chore(deps): bump actions/checkout from 4.3.1 to 7.0.0 by dependabot[bot] · Pull Request #227 · microsoft/bioemu

dependabot · 2026-07-17T12:29:08Z

Bumps actions/checkout from 4.3.1 to 7.0.0.

Release notes

Sourced from actions/checkout's releases.

v7.0.0

What's Changed

block checking out fork pr for pull_request_target and workflow_run by @aiqiaoy in actions/checkout#2454

Bump actions/publish-immutable-action from 0.0.3 to 0.0.4 in the minor-actions-dependencies group across 1 directory by @dependabot[bot] in actions/checkout#2458

Bump flatted from 3.3.1 to 3.4.2 by @dependabot[bot] in actions/checkout#2460

Bump js-yaml from 4.1.0 to 4.2.0 by @dependabot[bot] in actions/checkout#2461

Bump @actions/core and @actions/tool-cache and Remove uuid by @dependabot[bot] in actions/checkout#2459

upgrade module to esm and update dependencies by @aiqiaoy in actions/checkout#2463

Bump the minor-npm-dependencies group across 1 directory with 3 updates by @dependabot[bot] in actions/checkout#2462

getting ready for checkout v7 release by @aiqiaoy in actions/checkout#2464

update error wording by @aiqiaoy in actions/checkout#2467

New Contributors

@aiqiaoy made their first contribution in actions/checkout#2454

Full Changelog: actions/checkout@v6.0.3...v7.0.0

v6.0.3

What's Changed

Update changelog by @ericsciple in actions/checkout#2357

fix: expand merge commit SHA regex and add SHA-256 test cases by @yaananth in actions/checkout#2414

Fix checkout init for SHA-256 repositories by @yaananth in actions/checkout#2439

Update changelog for v6.0.3 by @yaananth in actions/checkout#2446

New Contributors

@yaananth made their first contribution in actions/checkout#2414

Full Changelog: actions/checkout@v6...v6.0.3

v6.0.2

What's Changed

Add orchestration_id to git user-agent when ACTIONS_ORCHESTRATION_ID is set by @TingluoHuang in actions/checkout#2355

Fix tag handling: preserve annotations and explicit fetch-tags by @ericsciple in actions/checkout#2356

Full Changelog: actions/checkout@v6.0.1...v6.0.2

v6.0.1

What's Changed

Update all references from v5 and v4 to v6 by @ericsciple in actions/checkout#2314

Add worktree support for persist-credentials includeIf by @ericsciple in actions/checkout#2327

Clarify v6 README by @ericsciple in actions/checkout#2328

Full Changelog: actions/checkout@v6...v6.0.1

v6.0.0

What's Changed

Update README to include Node.js 24 support details and requirements by @salmanmkc in actions/checkout#2248

Persist creds to a separate file by @ericsciple in actions/checkout#2286

v6-beta by @ericsciple in actions/checkout#2298

... (truncated)

Changelog

Sourced from actions/checkout's changelog.

Changelog

v7.0.1

Bump github/codeql-action from 3 to 4 by @dependabot[bot] in actions/checkout#2475

Bump actions/setup-node from 4 to 6 by @dependabot[bot] in actions/checkout#2477

Bump docker/build-push-action from 6.5.0 to 7.2.0 by @dependabot[bot] in actions/checkout#2478

Bump docker/login-action from 3.3.0 to 4.2.0 by @dependabot[bot] in actions/checkout#2479

Bump actions/checkout from 6 to 7 by @dependabot[bot] in actions/checkout#2488

Bump actions/upload-artifact from 4 to 7 by @dependabot[bot] in actions/checkout#2476

eslint 9 by @dependabot[bot] in actions/checkout#2474

Bump the minor-actions-dependencies group with 2 updates by @dependabot[bot] in actions/checkout#2499

skip running unsafe pr check if input is default by @aiqiaoy in actions/checkout#2518

trim only ascii whitespace for branch by @aiqiaoy in actions/checkout#2521

escape values passed to --unset by @aiqiaoy in actions/checkout#2530

v7.0.0

Block checking out fork PR for pull_request_target and workflow_run by @aiqiaoy in actions/checkout#2454

Bump actions/publish-immutable-action from 0.0.3 to 0.0.4 in the minor-actions-dependencies group across 1 directory by @dependabot[bot] in actions/checkout#2458

Bump flatted from 3.3.1 to 3.4.2 by @dependabot[bot] in actions/checkout#2460

Bump js-yaml from 4.1.0 to 4.2.0 by @dependabot[bot] in actions/checkout#2461

Bump @actions/core and @actions/tool-cache and Remove uuid by @dependabot[bot] in actions/checkout#2459

upgrade module to esm and update dependencies by @aiqiaoy in actions/checkout#2463

