Merge remote-tracking branch 'upstream/main' into tof_indexing_refine…

…ment
toastisme · Jun 19, 2024 · 427b805 · 427b805
2 parents 0a47047 + 64e6b8e
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diff --git a/.azure-pipelines/azure-pipelines.yml b/.azure-pipelines/azure-pipelines.yml
@@ -2,7 +2,7 @@ variables:
  CACHE_VERSION: 20201102
  isPullRequest: $[startsWith(variables['Build.SourceBranch'], 'refs/pull/')]
  PYTHON_MINIMUM_VERSION: "3.9"
- PYTHON_TESTING_VERSION: "3.11"
+ PYTHON_TESTING_VERSION: "3.12"
 
 stages:
 - stage: prepare

diff --git a/.conda-envs/linux.txt b/.conda-envs/linux.txt
@@ -11,14 +11,15 @@ conda-forge::eigen
 conda-forge::future
 conda-forge::gemmi>=0.6.5
 conda-forge::h5py>=3.1.0
-conda-forge::hdf5<1.13
+conda-forge::hdf5
 conda-forge::hdf5plugin
 conda-forge::iota
 conda-forge::jinja2
-conda-forge::jpeg
 conda-forge::libboost-devel
 conda-forge::libboost-python-devel
+conda-forge::libglu
 conda-forge::matplotlib-base>=3.0.2
+conda-forge::mesa-libgl-devel-cos7-x86_64
 conda-forge::mrcfile
 conda-forge::msgpack-cxx
 conda-forge::msgpack-python

diff --git a/.conda-envs/macos.txt b/.conda-envs/macos.txt
@@ -11,11 +11,10 @@ conda-forge::eigen
 conda-forge::future
 conda-forge::gemmi>=0.6.5
 conda-forge::h5py>=3.1.0
-conda-forge::hdf5<1.13
+conda-forge::hdf5
 conda-forge::hdf5plugin
 conda-forge::iota
 conda-forge::jinja2
-conda-forge::jpeg
 conda-forge::libboost-devel
 conda-forge::libboost-python-devel
 conda-forge::libcxx
@@ -53,6 +52,6 @@ conda-forge::sqlite
 conda-forge::tabulate
 conda-forge::tqdm
 conda-forge::urllib3
-conda-forge::wxpython>=4.2.0
+conda-forge::wxpython>=4.2.0=*_5
 conda-forge::xz
 conda-forge::zlib
diff --git a/.conda-envs/windows.txt b/.conda-envs/windows.txt
@@ -11,11 +11,10 @@ conda-forge::eigen
 conda-forge::future
 conda-forge::gemmi>=0.6.5
 conda-forge::h5py>=3.1.0
-conda-forge::hdf5<1.13
+conda-forge::hdf5
 conda-forge::hdf5plugin
 conda-forge::iota
 conda-forge::jinja2
-conda-forge::jpeg
 conda-forge::libboost-devel
 conda-forge::libboost-python-devel
 conda-forge::matplotlib-base>=3.0.2

diff --git a/AUTHORS b/AUTHORS
@@ -2,6 +2,7 @@ Contributors include:
 
 Aaron Brewster
 Ammaar Saeed
+Amy Thompson
 Asmit Bhowmick
 Benjamin Williams
 Billy Poon

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,3 +1,44 @@
+DIALS 3.19.1 (2024-05-23)
+=========================
+
+No significant changes.
+
+
+DIALS 3.19.0 (2024-04-17)
+=========================
+
+Features
+--------
+
+- ``dials.predict``: Allow usage when image data are not available. (`#2553 <https://github.com/dials/dials/issues/2553>`_)
+- Add ``TOFSpotFinder`` to tailor default params to time of flight experiments and add additional reflection table data. (`#2602 <https://github.com/dials/dials/issues/2602>`_)
+- ``dials.ssx_index``: Allow use of sequences indexer, pink_indexer and low_res_spot_match indexing algorithms. (`#2614 <https://github.com/dials/dials/issues/2614>`_)
+- ``dials.export``: Add option ``composition=`` to specify of asymmetric unit composition for SHELX ``.ins`` file output. (`#2623 <https://github.com/dials/dials/issues/2623>`_)
+
+
+Bugfixes
+--------
+
+- Fix building on RHEL8 and other more recent distributions. (`#1465 <https://github.com/dials/dials/issues/1465>`_)
+- ``dials.index``: Joint indexing is automatically set on for rotation data, off for still data. This can be overridden by explicit use of ``joint_indexing=``. (`#2605 <https://github.com/dials/dials/issues/2605>`_)
+- ``dials.export`` ``format=shelx``: Increased precision of unit cell parameters and their estimated standard deviations written to ``.ins`` file. (`#2624 <https://github.com/dials/dials/issues/2624>`_)
+- ``dials.ssx_index``: Don't combine detector models if individually refined. (`#2634 <https://github.com/dials/dials/issues/2634>`_)
+- ``dials.scale``: Fix error in propagation of partiality variance, when scaling still data. (`#2642 <https://github.com/dials/dials/issues/2642>`_)
+- ``dials.export``: Fix crash when exporting scaled still-shot data. (`#2646 <https://github.com/dials/dials/issues/2646>`_)
+
+
+Deprecations and Removals
+-------------------------
+
+- API: ``array_family/flex_ext.py``: remove ``nthread``s parameter from ``extract_shoeboxes``, as it was never implemented. (`#2638 <https://github.com/dials/dials/issues/2638>`_)
+
+
+Misc
+----
+
+- `#2617 <https://github.com/dials/dials/issues/2617>`_, `#2618 <https://github.com/dials/dials/issues/2618>`_, `#2619 <https://github.com/dials/dials/issues/2619>`_, `#2626 <https://github.com/dials/dials/issues/2626>`_, `#2633 <https://github.com/dials/dials/issues/2633>`_, `#2648 <https://github.com/dials/dials/issues/2648>`_
+
+
 DIALS 3.18.1 (2024-03-26)
 =========================
 

diff --git a/installer/bootstrap.py b/installer/bootstrap.py
@@ -50,7 +50,7 @@
 allowed_ssh_connections = {}
 concurrent_git_connection_limit = threading.Semaphore(5)
 
