--- name: DIALS core meeting 2022-03-03 tags: core meeting --- # DIALS core meeting 2022-03-03 [![hackmd-github-sync-badge](https://hackmd.io/zm2vjh9jSS2JMuFwFyxGyw/badge)](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.