2025.12.04

What's Changed

• fix colab badge by @atravitz in #258
• fixing a typo by @atravitz in #259
• footgun go boom by @mikemhenry in #257
• Start of workflow to test doc building by @mikemhenry in #262
• Start of workflow to test doc building by @mikemhenry in #263
• Add notebook for running OpenFE with OF3 generated inputs by @hannahbaumann in #266
• remove openmm_rbfe notebooks by @atravitz in #269
• remove unused binder image workflow by @atravitz in #270
• fix failing cells in example notebooks by @atravitz in #268

Full Changelog: 2025.10.2...2025.12.04

2025.10.2

What's Changed

• add torchvision and datetime workarounds to all notebooks using colab by @atravitz in #253
• Update download link for septop_results.zip by @IAlibay in #254
• Remove abfe results as they are breaking things otherwise by @IAlibay in #255

Full Changelog: 2025.10.1...2025.10.2

2025.10.1

What's Changed

• Add notebook for ABFE result analysis by @hannahbaumann in #235
• fix septop diagram aspect ratio by @atravitz in #242
• use ligandatommapping.view_3d in examples by @atravitz in #236
• Update showcase for v1.7 by @IAlibay in #240
• Update md notebook for v1.7 by @IAlibay in #238
• Update the tutorial notebooks for v1.7 by @IAlibay in #239
• Update cookbooks for v1.7 by @IAlibay in #237
• fix binder comment workflow syntax by @atravitz in #245
• fix septop png rendering in docs by @atravitz in #247
• Revert "Update cookbooks for v1.7" by @atravitz in #249
• Bump rc releases to 1.7 and python CI to 3.12 by @atravitz in #244
• updates to t4lysozyme rbfe example by @atravitz in #246

Full Changelog: oct-2025...2025.10.1

oct-2025

What's Changed

• Change the protocol repeat settings to 1 by @hannahbaumann in #219
• Adapt host min/max distance restraints + fix broken notebook by @hannahbaumann in #221
• bump to 1.6 by @atravitz in #214
• SepTop analysis notebook by @hannahbaumann in #225
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #233
• bump to 1.6.1 by @atravitz in #231
• CI autocomment should use colab, not binder by @atravitz in #232

Full Changelog: june-2025...oct-2025

june-2025

What's Changed

• see if notebooks will run on osx-arm64 by @mikemhenry in #147
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #151
• Issue 138 is no longer relevant by @IAlibay in #155
• Update openfe_showcase.ipynb to use openfe 1.0.1 by @mikemhenry in #158
• bumping openfe_showcase.ipynb from 1.0.1 to 1.1.0 by @atravitz in #166
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #162
• correcting cli --report option 'dg-raw' to 'raw' by @atravitz in #169
• Showcase proofreading by @atravitz in #163
• CLI tutorial proofreading by @atravitz in #170
• BespokeFit parameters notebook by @jthorton in #171
• Fix cookbook rendering issues by @jthorton in #173
• Update network viz cookbook to read from graphml too. by @IAlibay in #175
• bumping to openfe v1.2.0 by @atravitz in #179
• removing box vectors from 2.3 by @atravitz in #182
• CLI charging update by @jthorton in #187
• rename easy_rb(h)fe to rb(h)fe by @atravitz in #190
• Cookbook for plotting DG calc against DG exp when there are missing exp data by @hannahbaumann in #191
• bump openfe version to 1.3.1 by @atravitz in #198
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #196
• Update some settings in the MD tutorial to get outputs by @hannahbaumann in #201
• Add an ABFE tutorial by @hannahbaumann in #203
• Add a SepTop RBFE tutorial by @hannahbaumann in #202
• switch showcase install to 1.5.0dev by @atravitz in #204
• adding colab installs to some notebooks by @atravitz in #205
• notebooks clean up by @atravitz in #207
• adding a copy of rbfe tutorial notebook so fetch doesn't break for now by @atravitz in #208
• Change simulation length SepTop tutorial by @hannahbaumann in #210
• Adding details about --n-protocol-repeats to CLI tutorial by @IAlibay in #213

New Contributors

• @atravitz made their first contribution in #166
• @jthorton made their first contribution in #171

Full Changelog: april-2024...june-2025

1.5 DEV

What's Changed

• see if notebooks will run on osx-arm64 by @mikemhenry in #147
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #151
• Issue 138 is no longer relevant by @IAlibay in #155
• Update openfe_showcase.ipynb to use openfe 1.0.1 by @mikemhenry in #158
• bumping openfe_showcase.ipynb from 1.0.1 to 1.1.0 by @atravitz in #166
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #162
• correcting cli --report option 'dg-raw' to 'raw' by @atravitz in #169
• Showcase proofreading by @atravitz in #163
• CLI tutorial proofreading by @atravitz in #170
• BespokeFit parameters notebook by @jthorton in #171
• Fix cookbook rendering issues by @jthorton in #173
• Update network viz cookbook to read from graphml too. by @IAlibay in #175
• bumping to openfe v1.2.0 by @atravitz in #179
• removing box vectors from 2.3 by @atravitz in #182
• CLI charging update by @jthorton in #187
• rename easy_rb(h)fe to rb(h)fe by @atravitz in #190
• Cookbook for plotting DG calc against DG exp when there are missing exp data by @hannahbaumann in #191
• bump openfe version to 1.3.1 by @atravitz in #198
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #196
• Update some settings in the MD tutorial to get outputs by @hannahbaumann in #201
• Add an ABFE tutorial by @hannahbaumann in #203

