Dependency Dashboard

[renovate]

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

Config Migration Needed

• Select this checkbox to let Renovate create an automated Config Migration PR.

Rate-Limited

These updates are currently rate-limited. Click on a checkbox below to force their creation now.

• chore(deps): update crazy-max/ghaction-github-labeler action to v5.1.0
• chore(deps): update dependency einops to v0.8.0
• chore(deps): update dependency mypy to v1.13.0
• chore(deps): update dependency pandas to v2.2.3
• chore(deps): update dependency pybedtools to v0.10.0
• chore(deps): update dependency ruff to v0.7.4
• chore(deps): update dependency torch to v2.5.1
• chore(deps): update dependency torchvision to v0.20.1
• chore(deps): update dependency types-tqdm to v4.67.0.20241119
• chore(deps): update dependency wandb to v0.18.7
• chore(deps): update python docker tag to v3.13
• chore(deps): update actions/deploy-pages action to v4
• chore(deps): update actions/setup-python action to v5
• chore(deps): update actions/stale action to v9
• chore(deps): update actions/upload-pages-artifact action to v3
• chore(deps): update codecov/codecov-action action to v5
• chore(deps): update dependency accelerate to v1
• chore(deps): update dependency pytest to v8
• chore(deps): update dependency pytest-cov to v6
• chore(deps): update docker/build-push-action action to v6
• chore(deps): update release-drafter/release-drafter action to v6
• 🔐 Create all rate-limited PRs at once 🔐

Edited/Blocked

These updates have been manually edited so Renovate will no longer make changes. To discard all commits and start over, click on a checkbox.

• chore(deps): update dependency matplotlib to v3.9.2

Open

These updates have all been created already. Click a checkbox below to force a retry/rebase of any.

• chore(deps): update dependency jupyterlab to v4.2.5 [security]
• chore(deps): update dependency pytest to v7.4.4
• chore(deps): update dependency seaborn to v0.13.2
• chore(deps): update dependency sourmash to v4.8.11
• chore(deps): update dependency mkdocs-material to v9.5.44
• chore(deps): update dependency mkdocstrings to v0.27.0
• chore(deps): update dependency pytest-asyncio to v0.24.0
• chore(deps): update dependency xdoctest to v1.2.0
• chore(deps): update pypa/gh-action-pypi-publish action to v1.12.2
• Click on this checkbox to rebase all open PRs at once

Ignored or Blocked

These are blocked by an existing closed PR and will not be recreated unless you click a checkbox below.

• chore(deps): update dependency accelerate to v0.34.2
• chore(deps): update dependency gtfparse to v2

Detected dependencies

dockerfile

dockerfiles/Dockerfile

• python 3.10-slim

dockerfiles/Dockerfile.conda

• condaforge/mambaforge 23.1.0-4

github-actions

.github/workflows/build.yml

• actions/checkout v4
• actions/setup-python v4
• codecov/codecov-action v4

.github/workflows/docker.yml

• actions/checkout v4
• docker/setup-qemu-action v3
• docker/setup-buildx-action v3
• docker/login-action v3
• docker/metadata-action v5
• docker/build-push-action v5

.github/workflows/documentation.yml

• actions/checkout v4
• actions/setup-python v4
• actions/upload-pages-artifact v2
• actions/deploy-pages v2

.github/workflows/inactive-issues-prs.yml

• actions/stale v8

.github/workflows/labeler.yml

• actions/checkout v4
• crazy-max/ghaction-github-labeler v5.0.0

.github/workflows/release.yml

• actions/checkout v4
• actions/setup-python v4
• pypa/gh-action-pypi-publish v1.8.10
• release-drafter/release-drafter v5.25.0

.github/workflows/test-release.yml

• actions/checkout v4
• actions/setup-python v4
• salsify/action-detect-and-tag-new-version v2.0.3
• pypa/gh-action-pypi-publish v1.8.10
• release-drafter/release-drafter v5.25.0

pep621

pyproject.toml

• accelerate ==0.24.1
• click ==8.1.7
• einops ==0.7.0
• genomepy ==0.16.1
• gimmemotifs ==0.18.0
• gtfparse ==1.3.0
• jupyterlab ==4.0.9
• matplotlib ==3.8.1
• memory-efficient-attention-pytorch ==0.1.6
• pandas ==2.1.3
• pybedtools ==0.9.1
• seaborn ==0.13.0
• sourmash ==4.8.4
• torch ==2.3.1
• torchvision ==0.19.0
• wandb ==0.16.0
• mkdocs-material ==9.4.8
• mkdocstrings ==0.23.0
• mypy ==1.10.0
• pytest ==7.4.3
• pytest-asyncio ==0.21.1
• pytest-cov ==4.1.0
• ruff ==0.1.6
• types-tqdm ==4.66.0.4
• xdoctest ==1.1.2

---

• Check this box to trigger a request for Renovate to run again on this repository