---
# System prepended metadata

title: DIALS core meeting 2022-02-03
tags: [core meeting]

---

---
name: DIALS core meeting 2022-02-03
tags: core meeting
---

# DIALS core meeting 2022-02-03


## 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
- 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
    * [ ] `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
- [ ] (*) Nick: dxtbx and read-only base


## Agenda

### 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**


### 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)


### Merging of tables/experiments

- Make merging of tables and resolution of experiment identifiers easier **Action: JBE** - work out what we need to handle and how to do this
    - https://github.com/dials/dials/pull/1994
    - [x] **Aaron**: Write issue describing usage https://github.com/dials/dials/issues/1983
- Remove existing usage of std::string in XFEL modules


## 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

## Deferred to next meeting



### Next meeting
Thursday, February 17th, 4pm UK (GMT), 8am PT.