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Merge branch 'main' into remove-datablock
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dagewa authored Jul 25, 2023
2 parents 41d9c59 + 930be09 commit 004a99e
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20 changes: 11 additions & 9 deletions .azure-pipelines/azure-pipelines.yml
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Expand Up @@ -14,11 +14,11 @@ stages:
steps:
- checkout: none

# Use Python >=3.8 for syntax validation
# Use Python >=3.9 for syntax validation
- task: UsePythonVersion@0
displayName: Set up python
inputs:
versionSpec: 3.8
versionSpec: 3.9

# Run syntax validation on a shallow clone
- bash: |
Expand Down Expand Up @@ -78,7 +78,7 @@ stages:
vmImage: ubuntu-20.04
timeoutInMinutes: 60
variables:
PYTHON_VERSION: 3.8
PYTHON_VERSION: 3.9
steps:
- template: unix-build.yml

Expand All @@ -88,10 +88,10 @@ stages:
vmImage: ubuntu-20.04
strategy:
matrix:
python38:
PYTHON_VERSION: 3.8
python39:
PYTHON_VERSION: 3.9
python311:
PYTHON_VERSION: 3.11
timeoutInMinutes: 60
steps:
- template: unix-build.yml
Expand All @@ -101,10 +101,10 @@ stages:
vmImage: macOS-latest
strategy:
matrix:
python38:
PYTHON_VERSION: 3.8
python39:
PYTHON_VERSION: 3.9
python311:
PYTHON_VERSION: 3.11
timeoutInMinutes: 60
steps:
- template: unix-build.yml
Expand All @@ -114,8 +114,10 @@ stages:
vmImage: windows-2019
strategy:
matrix:
python38:
PYTHON_VERSION: 3.8
python39:
PYTHON_VERSION: 3.9
python311:
PYTHON_VERSION: 3.11
timeoutInMinutes: 20
steps:
- template: windows-build.yml
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2 changes: 1 addition & 1 deletion .azure-pipelines/bootstrap.py
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Expand Up @@ -847,7 +847,7 @@ def run():
"--python",
help="Install this minor version of Python (default: %(default)s)",
default="3.9",
choices=("3.8", "3.9", "3.10"),
choices=("3.9", "3.10", "3.11"),
)
parser.add_argument(
"--branch",
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4 changes: 2 additions & 2 deletions .azure-pipelines/ci-conda-env.txt
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Expand Up @@ -2,7 +2,7 @@ conda-forge::boost
conda-forge::boost-cpp
conda-forge::bzip2
conda-forge::c-compiler<1.5
conda-forge::cctbx-base==2022.12
conda-forge::cctbx-base==2023.5
conda-forge::conda
conda-forge::cxx-compiler<1.5
conda-forge::python-dateutil
Expand All @@ -18,10 +18,10 @@ conda-forge::matplotlib-base
conda-forge::mrcfile
conda-forge::numpy
conda-forge::nxmx
conda-forge::orderedset
conda-forge::pillow>=5.4.1
conda-forge::pint
conda-forge::pip
conda-forge::procrunner
conda-forge::psutil
conda-forge::pyrtf
conda-forge::pybind11
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2 changes: 1 addition & 1 deletion .bumpversion.cfg
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@@ -1,5 +1,5 @@
[bumpversion]
current_version = 3.15.dev
current_version = 3.16.dev
commit = True
tag = False
parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<release>[a-z]+)?(?P<patch>\d+)?
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1 change: 1 addition & 0 deletions AUTHORS
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ Graeme Winter
Ian Rees
Iris Young
James Beilsten-Edmands
James Hester
James Holton
James Parkhurst
Johan Hattne
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32 changes: 32 additions & 0 deletions CHANGELOG.rst
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@@ -1,3 +1,35 @@
DIALS 3.15.1 (2023-06-29)
=========================

Bugfixes
--------

- ``dxtbx.dlsnxs2cbf``: Fix import overwritten by local variable. (`#641 <https://github.com/cctbx/dxtbx/issues/641>`_)


dxtbx 3.15.0 (2023-06-13)
=========================

Features
--------

- Support for Bruker Photon detectors has been extended to include Photon-III. (`#637 <https://github.com/cctbx/dxtbx/issues/637>`_)


