[cctbxbb] use_internal_variance in iotbx.merging_statistics

[Keitaro Yamashita]

Dear Phenix/CCTBX developers,

iotbx/merging_statistics.py is used by phenix.merging_statistics,
phenix.table_one, and so on. By upgrading phenix from 1.10.1 to 1.11,
merging statistics-related codes were significantly changed.

Previously, miller.array.merge_equivalents() was always called with
argument use_internal_variance=False, which is consistent with XDS,
Aimless and so on. Currently, use_internal_variance=True is default,
and cannot be changed by users (see below).

These changes were made by @afonine and @rjgildea in rev. 22973 (Sep
26, 2015) and 23961 (Mar 8, 2016). Could anyone explain why these
changes were introduced?

https://sourceforge.net/p/cctbx/code/22973
https://sourceforge.net/p/cctbx/code/23961


My points are:

- We actually cannot control use_internal_variance= parameter because
it is not passed to merge_equivalents() in class
filter_intensities_by_sigma.

- In previous versions, if I gave XDS output to
phenix.merging_statistics, <I/sigma> values calculated in the same way
(as XDS does) were shown; but not in the current version.

- For (for example) phenix.table_one users who expect this behavior,
it can give inconsistency. The statistics would not be consistent with
the data used in refinement.


cf. the related discussion in cctbxbb:
http://phenix-online.org/pipermail/cctbxbb/2012-October/000611.html


Best regards,
Keitaro