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- Remove out of date comments (lefotver task from PR #2131) by @IAlibay in #2133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