Changelogs » Reciprocalspaceship

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- Update to minimal Pandas to 1.1
  - Improve handling of unmerged MTZ files




- 71 Support Pandas v1.3
  - 72 73 Update CrystFEL stream parser to return additional metadata


- 63 Fix sign of phase shifts in `DataSet.apply_symop()`
  - 64 Apply phase shifts to complex structure factors
  - 68 Fix implementation of `rs.utils.generate_reciprocal_asu()`
  - 70 Add `rs.read_pickle()` helper function
  - 71 Support pandas 1.3.0


Fix issue with NaNs when creating float32 arrays




- 58 Add methods for converting between wavelength and energy
  - 60 Add stats module for computing redundancy of observed reflections and completeness
  - 62 Change internals for float32-backed dtypes to improve performance


- 51 Update `rs.read_precognition()` API
  - 50 Add `rs.read_crystfel()` to support crystfel stream files
  - 53, 55 Documentation and error handling updates


-  49 Add MIT License to PyPI releases


- 40 Add `rs.read_csv()` to support plain text input sources to `DataSet`
  - 42 Update supported Pandas versions
  - 44 Add merging example to documentation using PyTorch to assess error models
  - 45, 46, 48 Improve French-Wilson scaling algorithm and testing to assess accuracy
  - 47 Add `DataSet.centrics` and `DataSet.acentrics` accessors


- 30 Add `rs.algorithms.merge()` for inverse-variance weighted merging of observed intensities
  - 35 Add `` for writing CCP4 map files from 3D NumPy arrays


- 20 Add `anomalous` flag to `DataSet.hkl_to_asu()`
  - 29 Fix handling of centric reflections in `DataSet.hkl_to_asu()`
  - 23 Rename `DataSet._cache_index_dtypes` to `DataSet._index_dtypes` and sensibly initialize values
  - Fix bug in `range_indexed()` decorator
  - 28 Improve handling of unmerged datasets and centrics in `DataSet.stack_anomalous()` and `DataSet.unstack_anomalous()`


- 17 Bug fix -- add decorators to facilitate inplace methods and enforcing consistent views of DataSet for methods
  -  19 Improve numerical stability for French-Wilson scaling
  - 18 Add type-checking for DataSet.cell and DataSet.spacegroup setter methods


- Adds `DataSet.expand_to_p1()`
  - Adds `DataSet.expand_anomalous()`
  - 14 Adds `DataSet.to_reciprocalgrid()` to organize `DataSet` column in a 3D NumPy array
  - Add `DataSet.to_structurefactor()` and `DataSet.from_structurefactor()` to facilitate converting to/from complex datatypes
  - 11 Add `DataSet.compute_multiplicity()` to avoid direct calls to. `rs.utils`
  - 10 Add `DataSet.label_absences()` for labeling systematic absences


- Bug fix to `rs.utils.bin_by_percentile()` in order to support data with repeated values -- enables `DataSet.assign_resolution_bins()` for unmerged data


- Add utility method for computing phase restrictions
  - Bug fixes to improve handling of the `MultiIndex` in `DataSet` built-in methods (6)
  - Add append/concat methods to `DataSet` and `rs` that preserve metadata/attributes
  - Argument to account for centering in epsilon calculation (7)
  - Improve performance of `hkl_is_absent()` and `is_centric()` through calls to `gemmi` vectorized functions
  - Add methods for binning reflections (e.g. by resolution: 9)
  - Most importantly: `rs` now has a logo... 1/:rocket:


Bug Fix:
  - Fix output of rs.mtzdump commandline tool


- Release reciprocalspaceship on PyPI


- Completed documentation including User Guide, API Reference, and For Developers sections
  - Support for reading/writing unmerged MTZ files by mapping indices based on M/ISYM flag
  - Support for converting anomalous data between 1-column and 2-column format
  - Added inference methods for MTZ dtypes
  - More complete tests for crystallographic methods over all supported spacegroups


This is the first public release of `reciprocalspaceship`.
  Updates since the last release:
  - Sphinx documentation with usage examples
  - compatibility with Pandas 1.0
  - removal of unnecessary utility functions that were specific to Hekstra lab projects
  - Change `Crystal` and `CrystalSeries` class names to `DataSet` and `DataSeries`
  - GitHub Actions for CI and publishing of documentation to gh-pages branch
  - Improved unit test coverage and report from


Initial release of reciprocalspaceship, containing a Crystal object for representing reflection tables using Pandas Dataframes.
  - Read and write MTZ files
  - Read HKL files from Precognition (Laue diffraction processing software)
  - Custom dtypes for representing crystallographic data (intensities, structure factor amplitudes, etc.)