v1.13.0

Changelog for humans

https://docs.openfree.energy/en/latest/CHANGELOG.html#v1-13-0

All PRs included in this release:

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #2064
• Update v1.12 changelog description for stdev update to cover all Prot… by @IAlibay in #2065
• [FIX] fix mypy checks by removing unused ignores by @IAlibay in #2066
• try pinning rdkit by @atravitz in #2068
• ci: update condalock ci by @atravitz in #2060
• ci: update docker build env by @atravitz in #2061
• return partial convergence analysis if mbar fails for individual fraction by @aqemia-benedict-tan in #1984
• Update docstrings and warnings with updated convergence analysis by @aqemia-benedict-tan in #2088
• Speed up HTF creation by @jthorton in #1858
• remove unused pytest.warns() check from test_gather by @atravitz in #2090
• Fix residue naming by @hannahbaumann in #2042
• docs: add announcement banner about user interviews by @atravitz in #2108
• Speed up tests a little w/ pre-assigned partial charges & other things by @IAlibay in #2110
• run mypy CI on PRs into all branches (not just main) by @atravitz in #2112
• Raise an error for empty HybridTopology atom mappings by @jthorton in #2120
• support pydantic 2.13 and python 3.14 by @atravitz in #2058
• Fix for forward and reverse analysis. by @IAlibay in #2131
• Remove out of date comments (lefotver task from PR #2131) by @IAlibay in #2133
• Check for bond breaks in Hybrid Topology validation by @jthorton in #2121
• Modify residue names of ligands and cofactors in the SepTop and ABFE protocols by @hannahbaumann in #2118
• Fix ligand order after multiprocessing charging by @jthorton in #2151
• Enable user defn boresch restraints in ABFE Protocol by @IAlibay in #2019
• Require at least 4 mapped heavy atoms in the Hybrid Topology protocol by @jthorton in #2122
• Move structural analysis methods to child classes in SepTop Protocol by @IAlibay in #2049
• remove unused storage classes by @atravitz in #2169
• remove user interview banner by @atravitz in #2175
• Fix residue names & numbers for the PlainMDProtocol by @IAlibay in #2178
• add user survey banner by @atravitz in #2184
• Validate the vacuum and solvent force field settings in ASFE by @jthorton in #2185
• Add new contributors section to guidelines by @IAlibay in #2189
• Let the force field resolve the partial charge assignment by @jthorton in #2152
• Catch errors in bulk charge assignment by @jthorton in #2180
• Update duecredit dependency in environment.yml by @jthorton in #2197
• Upper pin citeproc-py to get the harvard1 style by @jthorton in #2202
• build konnektor and kartograf from conda-forge by @atravitz in #2210
• CLI settings updates by @jthorton in #2212
• Return self in model_validator for BoreschRestraintSettings by @IAlibay in #2217
• Maint/clean up fixtures by @atravitz in #2225
• Epic: execution improvements by @atravitz in #2113
• Add new troubleshooting guide by @jthorton in #2213
• build docs with main branch of example notebooks by @atravitz in #2229
• Maint/compress test warehouse by @atravitz in #2224
• task-based execution user guide edits by @atravitz in #2211
• Fix mypy failure in Node.lock assignment by @IAlibay in #2235
• Add repair network cookbook to docs by @hannahbaumann in #2228
• Abfe structural analysis by @IAlibay in #2220
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #2242
• clean up compressed warehouse example data by @atravitz in #2238
• upper pin 3.15 until tested by @atravitz in #2243
• update max python pin by @atravitz in #2248
• clean up storage and orchestration APIs, expose to Reference docs by @atravitz in #2240
• upper pin click to <8.5.0 until we address deprecation warnings by @atravitz in #2253
• Allow reading of legacy restraint settings for SepTop by @IAlibay in #2237
• Decouple the solvent and vacuum lambda schedules for the AHFE Protocol and remove redundant windows. by @IAlibay in #2241
• add --name option to setup-task-campaign by @atravitz in #2249
• task-based execution: add option to increase max_tries by @atravitz in #2227
• add warnings for experimental features by @atravitz in #2256
• release prep: v1.13.0 by @atravitz in #2255
• add init.py to openfe/tests/storage by @atravitz in #2258

New Contributors

• @aqemia-benedict-tan made their first contribution in #1984

Full Changelog: v1.12.0...v1.13.0