v1.9.0

Changelog for humans

https://docs.openfree.energy/en/latest/CHANGELOG.html#v1-9-0

All PRs included in this release:

• add openeye w/ python 3.13 test to CI by @atravitz in #1745

• bump python version for conda cron by @atravitz in #1748

• remove mypy rdkit pin by @atravitz in #1753

• Make the multistate hybrid topology samplers not require the HybridTopologyFactory by @IAlibay in #1768

• Migrate validation to Protocol._validate in HybridTopologyProtocol by @IAlibay in #1740

• Move rfe protocol by @IAlibay in #1769

• Breakdown rfe protocolunit by @IAlibay in #1770

• Have two separate system generators for state A & B in hybrid protocol by @IAlibay in #1772

• HybridTop structural analysis via API rather than CLI by @IAlibay in #1771

• making some language clearer on github-facing things by @atravitz in #1758

• Moving AFE Protocols around a bit by @IAlibay in #1775

• Create setup, run, and analysis units for HybridTop Protocol by @IAlibay in #1773

• update docs for multiple protocol units by @atravitz in #1793

• Update docstring for hybridtop classes by @IAlibay in #1794

• Small improvement in RelativeHybridTopologyProtocol docstring by @IAlibay in #1797

• turn off zenodo retry by @atravitz in #1802

• only run CI on macos python 3.12 by @atravitz in #1803

• Turn AFE protocols into multiple units by @IAlibay in #1776

• move to src layout by @atravitz in #1805

• Temporarily build pooch from main w/ hotfix by @atravitz in #1806

• make CLI starting guide easier to find from the landing page by @atravitz in #1787

• Update pyproject.toml by @IAlibay in #1813

• refactor: clean up test data handling by @atravitz in #1815

• min pin pooch to fix data fetching by @atravitz in #1820

• fix api break check path by @atravitz in #1825

• fix scope mismatch with zenodo data by @atravitz in #1828

• numpy >=2.3.0 support by @atravitz in #1558

• pin smirnoff99frosst by @atravitz in #1837

• add --download-only option to openfe test by @atravitz in #1814

• Release/v1.9.0 by @atravitz in #1835

Full Changelog: v1.8.1...v1.9.0