Change log for humans

https://kartograf.openfree.energy/en/latest/CHANGELOG.html

Breaking Changes

• The default for KartografAtomMapper's map_hydrogens_on_hydrogens_only option is now True. Previously it was False.
• We moved the visualization widget to gufe. Instead of from kartograf.utils.mapping_visualization_widget import display_mappings_3d use from gufe.visualization.mapping_visualization import display_mappings_3d

What's Changed

• Add python version to package CI tests by @IAlibay in https://github.com/OpenFreeEnergy/kartograf/pull/98
• Package for PyPI by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/116
• Ensure PEP-639 Support by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/117
• Add API break test by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/118
• Change hydrogen on hydrogen mapping default to True by @jthorton in https://github.com/OpenFreeEnergy/kartograf/pull/69
• Add pre-commit + spruce up CI + add ruff config by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/119
• Feat/ruff fix fmt by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/120
• Run pre commit by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/124
• PR template update + setup a dependabot.yml by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/125
• ignore auto fixes in git blame by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/130
• Bump codecov/codecov-action from 3 to 5 by @dependabot[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/126
• Bump actions/github-script from 7 to 8 by @dependabot[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/128
• Bump actions/checkout from 4 to 6 by @dependabot[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/129
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/127
• Make sure we test with numpy 2 by @atravitz in https://github.com/OpenFreeEnergy/kartograf/pull/91
• add __version__ info by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/132
• Use scipy cdist to calculate distance matrix by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/133
• Remove colab link and add notebook to docs by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/135
• Use dict|list comprehension for speedups by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/137
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/140
• move viz over to gufe, switch to gufe branch with the viz for testing by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/138
• add alignment docs by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/144
• Bump mamba-org/setup-micromamba from 2 to 3 by @dependabot[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/145
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/147
• Bump codecov/codecov-action from 5 to 6 by @dependabot[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/146
• Update alignment docs with "method" details by @IAlibay in https://github.com/OpenFreeEnergy/kartograf/pull/149
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/150
• Bump actions/github-script from 8 to 9 by @dependabot[bot] in https://github.com/OpenFreeEnergy/kartograf/pull/148
• Improve warnings about atom mappings by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/151
• Missing News Items by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/134
• add news entry for PR 144 by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/153
• install gufe from conda-forge + include data needed for notebook example by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/154
• Remove viz deps + run pyupgrade 3.11 by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/155
• Updated CHANGELOG for 2.0 by @mikemhenry in https://github.com/OpenFreeEnergy/kartograf/pull/156

New Contributors

• @dependabot[bot] made their first contribution in https://github.com/OpenFreeEnergy/kartograf/pull/126
• @pre-commit-ci[bot] made their first contribution in https://github.com/OpenFreeEnergy/kartograf/pull/140

Full Changelog: https://github.com/OpenFreeEnergy/kartograf/compare/v1.2.0...v2.0