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...v2.0.0

Contributors

• @mikemhenry
• @IAlibay
• @dependabot
• @jthorton
• @atravitz
• @pre-commit-ci

What's Changed

• Remove outdated pip install instructions by @atravitz in #85
• Add check_packaging to ci by @atravitz in #87
• Add bond break filter by @jthorton in #89
• Optional bond breaking by @IAlibay in #92

Full Changelog: v1.1.0...v1.2.0

Contributors

• @IAlibay
• @jthorton
• @atravitz

What's Changed

• adding hybridization change filter by @RiesBen in #35
• ring hybridization filter by @RiesBen in #36
• Update element_change.py by @RiesBen in #39
• Update CI by @IAlibay in #43
• Create CITATION.cff by @RiesBen in #45
• Swap out from personal email by @IAlibay in #48
• Fix codecov action conditional by @IAlibay in #53
• Remove not tested scorer by @RiesBen in #54
• Fix fused ring mappings by @jthorton in #56
• Fix ring hybridization filter by @jthorton in #65
• Minor Docs clean up by @jthorton in #66
• Change optional filter ordering by @jthorton in #64
• Mapping multi chain components by @RiesBen in #47
• Pin to python >=3.10 by @jthorton in #78
• Add rever for changelog and backfill news by @jthorton in #77
• Add Zenodo link to the readme by @jthorton in #80
• switch to team authorship by @atravitz in #81
• Updated CHANGELOG for 1.1.0 by @jthorton in #83

New Contributors

• @IAlibay made their first contribution in #43
• @jthorton made their first contribution in #56
• @atravitz made their first contribution in #81

Full Changelog: https://kartograf.readthedocs.io/en/latest/CHANGELOG.html

Contributors

• @RiesBen
• @IAlibay
• @jthorton
• @atravitz

Minor release containing improved documentation and updates for gufe abc updates.

What's Changed

• Docs by @RiesBen in #27
• Update index.rst by @RiesBen in #28
• Update Install Instructions + May Other Fixes by @mikemhenry in #29
• include date in cache key by @mikemhenry in #31
• Add deps to colab notebook by @mikemhenry in #32
• Make Mapper tokenizable by @richardjgowers in #33

Full Changelog: 1.0.0...v1.0.1

Contributors

• @richardjgowers
• @mikemhenry
• @RiesBen

🥳 Kartograf is now at v1.0.0 🥳
Features:

• Mapping Geometry Based Atom Mapper
  • Fitlers for applying rules what not to map (ring breaks or ring size changes, element changes, no hydrogens, etc.)
• SmallCompound alignment tools - MCS or shape based
• Mapping Scoring Metrics (and an experimental Scorer - don't use for real business)
• visualization widget for multiple mappings in jupyter notebooks

Looking forward to get your Feedback! 😁

• minor refactor
• adding new optional visualization