completely changed build system for Python module, from setuptools to scikit-build-core - optimized electron density calculation: single-precision version is now about 2x faster and slightly less exact; some other grid-based calculations also got optimized in the process - as part of the above optimizations, some of the grid computations require that the model is in the standard orientation (conventional axis directions); in other cases (which are very rare after the [remediation of non-standard coordinate frames](https://www.wwpdb.org/news/news?year=2023#6525a09ad78e004e766a96af) in the PDB) call standardize_crystal_frame() - CIF output: more flexible formatting - mmCIF writing: category \_entity_poly is included by default, with pdbx_strand_id and pdbx_seq_one_letter_code - minor changes in reading mmCIF coordinate files - cif: added functions Loop::add_columns(), Loop::remove_column(), Column::erase() - MRC map format: ORIGIN record is ignored (previously, if ORIGIN was non-zero, Ccp4::full_cell() returned false and some map properties were not set) - new function Grid::symmetrize_avg() - fixed bug in ReciprocalGrid::prepare_asu_data() - added function read_pir_or_fasta() for reading sequences (previously it was undocumented and more limited) - added function pdbx_one_letter_code() which returns a string like AA(MSE)H…, for \_entity_poly.pdbx_seq_one_letter_code - new functions expand_one_letter() and expand_one_letter_sequence() that take ResidueKind.AA/RNA/DNA as argument replaced expand_protein_one_letter\*() - adjusted weights in align_sequence_to_polymer() - added function assign_best_sequences() - PDB reading: added Structure::ter_status flag to indicate if TER records were: absent, present, clearly in wrong places - experimental (not documented yet) new functions: Model::get_cra(), Model::get_parent_of() - Topo::Bond stores a flag for bonds between different symmetry images - ChemComp::Atom: store \_chem_comp_atom.alt_atom_id as old_id, use it in new function update_old_atom_names() - riding hydrogens: added H had wrong occupancy in special, rare cases - added Vec3f – Vec3 with single-precision numbers - minor API changes: Binner::setup() doesn't return anything, changed argument types of Scaling::scale_data(), align_sequences() Program - new tool gemmi-diff that compares categories and tags in two (mm)CIF files - gemmi-align prints vertical list with option --verbose - gemmi-residues has new options: -e, -sss, --chains - gemmi-rmsz: added option --missing to print missing atoms - gemmi-validate: more options for validating monomer files - gemmi-h: more options - gemmi-mtz: prints info about SYMM recordsConfiguration
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