DIALS 3.8.1

Improved Documentation
----------------------

- ``xia2.multiplex``: Add, and update, PHIL parameter descriptions. (xia2#644)

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.8.0
+current_version = 3.8.1
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<release>[a-z]+)?(?P<patch>\d+)?

CHANGELOG.rst

@@ -1,3 +1,12 @@
+xia2 3.8.1 (2022-01-25)
+=======================
+
+Improved Documentation
+----------------------
+
+- ``xia2.multiplex``: Add, and update, PHIL parameter descriptions. (`#644 <https://github.com/xia2/xia2/issues/644>`_)
+
+
 xia2 3.8.0 (2022-01-11)
 =======================
 

setup.py

@@ -4,7 +4,7 @@
 
 # Version number is determined either by git revision (which takes precendence)
 # or a static version number which is updated by bump2version
-__version_tag__ = "3.8.0"
+__version_tag__ = "3.8.1"
 
 console_scripts = [
     "dev.xia2.check_mosaic=xia2.cli.check_mosaic:run",

src/xia2/Modules/MultiCrystal/ScaleAndMerge.py

@@ -44,7 +44,9 @@
 # The phil scope
 phil_scope = iotbx.phil.parse(
     """
-unit_cell_clustering {
+unit_cell_clustering
+  .short_caption = "Unit cell clustering"
+{
   threshold = 5000
     .type = float(value_min=0)
     .help = 'Threshold value for the clustering'
@@ -54,6 +56,7 @@
 }
 
 scaling
+  .short_caption = "Scaling"
 {
   anomalous = False
     .help = "Separate anomalous pairs in scaling and error model optimisation."
@@ -74,22 +77,30 @@
     share.absorption = False
       .type = bool
       .expert_level = 2
-      .short_caption = "Apply a shared absorption correction between sweeps. Only"
-                       "suitable for scaling measurements from a single crystal."
+      .short_caption = "Shared absorption correction"
+      .help = "Apply a shared absorption correction between sweeps. Only"
+              "suitable for scaling measurements from a single crystal."
   }
   absorption_level = low medium high
     .type = choice
     .expert_level = 2
-    .short_caption = "Set the extent of absorption correction in scaling"
+    .help = "Set the extent of absorption correction in scaling"
+    .short_caption = "Absorption level"
   model = physical dose_decay array KB *auto
     .type = choice
+    .short_caption = "Scaling model"
   outlier_rejection = simple standard
     .type = choice
+    .short_caption = "Outlier rejection"
   min_partiality = None
     .type = float(value_min=0, value_max=1)
+    .short_caption = "Minimum partiality"
   partiality_cutoff = None
     .type = float(value_min=0, value_max=1)
-  reflection_selection {
+    .short_caption = "Partiality cutoff"
+  reflection_selection
+    .short_caption = "Reflection selection"
+  {
     method = quasi_random intensity_ranges use_all random
       .type = choice
       .help = "Method to use when choosing a reflection subset for scaling model"
@@ -106,22 +117,31 @@
               "slow for large datasets."
     Isigma_range = None
       .type = floats(size=2)
+      .short_caption = "I/σ range"
+      .help = "Minimum and maximum I/sigma values used to select a subset of"
+              "reflections for minimisation. A value of 0.0 for the maximum"
+              "indicates that no upper limit should be applied."
   }
 }
-symmetry {
+symmetry
+  .short_caption = "Symmetry"
+{
   resolve_indexing_ambiguity = True
     .type = bool
+    .short_caption = "Resolve indexing ambiguity"
   cosym {
     include scope dials.algorithms.symmetry.cosym.phil_scope
   }
   laue_group = None
     .type = space_group
-    .help = "Specify the Laue group. If None, then the Laue group will be determined "
+    .help = "Specify the Laue group. If None, then the Laue group will be determined"
             "by dials.cosym."
+    .short_caption = "Laue group"
   space_group = None
     .type = space_group
-    .help = "Specify the space group. If None, then the dials.symmetry will perform "
+    .help = "Specify the space group. If None, then the dials.symmetry will perform"
             "analysis of systematically absent reflections to determine the space group."
+    .short_caption = "Space group"
 }
 
 resolution
@@ -141,69 +161,91 @@
 rescale_after_resolution_cutoff = False
   .help = "Re-scale the data after application of a resolution cutoff"
   .type = bool
+  .short_caption = "Rescale after resolution cutoff"
 
-filtering {
+filtering
+  .short_caption = "Filtering"
+{
 
   method = None deltacchalf
     .type = choice
     .help = "Choice of whether to do any filtering cycles, default None."
 
-  deltacchalf {
+  deltacchalf
+    .short_caption = "ΔCC½"
+  {
     max_cycles = None
       .type = int(value_min=1)
+      .short_caption = "Maximum number of cycles"
     max_percent_removed = None
       .type = float
+      .short_caption = "Maximum percentage removed"
     min_completeness = None
       .type = float(value_min=0, value_max=100)
       .help = "Desired minimum completeness, as a percentage (0 - 100)."
+      .short_caption = "Minimum completeness"
     mode = dataset image_group
       .type = choice
       .help = "Perform analysis on whole datasets or batch groups"
     group_size = None
       .type = int(value_min=1)
       .help = "The number of images to group together when calculating delta"
               "cchalf in image_group mode"
+      .short_caption = "Group size"
     stdcutoff = None
       .type = float
       .help = "Datasets with a ΔCC½ below (mean - stdcutoff*std) are removed"
+      .short_caption = "Standard deviation cutoff"
   }
 }
 
 multi_crystal_analysis {
   include scope xia2.Modules.MultiCrystal.master_phil_scope
 }
 
-unit_cell {
+unit_cell
+  .short_caption = "Unit cell"
+{
   refine = *two_theta
     .type = choice(multi=True)
 }
 
-two_theta_refine {
+two_theta_refine
+  .short_caption = "2θ refinement"
+{
   combine_crystal_models = True
     .type = bool
+    .short_caption = "Combine crystal models"
 }
 
 min_completeness = None
   .type = float(value_min=0, value_max=1)
+  .short_caption = "Minimum completeness"
 min_multiplicity = None
   .type = float(value_min=0)
+  .short_caption = "Minimum multiplicity"
 max_clusters = None
   .type = int(value_min=1)
+  .short_caption = "Maximum number of clusters"
 cluster_method = *cos_angle correlation unit_cell
   .type = choice
+  .short_caption = "Metric on which to perform clustering"
 
 identifiers = None
   .type = strings
+  .short_caption = "Identifiers"
 
 dose = None
   .type = ints(size=2, value_min=0)
+  .short_caption = "Dose"
 
 nproc = Auto
   .type = int(value_min=1)
   .help = "The number of processors to use"
   .expert_level = 0
 remove_profile_fitting_failures = True
   .type = bool
+  .short_caption = "Remove profile fitting failures"
 
 """,
     process_includes=True,

src/xia2/Modules/MultiCrystal/__init__.py

@@ -27,10 +27,13 @@
     """\
 unit_cell = None
   .type = unit_cell
+  .short_caption = "Unit cell"
 n_bins = 20
   .type = int(value_min=1)
+  .short_caption = "Number of bins"
 d_min = None
   .type = float(value_min=0)
+  .short_caption = "High resolution cutoff"
 %s
 """
     % batch_phil_scope