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[renovate]

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

The following updates are currently rate-limited. To force their creation now, click on a checkbox below.

• chore(deps): update actions/checkout digest to 34e1148
• chore(deps): update cloudflare/wrangler-action digest to da0e0df
• chore(deps): update docker/login-action digest to c94ce9f
• chore(deps): update docker/metadata-action digest to c299e40
• chore(deps): update docker/setup-qemu-action digest to c7c5346
• chore(deps): update google-github-actions/auth digest to c200f36
• chore(deps): update google-github-actions/upload-cloud-storage digest to c0f6160
• chore(deps): update mxschmitt/action-tmate digest to c0afd6f
• chore(deps): update prefix-dev/rattler-build-action digest to d593d93
• chore(deps): update pypa/gh-action-pypi-publish digest to cef2210
• chore(deps): update rlespinasse/github-slug-action digest to e6f2616
• chore(deps): update actions/upload-artifact action to v4.6.2
• chore(deps): update dependency astropy to v6.1.7
• chore(deps): update dependency docformatter to v1.7.7
• chore(deps): update dependency jupyter-cache to v1.0.1
• chore(deps): update dependency matplotlib-venn to v0.11.10
• chore(deps): update dependency nbsphinx to v0.9.8
• chore(deps): update dependency polars to v0.20.31
• chore(deps): update dependency pyright to v1.1.408
• chore(deps): update dependency pyyaml to v6.0.3
• chore(deps): update dependency scvelo to v0.3.4
• chore(deps): update dependency sphinx-markdown-builder to v0.6.10
• chore(deps): update dependency statsmodels to v0.14.6
• chore(deps): update actions/cache action to v4.3.0
• chore(deps): update actions/checkout action to v4.3.1
• chore(deps): update actions/download-artifact action to v4.3.0
• chore(deps): update actions/setup-python action to v5.6.0
• chore(deps): update codecov/codecov-action action to v5.5.4
• chore(deps): update crazy-max/ghaction-github-labeler action to v5.3.0
• chore(deps): update dependency adjusttext to v1.3.0
• chore(deps): update dependency altair to v5.5.0
• chore(deps): update dependency anyio to v4.13.0
• chore(deps): update dependency arviz to v0.23.4
• chore(deps): update dependency aspect_bazel_lib to v2.22.5
• chore(deps): update dependency bazel to v7.7.1
• chore(deps): update dependency beartype to v0.22.9
• chore(deps): update dependency click to v8.3.2
• chore(deps): update dependency colorlog to v6.10.1
• chore(deps): update dependency coverage to v7.13.5
• chore(deps): update dependency daft to v0.7.9
• chore(deps): update dependency dataclasses-json to v0.6.7
• chore(deps): update dependency diffrax to v0.7.2
• chore(deps): update dependency dill to v0.4.1
• chore(deps): update dependency duckdb to v1.5.2
• chore(deps): update dependency dulwich to v0.25.2
• chore(deps): update dependency einops to v0.8.2
• chore(deps): update dependency expression to v5.6.0
• chore(deps): update dependency flytekit to v1.16.19
• chore(deps): update dependency frozenlist to v1.8.0
• chore(deps): update dependency fsspec to v2024.12.0
• chore(deps): update dependency furo to v2023.9.10
• chore(deps): update dependency google-api-python-client to v2.194.0
• chore(deps): update dependency google-cloud-storage to v2.19.0
• chore(deps): update dependency greenlet to v3.4.0
• chore(deps): update dependency h5py to v3.16.0
• chore(deps): update dependency httpx to v0.28.1
• chore(deps): update dependency hydra-zen to v0.16.0
• chore(deps): update dependency hypothesis to v6.151.14
• chore(deps): update dependency ibis-framework to v9.5.0
• chore(deps): update dependency ipython to v8.39.0
• chore(deps): update dependency jupytext to v1.19.1
• chore(deps): update dependency leidenalg to v0.11.0
• chore(deps): update dependency llvmlite to v0.47.0
• chore(deps): update dependency mashumaro to v3.20
• chore(deps): update dependency matplotlib to v3.10.8
• chore(deps): update dependency mlflow to v2.22.4
• chore(deps): update dependency mypy to v1.20.1
• chore(deps): update dependency nbconvert to v7.17.1
• chore(deps): update dependency nbformat to v5.10.4
• chore(deps): update dependency numpyro to v0.20.1
• chore(deps): update dependency pandas to v2.3.3
• chore(deps): update dependency papermill to v2.7.0
• chore(deps): update dependency pillow to v11.3.0
• chore(deps): update dependency plumbum to v1.10.0
• chore(deps): update dependency pre-commit to v3.8.0
• chore(deps): update dependency pre-commit-hooks to v4.6.0
• chore(deps): update dependency prettier to v3.8.2
• chore(deps): update dependency pydantic to v2.13.0
• chore(deps): update dependency pyensembl to v2.6.2
• chore(deps): update dependency pyfaidx to v0.9.0.4
• chore(deps): update dependency pygments to v2.20.0
• chore(deps): update dependency pyperclip to v1.11.0
