MDANSE 2.0.0 RC2

What's Changed

• Fix issues with GridQVectors and clean up by @oerc0122 in #871
• Update neutron weights squaring in analysis and documentation by @MBartkowiakSTFC in #873
• Updated to GUI so that the 3D viewer side panel can be hidden. by @ChiCheng45 in #876
• Add the missing character in IJob.save by @MBartkowiakSTFC in #883
• Adjust 3D view side panel size policy by @ChiCheng45 in #884
• Improve input of partial charges by @MBartkowiakSTFC in #879
• Invert icon colours if in dark mode by @MBartkowiakSTFC in #878
• Add new axes options to 3d viewer by @ChiCheng45 in #885
• Fixed 3d view controls while animation is playing by @ChiCheng45 in #890
• Remove part of the nested dependencies of configurators by @MBartkowiakSTFC in #875
• Added option to display atom labels in the 3D viewer by @ChiCheng45 in #897
• Fix PPS preview in TrajectoryFilter by @MBartkowiakSTFC in #895
• Fix #816 data preview bug by @oerc0122 in #901
• Rework plotter to add visible range to 'Use it?' by @oerc0122 in #903
• Avoid array scan in CoordinationNumber by @oerc0122 in #904
• Add optional CLI progress bars by @oerc0122 in #906
• Add comment about prog_bar availability by @oerc0122 in #910
• Remove iteration over directories; switch to explicit import/re-export by @oerc0122 in #912
• Stop column width in RunTable from resetting by @MBartkowiakSTFC in #915
• Fixed grouped results axis and updated compare hdf by @ChiCheng45 in #916
• Add timings to GUI by @oerc0122 in #908
• Clean up some gui repetition and add typing by @oerc0122 in #907
• Load trajectories in a background thread by @MBartkowiakSTFC in #881
• Allow users to change matplotlib settings in the GUI by @MBartkowiakSTFC in #900
• Stop counting elapsed time after job has finished by @MBartkowiakSTFC in #921
• Fix unit parsing in ASE by @oerc0122 in #919
• Replace custom encoders with a single centralised one by @oerc0122 in #923
• Show clearer error output from the plotter by @MBartkowiakSTFC in #920
• Force future annotations by @oerc0122 in #925
• Fix trajectory editor with atom selection and trajectories with molecules. by @ChiCheng45 in #924
• Add minimize and maximise to atom selection and related helpers. by @ChiCheng45 in #928
• Update compare_hdf5 and fix rmsf with molecule grouping by @ChiCheng45 in #929
• Reduce some code duplication in selection and add load from dict by @oerc0122 in #930
• Fix converter scripts saved from GUI by @ChiCheng45 in #931
• Adjust job categories by @MBartkowiakSTFC in #934
• Documentation for CLI progress bars by @MBartkowiakSTFC in #936
• Add warning to interpolation order input by @MBartkowiakSTFC in #937
• Speed up Action widget creation by @MBartkowiakSTFC in #938
• Update comments and refactor trajectories to ABC form by @oerc0122 in #892
• Update AtomSelectionWidget on selection change by @MBartkowiakSTFC in #945
• Updated MDANSE CLI by @MBartkowiakSTFC in #927
• Reimplemented molecule viewer axes options by @ChiCheng45 in #948
• Fix single-index analysis by @MBartkowiakSTFC in #940
• Include atom selection in CentreOfMassesTrajectory by @MBartkowiakSTFC in #950
• Prepare for RC2 by @MBartkowiakSTFC in #954
• Use only the real part of complex weights in analysis results (typically dynamic structure factors)