Bump the minor-npm-dependencies group across 1 directory with 3 updates by @dependabot[bot] in actions/checkout#2462

v6.0.3

Fix checkout init for SHA-256 repositories by @yaananth in actions/checkout#2439

fix: expand merge commit SHA regex and add SHA-256 test cases by @yaananth in actions/checkout#2414

v6.0.2

Fix tag handling: preserve annotations and explicit fetch-tags by @ericsciple in actions/checkout#2356

v6.0.1

Add worktree support for persist-credentials includeIf by @ericsciple in actions/checkout#2327

v6.0.0

Persist creds to a separate file by @ericsciple in actions/checkout#2286

Update README to include Node.js 24 support details and requirements by @salmanmkc in actions/checkout#2248

v5.0.1

Port v6 cleanup to v5 by @ericsciple in actions/checkout#2301

v5.0.0

Update actions checkout to use node 24 by @salmanmkc in actions/checkout#2226

v4.3.1

Port v6 cleanup to v4 by @ericsciple in actions/checkout#2305

v4.3.0

docs: update README.md by @motss in actions/checkout#1971

Add internal repos for checking out multiple repositories by @mouismail in actions/checkout#1977

... (truncated)

Commits

9c091bb update error wording (#2467)
1044a6d getting ready for checkout v7 release (#2464)
f028218 Bump the minor-npm-dependencies group across 1 directory with 3 updates (#2462)
d914b26 upgrade module to esm and update dependencies (#2463)
537c7ef Bump @actions/core and @actions/tool-cache and Remove uuid (#2459)
130a169 Bump js-yaml from 4.1.0 to 4.2.0 (#2461)
7d09575 Bump flatted from 3.3.1 to 3.4.2 (#2460)
0f9f3aa Bump actions/publish-immutable-action (#2458)
f9e715a block checking out fork pr for pull_request_target and workflow_run (#2454)
df4cb1c Update changelog for v6.0.3 (#2446)
Additional commits viewable in compare view

github-actions · 2026-07-17T12:54:15Z

Summary


Generated on:	07/17/2026 - 12:54:15
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 · 2026-07-20T09:00:41Z

Summary


Generated on:	07/20/2026 - 09:00:40
Parser:	Cobertura
Assemblies:	5
Classes:	32
Files:	32
Line coverage:	86.4% (2181 of 2524)
Covered lines:	2181
Uncovered lines:	343
Coverable lines:	2524
Total lines:	8079
Covered branches:	0
Total branches:	0
Method coverage:	Feature is only available for sponsors

Coverage

src.bioemu - 88.9%

Name	Line	Branch
src.bioemu	88.9%	****
init.py	100%
chemgraph.py	100%
convert_chemgraph.py	96.4%
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 · 2026-07-20T09:25:45Z

Summary


Generated on:	07/20/2026 - 09:25:42
Parser:	Cobertura
Assemblies:	5
Classes:	32
Files:	32
Line coverage:	86.4% (2181 of 2524)
Covered lines:	2181
Uncovered lines:	343
Coverable lines:	2524
Total lines:	8079
Covered branches:	0
Total branches:	0
Method coverage:	Feature is only available for sponsors

Coverage

src.bioemu - 88.9%

Name	Line	Branch
src.bioemu	88.9%	****
init.py	100%
chemgraph.py	100%
convert_chemgraph.py	96.4%
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 · 2026-07-20T09:46:24Z

Summary


Generated on:	07/20/2026 - 09:46:21
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%

Bumps [actions/checkout](https://github.com/actions/checkout) from 4.3.1 to 7.0.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@34e1148...9c091bb) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>

github-actions · 2026-07-20T13:08:51Z

Summary


Generated on:	07/20/2026 - 13:08:48
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%

dependabot Bot added dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code labels Jul 17, 2026

dependabot Bot force-pushed the dependabot/github_actions/actions/checkout-7.0.0 branch from 6c6de21 to 6384c56 Compare July 20, 2026 08:34

dependabot Bot force-pushed the dependabot/github_actions/actions/checkout-7.0.0 branch 2 times, most recently from 6cfd35c to 57c6f61 Compare July 20, 2026 09:23

dependabot Bot force-pushed the dependabot/github_actions/actions/checkout-7.0.0 branch from 57c6f61 to 3d6f053 Compare July 20, 2026 12:44

sarahnlewis approved these changes Jul 20, 2026

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sarahnlewis merged commit 81ff4e3 into main Jul 20, 2026
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sarahnlewis deleted the dependabot/github_actions/actions/checkout-7.0.0 branch July 20, 2026 13:42

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chore(deps): bump actions/checkout from 4.3.1 to 7.0.0#227

chore(deps): bump actions/checkout from 4.3.1 to 7.0.0#227
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v7.0.0

What's Changed

New Contributors

v6.0.3

What's Changed

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v6.0.2

What's Changed

v6.0.1

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v6.0.0

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v7.0.1

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v6.0.3

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v6.0.1

v6.0.0

v5.0.1

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v4.3.1

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