• chore(deps): update dependency pytest to v7.4.4
• chore(deps): update dependency pytest-asyncio to v0.26.0
• chore(deps): update dependency pytest-cov to v4.1.0
• chore(deps): update dependency pytest-mock to v3.15.1
• chore(deps): update dependency pytest-xdist to v3.8.0
• chore(deps): update dependency python-dotenv to v1.2.2
• chore(deps): update dependency pytorch-lightning to v2.6.1
• chore(deps): update dependency quartodoc to v0.11.1
• chore(deps): update dependency requests-mock to v1.12.1
• chore(deps): update dependency returns to v0.27.0
• chore(deps): update dependency rich to v13.9.4
• chore(deps): update dependency rich-click to v1.9.7
• chore(deps): update dependency ruff to v0.15.10
• chore(deps): update dependency rules_python to v0.40.0
• chore(deps): update dependency scanpy to v1.12.1
• chore(deps): update dependency scikit-learn to v1.8.0
• chore(deps): update dependency scipy to >=1.17.1,<1.18.0
• chore(deps): update dependency scvi-tools to v1.4.2
• chore(deps): update dependency sparse to v0.18.0
• chore(deps): update dependency sphinx to v7.4.7
• chore(deps): update dependency sphinx-autodoc-typehints to v1.25.3
• chore(deps): update dependency sympy to v1.14.0
• chore(deps): update dependency termcolor to v2.5.0
• chore(deps): update dependency tiledb to v0.36.1
• chore(deps): update dependency torch to v2.11.0
• chore(deps): update dependency torchmetrics to v1.9.0
• chore(deps): update dependency trio to v0.33.0
• chore(deps): update dependency validators to v0.35.0
• chore(deps): update dependency vl-convert-python to v1.9.0.post1
• chore(deps): update dependency zstandard to v0.25.0
• chore(deps): update mxschmitt/action-tmate action to v3.23
• chore(deps): update nvidia/cuda docker tag to v12.9.1
• chore(deps): update python to v3.14.4
• chore(deps): update r-base docker tag to v4.5.3
• chore(deps): update terraform google to v4.85.0
• chore(deps): update yarn to v4.13.0
• chore(deps): update actions/cache action to v5
• chore(deps): update actions/checkout action to v6
• chore(deps): update actions/deploy-pages action to v5
• chore(deps): update actions/setup-python action to v6
• chore(deps): update actions/upload-pages-artifact action to v5
• chore(deps): update cachix/cachix-action action to v17
• chore(deps): update codecov/codecov-action action to v6
• chore(deps): update crazy-max/ghaction-github-labeler action to v6
• chore(deps): update dependency altair to v6
• chore(deps): update dependency arviz to v1
• chore(deps): update dependency astropy to v7
• chore(deps): update dependency bazel to v9
• chore(deps): update dependency dulwich to v1
• chore(deps): update dependency fsspec to v2026
• chore(deps): update dependency furo to v2025
• chore(deps): update dependency google-cloud-storage to v3
• chore(deps): update dependency ibis-framework to v12
• chore(deps): update dependency ipython to v9
• chore(deps): update dependency matplotlib-venn to v1
• chore(deps): update dependency mlflow to v3
• chore(deps): update dependency myst-parser to v5
• chore(deps): update dependency pandas to v3
• chore(deps): update dependency pillow to v12
• chore(deps): update dependency poetry-core to v2
• chore(deps): update dependency polars to v1
• chore(deps): update dependency pre-commit to v4
• chore(deps): update dependency pre-commit-hooks to v6
• chore(deps): update dependency pyarrow to v23
• chore(deps): update dependency pytest to v9
• chore(deps): update dependency pytest-asyncio to v1
• chore(deps): update dependency pytest-cov to v7
• chore(deps): update dependency rich to v15
• chore(deps): update dependency rules_python to v1
• chore(deps): update dependency sphinx to v9
• chore(deps): update dependency sphinx-autobuild to v2025
• chore(deps): update dependency sphinx-autodoc-typehints to v3
• chore(deps): update dependency sphinx-click to v6
• chore(deps): update dependency termcolor to v3
• chore(deps): update dependency vegafusion to v2
• chore(deps): update determinatesystems/nix-installer-action action to v22
• chore(deps): update docker/build-push-action action to v7
• chore(deps): update docker/login-action action to v4
• chore(deps): update docker/metadata-action action to v6
• chore(deps): update docker/setup-buildx-action action to v4
• chore(deps): update docker/setup-qemu-action action to v4
• chore(deps): update github artifact actions (major) (actions/download-artifact, actions/upload-artifact)
• chore(deps): update google-github-actions/auth action to v3
• chore(deps): update google-github-actions/deploy-cloudrun action to v3
• chore(deps): update google-github-actions/upload-cloud-storage action to v3
• chore(deps): update nvidia/cuda docker tag to v13
• chore(deps): update rlespinasse/github-slug-action action to v5
• chore(deps): update terraform google to v7
• 🔐 Create all rate-limited PRs at once 🔐

