Dependency Dashboard

[renovate[bot]]

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

Rate-Limited

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• [ ] chore(deps): update dependency seaborn to v0.13.2
• [ ] chore(deps): update dependency sourmash to v4.8.8
• [ ] chore(deps): update dependency types-tqdm to v4.66.0.20240417
• [ ] chore(deps): update dependency xdoctest to v1.1.3
• [ ] chore(deps): update dependency einops to v0.8.0
• [ ] chore(deps): update dependency mkdocstrings to v0.25.1
• [ ] chore(deps): update dependency pandas to v2.2.2
• [ ] chore(deps): update dependency pybedtools to v0.10.0
• [ ] chore(deps): update dependency ruff to v0.4.4
• [ ] chore(deps): update dependency wandb to v0.17.0
• [ ] 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 dependency pytest to v8
• [ ] chore(deps): update dependency pytest-cov to v5
• [ ] chore(deps): update release-drafter/release-drafter action to v6
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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 v3.8.4

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 v4.0.11 [security]
• [ ] chore(deps): update dependency pytest to v7.4.4
• [ ] chore(deps): update pypa/gh-action-pypi-publish action to v1.8.14
• [ ] chore(deps): update dependency accelerate to v0.30.1
• [ ] chore(deps): update dependency mkdocs-material to v9.5.21
• [ ] chore(deps): update dependency mypy to v1.10.0
• [ ] chore(deps): update dependency pytest-asyncio to v0.23.6
• [ ] chore(deps): update dependency torch to v2.3.0
• [ ] chore(deps): update dependency torchvision to v0.18.0
• [ ] 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 python docker tag to v3.12
• [ ] chore(deps): update codecov/codecov-action action to v4
• [ ] 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 v3

.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 ==2.1.0
• torchvision ==0.16.0
• wandb ==0.16.0
• mkdocs-material ==9.4.8
• mkdocstrings ==0.23.0
• mypy ==1.6.1
• 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

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