format essnmx

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.24.dev
+current_version = 3.26.dev
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<release>[a-z]+)?(?P<patch>\d+)?
@@ -8,9 +8,9 @@ serialize =
 	{major}.{minor}.{release}
 	{major}.{minor}.{patch}
 
-[bumpversion:file:setup.py]
-search = __version_tag__ = "{current_version}"
-replace = __version_tag__ = "{new_version}"
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
 
 [bumpversion:part:patch]
 

.github/workflows/build_test.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macOS, windows]
-        python: ["3.9", "3.12"]
+        python: ["3.11", "3.12", "3.13"]
     runs-on: ${{ matrix.os }}-latest
     # Micromamba needs a login shell to activate
     defaults:
@@ -45,6 +45,7 @@ jobs:
         run: echo "CMAKE_GENERATOR=Ninja" >> $GITHUB_ENV
       - name: Build
         run: |
+          pip3 install "nxmx>=0.0.5"
           mkdir build
           cd build
           cmake ../dxtbx -DCMAKE_UNITY_BUILD=true -DPython_ROOT_DIR="${CONDA_PREFIX}"

.pre-commit-config.yaml

@@ -1,7 +1,10 @@
+ci:
+  autoupdate_schedule: quarterly
+
 repos:
 # Syntax validation and some basic sanity checks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-merge-conflict
   - id: check-ast
@@ -16,7 +19,7 @@ repos:
     name: "Don't commit to 'main' directly"
 
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.4.8
+  rev: v0.11.12
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix, --show-fixes]
@@ -25,7 +28,7 @@ repos:
       types: [file]
 
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v14.0.6
+  rev: v20.1.5
   hooks:
   - id: clang-format
     files: \.c(c|pp|xx)?$|\.h(pp)?$

AUTHORS

@@ -1,6 +1,7 @@
 Contributors include:
 
 Aaron Brewster
+Aaron Finke
 Asmit Bhowmick
 Ben Williams
 Billy K. Poon

CHANGELOG.rst

@@ -1,3 +1,108 @@
+dxtbx 3.25.0 (2025-06-20)
+=========================
+
+Features
+--------
+
+- DXTBX is now compatible with numpy 2. (`#751 <https://github.com/cctbx/dxtbx/issues/751>`_)
+- Allow the creation of a simple ``Crystal`` model from PHIL parameters. (`#819 <https://github.com/cctbx/dxtbx/issues/819>`_)
+- Python 3.13 compatibility. (`#826 <https://github.com/cctbx/dxtbx/issues/826>`_)
+
+
+Bugfixes
+--------
+
+- Convert tests to use ``dials-data``, rather than ``dials_regression``. This means they can be run outside of Diamond. (`#812 <https://github.com/cctbx/dxtbx/issues/812>`_)
+- Increase displayed precision of crystal U, B and A matrices. (`#823 <https://github.com/cctbx/dxtbx/issues/823>`_)
+- Add DECTRIS Singla to detectors.lib. (`#824 <https://github.com/cctbx/dxtbx/issues/824>`_)
+- Avoid reading h5 imagesets as having a single image, when a format class is not available (`#825 <https://github.com/cctbx/dxtbx/issues/825>`_)
+- ``dials.modify_experiments``: Bug fixes for ``CrystalFactory.from_phil``. (`#829 <https://github.com/cctbx/dxtbx/issues/829>`_)
+
+
+Deprecations and Removals
+-------------------------
+
+- The ``dials_regression`` and ``dials_regression_path`` fixtures are removed, as no tests use this repository any more. (`#815 <https://github.com/cctbx/dxtbx/issues/815>`_)
+
+
+Misc
+----
+
+- `#778 <https://github.com/cctbx/dxtbx/issues/778>`_, `#807 <https://github.com/cctbx/dxtbx/issues/807>`_, `#810 <https://github.com/cctbx/dxtbx/issues/810>`_, `#817 <https://github.com/cctbx/dxtbx/issues/817>`_, `#818 <https://github.com/cctbx/dxtbx/issues/818>`_, `#827 <https://github.com/cctbx/dxtbx/issues/827>`_
+
+
+DIALS 3.24.1 (2025-05-13)
+=========================
+
+Bugfixes
+--------
+
+- ``dxtbx.install_format``: Fix for modern setuptools versions which drop legacy ``setup.py`` features. (`#808 <https://github.com/cctbx/dxtbx/issues/808>`_)
+
+
+dxtbx 3.24.0 (2025-04-29)
+=========================
+
+Features
+--------
+
+- ``FormatROD_Arc``: Support for Rigaku HyPix-Arc 100° and 150° curved detectors. (`#787 <https://github.com/cctbx/dxtbx/issues/787>`_)
+- ``FormatBrukerELA``: Add support for the DECTRIS-ELA detector images in Bruker SFRM format. (`#802 <https://github.com/cctbx/dxtbx/issues/802>`_)
+- ``dxtbx.any2nexus``: Add ``sensor_material=`` and ``sensor_thickness=`` options. (`#803 <https://github.com/cctbx/dxtbx/issues/803>`_)
+- ``FormatXTC``: New features for managing wavelength calibration and an adjustment to the minimum trusted range for the ePix. (`#804 <https://github.com/cctbx/dxtbx/issues/804>`_)
+
+
+Bugfixes
+--------
+
+- Fix issue where attempting to group experiments would fail if the source images are currently inaccessible. This caused failures in downstream tooling such as ``xia2.ssx_reduce``. (`#772 <https://github.com/cctbx/dxtbx/issues/772>`_)
+- ``dials.import``: Reduce excessive memory usage when importing many (>100s) FormatNXMX files. (`#789 <https://github.com/cctbx/dxtbx/issues/789>`_)
+- ``FormatNXmxEigerFilewriter``: Use a lookup table when deciding whether to swap image dimensions, rather than relying on a firmware version check. (`#793 <https://github.com/cctbx/dxtbx/issues/793>`_)
+- ``FormatROD``: Use the weighted average of K-alpha1 and K-alpha2 as the monochromatic wavelength for the beam model. (`#800 <https://github.com/cctbx/dxtbx/issues/800>`_)
+- ``FormatRAXIS``: Allow the possibility of reading compressed files. (`#801 <https://github.com/cctbx/dxtbx/issues/801>`_)
+
+
+Improved Documentation
+----------------------
+
+- The user support mailing list is now ``dials-user-group@jiscmail.net`` (`#795 <https://github.com/cctbx/dxtbx/issues/795>`_)
+
+
+Misc
+----
+
+- `#197 <https://github.com/cctbx/dxtbx/issues/197>`_, `#788 <https://github.com/cctbx/dxtbx/issues/788>`_, `#796 <https://github.com/cctbx/dxtbx/issues/796>`_, `#797 <https://github.com/cctbx/dxtbx/issues/797>`_, `#805 <https://github.com/cctbx/dxtbx/issues/805>`_, `#978 <https://github.com/cctbx/dxtbx/issues/978>`_
+
+
+dxtbx 3.23.0 (2025-01-08)
+=========================
+
+Features
+--------
+
+- Nexus support: Handle reading new scale_factor fields (used for detector gain). (`#756 <https://github.com/cctbx/dxtbx/issues/756>`_)
+- ``dials.import``: Add a progress bar, so that it doesn't look like progress has stopped with large collections of images. (`#768 <https://github.com/cctbx/dxtbx/issues/768>`_)
+- Add ``FormatSMVADSCCetaD`` to allow easier processing of 3DED images from the Ceta-D detector, which have been converted to SMV. (`#770 <https://github.com/cctbx/dxtbx/issues/770>`_)
+
+
+Bugfixes
+--------
+
+- ``dials.show``: Hide progress bar if DIALS_NOBANNER (`#774 <https://github.com/cctbx/dxtbx/issues/774>`_)
+
+
+Deprecations and Removals
+-------------------------
+
+- Python 3.10 is now the minimum required (`#769 <https://github.com/cctbx/dxtbx/issues/769>`_)
+
+
+Misc
+----
+
+- `#767 <https://github.com/cctbx/dxtbx/issues/767>`_, `#773 <https://github.com/cctbx/dxtbx/issues/773>`_, `#775 <https://github.com/cctbx/dxtbx/issues/775>`_
+
+
 dxtbx 3.22.0 (2024-10-15)
 =========================
 

