2025.11.0

What's Changed

• Bump fastapi from 0.116.1 to 0.120.4 by @dependabot[bot] in #1434
• Bump coverage from 7.10.6 to 7.10.7 by @dependabot[bot] in #1435
• Minor: remove BioExcel User Survey 2025 link from log file by @AnnaKravchenko in #1441
• Bump pytest-cov from 6.2.1 to 7.0.0 by @dependabot[bot] in #1436
• Bump hypothesis from 6.140.2 to 6.141.1 by @dependabot[bot] in #1432
• Bump plotly from 6.3.0 to 6.3.1 by @dependabot[bot] in #1433
• Update download link for tutorial data by @amjjbonvin in #1440
• Added permanent link for Prot-ON results by @amjjbonvin in #1442
• Alascan with non-standard ligand/molecules/residues by @VGPReys in #1412
• Corrects verbosity settings - issue #1446 by @amjjbonvin in #1447
• Corrected verbose level to use all instead of verbose by @amjjbonvin in #1450
• Fixed the use of restraints in the presence of ions in flexref module by @amjjbonvin in #1449

Full Changelog: 2025.9.1...2025.11.0

2025.9.1

What's Changed

• Removed os.chdir command in installation cell of HADDOCK3-antibody-antigen.ipynb - issue #1383 by @amjjbonvin in #1384
• update minimum mpi4py version by @rvhonorato in #1386
• add mode=grid by @rvhonorato in #1381
• Bump pytest from 8.3.5 to 8.4.1 by @dependabot[bot] in #1365
• update Makefiles to make CNS compilation static by @rvhonorato in #1394
• use musl binaries from haddock-restraints by @rvhonorato in #1396
• Cleaned the antibody-antigen notebook by @amjjbonvin in #1400
• Corrected dead links by @amjjbonvin in #1402
• Bump hypothesis from 6.138.10 to 6.140.2 by @dependabot[bot] in #1403
• Bump prodigy-lig from 1.1.3 to 1.1.4 by @dependabot[bot] in #1407
• Bump pytest-mock from 3.14.1 to 3.15.1 by @dependabot[bot] in #1406
• Bump kaleido from 1.0.0 to 1.1.0 by @dependabot[bot] in #1405
• add action to identify stale issues/PRs by @rvhonorato in #1408
• add adaptative job concatenation to mode=grid by @rvhonorato in #1391
• force download of cns linux binary if arch!="x86_64-linux" by @rvhonorato in #1398
• support python3.14 by @rvhonorato in #1415
• fix test coverage report by @rvhonorato in #1427
• refactor libpdb.sanitize by @rvhonorato in #1426
• Allow for chain selection in CNS scoring modules by @VGPReys in #1421
• update coverage upload by @rvhonorato in #1431
• update CNS download links by @rvhonorato in #1439

Full Changelog: 2025.9.0...2025.9.1

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