Kevin Dalton

I am unsure if this is a bug in Gemmi or a bug in Sgtbx. Either way it is probably academic. The following script can be used to confirm that...

[Feature Request] dials.symmetry Should Use a Fourier Analysis to Detect Screw Axes

6

As discussed in #1742, Fourier analysis is an effective strategy to detect screw axes which is robust to systematic errors in background estimates. [Pointless](http://scripts.iucr.org/cgi-bin/paper?S090744491003982X), appears to use such a strategy...

Command line application unavailable from PyPI

3

Whenever I `pip install gemmi`, the `gemmi` program does not end up in my path. Actually, I'm not even certain the binary ends up on my disk at all. I...

Faster parser for CrystFEL stream files

10

I wrote a faster version of the stream file parser. It mostly just uses more numpy and less pandas while vectorizing operations within a crystal block.

mean_intensity_by_miller_index should use a grid

1

[Isotropic French-Wilson scaling](https://github.com/rs-station/reciprocalspaceship/blob/a4c97e4520101e9d4ff6b91a9af75e18124d3e4a/reciprocalspaceship/algorithms/scale_merged_intensities.py#L129) uses grid points to efficiently estimate the resolution-dependent average intensity. However, [anisotropic scaling](https://github.com/rs-station/reciprocalspaceship/blob/a4c97e4520101e9d4ff6b91a9af75e18124d3e4a/reciprocalspaceship/algorithms/scale_merged_intensities.py#L98) currently does not. It just computes the full kernel matrix one row at a...

No documentation of CrystFEL columns

1

The [docstring](https://github.com/rs-station/reciprocalspaceship/blob/3809a90c343e9e721dad4fcf0e09b58d8ed8467c/reciprocalspaceship/io/crystfel.py#L217) for `rs.read_crystfel`doesn't say anything about the columns in the dataset which it returns. I suggest the following descriptions as a start: - XDET,YDET : internal detector panel coordinates...

`rs.DataSet.reset_index()` call signature does not match pandas >1.5

1

With pandas version 2.0.3 and rs 1.0.1, calling `reset_index` on a `DataSeries` instance leads to a type error. ``` [nav] In [18]: rs.DataSeries(range(10)).reset_index() --------------------------------------------------------------------------- TypeError Traceback (most recent call last)...

unstack_anomalous makes data that phenix cannot interpret

3

When intensities and structure factors are both present in an unstacked, anomalous dataset, the stack_anomalous output cannot be interpreted by phenix because the column order is not as expected. In...

groupby apply drops cell and spacegroup

2

Installing `rs` from pypi with the following: ```bash conda create -n rs python=3.10 pip install --upgrade pip pip install reciprocalspaceship ``` I have `rs=0.10.3` and `pandas=1.4.4`. ```python import numpy as...

`stack_anomalous` inside `groupby` breaks `as_index=False`

1

When called inside a `groupby.apply` context, `stack_anomalous` overrides the `as_index=False` setting and appends the grouping column to the index of the returned dataset with name `None` ```python import numpy as...