v1.12.0

Changelog for humans

https://docs.openfree.energy/en/latest/CHANGELOG.html#v1-12-0

All PRs included in this release:

• Switch repeat id assignment from leg to repeat in AFE Protocols by @IAlibay in #1948
• Support for charge changes in the HybTop protocol for explicitly solvated systems by @hannahbaumann in #1978
• Cinnabar update by @jthorton in #1989
• Add structural analysis to the SepTop protocol by @hannahbaumann in #1982
• Use unbiased std for uncertainty estimates by @jthorton in #2000
• Updated the CLI to use unbiased std for errors by @jthorton in #2018
• add other cli commands to docs by @atravitz in #2017
• add contributing guidelines by @atravitz in #1580
• remove warning for element changes by @atravitz in #1965
• testing: catch konnektor warnings by @atravitz in #2027
• turn off api break check (for now) by @atravitz in #2034
• split api break test into two parts by @mikemhenry in #2037
• bump env to konnektor 0.4.0 by @atravitz in #2026
• Test kartograf 2.0 by @mikemhenry in #2031
• add to_rbfe_deprecation news item by @atravitz in #2044
• fix: add dep for example notebook testing by @atravitz in #2045
• Fix SepTop resume test by @IAlibay in #2048
• add contributing guide and code of conduct links to landing page by @atravitz in #2047
• remove perses atommapper and scorer by @atravitz in #1943
• Update pull request template for AI disclosure by @IAlibay in #2051
• Release/v1.12.0 by @atravitz in #2053

Full Changelog: v1.11.1...v1.12.0