v1.3.1

What's Changed

• fix: include .sh files in package data and improve hpacker docs by @sarahnlewis in #210
• fix: handle annotated tags in publish workflow by @sarahnlewis in #212

Full Changelog: v.1.3.0...v1.3.1

v1.3.1a3

Full Changelog: v1.3.1a2...v1.3.1a3

v1.3.1a2

Pre-release for testing hpacker setup.sh packaging fix.

v1.3.1a1

Pre-release for testing hpacker setup.sh packaging fix.

1.3.0

What's Changed

• Saves physics-filtered frame to topology.pdb, instead of 0th sample by @thempel in #186
• Report pytest durations by @sarahnlewis in #189
• Speed up md-relaxation test by @thempel in #190
• feat: steering to avoid chain breaks and clashes by @ludwigwinkler in #171
• chore: update OpenMM version by @thempel in #192
• Remove Disulfide Potential by @ludwigwinkler in #198
• feat: Inline ColabFold and AlphaFold2 into BioEmu by @sarahnlewis in #206

Full Changelog: v.1.2.0...v.1.3.0

1.2.0

What's Changed

• Toy example of PPFT training by @sarahnlewis in #134
• Check input sequence validity by @josejimenezluna in #130
• Various documentation and error message updates by @franknoe @josejimenezluna @sarahnlewis
• Default model changed by @josejimenezluna in #136
• Updates to the DPM solver by @YuuuXie in #148 and #151
• Use KDTree instead of mdtraj.compute_contacts in _filter_unphysical_traj_masks to mitigate MemoryError and improve performance by @ahmedselim2017 in #158
• Support extra_residue_embeds by @sarahnlewis in #174
• By default, use system time for random seed, not zero by @sarahnlewis in #180

New Contributors

• @ahmedselim2017 made their first contribution in #160

Full Changelog: v.0.1.12...v.1.2.0

1.1.0

What's Changed

• chore: remove hpacker citation from README.md by @josejimenezluna in #119
• chore: check for supported model names by @josejimenezluna in #126
• chore: Add instructions how to use the foundry endpoint by @ryotatomioka in #124
• chore: make sure input sequence is valid by @josejimenezluna in #130
• feat: PPFT training by @sarahnlewis in #134
• Update MODEL_CARD.md by @ryotatomioka in #125

Full Changelog: v.0.1.12...v.1.1.0

1.0.0pre

v.1.0.0pre

Merge branch 'main' into jjimenezluna/release1

0.1.12

What's Changed

• fix: don't require ensurepip by @ryotatomioka in #120

Full Changelog: v.0.1.11...v.0.1.12

0.1.11

What's Changed

• Increase --maxkb in pre-commit-config by @josejimenezluna in #110
• feat: add afdb cluster definitions by @oabdin in #109
• Update README.md by @franknoe in #112
• add hpacker reference to readme by @thempel in #115
• fix: colabfold install by @josejimenezluna in #116
• Revert "chore: tie colabfold dir to the python executable (#104)" by @ryotatomioka in #118

New Contributors

• @oabdin made their first contribution in #109

Full Changelog: v.0.1.10...v.0.1.11