xia2/xia2 issues and pull requests

#730 - Update test assertion in xia2.ssx

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 1 comment

#729 - Update xia2.ssx documentation to include new dose-series merging options

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 1 comment

#728 - Don't copy xia2.ssx[_reduce].log into LogFiles directory

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 1 comment

#727 - In xia2.html damage summary: overlay Rcp(d) and completeness(d)

Issue - State: open - Opened by graeme-winter almost 2 years ago

#726 - xia2.ssx: Fix handling of manually specified detector geometry parameters.

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 1 comment

#725 - xia2.ssx: make sure correct batch folders are generated correctly

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 1 comment

#724 - Don't use the beam reference from a reference geometry file in xia2.ssx

Pull Request - State: closed - Opened by jbeilstenedmands almost 2 years ago - 1 comment

#723 - small molecule chemical formula

Pull Request - State: closed - Opened by keeble about 2 years ago

#722 - Use `dials.util.mp.available_cores()`

Pull Request - State: closed - Opened by rjgildea about 2 years ago - 1 comment

#721 - xia2.ssx; report R-split statistic

Pull Request - State: closed - Opened by jbeilstenedmands about 2 years ago

#720 - Move type annotations from comments to actual annotations

Pull Request - State: closed - Opened by jbeilstenedmands about 2 years ago - 1 comment

#719 - Add support for processing PAL and SACLA data with xia2.ssx

Pull Request - State: closed - Opened by jbeilstenedmands about 2 years ago - 1 comment

#718 - xia2.multiplex: allow option to use ∂CC1/2 on individual clusters

Issue - State: open - Opened by graeme-winter about 2 years ago

#717 - Add CodeQL workflow for GitHub code scanning

Pull Request - State: closed - Opened by lgtm-com[bot] over 2 years ago

#716 - Add hdf5_plugin to parameters doc

Pull Request - State: closed - Opened by graeme-winter over 2 years ago - 1 comment

#715 - too many CPUs

Issue - State: open - Opened by jmholton over 2 years ago - 1 comment

#714 - undocumented hdf5_plugin

Issue - State: closed - Opened by jmholton over 2 years ago

#713 - Allow arbitrary groupings for merging in xia2.ssx

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago

#712 - DIALS 3.11.3

Pull Request - State: closed - Opened by DiamondLightSource-build-server over 2 years ago - 1 comment
Labels: PR: merge conflicts

#711 - Fix xia2.ssx crash if no images successfully integrated.

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#710 - Remove dev. from xia2.ssx/xia2.ssx_reduce

Pull Request - State: closed - Opened by ndevenish over 2 years ago - 1 comment

#709 - Explicitly set the log file encoding

Pull Request - State: closed - Opened by graeme-winter over 2 years ago - 1 comment

#708 - Explicitly set the codec for log files

Issue - State: closed - Opened by graeme-winter over 2 years ago - 2 comments

#707 - Fix potential dev.xia2.ssx crash during geometry refinement

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago

#706 - DIALS 3.11.3

Pull Request - State: closed - Opened by DiamondLightSource-build-server over 2 years ago - 2 comments

#705 - Fix error in checking whether need to assess for indexing ambiguity in dev.xia2.ssx

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#704 - Update xia2 ssx params

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#703 - No multi crystal analysis

Pull Request - State: closed - Opened by graeme-winter over 2 years ago - 6 comments

#702 - is xia2.multi_crystal_analysis useful?

Issue - State: closed - Opened by graeme-winter over 2 years ago - 1 comment

#701 - xia2.ssx: copy dials.merge.json to LogFiles directory

Pull Request - State: closed - Opened by rjgildea over 2 years ago - 1 comment

#700 - Multiplex set output filenames

Pull Request - State: open - Opened by graeme-winter over 2 years ago - 2 comments
Labels: PR: merge conflicts

#699 - Generate the DataFiles & LogFiles directories for xia2.ssx/ssx_reduce

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#698 - Update path to ExperimentListFactory to fix to_shelx crash. Fixes #697

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#697 - xia2.to_shelx crash with --cell option

Issue - State: closed - Opened by huwjenkins over 2 years ago - 1 comment

#696 - dev.xia2.ssx: Assess crystals & refine geometry up to a given number of crystals.

