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DIALS 3.15.2 #185

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wants to merge 26 commits into from
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DIALS 3.15.2 #185

wants to merge 26 commits into from

Commits on Jun 13, 2023

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Commits on Jun 16, 2023

  1. Remove dxtbx procrunner dependency (cctbx#640)

    There is no longer any reason to use procrunner in place of built-in subprocess
    rjgildea committed Jun 16, 2023
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Commits on Jun 27, 2023

  1. Fix for nxmx import overwritten by local variable (cctbx#641)

    * Unbreak help test
    * explicitly set program name
    * minor change to docstring
    
    * Fix for nxmx import overwritten by local variable
    
    Introduced by cctbx#597
    
    Another case were bugs have crept in through lack of tests (see cctbx#470)
    
    * news
    
    * Rename newsfragments/XXX.bugfix to newsfragments/641.bugfix
    rjgildea committed Jun 27, 2023
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Commits on Jun 29, 2023

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  2. Use importlib instead of pkg_resources (cctbx#643)

    pkg_resources is now deprecated, as importlib has covered
    most use-cases since python 3.8. This removes the code
    causing warnings in downstream tests.
    
    Also suppress numpy 'product' warnings when running pytest.
    ndevenish committed Jun 29, 2023
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Commits on Jun 30, 2023

  1. Drop Python 3.8 support (cctbx#642)

    Upstream dependencies (e.g. numpy, scipy) have now dropped Python 3.8
    support in latest releases.
    
    Add Python 3.11 support.
    
    See also https://dials.github.io/kb/proposals/dc3
    
    ---------
    
    Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>
    rjgildea and ndevenish committed Jun 30, 2023
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Commits on Jul 25, 2023

  1. Easier override of panel geometry (cctbx#644)

    When setting panels by PHIL, merge multiple definitions first by id. This fixes cctbx#299.
    dagewa committed Jul 25, 2023
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  2. Flumpy: Don't allow converting 1D vectors to vec2/3 (cctbx#648)

    Previously, a size (3,) array would have erroneously converted
    to a 0x3 length vec3.
    
    This is now explicitly forbidden; you must pass at least a (0, 3)
    multidimensional array.
    
    Fixes cctbx#439.
    ndevenish committed Jul 25, 2023
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Commits on Jul 26, 2023

  1. FormatROD (cctbx#645)

    Partial support for Rigaku Oxford Diffraction format images.
    ---------
    
    Co-authored-by: Takanori Nakane <nakane.t@gmail.com>
    Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>
    3 people committed Jul 26, 2023
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  2. Check Registry against refl/expt files (cctbx#650)

    This was previously done implicitly, but only when dials_regression
    was present. This makes the test explicit, and works with
    dials-data (so that it will work on e.g. CI with restricted access
    to test cases).
    ndevenish committed Jul 26, 2023
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  3. Make Imageset slices consistently index from 0

    Without this, slices sometimes needed to be indexed by their original
    image index, even inside the slice.
    
    The previous workaround in 67aab2 (cctbx#485) for negative offset was
    reacting to the erroneous behaviour introduced by including batch
    offsets in imagesequence slicing.
    dagewa committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. MNT: Update CMake modules path relative to script

    Without this, dxtbx did not work as a subdirectory in
    a larger CMakeLists project.
    ndevenish committed Jul 27, 2023
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Commits on Jul 31, 2023

  1. Fixes for EMBL beamlines at PETRA (cctbx#626)

    The E-32-0017 Eiger moved to P13 on 2021-5-22, where the goniometer axis no
    longer needs overriding.
    
    Check for that date in the MiniCBF, and check for the serial matching the date
    range.
    
    Co-authored-by: Christian Becke <christian.becke@fu-berlin.de>
    Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>
    3 people committed Jul 31, 2023
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Commits on Aug 2, 2023

  1. Add polychromatic beam (cctbx#621)

    Add new Beam class "PolychromaticBeam" for polychromatic/multi-wavelength/wide bandpass experiments.
    
    ---------
    
    Co-authored-by: DiamondLightSource-build-server <DiamondLightSource-build-server@users.noreply.github.com>
    Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>
    3 people committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. FormatROD - Multi-axis goniometer, faster decompression (cctbx#653)

    Co-authored-by: Takanori Nakane <nakane.t@gmail.com>
    2 people authored and ndevenish committed Aug 3, 2023
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Commits on Aug 4, 2023

  1. Add probe type to the Beam model (cctbx#647)

    At the moment this just adds the additional datum and allows
    serialisation etc. Old experiment files where this is not set are
    interpreted as having Probe.xray. Some electron diffraction format
    classes are updated here to record Probe.electron.
    
    Co-authored-by: davidmcdonagh <davidnmcdonagh@gmail.com>
    dagewa and toastisme committed Aug 4, 2023
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Commits on Aug 8, 2023

  1. Fix bit depth for Eiger / NXmx for i19-2 (cctbx#652)

    Fix bit depth for Eiger / NXmx for i19-2
    
    Add bit depth check from image metadata as implemented on other Diamond NXmx
    installations. Fixes dials/dials#2473
    graeme-winter committed Aug 8, 2023
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Commits on Aug 10, 2023

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Commits on Aug 11, 2023

  1. NXmx: handle multidimensional arrays (cctbx#612)

    Data in NeXus can be 3 or 4 dimensional.
    3D: Nimages by slow by fast
    4D: Nimages by Nmodules by slow fast
    
    Slice image_size and reshape the raw_data in these cases.
    
    Co-authored-by: Richard Gildea <rjgildea@users.noreply.github.com>
    phyy-nx and rjgildea committed Aug 11, 2023
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Commits on Aug 13, 2023

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Commits on Aug 14, 2023

  1. dxtbx 3.16.0 Changelog

        towncrier --name=dxtbx --version='3.16.0'
    DiamondLightSource-build-server committed Aug 14, 2023
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  2. Ignore trusted-range in dxtbx.average test

    This behaviour has changed in cctbx, however has not been
    backported to the release.
    ndevenish authored and DiamondLightSource-build-server committed Aug 14, 2023
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