---
name: DIALS core meeting 2022-03-03
tags: core meeting
---

# DIALS core meeting 2022-03-03

[](https://hackmd.io/zm2vjh9jSS2JMuFwFyxGyw)

This is a future meeting, please see the WIP agenda at [hackmd.io](https://hackmd.io/zm2vjh9jSS2JMuFwFyxGyw)

## Previous Actions

- [ ] dxtbx `src/` layout [[prev](https://dials.github.io/kb/core/20210715#src-layout-for-dxtbx)]
- [ ] Nick: Outstanding issues with dispatcher re-export on windows
- [ ] This is a higher priority now - David feeling pain of missing
- [ ] Also, seeing related errors "in the wild
- [ ] Nick: **Action before 3.9**
- [ ] Removal of DataBlock [[prev](https://dials.github.io/kb/core/20210909#datablock), [prev](https://dials.github.io/kb/core/20210826#removal-of-datablock)]
- [x] **Nick:** More visible deprecationwarning ([`cctbx/dxtbx#448`](https://github.com/cctbx/dxtbx/pull/448))
- Merged 23rd November. Do we want to set any plans for further?
- [ ] **Action: GW** Make a PR/branch to remove this so that we can run things against it
- [ ] Graeme _will_ do this on 18th March
- DXTBX/pycbf [[prev](https://dials.github.io/kb/core/20210826#cbflib-conda-forge-packagepycbf)]
* [ ] ND: conda-forge pycbf: Make new release to use dials-data directly for tests
* [ ] Nick: Add lots more attribution
* [x] `dxtbx`: Now 3.8.0 our can move forwards [`conda-forge/staged-recipes#16846`](https://github.com/conda-forge/staged-recipes/pull/16846)
- [ ] Nick: Make sure that HKLviewer ([prev](https://dials.github.io/kb/core/20211209#new-item-hklviewer)) works at Diamond on `module load`
- [ ] Aaron: Reduce zenodo dataset for contiguous nexus
- [ ] Put on Dan Paley backburner also - time is short
- [ ] (*) Nick: dxtbx and read-only base

## Agenda

### DXTBX read-only base
- Read only base by default would be the ideal
- Defer for two meetings - pinning on DIALS 3.2/virtualenv script working around for now

### Dropping Data Blocks

https://github.com/cctbx/dxtbx/pull/480

Drops data blocks from radial average. All good -> merge. We should enumerate where data blocks are actually used. DIALS, dxtbx, xia2, ... we should make that list.

- [ ] ASB to contact e.g. Mike Wall about this, too.
- [ ] Blocked behind GW PR

### DXTBX conda package

This we believe now exists and works. Does that mean that pycbf got in there with many attributions as we previously discussed?

### Add option for dxtbx's libtbx_refresh to not modify conda_base
- Issue [`cctbx/dxtbx#444`](https://github.com/cctbx/dxtbx/issues/444)
- ND: Add environment variable to do this
- Add this as default in the CCTBX
- Couple of false starts
- Currently awaiting feedback [`cctbx/dxtbx#474`](https://github.com/cctbx/dxtbx/pull/474)
- do for ~~DIALS~~, iota, dxtbx, xia2 when accepted
- **Top Priority**

This is queued behind catching up with Nick - it turned out to be involved.

### Contiguous Nexus

- [ ] "Contiguous Nexus" [`cctbx/dxtbx#356`](https://github.com/cctbx/dxtbx/pull/356)
- [ ] Non-draft state is pending checks against issues @dwpaley raised, and checking for non-contiguous cases [[prev](https://dials.github.io/kb/core/20210715#contiguous-nexus-pr)]
- AB wants this to be applied against new nexus writing
- RG: Probably useful to mock up an example in the nxmxtests
- **Action: Aaron** Reduce down zenodo dataset used in the issue ([`cctbx/dxtbx#93`](https://github.com/cctbx/dxtbx/issues/93))
so that we can include it in dials-data.
- Afterward: Coordinate with RG to make sure the ideas in this are integrated into new nexus reading

## PRs to remove std::string from messagepack

- ~~[`dials/dials#1982`](https://github.com/dials/dials/pull/1982)~~ DO NOT MERGE
- Discussion about how this is used in XFEL module
- **Action:** Actually try to fix this (https://github.com/dials/dials/issues/1858)

Commentary: ASB and crew have 5 experiments over the next few weeks; so yeh a bunch of stuff is gonna get bumped.

- Realistically not before April

## Still process
- Going to be a PR for "Diffbragg stage 1 refinement"
- Uses pixel models of image to refine crystal using polychromotic spectra as per Mendez 2020 paper.
- Implements an override in stills_process

ASB wants to put diffbrag stage 1 into dials.stills_process as a refinement engine. Depends on simtbx. This is very much dependent on GPU. Can use OMP etc.

- Derek Mendez going to send changes to Aaron

## Discussion

What should we do with "experimental" matters? Should new experimental programs go in? Trying to dig out legacy potatoes was a nightmare, so there is an argument for adding it on a live branch where you can merge main in from time to time.

- Discussion spawned by James explorations on dials.potatoes
- New work goes in as a branch, early on, kept up-to-date over main

### CCP4 / PHENIX

Release now held up by a program being broken, but only one. So therefore something of an unknown. Would bring CCP4 pretty much up to date.

PHENIX - depending on the readonly dxtbx stuff - until that is fixed DIALS will be pinned at 3.2 or similar. They also have a hard stop at Python 3.7, due to a slowly changing dependecy.

### Add reading and writing of flux to full CBF files
- https://github.com/cctbx/dxtbx/pull/493
- Add compatibility for current CCTBX release by calling twice with TypeError fallback
- Then merge

### Proposal for a time-of-flight beam in dxtbx.

- TOFBeam https://github.com/cctbx/dxtbx/pull/492
- Also scan object required to properly use neutron data in DIALS
- Discussion on motivation and fundings
- Add ND as a reviewer on the commit

### Mac Dispatchers
- Briefly discussed, participants not directly familiar with issue. Will continue discussing in tickets.

## Next meeting
- 13th March California clocks move forward
- 27th March UK clocks move forwards

so:

~~Thursday, March 17th, 3pm UK (GMT), 8am PDT.~~

or

~~Thursday, March 17th, 4pm UK (GMT), 9am PDT.~~

Conclusion: Skip March 17th. Next meeting will be 31st March, 4pm UK (BST), 8am PDT.