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Recent Releases of mdanse

mdanse - v2.0.0rc1

What's Changed

  • Correct dlpoly and instruments by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/590
  • 3d viewer fix when switching trajectories by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/601
  • Indicate job start and completion by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/604
  • Add MDAnalysis converter by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/611
  • Explicitly set the QLocale in the GUI by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/603
  • Modify the VASP converter to work with several XDATCAR formats by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/607
  • Split trajectory frames into chunks by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/602
  • Set charges using TrajectoryEditor by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/613
  • General GUI optimisations and atom selection inversion button by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/617
  • GUI optimisation - qvector and instrument resolution type change by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/618
  • Improved output file names by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/610
  • Fix tab switching performance issues. by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/623
  • Fixes runtime error seen after the GUI is closed when jobs have been terminated. by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/626
  • Add MDTraj converter and update to atom mapping code by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/622
  • Output files setting fix by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/631
  • Fixed dl-poly gradient conversion fix by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/632
  • Fixed failure to load up jobs after selecting the trajectory editor jobs. by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/633
  • Numerical derivatives configurators now check there are enough MD frames. by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/635
  • Documentation update: new converged results section by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/636
  • Fixed discover fold setting by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/645
  • Simplify Chemical System by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/616
  • Bond tolerance update and trajectory editor widget fixes. by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/652
  • Update analysis and converter unit tests so they check against reference values by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/647
  • Simplify packaging by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/648
  • Convert os.path to pathlib based Paths by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/646
  • Add ruff to GUI by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/653
  • Modernise strings by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/643
  • Add ruff by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/642
  • Improve H5MD trajectory support by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/655
  • Simplify test converter add gromacs test by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/671
  • Add Python 3.13 to the workflow matrix by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/674
  • Improve DISF+DCSF summation by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/619
  • Add ruff format to gui by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/662
  • Add ruff format to MDANSE main by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/666
  • Update the CP2K configurator and widget so that the velocity file is optional by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/668
  • Save the MSD results with equal weights to GDISF output by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/677
  • Add timeout to MDANSE unit tests by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/685
  • Use pytest for test_configurable by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/684
  • Simplify PDB reader and add docs by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/663
  • Removed broken SVG format by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/700
  • Add new adjusted weight scheme to work with DCSF and CCF jobs by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/689
  • New atom selection mechanism by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/672
  • Use pytest for test_units by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/681
  • Documentation clean up and update by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/712
  • Visualise atom trace by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/657
  • Rename workflow to include information by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/702
  • Fix to images, links and equations in documentation by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/716
  • Add test helpers by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/687
  • Rework IOutput and add tests by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/699
  • Use pytest for test_analysis and fix test by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/678
  • Fix saving paths in IJob.save by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/728
  • Remove almost, replace with np.isclose by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/729
  • Pytestise test_atom_mapping by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/688
  • Fix issue with 3.11 StrEnum by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/742
  • Treat all fields in ElementsDatabaseEditor as text fields by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/714
  • Atom database editor updates by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/748
  • Improve plotter code by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/719
  • Fix issue when MultiInput... has non-extant files by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/751
  • Re-use the job instance in Action.py by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/758
  • Update os env setting to make numpy use one thread when the GUI is used by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/762
  • Molecule preview using rdkit by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/756
  • Molecule preview button and fast plotting by @raunakkbanerjee in https://github.com/ISISNeutronMuon/MDANSE/pull/620
  • Save Q vectors in the output file by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/634
  • Fixed the structure factor from scattering function job. by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/766
  • Fix progress bar visual bug by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/768
  • Rework lammps parser by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/736
  • Add data normalisation to the plotter by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/761
  • Fix PDF calculation for non-orthogonal unit cells by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/735
  • Add ideal results when using the instrument resolution by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/773
