2024.10.0b6

What's Changed

• Openmm by @VGPReys in #654
• Interactive rescoring reviewed by @VGPReys in #778
• added chain ID by @mgiulini in #793
• Interactive rescoring and reclustering by @mgiulini in #769
• Zip structures by @mgiulini in #794
• Create action.yml by @amjjbonvin in #797
• Adding mirror pushing to the Castiel EuroHPC GitLab repo by @amjjbonvin in #798
• Add conditional execution for integration job by @rvhonorato in #801
• changed capri columns by @mgiulini in #805
• Side by side2 by @sverhoeven in #799
• Round other cluster + dont add score which was not there before by @sverhoeven in #810
• update codehub sync by @rvhonorato in #812
• Show top 10 ranked clusters + Other cluster by @sverhoeven in #813
• Improve docs by @mgiulini in #803
• Validate example workflows by @mgiulini in #816
• Low level docs by @mgiulini in #815
• Fine tuning Contact map module by @VGPReys in #749
• Mapping TIMEOUT output to failure in libhpc by @VGPReys in #727
• corrected parameter handling for cli-score by @mgiulini in #807
• Calc accessibility by @mgiulini in #820
• Work arround chain matching in IL-RMSDMatrix by @VGPReys in #828
• ordered traceback by @mgiulini in #831
• Fast rmsd by @mgiulini in #809
• Resolves issue #845 - adding missing parameters by @amjjbonvin in #847
• Interactivity fixes by @mgiulini in #823
• Graphical representation of clusters by @VGPReys in #772
• added traceback plot and sum of ranks file by @mgiulini in #850
• Offline mode by @VGPReys in #825
• Fix offlinemode by @VGPReys in #854
• Upgrade contact heatmap by @VGPReys in #855
• changing header info in contact map tsv files by @VGPReys in #856
• Fixing error in caprieval using shapes by @VGPReys in #851
• Fix auto analysis by @mgiulini in #853
• Improved seletopclusts by @VGPReys in #819
• Chain match coords load issue by @VGPReys in #864
• added groups data by @VGPReys in #872
• create new CNSScoringModule class by @VGPReys in #870
• Fair by @VGPReys in #868
• Added alascan modules to tests execution and comparison by @amjjbonvin in #876
• Add prefix to model names from input ensemble by @VGPReys in #878
• Save outputs in case of faulty tolerance by @VGPReys in #880
• Heavy atoms RMSD calculation in caprieval by @VGPReys in #837
• Add codacy/codacy-coverage-reporter-action action to tests.yml by @rvhonorato in #875
• Remove faulty outputs before saving io.json by @VGPReys in #883
• Define contact distance cutoff parameter in ilrmsdmatrix by @VGPReys in #881
• corrected absolute path in seletopclusts by @mgiulini in #888
• Improve alascan output by @mgiulini in #889
• Reclusts matrixplot by @VGPReys in #859
• check that file exists before renaming by @VGPReys in #893
• Update CONTRIBUTING.md by @AnnaKravchenko in #890
• Per interface scoring by @amjjbonvin in #896
• updating to latest main version by @amjjbonvin in #899
• Add option to keep the existing b-factor in the input PDB by @amjjbonvin in #898
• Updated CNS installation instructions by @amjjbonvin in #895
• Merge of main branch into the score branch by @amjjbonvin in #902
• Adds the HADDOCK score to the PDB headers - issue #901 by @amjjbonvin in #903
• only run codacy-coverage-reporter-action for same repo by @rvhonorato in #904
• Inverted chains by @mgiulini in #905
• added code of conduct by @mgiulini in #910
• improved postprocessing scaling by @mgiulini in #874
• remove deprecation warnings by @mgiulini in #907
• Reduce number of files in mode = "local" by @rvhonorato in #918
• add more good byes by @rvhonorato in #929
• Avoid generating .seed files by @rvhonorato in #924
• Makes haddock3 restraints subcommands available as web service by @sverhoeven in #841
• Refactor rigidbody module to allow the preparation of cns_input to be done in parallel by @rvhonorato in #933
• Use less_io parameter in caprieval by @rvhonorato in #928
• increased max sampling_factor by @mgiulini in #939
• removed duplicated w_air parameter by @amjjbonvin in #946
• Add MPI execution tests by @rvhonorato in #942
• Update repository templates by @rvhonorato in #951
• lazy load MPI module and COMM variable by @rvhonorato in #953
• Refactor capri.extract_data_from_capri_class to propagate the model's energy terms by @rvhonorato in #950
• changed min and max clust_cutoff by @mgiulini in #954
• Use prepare_cns_input_sequential when mode is not local by @rvhonorato in #943
• better description for some modules by @VGPReys in #947
• added ilrmsd to capri clt by @mgiulini in #957
• update caprieval integration tests by @rvhonorato in #958
• Handle exceptions in Worker.run by @rvhonorato in #962
• Clean intermediate files in batch mode by @VGPReys in #937
• change log level of exceptions in the Worker's run method by @rvhonorato in #966
• Update caprieval integration tests with new score values by @rvhonorato in #964
• Fix rescore by @mgiulini in #972
• Add logic to check for incompatible parameters by @rvhonorato in #935
• Propagate cluster related properties in caprieval by @rvhonorato in #978
• Ilrmsd onechain clarified by @mgiulini in #922
• Update README.md by @rvhonorato in #976
• Change the naming of the phoshpate oxygens to OP1/OP2 by @amjjbonvin in #985
• links to feedbacks by @VGPReys in #997
• Single chain caprieval by @VGPReys in #994
• remove dead code related to DNA in cm_restraints.cns by @amjjbonvin in #1001
• modifying amb_scale and unamb_scale parameter names by @VGPReys in #983
• avoid fileexist on empty strings by @amjjbonvin in #995
• Fileexist issue update by @amjjbonvin in #1010
• Set tolerance to 5 for non-topoaa modules by @sverhoeven in #1004
• ordering by size in clustrmsd by @mgiulini in #974
• added integration tests for scoring modules by @mgiulini in #968
• adding test to checks for duplicated parameters in defaults.yaml by @VGPReys in #913
• exposes cyclisation distance cutoffs by @amjjbonvin in #1003
• Add all global parameters description by @VGPReys in #1009
• make sure hbond restraints are read under a separate class by @amjjbonvin in #1015
• update pull_request_template.md by @rvhonorato in #1017
• refactor clustfcc and it's tests to use the proper path by @rvhonorato in #1016
• Enhance flexible definition in config files / defaults.yaml by @amjjbonvin in #969
• create libfcc.py by @rvhonorato in #1019
• Automatically reduce the tadfactor to 4 when fully flexible segments are defined by @amjjbonvin in #1020
• lower expertise level of ligands params by @VGPReys in #1023
• Integration tests by @amjjbonvin in #1014
• validate ncs parameters by @VGPReys in #1026
• Added DISCLAIMER statement by @amjjbonvin in #1031
• Detection of known CNS errors when failed run by @VGPReys in #1018
• re-work haddock3 installation by @rvhonorato in #1013
• less_io to debug by @VGPReys in #1035
• Update pages.yml by @rvhonorato in #1036
• Simplify definition of counted parameters by computing them on the fly from definition. by @VGPReys in #975
• Update main cli description by @VGPReys in #1043
• Update installation instructions by @rvhonorato in #1039
• add development instructions by @rvhonorato in #988
• Fixing some examples workflow configuration files by @VGPReys in #1045
• Cleaning of the random AIRs CNS code by @amjjbonvin in #1050
• removed NCS from rigidbody by @VGPReys in #1048
• Updating DNA examples to match parameters in tutorial by @VGPReys in #1055
• z-surface restraints scripts by @VGPReys in #839
• Refactor tempfile usage in tests by @rvhonorato in #1058
• update cyclic peptides examples by @VGPReys in #1057
• Make project compatible with recent python versions by @rvhonorato in #1042
• Update pandas requirement from ==1.* to ==2.* by @dependabot in #1065
• Bump mpi4py from 3.1.6 to 4.0.0 by @dependabot in #1064
• Bump pytest from 7.3.1 to 8.3.3 by @dependabot in #1066
• Bump hypothesis from 6.75.1 to 6.112.2 by @dependabot in #1067
• Parameter incompatibilities: Increase flexibility in incompatibilities handles. by @VGPReys in #991
• Corrected incompatibility values for the debug parameter by @amjjbonvin in #1071
• Import plotly offline mode by @VGPReys in #1041
• Replace haddock3-analysis-components with haddock3-ui package by @sverhoeven in #1025
• Add OpenMM module by @joaomcteixeira in #482
• Bump plotly from 5.11.0 to 5.24.1 by @dependabot in #1080
• Bump coverage from 7.2.5 to 7.6.1 by @dependabot in #1076
• Bump fastapi from 0.110.1 to 0.115.0 by @dependabot in #1077
• Bump pytest-mock from 3.12.0 to 3.14.0 by @dependabot in #1079
• Use YYYY.MM.PATCH for versioning by @rvhonorato in #1083
• limiting cpu usage in [openmm] by @VGPReys in #1075
• Add pipeline to publish image to ghcr.io by @rvhonorato in #1085
• add pipeline to automatically publish package in pypi on every release by @rvhonorato in #1087

New Contributors

• @AnnaKravchenko made their first contribution in #890

Full Changelog: v3.0.0-beta.5...2024.10.0b6