Merge remote-tracking branch 'origin/main' into fix_ssx_integrate_ima…

…geviewer

newsfragments/2590.misc

@@ -0,0 +1 @@
+Updated interfaces between DIALS and cctbx

newsfragments/2592.bugfix

@@ -0,0 +1 @@
+Reorganize imports in ``export_mtz.py`` so that its gemmi-less objects can be used by other gemmi-less software

src/dials/util/export_mtz.py

@@ -8,9 +8,13 @@
 from math import isclose
 from typing import List, Optional
 
-import gemmi
 import numpy as np
 import pandas as pd
+try:
+    import gemmi
+except ModuleNotFoundError as e:
+    gemmi = None
+    gemmi_import_error = e
 
 from cctbx import uctbx
 from dxtbx import flumpy
@@ -310,6 +314,8 @@ def add_batch_list(
     if max_batch_number > batch_offset:
         batch_offset = max_batch_number
 
+    if gemmi is None:
+        raise gemmi_import_error
     batch = gemmi.Mtz.Batch()
 
     # Setting fields that are the same for all batches
@@ -670,6 +676,8 @@ def export_mtz(
         )
 
     # Create the mtz file
+    if gemmi is None:
+        raise gemmi_import_error
     mtz = gemmi.Mtz(with_base=True)
     mtz.title = f"From {env.dispatcher_name}"
     date_str = time.strftime("%Y-%m-%d at %H:%M:%S %Z")

src/dials/util/reference.py

@@ -1,7 +1,13 @@
 from __future__ import annotations
 
 from iotbx import cif, mtz, pdb
-from mmtbx.command_line.fmodel import fmodel_from_xray_structure_master_params
+
+try:
+    from mmtbx.command_line.fmodel import (
+        fmodel_from_xray_structure_master_params as fmodel_phil,
+    )
+except ImportError:
+    from mmtbx.programs.fmodel import master_phil as fmodel_phil
 from mmtbx.utils import fmodel_from_xray_structure
 
 reference_phil_str = """
@@ -133,7 +139,7 @@ def _mmtbx_intensity_from_structure(
     """Use the mmtbx methods for quick calculation of fs from model."""
     if wavelength:
         xray_structure.set_inelastic_form_factors(photon=wavelength, table="sasaki")
-    params = fmodel_from_xray_structure_master_params.extract()
+    params = fmodel_phil.extract()
     params.high_resolution = d_min
     params.fmodel.k_sol = k_sol
     params.fmodel.b_sol = b_sol