Full Changelog: v2.0.0rc1...v2.0.0rc2

v2.0.0rc1

What's Changed

• Correct dlpoly and instruments by @MBartkowiakSTFC in #590
• 3d viewer fix when switching trajectories by @ChiCheng45 in #601
• Indicate job start and completion by @MBartkowiakSTFC in #604
• Add MDAnalysis converter by @ChiCheng45 in #611
• Explicitly set the QLocale in the GUI by @MBartkowiakSTFC in #603
• Modify the VASP converter to work with several XDATCAR formats by @MBartkowiakSTFC in #607
• Split trajectory frames into chunks by @MBartkowiakSTFC in #602
• Set charges using TrajectoryEditor by @MBartkowiakSTFC in #613
• General GUI optimisations and atom selection inversion button by @ChiCheng45 in #617
• GUI optimisation - qvector and instrument resolution type change by @ChiCheng45 in #618
• Improved output file names by @MBartkowiakSTFC in #610
• Fix tab switching performance issues. by @ChiCheng45 in #623
• Fixes runtime error seen after the GUI is closed when jobs have been terminated. by @ChiCheng45 in #626
• Add MDTraj converter and update to atom mapping code by @ChiCheng45 in #622
• Output files setting fix by @ChiCheng45 in #631
• Fixed dl-poly gradient conversion fix by @ChiCheng45 in #632
• Fixed failure to load up jobs after selecting the trajectory editor jobs. by @ChiCheng45 in #633
• Numerical derivatives configurators now check there are enough MD frames. by @ChiCheng45 in #635
• Documentation update: new converged results section by @ChiCheng45 in #636
• Fixed discover fold setting by @ChiCheng45 in #645
• Simplify Chemical System by @MBartkowiakSTFC in #616
• Bond tolerance update and trajectory editor widget fixes. by @ChiCheng45 in #652
• Update analysis and converter unit tests so they check against reference values by @ChiCheng45 in #647
• Simplify packaging by @oerc0122 in #648
• Convert os.path to pathlib based Paths by @oerc0122 in #646
• Add ruff to GUI by @oerc0122 in #653
• Modernise strings by @oerc0122 in #643
• Add ruff by @oerc0122 in #642
• Improve H5MD trajectory support by @MBartkowiakSTFC in #655
• Simplify test converter add gromacs test by @oerc0122 in #671
• Add Python 3.13 to the workflow matrix by @MBartkowiakSTFC in #674
• Improve DISF+DCSF summation by @MBartkowiakSTFC in #619
• Add ruff format to gui by @oerc0122 in #662
• Add ruff format to MDANSE main by @oerc0122 in #666
• Update the CP2K configurator and widget so that the velocity file is optional by @ChiCheng45 in #668
• Save the MSD results with equal weights to GDISF output by @ChiCheng45 in #677
• Add timeout to MDANSE unit tests by @MBartkowiakSTFC in #685
• Use pytest for test_configurable by @oerc0122 in #684
• Simplify PDB reader and add docs by @oerc0122 in #663
• Removed broken SVG format by @oerc0122 in #700
• Add new adjusted weight scheme to work with DCSF and CCF jobs by @ChiCheng45 in #689
• New atom selection mechanism by @MBartkowiakSTFC in #672
• Use pytest for test_units by @oerc0122 in #681
• Documentation clean up and update by @ChiCheng45 in #712
• Visualise atom trace by @MBartkowiakSTFC in #657
• Rename workflow to include information by @oerc0122 in #702
• Fix to images, links and equations in documentation by @ChiCheng45 in #716
• Add test helpers by @oerc0122 in #687
• Rework IOutput and add tests by @oerc0122 in #699
• Use pytest for test_analysis and fix test by @oerc0122 in #678
• Fix saving paths in IJob.save by @oerc0122 in #728
• Remove almost, replace with np.isclose by @oerc0122 in #729
• Pytestise test_atom_mapping by @oerc0122 in #688
• Fix issue with 3.11 StrEnum by @oerc0122 in #742
• Treat all fields in ElementsDatabaseEditor as text fields by @MBartkowiakSTFC in #714
• Atom database editor updates by @ChiCheng45 in #748
• Improve plotter code by @MBartkowiakSTFC in #719
• Fix issue when MultiInput... has non-extant files by @oerc0122 in #751
• Re-use the job instance in Action.py by @MBartkowiakSTFC in #758
• Update os env setting to make numpy use one thread when the GUI is used by @ChiCheng45 in #762
• Molecule preview using rdkit by @MBartkowiakSTFC in #756
• Molecule preview button and fast plotting by @raunakkbanerjee in #620
• Save Q vectors in the output file by @MBartkowiakSTFC in #634
• Fixed the structure factor from scattering function job. by @ChiCheng45 in #766
• Fix progress bar visual bug by @ChiCheng45 in #768
• Rework lammps parser by @oerc0122 in #736
• Add data normalisation to the plotter by @MBartkowiakSTFC in #761
• Fix PDF calculation for non-orthogonal unit cells by @MBartkowiakSTFC in #735
• Add ideal results when using the instrument resolution by @ChiCheng45 in #773
• Add the final progress update to IJob._run_multicore by @MBartkowiakSTFC in #779
• Clean up widget base and move arguments to documented interface by @oerc0122 in #757
• Check for length-1 arrays in PlottingContext by @MBartkowiakSTFC in #787
• T20 remove print by @oerc0122 in #785
• Add simulation time step section to converged results by @ChiCheng45 in #784
• Fix gui so that trajectory editor loads up correctly by @ChiCheng45 in #790
• Improve atom type recognition in LAMMPS parser by @oerc0122 in #771
• Use coordinates and not unit cell in SelectionWidgets by @MBartkowiakSTFC in #788
• Remove print to satisfy T201 by @oerc0122 in #791
• Fix to unit conversion by @ChiCheng45 in #796
• Split distinct van Hove calculation into segments by @MBartkowiakSTFC in #738
• 778 lammps read vel by @oerc0122 in #782
• Port citation to CITATION.cff format by @oerc0122 in #654
• Adjust the MDANSE GUI logo by @ChiCheng45 in #799
• Add missing attributes when axis=index in plotters by @MBartkowiakSTFC in #805
• Fix unit conversion in MDAnalysis for velocity and forces by @ChiCheng45 in #803
• Improve atom property caching in MdanseTrajectory by @MBartkowiakSTFC in #802
• Rework DLPoly parser to support more diverse inputs by @oerc0122 in #798
• Use configurator defaults for VectorWidget by @oerc0122 in https://github.com/ISISNeutronMuon/MD...