Bugfixes
--------

- Rigaku Saturn SMV images with multi-axis crystal goniometers are now handledi, instead of being silently ignored. With thanks to James Hester for this contribution. (`#617 <https://github.com/cctbx/dxtbx/issues/617>`_)
- FormatCBFFull: If rotation angles are decreasing, then invert the rotation axis as well as the angles, to be consistent. (`#623 <https://github.com/cctbx/dxtbx/issues/623>`_)
- Bugfix for CCTBX bootstrapped environments, without conda. (`#630 <https://github.com/cctbx/dxtbx/issues/630>`_)


Misc
----

- `#625 <https://github.com/cctbx/dxtbx/issues/625>`_, `#636 <https://github.com/cctbx/dxtbx/issues/636>`_, `#639 <https://github.com/cctbx/dxtbx/issues/639>`_


DIALS 3.14.2 (2023-05-16)
=========================

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2 changes: 1 addition & 1 deletion SConscript
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Expand Up @@ -119,7 +119,7 @@ if not env_etc.no_boost_python and hasattr(env_etc, "boost_adaptbx_include"):
env = env_no_includes_boost_python_ext.Clone()

# Don't surface warnings from system or cctbx_project headers
system_includes = [x for x in env_etc.conda_cpppath if x]
system_includes = [x for x in env_etc.conda_cpppath if x] if libtbx.env.build_options.use_conda else []
system_includes.append(str(Path(env_etc.scitbx_dist).parent))
env.Append(CXXFLAGS=[f"-isystem{x}" for x in system_includes])
env.Append(SHCXXFLAGS=[f"-isystem{x}" for x in system_includes])
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1 change: 0 additions & 1 deletion libtbx_config
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@
"python_required": [
"dials-data>=2.0.30",
"pint",
"procrunner>=1.0.2",
"pytest>=4.5,<5.0",
],
}
11 changes: 3 additions & 8 deletions libtbx_refresh.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import contextlib
import importlib
import inspect
import io
import os
Expand All @@ -17,11 +18,6 @@
except ModuleNotFoundError:
pass

try:
import pkg_resources
except ModuleNotFoundError:
pkg_resources = None


def _install_setup_readonly_fallback(package_name: str):
"""
Expand Down Expand Up @@ -67,9 +63,8 @@ def _install_setup_readonly_fallback(package_name: str):
if import_path not in sys.path:
sys.path.insert(0, import_path)

# ...and add to the existing pkg_resources working_set
if pkg_resources:
pkg_resources.working_set.add_entry(import_path)
# ...and make sure it is picked up by the import system
importlib.invalidate_caches()

# This is already generated by this point, but will get picked up
# on the second libtbx.refresh.
Expand Down
1 change: 1 addition & 0 deletions newsfragments/299.bugfix
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@@ -0,0 +1 @@
Panel geometry definitions in PHIL are merged by panel id before constructing panels
2 changes: 0 additions & 2 deletions newsfragments/623.bugfix

This file was deleted.

1 change: 0 additions & 1 deletion newsfragments/625.misc

This file was deleted.

1 change: 0 additions & 1 deletion newsfragments/636.misc

This file was deleted.

1 change: 1 addition & 0 deletions newsfragments/640.misc
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@@ -0,0 +1 @@
Use Python built-in ``subprocess`` in place of external dependency ``procrunner`` for running CLI tests.
1 change: 1 addition & 0 deletions newsfragments/642.misc
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@@ -0,0 +1 @@
Drop Python 3.8 support in line with https://dials.github.io/kb/proposals/dc3. Add Python 3.11 support.
1 change: 1 addition & 0 deletions newsfragments/643.misc
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@@ -0,0 +1 @@
Move from deprecated pkg_resources to importlib.
1 change: 1 addition & 0 deletions pytest.ini
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ filterwarnings =
ignore:numpy.dtype size changed:RuntimeWarning
ignore:Datablocks are deprecated:UserWarning
ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning
ignore:`product` is deprecated as of NumPy:DeprecationWarning:h5py|numpy
junit_family = legacy
markers =
regression: dxtbx regression test
3 changes: 2 additions & 1 deletion setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,9 @@ classifiers =
Operating System :: Microsoft :: Windows
Operating System :: POSIX :: Linux
Programming Language :: Python :: 3
Programming Language :: Python :: 3.8
Programming Language :: Python :: 3.9
Programming Language :: Python :: 3.10
Programming Language :: Python :: 3.11

[flake8]
# Black disagrees with flake8 on a few points. Ignore those.
Expand Down
2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@

