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chore(deps): bump github/codeql-action/init from 4.37.1 to 4.37.3 - #246

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Ludwig Winkler (ludwigwinkler) merged 4 commits into
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dependabot/github_actions/github/codeql-action/init-4.37.3
Aug 12, 2026
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chore(deps): bump github/codeql-action/init from 4.37.1 to 4.37.3#246
Ludwig Winkler (ludwigwinkler) merged 4 commits into
mainfrom
dependabot/github_actions/github/codeql-action/init-4.37.3

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@dependabot dependabot Bot commented on behalf of github Jul 30, 2026 •
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Bumps github/codeql-action/init from 4.37.1 to 4.37.3.

Release notes

Sourced from github/codeql-action/init's releases.

v4.37.3

No user facing changes.

v4.37.2

  • The new address format for the config-file input that was introduced in CodeQL Action 4.37.0 is now enabled by default. In addition to the format described there, the remote= prefix can now be used to explicitly indicate that the input refers to a remote file. All previous input formats continue to be accepted as well. #4023
  • The CodeQL Action can now make use of configured private registries in Default Setup to retrieve CodeQL configuration files from remote repositories that require authentication. This will allow customers to store their CodeQL configuration in a single repository that can then be referenced by Default Setup workflows in other repositories. We expect to roll this and other, related changes out to everyone in July. #4007
Changelog

Sourced from github/codeql-action/init's changelog.

CodeQL Action Changelog

See the releases page for the relevant changes to the CodeQL CLI and language packs.

[UNRELEASED]

No user facing changes.

4.37.4 - 29 Jul 2026

  • This version of the CodeQL Action adds support for the tools input for the codeql-action/init step to be specified using a github-codeql-tools repository property. This feature will gradually be rolled out following the release of this version. Once rolled out, this allows for the CodeQL CLI version that is used in GitHub-managed workflows, such as Default Setup, to be set to a custom value. For example, customers who run into issues with rate limits when a new CodeQL CLI version is released can set the value to toolcache to always use the CodeQL CLI version that is available in the runner toolcache. For Advanced Setup workflows, the value provided for tools in the workflow definition always takes precedence unless the value of the repository property starts with !. #4037
  • Update default CodeQL bundle version to 2.26.2. #4051

4.37.3 - 22 Jul 2026

No user facing changes.

4.37.2 - 21 Jul 2026

  • The new address format for the config-file input that was introduced in CodeQL Action 4.37.0 is now enabled by default. In addition to the format described there, the remote= prefix can now be used to explicitly indicate that the input refers to a remote file. All previous input formats continue to be accepted as well. #4023
  • The CodeQL Action can now make use of configured private registries in Default Setup to retrieve CodeQL configuration files from remote repositories that require authentication. This will allow customers to store their CodeQL configuration in a single repository that can then be referenced by Default Setup workflows in other repositories. We expect to roll this and other, related changes out to everyone in July. #4007

4.37.1 - 16 Jul 2026

  • Upcoming breaking change: Add a deprecation warning for customers using CodeQL version 2.20.6 and earlier. These versions of CodeQL were discontinued on 1 July 2026 alongside GitHub Enterprise Server 3.16, and will be unsupported by the next minor release of the CodeQL Action. #3956
  • Update default CodeQL bundle version to 2.26.1. #4019

4.37.0 - 08 Jul 2026

  • Update default CodeQL bundle version to 2.26.0. #3995
  • In addition to the existing input format, the config-file input for the codeql-action/init step will soon support a new [owner/]repo[@ref][:path] format. All components except the repository name are optional. If omitted, owner defaults to the same owner as the repository the analysis is running for, ref to main, and path to .github/codeql-action.yaml. Support for this format ships in this version of the CodeQL Action, but will only be enabled over the coming weeks. #3973

4.36.3 - 01 Jul 2026

No user facing changes.

4.36.2 - 04 Jun 2026

  • Cache CodeQL CLI version information across Actions steps. #3943
  • Reduce requests while waiting for analysis processing by using exponential backoff when polling SARIF processing status. #3937
  • Update default CodeQL bundle version to 2.25.6. #3948

4.36.1 - 02 Jun 2026

No user facing changes.

4.36.0 - 22 May 2026

  • Breaking change: Bump the minimum required CodeQL bundle version to 2.19.4. #3894
  • Add support for SHA-256 Git object IDs. #3893

... (truncated)

Commits
  • e4fba86 Merge pull request #4031 from github/update-v4.37.3-72f6a9da0
  • fb50ab5 Update changelog for v4.37.3
  • 72f6a9d Merge pull request #4030 from github/mbg/fix/no-proxy
  • 3b5ee58 Use default request options instead of undefined
  • bfb6be4 Merge pull request #4028 from github/mergeback/v4.37.2-to-main-e0647621
  • 526ab84 Rebuild
  • d6217b9 Update changelog and version after v4.37.2
  • e064762 Merge pull request #4027 from github/update-v4.37.2-385bcdc5a
  • e0faed8 Add a couple of change notes
  • 73aad0e Update changelog for v4.37.2
  • Additional commits viewable in compare view