Release Version 2.0.0b1

This is the beta release of MDANSE and MDANSE_GUI. We would like to thank all the contributors who made this release possible and all the users who reported problems with the previous alpha release.

The release includes new analysis (van Hove functions), new GUI functionality (saving resolution and q-vector settings via instrument profiles), improvements to the plotting interface and multiple improvements of converter and analysis code. Please refer to the changelog for a more detailed description of this release.

Both MDANSE and MDANSE_GUI have been published on PyPI and can be installed using pip install. You are welcome to visit their project websites:
https://pypi.org/project/MDANSE/
https://pypi.org/project/MDANSE-GUI/

Release Version 2.0.0a2

This is the second alpha release of MDANSE and MDANSE_GUI based on Python 3. We would like to thank all the contributors who made this release possible.

This release includes the new plotting interface, TOML-based user settings, automatic loading of results into the GUI, and per-task logging. Additionally, there is more control over multicore jobs, which can be paused and terminated without significant delay.

We would like to encourage all the users to provide feedback on this release. Any comments you may have on this alpha version will help us improve the upcoming beta release.

Both MDANSE and MDANSE_GUI have been published on PyPI and can be installed using pip install. You are welcome to visit their project websites:
https://pypi.org/project/MDANSE/
https://pypi.org/project/MDANSE-GUI/

Release Version 2.0.0a1

This is the first (alpha) release of MDANSE and MDANSE_GUI based on Python 3. We would like to thank all the contributors who made this release possible.

We would like to encourage all the users to provide feedback on this release. Any comments you may have on this alpha version will help us improve the upcoming beta release.

Both MDANSE and MDANSE_GUI have been published on PyPI and can be installed using pip install. You are welcome to visit their project websites:
https://pypi.org/project/MDANSE/
https://pypi.org/project/MDANSE-GUI/
The conda packages will be available shortly.

Release Version 1.5.2

We are pleased to announce version 1.5.2 of MDANSE

This is the last version of MDANSE software based on python 2.0. In this version we focus on a stable version of MDANSE along with fixed bugs and improvements in performances. Please take a look on release notes for important changes and improvements.

The development team has put a lot of efforts to make these improvements in MDANSE. We also would like to thank all beta testers and users for testing and reporting all bugs Please keep on reporting bugs and send us requirements for further improvements to MDANSE.

Information about installation of packages will be found in the MDANSE project webpage

Full Changelog: https://github.com/ISISNeutronMuon/MDANSE/commits/v1.5.2

Release Version 1.5.1

We are pleased to announce version 1.5.1 of MDANSE

Some bugs are fixed in this version to focus on a stable version of MDANSE. Please take a look on release notes for important changes and improvements.

The development team has put a lot of efforts to make these improvements in MDANSE. We also would like to thank all beta testers and users for testing and reporting all bugs Please keep on reporting bugs and send us requirements for further improvements to MDANSE.

Information about installation of packages will be found in the MDANSE webpage
as well as in MDANSE project webpage

Full Changelog: https://github.com/ISISNeutronMuon/MDANSE/commits/v1.5.1

Release Version 1.5.0

We are pleased to announce version 1.5.0 of MDANSE

Many of the updates in this version have focused on a stable version of MDANSE. Please take a look on release notes for important changes and improvements.

The development team has put a lot of efforts to make these improvements in MDANSE. We also would like to thank all beta testers and users for testing and reporting all bugs Please keep on reporting bugs and send us requirements for further improvements to MDANSE.

Information about installation of packages will be found in the MDANSE webpage
as well as in MDANSE project webpage

Full Changelog: https://github.com/ISISNeutronMuon/MDANSE/commits/v1.5.0