From d2f8e5f5ca3ec26a89be840da24e5e4ff75a9a77 Mon Sep 17 00:00:00 2001 From: James Beilsten-Edmands <30625594+jbeilstenedmands@users.noreply.github.com> Date: Mon, 26 Feb 2024 12:14:07 +0000 Subject: [PATCH] Fix scipy deprecation warning and doc build failure in pinkindexer.py (#2617) --- newsfragments/2617.misc | 1 + src/dials/algorithms/indexing/lattice_search/pinkindexer.py | 6 +++++- 2 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 newsfragments/2617.misc diff --git a/newsfragments/2617.misc b/newsfragments/2617.misc new file mode 100644 index 0000000000..b7adf88987 --- /dev/null +++ b/newsfragments/2617.misc @@ -0,0 +1 @@ +Fix Deprecation warning and doc build failure for pinkindexer file diff --git a/src/dials/algorithms/indexing/lattice_search/pinkindexer.py b/src/dials/algorithms/indexing/lattice_search/pinkindexer.py index dd1123b72c..4a11c029e2 100644 --- a/src/dials/algorithms/indexing/lattice_search/pinkindexer.py +++ b/src/dials/algorithms/indexing/lattice_search/pinkindexer.py @@ -4,7 +4,7 @@ import gemmi import numpy as np -from scipy.spatial.transform.rotation import Rotation +from scipy.spatial.transform import Rotation import iotbx.phil from dxtbx.model import Crystal @@ -348,6 +348,7 @@ def index_pink( class PinkIndexer(Strategy): """ A lattice search strategy using the pinkIndexer algorithm. + For more info, see: [Gevorkov Y, et al. pinkIndexer – a universal indexer for pink-beam X-ray and electron diffraction snapshots. Acta Cryst A. 2020 Mar 1;76(2):121–31.](https://doi.org/10.1107/S2053273319015559) """ @@ -364,10 +365,13 @@ def __init__( self, target_symmetry_primitive, max_lattices, params=None, *args, **kwargs ): """Construct PinkIndexer object. + Args: target_symmetry_primitive (cctbx.crystal.symmetry): The target crystal symmetry and unit cell + max_lattices (int): The maximum number of lattice models to find + params (phil,optional): Phil params """ super().__init__(params=None, *args, **kwargs)