Add uv.lock, unpin deps, use --locked in CI

[sarahnlewis]

• Remove uv from runtime deps
• Unpin modelcif, fire, jax, openmm, openmm-cuda-12, nvidia-cuda-nvcc-cu12 to >= lower bounds; lockfile pins exact versions
• Cap jax<0.11 (dm-haiku incompatible with 0.11+)
• Drop Python 3.10 (EOL Oct 2026)
• Add uv.lock (150 packages)
• Use uv sync --locked in CI
• Switch publish workflow from pip to uv
• Fix vendored alphafold for jax 0.10: tree_map, jnp.clip kwargs, jax.util.wraps, PRNGKey

Closes dependabot PRs #233 #235 #236 #231 #229

[temporaer]

Thank you!

[github-actions]

Summary

Summary

Generated on:	07/17/2026 - 16:23:21
Parser:	Cobertura
Assemblies:	5
Classes:	32
Files:	32
Line coverage:	86.4% (2182 of 2524)
Covered lines:	2182
Uncovered lines:	342
Coverable lines:	2524
Total lines:	8079
Covered branches:	0
Total branches:	0
Method coverage:	Feature is only available for sponsors

Coverage

src.bioemu - 89%

Name	Line	Branch
src.bioemu	89%	****
init.py	100%
chemgraph.py	100%
convert_chemgraph.py	97%
denoiser.py	98.3%
get_embeds.py	92.1%
md_utils.py	85.8%
model_utils.py	78%
models.py	94.1%
run_hpacker.py	0%
sample.py	92.2%
sde_lib.py	88.3%
seq_io.py	100%
shortcuts.py	100%
sidechain_relax.py	75%
so3_sde.py	90.3%
structure_module.py	84.3%
utils.py	65.6%

src.bioemu.colabfold_inline - 79.1%

Name	Line	Branch
src.bioemu.colabfold_inline	79.1%	****
init.py
features.py	100%
input_parsing.py	100%
model_runner.py	99%
msa_client.py	60.8%

src.bioemu.hpacker_setup - 69.2%

Name	Line	Branch
src.bioemu.hpacker_setup	69.2%	****
init.py
setup_hpacker.py	69.2%

src.bioemu.steering - 79.5%

Name	Line	Branch
src.bioemu.steering	79.5%	****
init.py	100%
collective_variables.py	34.8%
dpm_fkc.py	100%
dpm_smc.py	100%
potentials.py	95.3%
utils.py	83.5%

src.bioemu.training - 100%

Name	Line	Branch
src.bioemu.training	100%	****
foldedness.py	100%
loss.py	100%

[github-actions]

Summary

Summary

Generated on:	07/17/2026 - 16:33:11
Parser:	Cobertura
Assemblies:	5
Classes:	32
Files:	32
Line coverage:	86.4% (2182 of 2524)
Covered lines:	2182
Uncovered lines:	342
Coverable lines:	2524
Total lines:	8079
Covered branches:	0
Total branches:	0
Method coverage:	Feature is only available for sponsors

Coverage

src.bioemu - 89%

Name	Line	Branch
src.bioemu	89%	****
init.py	100%
chemgraph.py	100%
convert_chemgraph.py	97%
denoiser.py	98.3%
get_embeds.py	92.1%
md_utils.py	85.8%
model_utils.py	78%
models.py	94.1%
run_hpacker.py	0%
sample.py	92.2%
sde_lib.py	88.3%
seq_io.py	100%
shortcuts.py	100%
sidechain_relax.py	75%
so3_sde.py	90.3%
structure_module.py	84.3%
utils.py	65.6%

src.bioemu.colabfold_inline - 79.1%

Name	Line	Branch
src.bioemu.colabfold_inline	79.1%	****
init.py
features.py	100%
input_parsing.py	100%
model_runner.py	99%
msa_client.py	60.8%

src.bioemu.hpacker_setup - 69.2%

Name	Line	Branch
src.bioemu.hpacker_setup	69.2%	****
init.py
setup_hpacker.py	69.2%

src.bioemu.steering - 79.5%

Name	Line	Branch
src.bioemu.steering	79.5%	****
init.py	100%
collective_variables.py	34.8%
dpm_fkc.py	100%
dpm_smc.py	100%
potentials.py	95.3%
utils.py	83.5%

src.bioemu.training - 100%

Name	Line	Branch
src.bioemu.training	100%	****
foldedness.py	100%
loss.py	100%