CMakeLists.txt

@@ -11,6 +11,11 @@ include(AlwaysColourCompilation) # Always show coloured compiler output
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON) # Generate compile_commands.json
 set(CMAKE_CXX_STANDARD 14)
 
+# Handle unity build on Windows
+if (CMAKE_UNITY_BUILD AND MSVC)
+    add_compile_options(/bigobj)
+endif()
+
 find_package(Python REQUIRED COMPONENTS Interpreter Development)
 find_package(CCTBX COMPONENTS scitbx cctbx REQUIRED)
 find_package(pybind11 REQUIRED)

SConscript

@@ -215,6 +215,7 @@ if not env_etc.no_boost_python and hasattr(env_etc, "boost_adaptbx_include"):
             "src/dxtbx/model/boost_python/crystal.cc",
             "src/dxtbx/model/boost_python/parallax_correction.cc",
             "src/dxtbx/model/boost_python/pixel_to_millimeter.cc",
+            "src/dxtbx/model/boost_python/history.cc",
             "src/dxtbx/model/boost_python/experiment.cc",
             "src/dxtbx/model/boost_python/experiment_list.cc",
             "src/dxtbx/model/boost_python/model_ext.cc",

conftest.py

@@ -5,50 +5,11 @@
 
 from __future__ import annotations
 
-import os
-import socket
-
 import pytest
 
 collect_ignore = []
 
 
-def dials_regression_path():
-    """Return the absolute path to the dials_regression module as a string.
-    This function is used directly by tests/test_regression_images.py"""
-
-    if "DIALS_REGRESSION" in os.environ:
-        return os.environ["DIALS_REGRESSION"]
-
-    try:
-        import dials_regression as dr
-
-        return os.path.abspath(os.path.dirname(dr.__file__))
-    except ImportError:
-        pass  # dials_regression not configured
-
-    # Check if we are in a known location
-    reference_copy = (
-        "/dls/science/groups/scisoft/DIALS/repositories/git-reference/dials_regression"
-    )
-    if (
-        os.name == "posix"
-        and socket.gethostname().endswith(".diamond.ac.uk")
-        and os.path.exists(reference_copy)
-    ):
-        return reference_copy
-
-
-@pytest.fixture(scope="session")
-def dials_regression():
-    """Return the absolute path to the dials_regression module as a string.
-    Skip the test if dials_regression is not available."""
-    d_r = dials_regression_path()
-    if d_r:
-        return d_r
-    pytest.skip("dials_regression required for this test")
-
-
 def pytest_addoption(parser):
     """Add '--regression' options to pytest."""
     try: