2025.9.0

What's Changed

• Addresses issue #1350 - coordinates check by @amjjbonvin in #1351
• add PostInstallCommand to check if CNS is executable by @rvhonorato in #1356
• distribute haddock-restraints binary by @rvhonorato in #1354
• download binaries in editable mode by @rvhonorato in #1358
• Bump plotly from 6.2.0 to 6.3.0 by @dependabot[bot] in #1364
• Bump fastapi from 0.115.12 to 0.116.1 by @dependabot[bot] in #1363
• Bump coverage from 7.10.1 to 7.10.6 by @dependabot[bot] in #1361
• Bump hypothesis from 6.136.6 to 6.138.10 by @dependabot[bot] in #1362
• add libnotebooks by @rvhonorato in #1368
• Adding support for THR-glycosylation - Issue #1371 by @amjjbonvin in #1373
• Added missing parameters for all atoms thr-glycans - Issue #1371 by @amjjbonvin in #1377
• Consistancy in cluster naming in contactmap by @VGPReys in #1374
• Update pull_request_template.md by @amjjbonvin in #1378
• Adding the notebooks directory by @amjjbonvin in #1376
• Remove tmp dir in alascan test by @VGPReys in #1379

Full Changelog: 2025.8.0...2025.9.0

2025.8.0

Haddock3 v.2025.8.0 - Hot summer stable release

What's Changed

• adding random removal in haddock3-restraint cli by @VGPReys in #1232
• correction to alascan mutants by @mgiulini in #1275
• Update README with url to user manual by @VGPReys in #1278
• fix path to access matrix in tests cli re clustrmsd by @VGPReys in #1280
• Bump plotly from 6.0.1 to 6.1.2 by @dependabot[bot] in #1287
• Bump pytest-mock from 3.14.0 to 3.14.1 by @dependabot[bot] in #1285
• Bump coverage from 7.8.0 to 7.8.2 by @dependabot[bot] in #1286
• Bump hypothesis from 6.131.9 to 6.132.0 by @dependabot[bot] in #1284
• Selection of Nter, Cter and 5'end states at topology generation by @VGPReys in #1273
• Update CHANGELOG.md by @amjjbonvin in #1295
• Added support for pyroglutamic acid - issue #1228 by @amjjbonvin in #1290
• make deepcopy of molecule params so they can be used multiple times by @VGPReys in #1297
• fix url to user manual in readme by @VGPReys in #1303
• Restrain ligand by @VGPReys in #1301
• update readme with link to publication by @VGPReys in #1306
• adding citruline parameters/topology definition by @VGPReys in #1304
• add permissions to actions by @rvhonorato in #1308
• Added separate mpi install option by @amjjbonvin in #1294
• Bump hypothesis from 6.133.2 to 6.135.20 by @dependabot[bot] in #1311
• Bump coverage from 7.8.2 to 7.9.1 by @dependabot[bot] in #1313
• Bump pytest-cov from 6.1.1 to 6.2.1 by @dependabot[bot] in #1310
• Bump plotly from 6.1.2 to 6.2.0 by @dependabot[bot] in #1314
• Bump mpi4py from 4.0.3 to 4.1.0 by @dependabot[bot] in #1312
• Fix restrain lig test by @VGPReys in #1316
• Alascan parallel tests by @AnnaKravchenko in #1322
• Implements feature #1323 - adding bonded energies to the PDB headers by @amjjbonvin in #1330
• allow zero steps of energy minimization by @sjdv1982 in #1331
• computing std dev in alascan by @VGPReys in #1334
• version incrementation by @VGPReys in #1335
• Per-residue parallelization in alasan by @AnnaKravchenko in #1317
• Bump pytest-random-order from 1.1.1 to 1.2.0 by @dependabot[bot] in #1342
• Bump kaleido from 0.2.1 to 1.0.0 by @dependabot[bot] in #1341
• Bump coverage from 7.9.1 to 7.10.1 by @dependabot[bot] in #1340
• Bump hypothesis from 6.135.20 to 6.136.6 by @dependabot[bot] in #1339
• Bump pytest from 8.3.5 to 8.4.1 by @dependabot[bot] in #1338
• adding support for HETATM in caprieval by @VGPReys in #1279
• Increase parallelism in alascan by @VGPReys in #1337
• add no-restraints guardrail in rigidbody module by @VGPReys in #1346
• Allow clustering of single model in clustfcc by @VGPReys in #1348
• August package bumps by @VGPReys in #1344
• haddock3 v.2025.08.0 stable release by @VGPReys in #1347

New Contributors

• @sjdv1982 made their first contribution in #1331

Full Changelog: 2025.5.0...2025.8.0

HADDOCK3 2025.5.0

What's Changed

• Bump httpx from 0.27.2 to 0.28.0 by @dependabot in #1164
• Bump hypothesis from 6.119.3 to 6.122.0 by @dependabot in #1162
• Bump coverage from 7.6.7 to 7.6.8 by @dependabot in #1163
• [caprieval] comparisons against multiple references by @VGPReys in #1136
• Remove tox and adjust markdown files by @mgiulini in #1159
• Increased parameters in various CNS files for max path length by @amjjbonvin in #1170
• back to kaleido 0.2.1 until they fix it by @VGPReys in #1175
• refactored check for chain combinations by @mgiulini in #1176
• added flat tar extraction by @mgiulini in #1180
• modify way of getting the ncores by @VGPReys in #1172
• back to basics for macos users when detecting number of cores by @VGPReys in #1183
• allow for digit fluctuation in mdscoring integration tests by @VGPReys in #1185
• quick fix openm install and 8.2 version by @VGPReys in #1145
• Handle reference issue when multiple conformation provided in [caprieval] by @VGPReys in #1133
• Bump httpx from 0.28.0 to 0.28.1 by @dependabot in #1189
• Bump coverage from 7.6.8 to 7.6.10 by @dependabot in #1188
• Bump fastapi from 0.115.5 to 0.115.6 by @dependabot in #1186
• Bump hypothesis from 6.122.0 to 6.123.2 by @dependabot in #1187
• Bump pytest from 8.3.3 to 8.3.4 by @dependabot in #1190
• Added CNS troubleshooting instructions (issue #1191) by @amjjbonvin in #1197
• Bump hypothesis from 6.123.2 to 6.124.7 by @dependabot in #1194
• Bump fastapi from 0.115.6 to 0.115.8 by @dependabot in #1196
• removed debug log calls by @mgiulini in #1199
• Upgrade plotly by @mgiulini in #1200
• Add radius passive from active by @mgiulini in #1206
• add python3.13 to automatic pipelines by @rvhonorato in #1209
• Bump coverage from 7.6.10 to 7.6.12 by @dependabot in #1211
• Bump fastapi from 0.115.8 to 0.115.11 by @dependabot in #1218
• Bump mpi4py from 4.0.1 to 4.0.3 by @dependabot in #1213
• Bump hypothesis from 6.124.7 to 6.127.4 by @dependabot in #1217
• modified alascan by @mgiulini in #1219
• Adding rank to filenames in [contactmap] module by @VGPReys in #1228
• Bump plotly from 6.0.0 to 6.0.1 by @dependabot in #1237
• Increase number of supported molecules with common co-factors by @VGPReys in #1233
• Bump fastapi from 0.115.11 to 0.115.12 by @dependabot in #1238
• Bump pytest from 8.3.4 to 8.3.5 by @dependabot in #1236
• Update README.md by @amjjbonvin in #1245
• Bump coverage from 7.6.12 to 7.8.0 by @dependabot in #1234
• Bump hypothesis from 6.127.4 to 6.130.6 by @dependabot in #1235
• [prodigyligand] and [prodigyprotein] scoring modules by @VGPReys in #1069
• Updating Pull Request template checklist by @VGPReys in #1230
• Returning unequilibrated structure in openmm by @VGPReys in #1243
• pin prodigy-prot version by @rvhonorato in #1250
• add schedule to ci.yml by @rvhonorato in #1253
• Fine tuning for web app purpose by @VGPReys in #1126
• fix inconsistent use of top_cluster parameter by @amjjbonvin in #1222
• Added link to BioExcel 2025 survey by @AnnaKravchenko in #1254
• added nanobody example data by @mgiulini in #1207
• Bump prodigy-prot version + small ugrades on prodigy modules by @VGPReys in #1252
• Adding new filtering module [filter] by @VGPReys in #1226
• fix path in CONTRIBUTING.md by @VGPReys in #1256
• Active passive to ambig exception by @mgiulini in #1258
• Bump hypothesis from 6.130.6 to 6.131.9 by @dependabot in #1261
• Bump pytest-cov from 6.0.0 to 6.1.1 by @dependabot in #1260
• removed verbose log call from seletopclusts by @mgiulini in #1263
• added biorxiv ref by @mgiulini in #1265
• changed version by @mgiulini in #1266

Full Changelog: 2024.12.0b7...2025.5.0

2024.12.0b7

What's Changed

• Workaround plotly / kaleido static figure generation by @VGPReys in #1086
• Remove self.params["debug"] logic in caprieval by @rvhonorato in #1088
• numpy upgrade by @mgiulini in #1091
• Bump mpi4py from 4.0.0 to 4.0.1 by @dependabot in #1093
• Bump hypothesis from 6.112.2 to 6.115.0 by @dependabot in #1094
• Bump pytest-cov from 4.0.0 to 5.0.0 by @dependabot in #1097
• Bump fastapi from 0.115.0 to 0.115.2 by @dependabot in #1095
• Bump httpx from 0.27.0 to 0.27.2 by @dependabot in #1096
• Fix z restraints examples by @VGPReys in #1101
• Remove dead cli_bm by @rvhonorato in #1102
• sasascore module by @mgiulini in #862
• Remove adaptative sleep logic in libhpc by @rvhonorato in #1103
• Bump coverage from 7.6.1 to 7.6.4 by @dependabot in #1110
• Bump hypothesis from 6.115.0 to 6.115.3 by @dependabot in #1111
• Bump fastapi from 0.115.2 to 0.115.4 by @dependabot in #1118
• Bump hypothesis from 6.115.3 to 6.115.5 by @dependabot in #1117
• Correct auto documentation by @mgiulini in #1109
• Fix tests by @mgiulini in #1123
• Solves issue #1119 related to MPI execution with mpirun or run by @amjjbonvin in #1127
• fix random error by @mgiulini in #1129
• Bump hypothesis from 6.115.5 to 6.116.0 by @dependabot in #1130
• Bump pytest-cov from 5.0.0 to 6.0.0 by @dependabot in #1131
• Analysis not capri by @mgiulini in #1120
• Bump hypothesis from 6.116.0 to 6.118.7 by @dependabot in #1137
• fixed analysis on cleaned, downloaded runs by @mgiulini in #1124
• caught CNS exception in scoring modules by @mgiulini in #1138
• Per interface scoring for dimers by @mgiulini in #1143
• Reducing number of steps in openmm examples by @VGPReys in #1142
• Bump hypothesis from 6.118.7 to 6.119.3 by @dependabot in #1151
• Bump coverage from 7.6.4 to 7.6.7 by @dependabot in #1148
• Bump fastapi from 0.115.4 to 0.115.5 by @dependabot in #1150
• add new glycans by @mgiulini in #1134
• Update README.md by @amjjbonvin in #1146
• Bump kaleido from 0.2.1 to 0.4.1 by @dependabot in #1149
• Create validate_citation.yml by @mgiulini in #1156
• adding bioexcel forum by @VGPReys in #1161

Full Changelog: 2024.10.0b6...2024.12.0b7

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
  *...

v3.0.0-beta.5

haddock3 beta 5 release

What's Changed

• Clean and postprocess true by @mgiulini in #712
• Glycan example by @mgiulini in #711
• Tweak CI by @rvhonorato in #717
• Add topoaa integration test stub by @rvhonorato in #716
• Glycan 1 6 by @amjjbonvin in #714
• add function and variable annotations by @alchemistcai in #645
• added symmetry energy to output by @mgiulini in #723
• Integration tweak by @rvhonorato in #726
• Implement type annotations by @rvhonorato in #724
• commented workdir parameter by @mgiulini in #708
• Randomisation of starting orientations at flexref by @amjjbonvin in #729
• Haddock3 restraints by @mgiulini in #732
• removed xaxis sharing in report by @mgiulini in #736
• alascan module by @mgiulini in #690
• added bsa box plot by @mgiulini in #737
• added fnat - energy scatter plots by @mgiulini in #725
• Add missing parameters and update compare_runs.py by @amjjbonvin in #743
• contact map analysis module by @VGPReys in #731
• Updated color scheme of chord chart by @amjjbonvin in #745
• updated freesasa by @mgiulini in #748
• short description in haddock3-cfg CLI by @mgiulini in #753
• Bugfix traceback contactmap by @mgiulini in #751
• added description to analysis modules by @mgiulini in #688
• show gzipped structures in analysis report by @mgiulini in #758
• modif float comparisons in contact map tests by @VGPReys in #764
• Deep CNS scripts checking and example cleaning by @amjjbonvin in #763
• update protein-peptide examples/ files by @amjjbonvin in #768
• update key deletion logic in topoaa by @VGPReys in #766
• corrected crossbar values by @mgiulini in #771
• ilrmsdmatrix module by @mgiulini in #685
• Cli score fix by @mgiulini in #783
• uniform running modes by @mgiulini in #775
• Solves issue #785 about unstable energies when changing the param file by @amjjbonvin in #787
• Add topo/params for covalent docking Serine (SEC) - issue #757 by @amjjbonvin in #788
• Fix prot segid by @mgiulini in #780

New Contributors

• @alchemistcai made their first contribution in #645

Full Changelog: v3.0.0-beta.4...v3.0.0-beta.5

v3.0.0-beta.4

What's Changed

• solve unicode problem in restarting and copying runs by @mgiulini in #610
• change log handler by @rvhonorato in #616
• added score components to capri_clt by @mgiulini in #618
• Update pull_request_template.md by @rvhonorato in #620
• added packages to std envs by @mgiulini in #622
• added postprocess option to workflow by @mgiulini in #619
• Test cli analyse and remove matplotlib plots by @mgiulini in #627
• Remove duplicated key in src/haddock/modules/refinement/flexref/defaults.yaml by @rvhonorato in #630
• correct model-cluster-ranking by @mgiulini in #626
• updated paths in capri_ss cli_analyse by @mgiulini in #615
• Postprocess example workflows by @mgiulini in #634
• removed other_params from call to postprocess by @mgiulini in #636
• Adjust clustrmsd by @mgiulini in #632
• haddock3-analyse: create report html page based on individual plots by @SarahAlidoost in #611
• Add support for new carbohydrate linkages in line with 2.4 by @amjjbonvin in #640
• bugfix for when nemsteps=0 by @amjjbonvin in #646
• correct existing linting errors by @mgiulini in #649
• changed exported file names by @mgiulini in #650
• Update INSTALL.md sementic on various haddock3 by @VGPReys in #652
• change codecov fail_ci_if_error by @rvhonorato in #656
• Fixes b16 glycan linkage issue #659 by @amjjbonvin in #660
• Add structure viewer to the analysis report by @SarahAlidoost in #639
• Increased dihedral restraints array size - in line with haddock2.4/5 by @amjjbonvin in #664
• Add caprieval_rank to hover text in scatter and box plots by @SarahAlidoost in #666
• score-sorted scoring files by @mgiulini in #669
• Bump scipy from 1.8.0 to 1.10.0 by @dependabot in #671
• fixes issue #662 by @amjjbonvin in #672
• Hide install deprecation warnings by @VGPReys in #661
• modify location of SetuptoolsDeprecationWarning by @VGPReys in #674
• Make the table sortable(Use a React component in libplots) by @SarahAlidoost in #667
• fix max_molecules_allowed formatting by @VGPReys in #678
• haddock3-traceback by @mgiulini in #668
• Issuefixes by @VGPReys in #658
• Pin versions of react libraries by @SarahAlidoost in #682
• Chain matching and multibody capri by @mgiulini in #675
• update CI by @rvhonorato in #693
• handled max sampling_factor by @mgiulini in #691
• Access long description of module parameters by @VGPReys in #695
• Use ngl component by @SarahAlidoost in #683
• no traceback on pure analysis runs by @mgiulini in #702
• Fixing issues running examples by @VGPReys in #703
• Input to json by @mgiulini in #705

New Contributors

• @SarahAlidoost made their first contribution in #611
• @dependabot made their first contribution in #671

Full Changelog: v3.0.0-beta.3...v3.0.0-beta.4

v3.0.0-beta.3

What's Changed

• Added new antibody-antigen example using epitope definition from NMR by @amjjbonvin in #491
• Improve two titles in documentation by @joaomcteixeira in #490
• Added exit module by @joaomcteixeira in #494
• Improve running topoaa as an intermediate step in the workflow by @mgiulini in #498
• Update pdb-tools version. by @joaomcteixeira in #493
• Add documentation to the limit parameter in topoaa by @joaomcteixeira in #499
• Correct function selection in topoaa when order=0 and limit is used (or not) by @joaomcteixeira in #500
• Add missing parameter in run_tests.py after #494 by @joaomcteixeira in #501
• PDB pre-processing by @joaomcteixeira in #144
• Added shape.top to the supported residues by @joaomcteixeira in #508
• implemented check_chains by @mgiulini in #507
• Add documentation paragraph to rigidbody module description by @joaomcteixeira in #511
• add missing init file by @joaomcteixeira in #512
• Added a brief intro do HADDOCK3 by @joaomcteixeira in #514
• Correct typo in documentation by @joaomcteixeira in #513
• Removes --verbosity in isort lint check by @joaomcteixeira in #521
• Add action to deploy pages by @joaomcteixeira in #525
• changed to py39 in GA for pages by @joaomcteixeira in #526
• Updates docs theme to Karma theme by @joaomcteixeira in #524
• Uses action to deploy pages by @joaomcteixeira in #527
• add nojekyll file to GA generating pages by @joaomcteixeira in #530
• Corrects minor lint issues by @joaomcteixeira in #523
• Update guidelines to contribute to documentation by @joaomcteixeira in #531
• Add template to write new modules by @joaomcteixeira in #520
• Added support for 3-hydroxyproline (HY3) by @amjjbonvin in #533
• Update the --restart option to cope with subfolders in steps. by @joaomcteixeira in #522
• Rank capri_ss.tsv by score and sort by sortkey by @rvhonorato in #537
• Add full support to toml by @joaomcteixeira in #539
• changed retrieve_models logic by @mgiulini in #543
• Create haddock3-score CLI by @rvhonorato in #510
• Update the docs badge to match the pages.yml file. by @joaomcteixeira in #540
• Revert "changed retrieve_models logic" by @mgiulini in #553
• removed sampling parameter by @mgiulini in #552
• Add missing transfor_to_list in molecules when reading config by @joaomcteixeira in #554
• addressed bug in haddock3-copy cli by @mgiulini in #560
• Unclustered structures by @mgiulini in #556
• Handle single chains caprieval by @mgiulini in #548
• removed absolute paths in topoaa by @mgiulini in #562
• fixed dockq calculation by @mgiulini in #572
• Fault tolerant caprieval by @mgiulini in #574
• Add --ncores param to clean clients by @joaomcteixeira in #579
• Top cluster integer by @mgiulini in #576
• Fix clt order by @mgiulini in #582
• removed cluster file from tests and prettified code by @mgiulini in #583
• Add CNS installation instructions by @cvnoort in #469
• Multiple ambig files by @mgiulini in #563
• Adding the varia directory containing the CNS and lmod code by @amjjbonvin in #571
• Updates haddock3-cfg for toml compatibility - bool variables by @joaomcteixeira in #591
• Changed in yaml files some boeleans to use lowercase for consistency by @amjjbonvin in #592
• Update INSTALL.md to add an optional MPI dependency by @amjjbonvin in #577
• fixed handling of restr_fname in refinement modules by @mgiulini in #590
• Compress .inp, .out, and .seed in CNS Jobs on the fly by @joaomcteixeira in #594
• Implement option to use MAX CPUs and bypass the N-1 rule for local mode. by @joaomcteixeira in #597
• add w+ to data dir by @joaomcteixeira in #599
• Related to issue #598 - now compatible with OSX as well by @amjjbonvin in #600
• implement haddock3 postprocessing by @mgiulini in #567
• minor: correct test for #597 by @joaomcteixeira in #602
• Correct rmsds by @mgiulini in #604
• Capri memory error by @mgiulini in #585
• Changed max_cpus to true as default (and its description) by @amjjbonvin in #605
• added png option by @mgiulini in #606
• increased tolerance for MD modules by @mgiulini in #609
• text/typo edits in the documentation by @bvreede in #607

New Contributors

• @cvnoort made their first contribution in #469
• @bvreede made their first contribution in #607

Full Changelog: v3.0.0-beta.2...v3.0.0-beta.3

v3.0.0-beta.2

What's Changed since v3.0.0-beta.1

• Refactor caprieval by @rvhonorato in #441
• Generate .rst documentation page for .yaml default configuration files by @joaomcteixeira in #436
• Add user documentation on configuration files by @joaomcteixeira in #445
• Update MANIFEST.in by @joaomcteixeira in #455
• Enhance clustering protocols by @rvhonorato in #454
• amended clt_threshold behavior by @mgiulini in #460
• Add md5 property to libontology by @rvhonorato in #459
• Populate mol_ expandable parameters when using --extend-run by @joaomcteixeira in #450
• Allows single entries in molecules parameter by @joaomcteixeira in #439
• add cluster name to seletopclusts.txt by @rvhonorato in #462
• add tests to topoaa by @rvhonorato in #461
• add haddock3-docs to .gitignore by @joaomcteixeira in #463
• remove duplicated entry in clustfcc.txt by @rvhonorato in #465
• Corrects bug in --restart option by @joaomcteixeira in #467
• Add missing header to seletopclusts.txt by @rvhonorato in #471
• Implements clean output - compress/archive output files by @joaomcteixeira in #468
• Corrects check modules names in config on startup by @joaomcteixeira in #477
• Update CI workflows by @joaomcteixeira in #478
• Improve reading md5 from REMARK lines by @joaomcteixeira in #475
• Allows topoaa to run in different parts of the workflow by @joaomcteixeira in #474
• Adds parameter validation to general parameters by @joaomcteixeira in #479
• Improves mandatory parameter check by @joaomcteixeira in #481
• added chain-matching AlignError by @mgiulini in #483
• added single linkage as clustrmsd default by @mgiulini in #486
• added check on tolerance in clustrmsd by @mgiulini in #489
• run analysis modules after topoaa by @mgiulini in #484
• Add general parameters to haddock3-cfg client by @joaomcteixeira in #476

Full Changelog: v3.0.0-beta.1...v3.0.0-beta.2

v3.0.0-beta.1

What's Changed

• activate exports by @SSchott in #18
• LightDock sampling by @brianjimenez in #20
• Drop class name analogies favoring technical names by @rvhonorato in #21
• Clarifies main branch status by @joaomcteixeira in #23
• data_path not being found by @joaomcteixeira in #24
• renames flavour to mode missing files by @joaomcteixeira in #26
• Update installation instructions by @joaomcteixeira in #25
• Transforms haddock3 into a python package by @joaomcteixeira in #28
• Reduces code repetition in pdbutil when checking for new files by @joaomcteixeira in #31
• Correct ln command typo and updates CNS_EXE path to bin/cns by @rvhonorato in #34
• Example cleaning by @rvhonorato in #36
• Refactor scoring pipeline by @rvhonorato in #38
• corrects ln typo by @joaomcteixeira in #46
• Re-implement rigid body docking by @rvhonorato in #41
• Implement the semi flexible refinement module (flexref) by @rvhonorato in #50
• Implement water refinement (waterref) module by @rvhonorato in #51
• Add emref module by @rvhonorato in #56
• Rename waterref to mdref by @rvhonorato in #58
• Example fix by @rvhonorato in #60
• Remove input layer from configuration file by @joaomcteixeira in #62
• New modules structure and names by @joaomcteixeira in #59
• Removing stage key as a requirement for the configuration file by @joaomcteixeira in #63
• Moves and adjusts greeting messages by @joaomcteixeira in #65
• Implement clustfcc module by @rvhonorato in #67
• Update readme and minor path after #67 by @joaomcteixeira in #70
• Move examples data to its own folder by @rvhonorato in #73
• Add third-party module gdock by @rvhonorato in #72
• Handling defaults by @joaomcteixeira in #64
• Corrects path to example/data in lightdock.toml file by @joaomcteixeira in #79
• Add seletop module by @rvhonorato in #77
• reviewing subprocesses by @joaomcteixeira in #66
• Ensures misspelled keys in config files do not pass silently by @joaomcteixeira in #83
• adds setup only option by @joaomcteixeira in #84
• Modularizes cli.py by @joaomcteixeira in #85
• Updates clusterfcc to #66 - missing by @joaomcteixeira in #87
• moves mathutil to libmath by @joaomcteixeira in #86
• Reactivates --restart option by @joaomcteixeira in #88
• ReOrganizes some files, folder, and code by @joaomcteixeira in #89
• Inspect dependencies are installed for thirdparty libraries by @joaomcteixeira in #93
• Make weights configurable parameters by @joaomcteixeira in #91
• Implements dedicated configuration reader by @joaomcteixeira in #81
• Removes the need for activate_haddock global variables setup by @joaomcteixeira in #104
• Corrects for the rare case of number of CPUs = 0 by @joaomcteixeira in #107
• Removes remaining toml dependency after #81 by @joaomcteixeira in #109
• Implements CI for python modules by @joaomcteixeira in #110
• remove py310 action and env by @joaomcteixeira in #111
• Updates the logging system by @joaomcteixeira in #106
• Improves Scheduler ctrl+c handling by @joaomcteixeira in #105
• Corrects var names critical errors by @joaomcteixeira in #112
• Codecoving by @joaomcteixeira in #114
• Lints the code so far by @joaomcteixeira in #113
• removed py310 from tox by @joaomcteixeira in #115
• Clean the CNS part of the rigidbody docking module by @amjjbonvin in #124
• Further cleaning of the topoaa, rigidbody and flexref modules by @amjjbonvin in #127
• Models start 1-index by @joaomcteixeira in #129
• Implement caprieval by @rvhonorato in #130
• Update caprieval defaults.cfg by @rvhonorato in #135
• Correct enumerate syntax by @joaomcteixeira in #137
• Adds support for global variables for CNS by @joaomcteixeira in #136
• Cleaned emref module and adapted other to new env variables by @amjjbonvin in #140
• Added example, some cns module corrections/additions by @amjjbonvin in #145
• Bugfix caprieval by @rvhonorato in #147
• Solves missing repeated modules during prepare_run by @joaomcteixeira in #150
• Fixes arrays being overwritten in caprieval by @rvhonorato in #155
• Implement ensemble support for docking in CNS-based modules by @rvhonorato in #152
• Add support for ligands and DNA and refactor mdref module by @amjjbonvin in #156
• Add homotrimer docking example with C3 symmetry by @amjjbonvin in #161
• None variables are NOT written to CNS by @joaomcteixeira in #163
• improves on #163 by @joaomcteixeira in #167
• empty strings are written to CNS by @joaomcteixeira in #168
• input params in topoaa/defaults.cfg now with proper behaviour by @joaomcteixeira in #169
• Added protein-ligand-shape example by @amjjbonvin in #170
• Improves regex for scientific notation in config reader by @joaomcteixeira in #174
• Added check to make sure the seed file is present before reading. by @amjjbonvin in #175
• Add scores to caprieval output by @rvhonorato in #180
• Add .vscode to gitignore by @rvhonorato in #181
• Add option to "sortby" in caprieval by @rvhonorato in #182
• Revert "Merge pull request #182 from haddocking/153" by @rvhonorato in #184
• Change log statements by @rvhonorato in #159
• Benchmarking system and configuration. by @joaomcteixeira in #116
• Add option to sort-by in caprieval by @rvhonorato in #185
• Tweak logs by @rvhonorato in #188
• Refactor code to allow for Refinement by @rvhonorato in #187
• Add sampling_factor parameter to refinement modules by @rvhonorato in #189
• Implement HPC execution by @rvhonorato in #192
• Fix HPC completed percentage by @rvhonorato in #193
• Sort tasks while initializing libparallel by @rvhonorato in #197
• Small tweaks to the benchmark scripts by @rvhonorato in #195
• Fix sorting of paralel jobs by @rvhonorato in #202
• Updates clarifies install instructions by @joaomcteixeira in #203
• Refactor code to allow for scoring by @rvhonorato in #199
• Use MODDIR instead of MODRUN rigidbody.cns by @amjjbonvin in #207
• Do not delete the run dir. by @joaomcteixeira ...