v2.0.0

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

New Contributors

• @dependabot[bot] made their first contribution in #126
• @pre-commit-ci[bot] made their first contribution in #140

Full Changelog: v1.2.0...v2.0