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#695 - Multiplex: provide ability to override output filenames

Issue - State: open - Opened by graeme-winter over 2 years ago

#694 - Multiplex: please provide an option to split output experiments

Issue - State: open - Opened by graeme-winter over 2 years ago - 1 comment

#693 - dev.xia2.ssx: Fix parallelisation for njobs>1

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#692 - Fix dev.xia2.ssx_reduce crash when an input refl file has no data

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#691 - Improve helpfulness of output from dev.xia2.ssx upon dials.import failure

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#690 - Updates to track changes to dials.merge

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#689 - Correctly handle xia2.ssx warning handlers

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#688 - Fix xia2.ssx test

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#687 - DIALS 3.10.1

Pull Request - State: closed - Opened by DiamondLightSource-build-server over 2 years ago

#686 - Fix a few issues in dev.xia2.ssx identified in user testing

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment
Labels: backported

#685 - xia2.Handlers.CommandLine is overdue a refactor

Issue - State: open - Opened by benjaminhwilliams over 2 years ago

#684 - Replace procrunner use with subprocess

Pull Request - State: closed - Opened by rjgildea over 2 years ago - 2 comments

#683 - Add dev.xia2.ssx_reduce

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 2 comments

#682 - Update help strings in dev.xia2.ssx

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#681 - Fix read-only-base dispatcher generation on windows

Pull Request - State: closed - Opened by ndevenish over 2 years ago

#680 - DIALS 3.8.6

Pull Request - State: closed - Opened by DiamondLightSource-build-server over 2 years ago

#679 - citations.xml -> citations.yaml

Pull Request - State: closed - Opened by rjgildea over 2 years ago - 4 comments

#678 - Fix xia2.ssx spotfinding reporting for multiple imagesets

Pull Request - State: closed - Opened by jbeilstenedmands over 2 years ago - 1 comment

#677 - Add page numbers to multiplex citation

Pull Request - State: closed - Opened by rjgildea over 2 years ago - 1 comment

#676 - Always assume read-only base with libtbx_refresh

Pull Request - State: closed - Opened by ndevenish over 2 years ago

#675 - Add citations to xia2.multiplex

Pull Request - State: closed - Opened by rjgildea over 2 years ago - 1 comment

#674 - Slightly less stupid MTZ rename

Pull Request - State: closed - Opened by graeme-winter over 2 years ago - 1 comment

#673 - If you run xia2 in a directory which contains the letters "mtz" you will not go to space that day

Issue - State: closed - Opened by graeme-winter over 2 years ago - 1 comment

#672 - Bugfix for finding NeXus data

Pull Request - State: closed - Opened by graeme-winter over 2 years ago - 9 comments

#671 - processing multiple run datasets - nxs files from Tristan 10M detector

Issue - State: closed - Opened by drmrw almost 3 years ago - 3 comments

#670 - Add new SSX processing pipeline dev.xia2.ssx for data integration

Pull Request - State: closed - Opened by jbeilstenedmands almost 3 years ago - 1 comment

#669 - Move DataManager to separate module

Pull Request - State: closed - Opened by rjgildea almost 3 years ago - 1 comment

#668 - Unit cell clustering fixes for dials/dials#2081

Pull Request - State: closed - Opened by rjgildea almost 3 years ago - 2 comments

#667 - Update mmcif output to conform to latest version of v5 mmcif pdbx dict

Pull Request - State: closed - Opened by jbeilstenedmands almost 3 years ago - 1 comment

#666 - Deprecate PHIL parameter 'report.resolution_bins'

Pull Request - State: closed - Opened by benjaminhwilliams almost 3 years ago - 2 comments

#665 - Synchronise n_bins across text output and report output

Issue - State: closed - Opened by graeme-winter almost 3 years ago

#664 - Use smaller datasets in some regression tests

Pull Request - State: closed - Opened by Anthchirp almost 3 years ago - 1 comment

#663 - OptionParser -> ArgumentParser

Pull Request - State: closed - Opened by Anthchirp almost 3 years ago - 1 comment

#662 - Enable type checking with mypy

Pull Request - State: closed - Opened by Anthchirp almost 3 years ago - 1 comment

