Configure Renovate

[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

• SARS-CoV-2_parser/Dockerfile (dockerfile)
• SARS-CoV-2_parser/requirements.txt (pip_requirements)
• Virulence-Analysis/methodology/requirements.txt (pip_requirements)

Configuration Summary

Based on the default config's presets, Renovate will:

• Start dependency updates only once this onboarding PR is merged
• Hopefully safe environment variables to allow users to configure.
• Show all Merge Confidence badges for pull requests.
• Enable Renovate Dependency Dashboard creation.
• Use semantic commit type fix for dependencies and chore for all others if semantic commits are in use.
• Ignore node_modules, bower_components, vendor and various test/tests (except for nuget) directories.
• Group known monorepo packages together.
• Use curated list of recommended non-monorepo package groupings.
• Apply crowd-sourced package replacement rules.
• Apply crowd-sourced workarounds for known problems with packages.

🔡 Do you want to change how Renovate upgrades your dependencies? Add your custom config to renovate.json in this branch. Renovate will update the Pull Request description the next time it runs.

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What to Expect

With your current configuration, Renovate will create 31 Pull Requests:

Update dependency pyspark to v3.3.2 [SECURITY]

• Branch name: renovate/pypi-pyspark-vulnerability
• Merge into: master
• Upgrade pyspark to ==3.3.2

Update dependency urllib3 to v1.26.19 [SECURITY]

• Branch name: renovate/pypi-urllib3-vulnerability
• Merge into: master
• Upgrade urllib3 to ==1.26.19

Update dependency fonttools to v4.43.0 [SECURITY]

• Branch name: renovate/pypi-fonttools-vulnerability
• Merge into: master
• Upgrade fonttools to ==4.43.0

Update dependency idna to v3.7 [SECURITY]

• Branch name: renovate/pypi-idna-vulnerability
• Merge into: master
• Upgrade idna to ==3.7

Update dependency requests to v2.32.2 [SECURITY]

• Branch name: renovate/pypi-requests-vulnerability
• Merge into: master
• Upgrade requests to ==2.32.2

Update dependency certifi to v2024 [SECURITY]

• Branch name: renovate/pypi-certifi-vulnerability
• Merge into: master
• Upgrade certifi to ==2024.7.4

Update dependency Pillow to v10 [SECURITY]

• Branch name: renovate/pypi-pillow-vulnerability
• Merge into: master
• Upgrade Pillow to ==10.3.0

Update dependency kiwisolver to v1.4.8

• Schedule: ["at any time"]
• Branch name: renovate/kiwisolver-1.x
• Merge into: master
• Upgrade kiwisolver to ==1.4.8

Update dependency kneed to v0.8.5

• Schedule: ["at any time"]
• Branch name: renovate/kneed-0.x
• Merge into: master
• Upgrade kneed to ==0.8.5

Update dependency pandas to v1.5.3

• Schedule: ["at any time"]
• Branch name: renovate/pandas-1.x
• Merge into: master
• Upgrade pandas to ==1.5.3
• Upgrade pandas to ~=1.5.3

Update dependency py4j to v0.10.9.9

• Schedule: ["at any time"]
• Branch name: renovate/py4j-0.x
• Merge into: master
• Upgrade py4j to ==0.10.9.9

Update dependency pytz to v2022.7.1

• Schedule: ["at any time"]
• Branch name: renovate/pytz-2022.x
• Merge into: master
• Upgrade pytz to ==2022.7.1

Update dependency sklearn to v0.0.post12

• Schedule: ["at any time"]
• Branch name: renovate/sklearn-0.x
• Merge into: master
• Upgrade sklearn to ==0.0.post12

Update dependency biopython to v1.85

• Schedule: ["at any time"]
• Branch name: renovate/biopython-1.x
• Merge into: master
• Upgrade biopython to ==1.85

Update dependency contourpy to v1.3.2

• Schedule: ["at any time"]
• Branch name: renovate/contourpy-1.x
• Merge into: master
• Upgrade contourpy to ==1.3.2

Update dependency cycler to v0.12.1

• Schedule: ["at any time"]
• Branch name: renovate/cycler-0.x
• Merge into: master
• Upgrade cycler to ==0.12.1

Update dependency fastcluster to v1.3.0

• Schedule: ["at any time"]
• Branch name: renovate/fastcluster-1.x
• Merge into: master
• Upgrade fastcluster to ==1.3.0

Update dependency matplotlib to v3.10.1

• Schedule: ["at any time"]
• Branch name: renovate/matplotlib-3.x
• Merge into: master
• Upgrade matplotlib to ==3.10.1

Update dependency numpy to v1.26.4

• Schedule: ["at any time"]
• Branch name: renovate/numpy-1.x
• Merge into: master
• Upgrade numpy to ==1.26.4

Update dependency pyparsing to v3.2.3

• Schedule: ["at any time"]
• Branch name: renovate/pyparsing-3.x
• Merge into: master
• Upgrade pyparsing to ==3.2.3

Update dependency python-dateutil to v2.9.0.post0

• Schedule: ["at any time"]
• Branch name: renovate/python-dateutil-2.x
• Merge into: master
• Upgrade python-dateutil to ==2.9.0.post0

Update dependency scipy to v1.15.2

• Schedule: ["at any time"]
• Branch name: renovate/scipy-1.x
• Merge into: master
• Upgrade scipy to ==1.15.2

Update dependency seaborn to v0.13.2

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

Update dependency six to v1.17.0

• Schedule: ["at any time"]
• Branch name: renovate/six-1.x
• Merge into: master
• Upgrade six to ==1.17.0

Update dependency charset-normalizer to v3

• Schedule: ["at any time"]
• Branch name: renovate/charset-normalizer-3.x
• Merge into: master
• Upgrade charset-normalizer to ==3.4.2

Update dependency docker to v7

• Schedule: ["at any time"]
• Branch name: renovate/docker-7.x
• Merge into: master
• Upgrade docker to ~=7.1.0

Update dependency numpy to v2

• Schedule: ["at any time"]
• Branch name: renovate/numpy-2.x
• Merge into: master
• Upgrade numpy to ==2.2.5

Update dependency packaging to v25

• Schedule: ["at any time"]
• Branch name: renovate/packaging-25.x
• Merge into: master
• Upgrade packaging to ==25.0

Update dependency pandas to v2

• Schedule: ["at any time"]
• Branch name: renovate/pandas-2.x
• Merge into: master
• Upgrade pandas to ==2.2.3
• Upgrade pandas to ~=2.2.3

Update dependency pytz to v2025

• Schedule: ["at any time"]
• Branch name: renovate/pytz-2025.x
• Merge into: master
• Upgrade pytz to ==2025.2

Update ubuntu Docker tag to v24

• Schedule: ["at any time"]
• Branch name: renovate/ubuntu-24.x
• Merge into: master
• Upgrade ubuntu to noble

🚸 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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❓ 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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