Nicholas Devenish

Rework/Enhance help and usage

1

Generally reworked help output to be a little more like what I expect (or, at least, like python's argparse) - Added metavars. If set, then will be used in help...

So that you can pass long options as `./test --option=value` in addition to the currently supported `./test --option value`. This is done by simply pre-parsing the argument list and splitting...

GUI dispatchers don't seem to work on Mac

5

Saw a while ago on DIALS, but intermittently. It seems to have come back: https://github.com/dials/dials/issues/1460 Reproducible directly for me with conda-forge `cctbx=2022.1` on macOS Big Sur 11.5.2/arm64: ``` $ mamba...

Linux base build fails recent ubuntu (glib, etc)

8

I'm bootstrapping on a fresh Ubuntu 17.10 VM, `gcc 7.2.0`. The base installation fails on `glib` with: ``` CC libglib_2_0_la-gdate.lo gdate.c: In function 'g_date_strftime': gdate.c:2497:7: error: format not a string...

bootstrap base fails with (inactive) unicode conda environments

2

``` $ conda create -p "some_🤔" $ ./bootstrap.py base --use-conda Performing actions: base Installing base packages using: python modules/cctbx_project/libtbx/auto_build/install_conda.py --builder=cctbx --install_conda removing .pyc files in /Users/nickd/dials/dist_1.14/modules, walk? True removed 1...

Conda issues

7

Mentioned in https://github.com/cctbx/cctbx_project/commit/6a8503a98b2e251be0b31806a0e5e20751b10055#commitcomment-32583542 that I'd had some problems using conda. Decided to post in a separate issue. I also had a quick poke over the weekend and noticed a few...

The deprecated parts removed: - ``dials.algorithms.symmetry.cosym.target.Target.get_sym_ops()`` function (deprecated in December 2020). - The ``nproc`` argument to the `Target` constructor (deprecated 2021) - ``dials.util.mp.parallel_map`` function (deprecated DIALS 3.9 https://github.com/dials/dials/commit/aed9914672df354180a82836759be452c673342d) - ``dials.command_line.dials_import.ImageImporter``...

Minor find_spots_server tweaks

1

Fixed a case where it would fail to start, but this would not be detected. Tidy up termination logic so that you don't need to send `nproc=` termination signals to...

reflection_table std::string messagepack writing is completely broken

6

It supports writing of `std::string` arrays https://github.com/dials/dials/blob/e129e6c3870e2d606ac8c39e65f2e5aa1027eed8/array_family/reflection_table_msgpack_adapter.h#L665-L666 but does so in a broken way; It uses the same "ref/versa" writing as all the standard objects: https://github.com/dials/dials/blob/e129e6c3870e2d606ac8c39e65f2e5aa1027eed8/array_family/reflection_table_msgpack_adapter.h#L171-L173 This means that it...

Cosym dimensions=auto: exit early if found elbow point

1

[Restoration of reverted #1699, as it had test failures] If there are at least two "flat" points after a potential elbow point then exit the optimisation early, rather than continuing...