Configure Renovate

[dnastack-renovate]

Welcome to Renovate! This is an onboarding PR to help you understand and configure settings before regular Pull Requests begin.

🚦 To activate Renovate, merge this Pull Request. To disable Renovate, simply close this Pull Request unmerged.

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Detected Package Files

• docker/cellbender/Dockerfile (dockerfile)
• docker/cellranger/Dockerfile (dockerfile)
• docker/multiome/Dockerfile (dockerfile)
• docker/sc_tools/Dockerfile (dockerfile)
• .github/workflows/lint-test-workflows.yml (github-actions)
• .github/workflows/sync-fork.yml (github-actions)
• docker/sc_tools/requirements.txt (pip_requirements)

What to Expect

With your current configuration, Renovate will create 23 Pull Requests:

Update dependency torch to v2.13.0 [SECURITY]

• Branch name: renovate/pypi-torch-vulnerability
• Merge into: main
• Upgrade torch to ==2.13.0

Update dependency pyarrow to v23 [SECURITY]

• Branch name: renovate/pypi-pyarrow-vulnerability
• Merge into: main
• Upgrade pyarrow to ==23.0.1

Update dependency muon to v0.1.9

• Schedule: ["at any time"]
• Branch name: renovate/muon-0.x
• Merge into: main
• Upgrade muon to ==0.1.9

Update dependency pandas to v2.3.3

• Schedule: ["at any time"]
• Branch name: renovate/pandas-2.x
• Merge into: main
• Upgrade pandas to ==2.3.3

Update continuumio/miniconda3 Docker tag to v23.9.0

• Schedule: ["at any time"]
• Branch name: renovate/continuumio-miniconda3-23.x
• Merge into: main
• Upgrade continuumio/miniconda3 to 23.9.0-0

Update dependency anndata to v0.13.2

• Schedule: ["at any time"]
• Branch name: renovate/anndata-0.x
• Merge into: main
• Upgrade anndata to ==0.13.2

Update dependency h5py to v3.16.0

• Schedule: ["at any time"]
• Branch name: renovate/h5py-3.x
• Merge into: main
• Upgrade h5py to ==3.16.0

Update dependency harmonypy to v0.2.0

• Schedule: ["at any time"]
• Branch name: renovate/harmonypy-0.x
• Merge into: main
• Upgrade harmonypy to ==0.2.0

Update dependency jax to v0.11.0

• Schedule: ["at any time"]
• Branch name: renovate/jax-0.x
• Merge into: main
• Upgrade jax to ==0.11.0

Update dependency matplotlib to v3.11.1

• Schedule: ["at any time"]
• Branch name: renovate/matplotlib-3.x
• Merge into: main
• Upgrade matplotlib to ==3.11.1

Update dependency numpy to v2.5.1

• Schedule: ["at any time"]
• Branch name: renovate/numpy-2.x
• Merge into: main
• Upgrade numpy to ==2.5.1

Update dependency scanpy to v1.12.3

• Schedule: ["at any time"]
• Branch name: renovate/scanpy-1.x
• Merge into: main
• Upgrade scanpy to ==1.12.3

Update dependency scib-metrics to v0.6.0

• Schedule: ["at any time"]
• Branch name: renovate/scib-metrics-0.x
• Merge into: main
• Upgrade scib-metrics to ==0.6.0

Update dependency scikit-learn to v1.9.0

• Schedule: ["at any time"]
• Branch name: renovate/scikit-learn-1.x
• Merge into: main
• Upgrade scikit-learn to ==1.9.0

Update dependency scipy to v1.18.0

• Schedule: ["at any time"]
• Branch name: renovate/scipy-1.x
• Merge into: main
• Upgrade scipy to ==1.18.0

Update dependency scvi-tools to v1.5.0.post1

• Schedule: ["at any time"]
• Branch name: renovate/scvi-tools-1.x
• Merge into: main
• Upgrade scvi-tools to ==1.5.0.post1

Update dependency tables to v3.11.1

• Schedule: ["at any time"]
• Branch name: renovate/tables-3.x
• Merge into: main
• Upgrade tables to ==3.11.1

Update dnastack/wdl-ci action to v2.2.0

• Schedule: ["at any time"]
• Branch name: renovate/dnastack-wdl-ci-2.x
• Merge into: main
• Upgrade dnastack/wdl-ci to v2.2.0

Update actions/checkout action to v7

• Schedule: ["at any time"]
• Branch name: renovate/actions-checkout-7.x
• Merge into: main
• Upgrade actions/checkout to v7

Update continuumio/miniconda3 Docker tag to v25

• Schedule: ["at any time"]
• Branch name: renovate/continuumio-miniconda3-25.x
• Merge into: main
• Upgrade continuumio/miniconda3 to 25.1.1-0

Update dependency harmonypy to v2

• Schedule: ["at any time"]
• Branch name: renovate/harmonypy-2.x
• Merge into: main
• Upgrade harmonypy to ==2.0.0

Update dependency pandas to v3

• Schedule: ["at any time"]
• Branch name: renovate/pandas-3.x
• Merge into: main
• Upgrade pandas to ==3.0.5

Update ubuntu Docker tag to v26

• Schedule: ["at any time"]
• Branch name: renovate/ubuntu-26.x
• Merge into: main
• Upgrade ubuntu to resolute

🚸 Branch creation will be limited to maximum 2 per hour, so it doesn't swamp any CI resources or overwhelm the project. See docs for prhourlylimit for details.

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Warning

Please correct - or verify that you can safely ignore - these dependency lookup failures before you merge this PR.

• Failed to look up docker package us-central1-docker.pkg.dev/dnastack-asap-parkinsons/workflow-images/util

Files affected: docker/cellbender/Dockerfile, docker/cellranger/Dockerfile, docker/multiome/Dockerfile, docker/sc_tools/Dockerfile

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❓ Got questions? Check out Renovate's Docs, particularly the Getting Started section.
If you need any further assistance then you can also request help here.

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This PR has been generated by Renovate Bot.