New Contributors

• @atravitz made their first contribution in #166
• @jthorton made their first contribution in #171

Full Changelog: april-2024...april-2025

April 2024

What's Changed

• Update network example notebook by @dwhswenson in #30
• *.nc in .gitignore by @dwhswenson in #38
• update pins for v0.6 by @richardjgowers in #37
• Update README.md by @richardjgowers in #32
• Alchemicalnetwork tutorial by @richardjgowers in #42
• CLI tutorial (markdown) by @dwhswenson in #50
• [WIP] Update cli-tutorial.md by @mikemhenry in #52
• Switch to tyk2 from p38 by @IAlibay in #53
• Add RHFE Python tutorial by @dwhswenson in #56
• Update MacOS runners so they exist by @dwhswenson in #58
• Update CLI tutorial by @dwhswenson in #57
• Switching tutorials over to RBFE by @dwhswenson in #59
• RBFE tutorial: next revisions by @dwhswenson in #60
• Make notebook transformations identical to CLI by @dwhswenson in #61
• [WIP] Fixes for feedback by @dwhswenson in #62
• Fix missing update to viewer => view by @dwhswenson in #63
• update tutorial to mention complex of vacuum by @IAlibay in #65
• Fix typos in cli_tutorial.md (#64) by @dwhswenson in #66
• Update tutorial with more details on running. by @dwhswenson in #68
• Add README to tutorial by @dwhswenson in #71
• Fix bug in cli_tutorial.md by @mikemhenry in #73
• Switch to colab by @mikemhenry in #69
• Add notebook for plotting out free energies using Cinnabar v0.3 by @IAlibay in #78
• Add notebook for creating AlchemicalNetworks from external files by @IAlibay in #79
• Openfe 13 updates by @richardjgowers in #83
• Showcase Notebook updates for OpenFE #538 by @Yoshanuikabundi in #81
• Add dG obtaining code and showing how to shift the absolutes by @IAlibay in #86
• Add notebooks for cookbook by @Yoshanuikabundi in #84
• Adapt notebook to work with cinnabar 0.4 by @hannahbaumann in #88
• Add cookbook entry for user charges by @IAlibay in #90
• Update cli_tutorial.md for new gather options by @mikemhenry in #85
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #92
• Add information about the settings flag to cli tutorial. by @RiesBen in #89
• Add LOMAP network examples by @hannahbaumann in #98
• Just testing table stuff - please ignore by @IAlibay in #116
• Update README.md by @richardjgowers in #72
• Add AHFE tutorial by @hannahbaumann in #100
• Add tutorial for MD simulations by @hannahbaumann in #97
• Fix for openfe docs rendering by @IAlibay in #120
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #121
• Update cookbooks for openfe 1.0 by @IAlibay in #122
• Add alchemical planners cookbook by @IAlibay in #124
• Fix title rendering MD tutorial by @hannahbaumann in #127
• Fix old showcase for 1.0 release by @hannahbaumann in #128
• Polish up the RBFE CLI tutorial for 1.0 release by @jameseastwood in #137
• Pin macos runner to v12 by @IAlibay in #134
• Test openfe 1.0.0rc0 + refresh showcase by @mikemhenry in #99

New Contributors

• @Yoshanuikabundi made their first contribution in #81
• @RiesBen made their first contribution in #89
• @jameseastwood made their first contribution in #137

Full Changelog: nov-2022...april-2024

November beta release

This is the beta release of the OpenFE toolkit.

The original showcase notebook is updated to include using the latest gufe Protocol API

A new notebook showing how to plan a free energy network, apply a Protocol, serialise Transformations and use the quickrun command is added.

April 2022 Demo

Install

Use this command to install the necessary packages for the notebook:
conda env create openfe/openfe-notebooks

What's Changed

• Add CI and mybinder to Example Notebooks by @mikemhenry in #1
• Setup openmm-rbfe Environment by @mikemhenry in #2
• use new tags for lomap and openfe by @mikemhenry in #6
• Improve performance of _remove_constraints by @dwhswenson in #8
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #10
• added CITATION file by @mikemhenry in #9
• Updating notebook for april 2022 release by @IAlibay in #11

New Contributors

• @mikemhenry made their first contribution in #1
• @dwhswenson made their first contribution in #8
• @pre-commit-ci made their first contribution in #10
• @IAlibay made their first contribution in #11

Full Changelog: https://github.com/OpenFreeEnergy/ExampleNotebooks/commits/april-2022