Dependency Dashboard

[tjboller]

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

Pending Approval

The following branches are pending approval. To create them, click on a checkbox below.

• [renovate] Update python versions
• [renovate] Update python versions
• [renovate] Update python versions
• [renovate] Update python versions
• [renovate] Update actions/checkout action to v5
• [renovate] Update actions/checkout action to v6
• [renovate] Update actions/checkout action to v7
• [renovate] Update actions/setup-python action to v6
• [renovate] Update astral-sh/setup-uv action to v4
• [renovate] Update astral-sh/setup-uv action to v5
• [renovate] Update astral-sh/setup-uv action to v6
• [renovate] Update astral-sh/setup-uv action to v7
• [renovate] Update astral-sh/setup-uv action to v8
• [renovate] Update pre-commit hook pre-commit/pre-commit-hooks to v6
• [renovate] Update pre-commit hook psf/black to v25
• [renovate] Update pre-commit hook psf/black to v26
• 🔐 Create all pending approval PRs at once 🔐

Awaiting Schedule

The following updates are awaiting their schedule. To get an update now, click on a checkbox below.

• [renovate] Update pre-commit hook astral-sh/ruff-pre-commit to v0.15.21
• [renovate] Update pre-commit hook astral-sh/uv-pre-commit to v0.11.28
• [renovate] Update dependency python to 3.14
• [renovate] Lock file maintenance
• 🔐 Create all awaiting schedule PRs at once 🔐

Pending Status Checks

The following updates await pending status checks. To force their creation now, click on a checkbox below.

• [renovate] Update dependency rdkit to v2025.9.6
• [renovate] Update dependency ruff to v0.15.22
• [renovate] Update dependency black to v26.5.1
• [renovate] Update dependency fastparquet to v2026.5.0
• [renovate] Update dependency matplotlib to v3.11.1
• [renovate] Update dependency mdanalysis to v2.10.0
• [renovate] Update dependency plotly to v6.9.0
• [renovate] Update dependency pytest to v9.1.1
• [renovate] Update dependency scikit-learn to v1.9.0
• [renovate] Update dependency scipy to v1.18.0
• [renovate] Update dependency torch to v2.13.0
• [renovate] Update dependency torch-geometric to v2.8.0
• [renovate] Update actions/setup-python action to v7
• [renovate] Update astral-sh/setup-uv action to v9
• [renovate] Update dependency ipykernel to v7
• [renovate] Update dependency numpy to v2
• [renovate] Update dependency pandas to v3
• [renovate] Update dependency pyarrow to v25
• [renovate] Update dependency rdkit to v2026

Detected Dependencies

dockerfile (2)

Dockerfile (2)

• docker/dockerfile 1
• python 3.10-slim-bookworm → [Updates: 3.11-slim-bookworm, 3.12-slim-bookworm, 3.13-slim-bookworm, 3.14-slim-bookworm]

Dockerfile.gnina-bundle (1)

• docker/dockerfile 1

github-actions (2)

.github/workflows/lint.yml (4)

• actions/checkout v4 → [Updates: v5, v6, v7]
• actions/setup-python v5 → [Updates: v6, v7]
• astral-sh/setup-uv v3 → [Updates: v4, v5, v6, v7, v8.3.2, v9.0.0]
• python 3.10 → [Updates: 3.14]

.github/workflows/test.yml (1)

• actions/checkout v4 → [Updates: v5, v6, v7]

pep621 (1)

pyproject.toml (37)

• python >=3.10,<3.11 → [Updates: >=3.11,<3.12, >=3.12,<3.13, >=3.13,<3.14, >=3.14,<3.15]
• mdanalysis ==2.3.0 → [Updates: ==2.10.0]
• prody >=2.4.1,<3
• pandas >=2.0.3,<3 → [Updates: >=3.0.3,<4]
• rmsd ==1.6.5
• prefetch-generator ==1.0.3
• seaborn >=0.13.2,<0.14
• chembl-webresource-client >=0.10.9,<0.11
• matplotlib-venn >=1.1.1,<2
• numpy >=1.23.0,<2 → [Updates: >=2.5.1,<3]
• chembl-downloader >=0.5.2,<0.6
• unipressed >=1.4.0,<2
• scikit-learn >=1.6.1,<2 → [Updates: >=1.6.1,<2]
• scipy >=1.13.1 → [Updates: >=1.13.1]
• vina >=1.2.7
• meeko >=0.6.1
• boltz >=1.0.0
• rdkit >=2022.9.5 → [Updates: >=2022.9.5]
• torch-geometric >=2.7.0 → [Updates: >=2.7.0]
• torch >=2.9.0 → [Updates: >=2.9.0]
• torch-cluster >=1.6.3
• torch-scatter >=2.1.2
• torch-sparse >=0.6.18
• e3nn >=0.5.8
• fair-esm ==2.0.0
• pyarrow >=22.0.0 → [Updates: >=22.0.0]
• fastparquet >=2024.11.0 → [Updates: >=2024.11.0]
• plotly >=6.5.2 → [Updates: >=6.5.2]
• nbformat >=5.10.4
• plip >=3.0.0
• scikit-fingerprints >=1.18.0
• matplotlib >=3.10.8 → [Updates: >=3.10.8]
• black >=26.3.1,<27 → [Updates: >=26.3.1,<27]
• ruff >=0.8.0,<1 → [Updates: >=0.8.0,<1]
• ipykernel >=6.29.5,<7 → [Updates: >=7.3,<8]
• pre-commit >=4.1.0,<5
• pytest >=9.0.3,<10 → [Updates: >=9.0.3,<10]

pre-commit (1)

.pre-commit-config.yaml (5)

• kynan/nbstripout 0.9.1
• astral-sh/ruff-pre-commit v0.15.15 → [Updates: v0.15.21]
• psf/black 24.10.0 → [Updates: 25.12.0, 26.5.1]
• pre-commit/pre-commit-hooks v5.0.0 → [Updates: v6.0.0]
• astral-sh/uv-pre-commit 0.11.18 → [Updates: 0.11.28]