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.

---

Detected Package Files

• docker/geomx_ngs/Dockerfile (dockerfile)
• docker/spaceranger/Dockerfile (dockerfile)
• docker/spatial_py/Dockerfile (dockerfile)
• docker/spatial_r/Dockerfile (dockerfile)
• .github/workflows/lint-test-workflows.yml (github-actions)
• .github/workflows/sync-fork.yml (github-actions)
• docker/spatial_py/requirements.txt (pip_requirements)
• docker/spatial_r/requirements.txt (pip_requirements)

What to Expect

With your current configuration, Renovate will create 14 Pull Requests:

Update dependency distributed to v2026 [SECURITY]

• Branch name: renovate/pypi-distributed-vulnerability
• Merge into: main
• Upgrade distributed to ==2026.1.0

Update dependency matplotlib to v3.10.8

• Schedule: ["at any time"]
• Branch name: renovate/matplotlib-3.x
• Merge into: main
• Upgrade matplotlib to ==3.10.8

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 dependency anndata to v0.12.10

• Schedule: ["at any time"]
• Branch name: renovate/anndata-0.x
• Merge into: main
• Upgrade anndata to ==0.12.10

Update dependency dask to v2024.12.1

• Schedule: ["at any time"]
• Branch name: renovate/dask-2024.x
• Merge into: main
• Upgrade dask to ==2024.12.1

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 numcodecs to v0.16.5

• Schedule: ["at any time"]
• Branch name: renovate/numcodecs-0.x
• Merge into: main
• Upgrade numcodecs to ==0.16.5

Update dependency numpy to v2.4.2

• Schedule: ["at any time"]
• Branch name: renovate/numpy-2.x
• Merge into: main
• Upgrade numpy to ==2.4.2

Update dependency scanpy to v1.12

• Schedule: ["at any time"]
• Branch name: renovate/scanpy-1.x
• Merge into: main
• Upgrade scanpy to ==1.12

Update dependency scipy to v1.17.1

• Schedule: ["at any time"]
• Branch name: renovate/scipy-1.x
• Merge into: main
• Upgrade scipy to ==1.17.1

Update dependency squidpy to v1.8.1

• Schedule: ["at any time"]
• Branch name: renovate/squidpy-1.x
• Merge into: main
• Upgrade squidpy to ==1.8.1

Update actions/checkout action to v6

• Schedule: ["at any time"]
• Branch name: renovate/actions-checkout-6.x
• Merge into: main
• Upgrade actions/checkout to v6

Update dependency dask to v2026

• Schedule: ["at any time"]
• Branch name: renovate/dask-2026.x
• Merge into: main
• Upgrade dask to ==2026.1.2

Update dependency pandas to v3

• Schedule: ["at any time"]
• Branch name: renovate/pandas-3.x
• Merge into: main
• Upgrade pandas to ==3.0.1

🚸 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.

---

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
• Failed to look up pypi package biocmanager
• Failed to look up pypi package hdf5r
• Failed to look up pypi package openxlsx
• Failed to look up pypi package ragg

Files affected: docker/geomx_ngs/Dockerfile, docker/spaceranger/Dockerfile, docker/spatial_py/Dockerfile, docker/spatial_r/Dockerfile, docker/spatial_r/requirements.txt

---

❓ 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.

---

This PR has been generated by Renovate Bot.