2026.06.29

What's Changed

• Add simulation extraction and viewing notebook by @jthorton in #226
• Add membrane tutorial with packmol-memgen setup by @hannahbaumann in #310
• update for new cinnabar API by @jthorton in #311
• Test kartograf 2.0 by @mikemhenry in #316
• bump to konnektor v0.4.0 by @atravitz in #317
• test lomap v3.3.0 by @atravitz in #318

Full Changelog: 2026.05.01...2026.06.29

2026.05.01

What's Changed

• update data and reorg openfold->openfe notebook by @atravitz in #307

Full Changelog: 2026.04.28...2026.05.01

2026.04.28

What's Changed

• comment out md simulation exectution so it doesn't auto-run in testing by @atravitz in #289
• pin interchange by @atravitz in #293
• update pin from interchange to interchange-base by @atravitz in #294
• Add workflow_dispatch to CI configuration by @IAlibay in #296
• Fix command path in CLI tutorial for quickrun by @ethanholz in #299
• bump to openfe v1.10.0 and update settings to include lipid17_merged by @atravitz in #302
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #303
• adding note about membranes in cli tutorial by @atravitz in #304
• Tutorial for membrane RBFE calculation by @hannahbaumann in #286
• update abfe_analysis notebook by @atravitz in #305
• updating septop analysis notebook for new results structure by @atravitz in #306

New Contributors

• @ethanholz made their first contribution in #299

Full Changelog: 2026.01.26...2026.04.28

2026.01.26

What's Changed

• update git ignore by @atravitz in #273
• clean up CI env and workflow by @atravitz in #272
• consolidate instructions for building networks from orion or fep+ files by @atravitz in #275
• consolidate instructions for creating an alchemical network by @atravitz in #276
• remove redundant generate_lomap_network.ipynb by @atravitz in #278
• remove unused data from networks/ dir by @atravitz in #281
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #282
• update ligandnetwork generation notebooks by @atravitz in #274
• update cli docs for clarity and accuracy by @atravitz in #283
• add cofactor example as a cookbook by @atravitz in #284
• Using cofactors example notebook by @IAlibay in #91

Full Changelog: 2025.12.04...2026.01.26

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