# Static version number which is updated by bump2version
# Do not change this manually - use 'bump2version <major/minor/patch/release>'
__version_tag__ = "3.15.dev"
__version_tag__ = "3.16.dev"

setup_kwargs = {
"name": "dxtbx",
Expand Down
4 changes: 2 additions & 2 deletions src/dxtbx/command_line/dlsnxs2cbf.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
Convert a NXmx-format NeXus file to a set of CBF-format image files.
Note that this tool does not produce full imgCIF-format files, only
Dectris-style mini-CBF files consisting of a plain text simplified
DECTRIS-style mini-CBF files consisting of a plain text simplified
header and the binary compressed image data. The simplified header
does not contain a full description of the experiment geometry and some
metadata, including the detector orientation, are unspecified. As
Expand All @@ -18,7 +18,7 @@

import dxtbx.util.dlsnxs2cbf

parser = argparse.ArgumentParser(description=__doc__)
parser = argparse.ArgumentParser(description=__doc__, prog="dxtbx.dlsnxs2cbf")
parser.add_argument(
"nexus_file", metavar="nexus-file", help="Input NeXus file.", type=Path
)
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
from dxtbx.format.FormatBruker import FormatBruker


class FormatBrukerPhotonII(FormatBruker):
class FormatBrukerPhoton(FormatBruker):
@staticmethod
def understand(image_file):

Expand All @@ -32,6 +32,7 @@ def understand(image_file):
dettype = header_dic.get("DETTYPE")
if dettype is None:
return False
# We support Photon-II and Photon-III detectors
if not dettype.startswith("CMOS-PHOTONII"):
return False

Expand All @@ -44,9 +45,9 @@ def _start(self):
except OSError:
return False

self.header_dict = FormatBrukerPhotonII.parse_header(header_lines)
self.header_dict = FormatBrukerPhoton.parse_header(header_lines)

# The Photon II format can't currently use BrukerImage, see
# The Photon II/III format can't currently use BrukerImage, see
# https://github.com/cctbx/cctbx_project/issues/65
# from iotbx.detectors.bruker import BrukerImage
# self.detectorbase = BrukerImage(self._image_file)
Expand All @@ -73,24 +74,21 @@ def _goniometer(self):
axes, angles, names, scan_axis
)

@staticmethod
def _estimate_gain(wavelength):
"""Estimate the detector gain based on values provided by Bruker. Each ADU
corresponds to 36.6 electrons. The X-ray conversion results in deposited
charge according to the following table for typical home sources:
In (0.5136 A): 359.6893 e/X-ray
Ag (0.5609 A): 329.3748 e/X-ray
Mo (0.7107 A): 259.9139 e/X-ray
Ga (1.3414 A): 137.6781 e/X-ray
Cu (1.5418 A): 119.8156 e/X-ray
This fits the linear model (1/G) = -0.0000193358 + 0.1981607255 * wavelength
extremely well.
def _calculate_gain(self, wavelength):
"""The CCDPARM header item contains 5 items:
1. readnoise
2. e/ADU
3. e/photon
4. bias
5. full scale
The gain in ADU/X-ray is given by (e/photon) / (e/ADU).
"""
inv_gain = -0.0000193358 + 0.1981607255 * wavelength
assert inv_gain > 0.1
return 1.0 / inv_gain
ccdparm = self.header_dict["CCDPARM"].split()
e_ADU = float(ccdparm[1])
e_photon = float(ccdparm[2])
if e_ADU == 0:
return 1.0
return e_photon / e_ADU

def _detector(self):
# goniometer angles in ANGLES are 2-theta, omega, phi, chi (FIXED)
Expand Down Expand Up @@ -123,7 +121,7 @@ def _detector(self):

# Not a CCD, but is an integrating detector. Photon II has a 90 um Gadox
# scintillator.
gain = self._estimate_gain(float(self.header_dict["WAVELEN"].split()[0]))
gain = self._calculate_gain(float(self.header_dict["WAVELEN"].split()[0]))
return self._detector_factory.complex(
"CCD",
origin.elems,
Expand All @@ -136,9 +134,15 @@ def _detector(self):
)

def _beam(self):
"""Assume home source, so make unpolarized beam"""
wavelength = float(self.header_dict["WAVELEN"].split()[0])

return self._beam_factory.simple(wavelength)
return self._beam_factory.make_polarized_beam(
sample_to_source=(0.0, 0.0, 1.0),
wavelength=wavelength,
polarization=(0, 1, 0),
polarization_fraction=0.5,
)

def _scan(self):

Expand Down Expand Up @@ -257,4 +261,4 @@ def get_raw_data(self):

if __name__ == "__main__":
for arg in sys.argv[1:]:
print(FormatBrukerPhotonII.understand(arg))
print(FormatBrukerPhoton.understand(arg))
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