v0.14.0

Highlights

• Fixes errors caused by conformer generation failing
• Addresses high variance in partial charge generation through Ambertools giving high variance to estimates
• By default the OpenMM_RFE protocol produces energetic analysis of the simulations
• Adds openfe.setup.ligand_network_planning.generate_minimal_redundant_network for more robust ligand networks
• Allows gather CLI command to process partially finished/complete results

What's Changed

• test pydantic v2 by @mikemhenry in #541
• Analysing free energies by @IAlibay in #531
• fix forwards/backwards analysis for very small files by @richardjgowers in #545
• Fix Zenodo by @mikemhenry in #547
• Update CITATION.cff by @richardjgowers in #553
• ci: update to use setup-micromamba by @richardjgowers in #552
• don't include central ligand self edge in radial networks by @richardjgowers in #546
• Log system probe info by @dwhswenson in #513
• Update CITATION.cff by @richardjgowers in #554
• Add Zenodo badge to README by @richardjgowers in #555
• [WIP] Fix RTHP results serialization and test results load by @IAlibay in #550
• Fix energy results out by @richardjgowers in #556
• Added missing nc file by @mikemhenry in #562
• Tests: Test coverage for RFE ProtocolResult by @richardjgowers in #560
• Improve error message if missing one leg for ligand pair by @dwhswenson in #568
• Switch to a unified Sphinx theme by @Yoshanuikabundi in #563
• Fixup mypy matplotlib by @richardjgowers in #575
• add function to create a minimal network with redundancy for all nodes by @JenkeScheen in #559
• Combine installation guides and fix typos by @Yoshanuikabundi in #561
• Get ExampleNotebooks into docs by @Yoshanuikabundi in #538
• clear up language a bit for dg report help text by @mikemhenry in #549
• Absolute solvation free energies + base things for ABFEs by @IAlibay in #573
• rfe protocol: partial charges fix by @richardjgowers in #577
• Explicitly set navigation_keys to False to avoid warning by @IAlibay in #584
• Test AHFE user charges by @IAlibay in #586
• Enforce charges generated by input conformer by @IAlibay in #587
• Add gather --allow-partial, improve related error message by @dwhswenson in #588

New Contributors

• @JenkeScheen made their first contribution in #559

Full Changelog: v0.13.0...v0.14.0