#661 - Retire py.path in favour of pathlib

Pull Request - State: closed - Opened by benjaminhwilliams almost 3 years ago - 9 comments

#660 - Add new experimental SSX processing pipeline dev.xia2.ssx

Pull Request - State: closed - Opened by jbeilstenedmands almost 3 years ago - 7 comments

#659 - Replace own which() function with shutil.which()

Pull Request - State: closed - Opened by Anthchirp almost 3 years ago - 2 comments

#658 - Remove a few unnecessary `run_in_tmpdir` instances

Pull Request - State: closed - Opened by Anthchirp almost 3 years ago - 1 comment

#657 - Remove placeholder option from cluster_method param

Pull Request - State: closed - Opened by rjgildea almost 3 years ago - 1 comment

#656 - Revert "Never install into conda_base/ when running under libtbx (#6…

Pull Request - State: closed - Opened by graeme-winter about 3 years ago

#655 - Add an updated setup.py

Pull Request - State: closed - Opened by ndevenish about 3 years ago - 5 comments

#654 - cluster_method=unit_cell causes an "Invalid cluster method" error

Issue - State: closed - Opened by biochem-fan about 3 years ago - 1 comment

#653 - DIALS 3.8.2

Pull Request - State: closed - Opened by DiamondLightSource-build-server about 3 years ago - 1 comment

#652 - Add environment variable to force installation in build/

Pull Request - State: closed - Opened by ndevenish about 3 years ago - 1 comment

#651 - Fix for xia2/xds hanging when run from ccp4i2

Pull Request - State: closed - Opened by dagewa about 3 years ago - 6 comments

#650 - DIALS 3.8.1

Pull Request - State: closed - Opened by DiamondLightSource-build-server about 3 years ago - 1 comment

#649 - Reapply pre-commit updates

Pull Request - State: closed - Opened by ndevenish about 3 years ago - 1 comment

#648 - Update pre-commit environments

Pull Request - State: closed - Opened by ndevenish about 3 years ago

#647 - More explicit error message

Pull Request - State: closed - Opened by rjgildea about 3 years ago - 1 comment

#646 - Drop Python 3.7 support

Pull Request - State: closed - Opened by Anthchirp about 3 years ago - 1 comment

#645 - Extra output for xia2.delta_cc_half

Pull Request - State: closed - Opened by dagewa about 3 years ago - 2 comments

#641 - Multiplex imported mtz

Pull Request - State: closed - Opened by dagewa about 3 years ago - 4 comments

#632 - Handling of multiple wavelengths in xia2.multiplex

Issue - State: closed - Opened by jbeilstenedmands over 3 years ago - 1 comment

#627 - Remove driver type concepts

Pull Request - State: closed - Opened by graeme-winter over 3 years ago - 4 comments
Labels: PR: merge conflicts

#594 - xia2 broken on Windows

Issue - State: closed - Opened by graeme-winter over 3 years ago - 3 comments

#571 - DIALS 3.3.4

Pull Request - State: closed - Opened by DiamondLightSource-build-server almost 4 years ago

#560 - DialsScaler.py should not conflate the concept of logical WAVELENGTH with physical X-ray wavelength

Issue - State: open - Opened by benjaminhwilliams about 4 years ago - 2 comments

#543 - Should xia2 PHIL parameters expose the full DIALS spot-finding PHIL scope?

Issue - State: open - Opened by benjaminhwilliams about 4 years ago - 2 comments

#442 - Tidy up processing summary

Issue - State: open - Opened by benjaminhwilliams almost 5 years ago - 14 comments
Labels: enhancement

#430 - xia2.multiplex fails because "Duplicate batch offsets detected"

Issue - State: closed - Opened by dagewa almost 5 years ago - 8 comments
Labels: multiplex

#236 - Add i19.screen reporting to xia2, if small molecule, if inexpensive

Issue - State: open - Opened by graeme-winter over 6 years ago - 7 comments

#230 - In xia2 integration with DIALS, if I19-screen thinks reflections are overloaded; remove

Issue - State: open - Opened by graeme-winter over 6 years ago - 7 comments

GitHub / xia2/xia2 issues and pull requests