-_prebuilt_cctbx_base = "2023" # Latest Nightly release
+_prebuilt_cctbx_base = "2024"
 
 
 def make_executable(filepath):
@@ -1432,8 +1432,8 @@ def run():
  parser.add_argument(
  "--python",
  help="Install this minor version of Python (default: %(default)s)",
- default="3.10",
- choices=("3.9", "3.10", "3.11"),
+ default="3.11",
+ choices=("3.9", "3.10", "3.11", "3.12"),
  )
  parser.add_argument(
  "--branch",

diff --git a/newsfragments/2553.feature b/newsfragments/2553.feature
diff --git a/newsfragments/2602.feature b/newsfragments/2602.feature
diff --git a/newsfragments/2605.bugfix b/newsfragments/2605.bugfix
diff --git a/newsfragments/2613.misc b/newsfragments/2613.misc
@@ -0,0 +1 @@
+Update cctbx-base dependency to 2024 versions.
diff --git a/newsfragments/2614.feature b/newsfragments/2614.feature
diff --git a/newsfragments/2616.misc b/newsfragments/2616.misc
@@ -0,0 +1 @@
+``dials.import``: add a test for distance overrides for a multi-panel detector.
diff --git a/newsfragments/2617.misc b/newsfragments/2617.misc
diff --git a/newsfragments/2618.misc b/newsfragments/2618.misc
diff --git a/newsfragments/2619.misc b/newsfragments/2619.misc
diff --git a/newsfragments/2626.misc b/newsfragments/2626.misc
diff --git a/newsfragments/2632.feature b/newsfragments/2632.feature
@@ -0,0 +1 @@
+``dials.correlation_matrix``: A new command-line tool for correlation and cosine similarity clustering of multi-crystal datasets, independent of ``xia2.multiplex``. It provides HTML output, including clustering heatmaps, dendrograms and corresponding ``dials.cosym`` graphs.
diff --git a/newsfragments/2633.misc b/newsfragments/2633.misc
diff --git a/newsfragments/2634.bugfix b/newsfragments/2634.bugfix
diff --git a/newsfragments/2641.misc b/newsfragments/2641.misc
@@ -0,0 +1 @@
+Remove find_spots_server_client tests.
diff --git a/newsfragments/2651.feature b/newsfragments/2651.feature
@@ -0,0 +1 @@
+DIALS is now compatible with Python 3.12.
diff --git a/newsfragments/2654.feature b/newsfragments/2654.feature
@@ -0,0 +1 @@
+``dials.scale``: Add filtering options to default basic error model to allow error modelling of stills data
diff --git a/newsfragments/2658.bugfix b/newsfragments/2658.bugfix
@@ -0,0 +1 @@
+``dials.find_rotation_axis``: Correctly set the orientation of the rotation axis for a multi-axis goniometer.
diff --git a/newsfragments/2660.bugfix b/newsfragments/2660.bugfix
@@ -0,0 +1 @@
+Fix `dials.show` beam checks for time of flight experiments.
diff --git a/newsfragments/2664.bugfix b/newsfragments/2664.bugfix
@@ -0,0 +1 @@
+d_min, d_max in masking: raise error if d_min > d_max so no spots will be found
diff --git a/newsfragments/2666.feature b/newsfragments/2666.feature
@@ -0,0 +1 @@
+``dials.cosym``: Add alternative weighting during cosym CC calculation
diff --git a/newsfragments/2667.misc b/newsfragments/2667.misc
@@ -0,0 +1 @@
+Reset ids in image grouping code to enable use in scripts
diff --git a/newsfragments/2668.bugfix b/newsfragments/2668.bugfix
@@ -0,0 +1 @@
+``dials.cosym``: Make function return structure correct in recently added cc_weights option
diff --git a/newsfragments/2670.bugfix b/newsfragments/2670.bugfix
@@ -0,0 +1 @@
+``dials.find_rotation_axis``: Add reflection selection criteria to avoid runs that use a very large amount of memory.
diff --git a/newsfragments/2671.feature b/newsfragments/2671.feature
@@ -0,0 +1 @@
+``dials.correlation_matrix``: Add tables with cluster information to html output
diff --git a/newsfragments/2672.feature b/newsfragments/2672.feature
@@ -0,0 +1 @@
+XXX.feature: Add dials.split_still_data for splitting dials-processed still data based on image number (e.g. dose series)
diff --git a/newsfragments/2673.bugfix b/newsfragments/2673.bugfix
@@ -0,0 +1 @@
+``dials.cosym``: For cc_weights=sigma, ensure correct filtering based on min_pairs parameters
diff --git a/newsfragments/2674.bugfix b/newsfragments/2674.bugfix
@@ -0,0 +1 @@
+``dials.cosym``: Fix to give more accurate cc calculation when running with a space_group set
diff --git a/newsfragments/2679.bugfix b/newsfragments/2679.bugfix
@@ -0,0 +1 @@
+Fix flex.reflection_table.concat to not modify in-place.
diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 from build import build
 
-__version_tag__ = "3.18.dev"
+__version_tag__ = "3.20.dev"
 
 setup_kwargs = {
  "name": "dials",

diff --git a/src/dials/algorithms/correlation/__init__.py b/src/dials/algorithms/correlation/__init__.py