  • Add the final progress update to IJob.runmulticore by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/779
  • Clean up widget base and move arguments to documented interface by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/757
  • Check for length-1 arrays in PlottingContext by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/787
  • T20 remove print by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/785
  • Add simulation time step section to converged results by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/784
  • Fix gui so that trajectory editor loads up correctly by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/790
  • Improve atom type recognition in LAMMPS parser by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/771
  • Use coordinates and not unit cell in SelectionWidgets by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/788
  • Remove print to satisfy T201 by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/791
  • Fix to unit conversion by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/796
  • Split distinct van Hove calculation into segments by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/738
  • 778 lammps read vel by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/782
  • Port citation to CITATION.cff format by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/654
  • Adjust the MDANSE GUI logo by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/799
  • Add missing attributes when axis=index in plotters by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/805
  • Fix unit conversion in MDAnalysis for velocity and forces by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/803
  • Improve atom property caching in MdanseTrajectory by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/802
  • Rework DLPoly parser to support more diverse inputs by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/798
  • Use configurator defaults for VectorWidget by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/800
  • Show file header in the GUI, remove unused code by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/808
  • Fix issues with density profile by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/819
  • Update ruff to encourage use of modern typing by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/795
  • Atom selection saving and loading by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/814
  • Add ability to nest data in .mda files by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/817
  • Fixed plot holder for windows by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/825
  • Use a subset of molecule indices array for distance histograms by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/827
  • Documentation update: atom selection and plotting by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/821
  • Updated to custom atom and property rename in database editor by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/830
  • Rob/mdanse trajectory filter by @RobBuchananCompPhys in https://github.com/ISISNeutronMuon/MDANSE/pull/615
  • Reimplement grouping as analysis input - 2 by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/810
  • Update doc conf.py by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/832
  • Add widgets back into widget lookup by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/837
  • Fix GUI bugs by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/834
  • Add optional file widget by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/812
  • Sort all imports with ruff by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/759
  • Atom selection normalisation update. by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/831
  • Add GUI warnings for the trajectory widget by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/841
  • Remove Discover trajectories by @RobBuchananCompPhys in https://github.com/ISISNeutronMuon/MDANSE/pull/839
  • Add missing getwidgetvalue in transmutation and charge widgets by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/840
  • User can not run IJob instance more than once in MDANSE script by @RobBuchananCompPhys in https://github.com/ISISNeutronMuon/MDANSE/pull/844
  • Limit IJob test to the CLI case by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/849
  • Deselect dummy atoms by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/838
  • Extend fast plotting to datasets and groups by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/847
  • Rework job status by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/754
  • Atoms selection and molecule grouping results in the documentation by @ChiCheng45 in https://github.com/ISISNeutronMuon/MDANSE/pull/851
  • Extended atom database by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/809
  • Scattering Length Density Profile by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/850
  • GUI warning for trajectories without a fixed cell by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/780
  • Test benchmark auto-generation by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/852
  • Correct AtomSelectionWidget by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/855
  • Documentation update, part 2 by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/829
  • Plot all files by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/860
  • Update GUI tab descriptions by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/862
  • Reorder jobs by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/856
  • Rework hdf trees by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/854
  • Skip key splitting for dummy index axes by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/865
  • Make COM trajectory use real cluster composition by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/863
  • Remove unnecessary outputs from SLDP by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/866
  • Enable more ruff checks and fix resulting errors by @oerc0122 in https://github.com/ISISNeutronMuon/MDANSE/pull/822
  • AngularCorrelation input change by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/835
  • Latest GUI corrections by @MBartkowiakSTFC in https://github.com/ISISNeutronMuon/MDANSE/pull/867

Full Changelog: https://github.com/ISISNeutronMuon/MDANSE/compare/v2.0.0b1...v2.0.0rc1

- Python
Published by MBartkowiakSTFC 8 months ago

mdanse - 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/

- Python
Published by MBartkowiakSTFC over 1 year ago

mdanse - 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/

- Python
Published by MBartkowiakSTFC over 1 year ago

mdanse - 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.

- Python
Published by MBartkowiakSTFC almost 2 years ago

mdanse - 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

- Python
Published by sanghamitra-mukhopadhyay almost 3 years ago

mdanse - 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

- Python
Published by sanghamitra-mukhopadhyay over 3 years ago

mdanse - 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

- Python
Published by sanghamitra-mukhopadhyay over 3 years ago