@dependabot dependabot Bot added dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code labels Jul 30, 2026
@github-actions

github-actions Bot commented Jul 30, 2026

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Summary

Summary
Generated on: 07/30/2026 - 14:40:32
Parser: Cobertura
Assemblies: 5
Classes: 32
Files: 32
Line coverage: 85.3% (2153 of 2524)
Covered lines: 2153
Uncovered lines: 371
Coverable lines: 2524
Total lines: 8079
Covered branches: 0
Total branches: 0
Method coverage: Feature is only available for sponsors

Coverage

src.bioemu - 87.2%
Name Line Branch
src.bioemu 87.2% ****
init.py 100%
chemgraph.py 100%
convert_chemgraph.py 79.5%
denoiser.py 98.3%
get_embeds.py 92.1%
md_utils.py 85.8%
model_utils.py 80.4%
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
chore(deps): bump github/codeql-action/init from 4.37.1 to 4.37.3
911ce09 
Bumps [github/codeql-action/init](https://github.com/github/codeql-action) from 4.37.1 to 4.37.3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@7188fc3...e4fba86)

---
updated-dependencies:
- dependency-name: github/codeql-action/init
  dependency-version: 4.37.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
dependabot Bot force-pushed the dependabot/github_actions/github/codeql-action/init-4.37.3 branch from a580659 to 911ce09 Compare July 30, 2026 14:47
@sarahnlewis
Keep CodeQL action versions aligned
9fb4b8a 
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Copilot-Session: 7f9be49e-44c6-4173-a5af-0bf1d98abe8b
@github-actions

github-actions Bot commented Jul 30, 2026

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Summary

Summary
Generated on: 07/30/2026 - 15:00:22
Parser: Cobertura
Assemblies: 5
Classes: 32
Files: 32
Line coverage: 85.3% (2153 of 2524)
Covered lines: 2153
Uncovered lines: 371
Coverable lines: 2524
Total lines: 8079
Covered branches: 0
Total branches: 0
Method coverage: Feature is only available for sponsors

Coverage

src.bioemu - 87.2%
Name Line Branch
src.bioemu 87.2% ****
init.py 100%
chemgraph.py 100%
convert_chemgraph.py 79.5%
denoiser.py 98.3%
get_embeds.py 92.1%
md_utils.py 85.8%
model_utils.py 80.4%
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

github-actions Bot commented Jul 30, 2026

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Summary

Summary
Generated on: 07/30/2026 - 15:09:04
Parser: Cobertura
Assemblies: 5
Classes: 32
Files: 32
Line coverage: 85.3% (2153 of 2524)
Covered lines: 2153
Uncovered lines: 371
Coverable lines: 2524
Total lines: 8079
Covered branches: 0
Total branches: 0
Method coverage: Feature is only available for sponsors

Coverage

src.bioemu - 87.2%
Name Line Branch
src.bioemu 87.2% ****
init.py 100%
chemgraph.py 100%
convert_chemgraph.py 79.5%
denoiser.py 98.3%
get_embeds.py 92.1%
md_utils.py 85.8%
model_utils.py 80.4%
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 @github

dependabot Bot commented on behalf of github Aug 6, 2026

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Contributor Author

A newer version of github/codeql-action/init exists, but since this PR has been edited by someone other than Dependabot I haven't updated it. You'll get a PR for the updated version as normal once this PR is merged.

@github-actions

github-actions Bot commented Aug 12, 2026

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Summary

Summary
Generated on: 08/12/2026 - 09:22:06
Parser: Cobertura
Assemblies: 5
Classes: 32
Files: 32
Line coverage: 85.3% (2153 of 2524)
Covered lines: 2153
Uncovered lines: 371
Coverable lines: 2524
Total lines: 8079
Covered branches: 0
Total branches: 0
Method coverage: Feature is only available for sponsors

Coverage

src.bioemu - 87.2%
Name Line Branch
src.bioemu 87.2% ****
init.py 100%
chemgraph.py 100%
convert_chemgraph.py 79.5%
denoiser.py 98.3%
get_embeds.py 92.1%
md_utils.py 85.8%
model_utils.py 80.4%
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

github-actions Bot commented Aug 12, 2026

Copy link
Copy Markdown

Summary

Summary
Generated on: 08/12/2026 - 09:42:27
Parser: Cobertura
Assemblies: 5
Classes: 32
Files: 32
Line coverage: 85.3% (2153 of 2524)
Covered lines: 2153
Uncovered lines: 371
Coverable lines: 2524
Total lines: 8079
Covered branches: 0
Total branches: 0
Method coverage: Feature is only available for sponsors

Coverage

src.bioemu - 87.2%
Name Line Branch
src.bioemu 87.2% ****
init.py 100%
chemgraph.py 100%
convert_chemgraph.py 79.5%
denoiser.py 98.3%
get_embeds.py 92.1%
md_utils.py 85.8%
model_utils.py 80.4%
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%

@ludwigwinkler
Ludwig Winkler (ludwigwinkler) merged commit 6528bbf into main Aug 12, 2026
6 checks passed
@ludwigwinkler
Ludwig Winkler (ludwigwinkler) deleted the dependabot/github_actions/github/codeql-action/init-4.37.3 branch August 12, 2026 09:42
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@temporaer Hannes Schulz (temporaer) temporaer approved these changes

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