--- name: DIALS core meeting 2022-03-31 tags: core meeting --- # DIALS core meeting 2022-03-31 [![hackmd-github-sync-badge](https://hackmd.io/s8v-dkcDSPibqZ3VtG_6ZA/badge)](https://hackmd.io/s8v-dkcDSPibqZ3VtG_6ZA) ## Previous Actions - [ ] (*) Removal of DataBlock [[prev](https://dials.github.io/kb/core/20210909#datablock), [prev](https://dials.github.io/kb/core/20210826#removal-of-datablock)] - [ ] **Action: GW** Make a PR/branch to remove this so that we can run things against it - [ ] Graeme _will_ do this on 18th March - [ ] Behold \o/ [`cctbx/dxtbx#504`](https://github.com/cctbx/dxtbx/pull/504) - [x] (*) DXTBX/pycbf [[prev](https://dials.github.io/kb/core/20210826#cbflib-conda-forge-packagepycbf)] * [x] ND: conda-forge pycbf: Make new release to use dials-data directly for tests * [x] Nick: Add lots more attribution - [ ] (*) Nick: dxtbx and read-only base - [ ] Nick: Make sure that HKLviewer ([prev](https://dials.github.io/kb/core/20211209#new-item-hklviewer)) works at Diamond on `module load` - [ ] Attempted, installing pyside2 is easy, but fails after that ([log](https://gist.github.com/ndevenish/fce20861a335385a5a65ed27c982e141)) - [ ] **Action** ND: ask RO about this - [ ] Aaron: Reduce zenodo dataset for contiguous nexus - [ ] Put on Dan Paley backburner also - time is short - [x] On the Todo list now! - [ ] ND to review: TOFBeam - A time-of-flight beam in dxtbx [`cctbx/dxtbx#492`](https://github.com/cctbx/dxtbx/pull/492) ([prev](https://dials.github.io/kb/core/20220303#proposal-for-a-time-of-flight-beam-in-dxtbx)) - [ ] Continue to discuss mac dispatcher issues (e.g. no GUI launch for image_viewer etc) in issues ([`cctbx/cctbx_project#739`](https://github.com/cctbx/cctbx_project/issues/739)) - [ ] `std::string` support for messagepack. This is used in XFEL module, should try to fix. [`dials/dials#1858`](https://github.com/dials/dials/issues/1858). - [ ] Actually try to fix this - [x] This is not going to happen before April at the earliest ## Agenda ### Dropping Data Blocks https://github.com/cctbx/dxtbx/pull/504 - [x] GW PR - [ ] After PR/PRs, ASB to contact e.g. Mike Wall about this, too. - GW thinks reasonable to merge when these concerns addressed ### 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 ### Add known_orientations to dials.stills_process https://github.com/dials/dials/commit/eb7967fbd4be133b6f631af2ac14ac5e2697bca2 ### Pathlib changes https://github.com/dials/dials/pull/2038 - Expecting this to be ready soon - Is a big pull request - Send out notice - **Action**: GW to send out notice to dials-support ## Deferred to next meeting ### PyCBF - Version 0.9.6.5 now out - Added more attribution in [`dials/pycbf@b8d4f6`](https://github.com/dials/pycbf/commit/b8d4f6ed47588a1145430f6fb53dbea9aec51e5d) and [`conda-forge/pycbf-feedstock#10`](https://github.com/conda-forge/pycbf-feedstock/pull/10) - Now uses dials-data for testing data - Added windows build: [`dials/pycbf#21`](https://github.com/dials/pycbf/pull/21) - somewhat scattered list of changes applied to CBFlib, at pycbf-build-time in [`002_windows.patch`](https://github.com/dials/pycbf/blob/56e99bafe9fded6d4a738febb943bf102d58b414/patches/002_windows.patch) - Wheels live for multiple manylinux flavors, MacOS x86/arm, windows 64bit/32bit, for Pythons 3.6/3.7/3.8/3.9 live on pypi and, conda-forge mac/mac-arm/linux/windows 3.6/7/8/9/10. ### DXTBX read-only base - Read only base by default would be the ideal - Turned out to be more involved - Previously discussed downstream use cases and if DIALS needs to be included - 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 dependency. - Defer for two meetings - pinning on DIALS 3.2/virtualenv script working around for now - Issue [`cctbx/dxtbx#444`](https://github.com/cctbx/dxtbx/issues/444) - **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 ### Next meeting Thursday, April 14th, 4pm UK (BST), 8am PDT.