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