---

Warning

Renovate failed to look up the following dependencies: Could not determine new digest for update (github-digest package r-lib/actions), Could not determine new digest for update (github-digest package mikefarah/yq), Could not determine new digest for update (github-digest package cachix/cachix-action), Could not determine new digest for update (github-digest package DeterminateSystems/flakehub-push), Could not determine new digest for update (github-digest package cameronraysmith/maximize-build-space), Could not determine new digest for update (github-tags package iterative/setup-dvc), Could not determine new digest for update (github-digest package quarto-dev/quarto-actions), Could not determine new digest for update (github-digest package sequoia-pgp/fast-forward).

Files affected: .github/actions/setup_environment/action.yml, .github/workflows/cid.yaml, .github/workflows/colab.yml, .github/workflows/conda.yaml, .github/workflows/deploy-docs-cloudflare.yaml, .github/workflows/manuscript.yaml, .github/workflows/pr-check.yaml, .github/workflows/pr-merge.yaml

---

Open

The following updates have all been created. To force a retry/rebase of any, click on a checkbox below.

• chore(deps): update dependency jupyterlab to v4.0.11 [security]
• chore(deps): update dependency lightning to v2.3.3 [security]
• chore(deps): update dependency black to v24 [security]
• chore(deps): update actions/cache digest to 0057852
• chore(deps): update dependency chex to v0.1.91
• chore(deps): update dependency diskcache to v5.6.3
• chore(deps): update dependency ipywidgets to v8.1.8
• chore(deps): update dependency anndata to v0.12.10
• chore(deps): update dependency flax to v0.12.6
• chore(deps): update dependency jax to v0.9.2
• chore(deps): update dependency jaxlib to v0.9.2
• chore(deps): update dependency jaxtyping to v0.3.9
• chore(deps): update dependency xdoctest to v1.3.2
• Click on this checkbox to rebase all open PRs at once

Detected Dependencies

bazel-module (1)

MODULE.bazel (2)

• aspect_bazel_lib 2.7.9 → [Updates: 2.22.5]
• rules_python 0.29.0 → [Updates: 0.40.0, 1.9.0]

bazelisk (1)

.bazelversion (1)

• bazel 7.2.1 → [Updates: 7.7.1, 9.0.2]

devcontainer (1)

.devcontainer/devcontainer.json (1)

• ghcr.io/devcontainers/features/docker-in-docker 2

docker-compose (1)

containers/compose.yaml

dockerfile (10)

.devcontainer/devcontainer.Dockerfile

containers/Dockerfile (2)

• docker/dockerfile 1
• ghcr.io/iterative/cml 0-dvc3-base1-gpu

containers/Dockerfile.app (2)

• docker/dockerfile 1
• condaforge/mambaforge 23.3.1-1

containers/Dockerfile.app.local (2)

• docker/dockerfile 1
• condaforge/mambaforge 23.3.1-1

containers/Dockerfile.conda (1)

• condaforge/mambaforge 23.3.1-1

containers/Dockerfile.conda.cpu (2)

• docker/dockerfile 1
• condaforge/mambaforge 23.3.1-1

containers/dyngen.Dockerfile (1)

• r-base 4.2.3 → [Updates: 4.5.3]

containers/gpu.Dockerfile (1)

• nvidia/cuda 12.3.0-runtime-ubuntu22.04 → [Updates: 12.9.1-runtime-ubuntu22.04, 13.2.0-runtime-ubuntu22.04]

containers/nix.Dockerfile (1)

• ghcr.io/pinellolab/pyrovelocity 520-sum

containers/pkg.Dockerfile (1)

• python 3.10.13-slim → [Updates: 3.14.4-slim]

github-actions (16)

.github/actions/build_nix_image/action.yml (4)

• docker/setup-qemu-action v3@5927c834f5b4fdf503fca6f4c7eccda82949e1ee → [Updates: v4, v3]
• DeterminateSystems/nix-installer-action v12@7993355175c2765e5733dae74f3e0786fe0e5c4f → [Updates: v22]
• cachix/cachix-action v15@ad2ddac53f961de1989924296a1f236fcfbaa4fc → [Updates: v17]
• rlespinasse/github-slug-action v4@797d68864753cbceedc271349d402da4590e6302 → [Updates: v5]

.github/actions/setup_environment/action.yml (5)

• actions/setup-python v5.4.0@42375524e23c412d93fb67b49958b491fce71c38 → [Updates: v5.6.0, v6.2.0]
• r-lib/actions ratchet:r-lib/actions/setup-pandoc@v2@14a7e741c1cb130261263aa1593718ba42cf443b
• snok/install-poetry v1@76e04a911780d5b312d89783f7b1cd627778900a
• actions/cache v4.2.2@d4323d4df104b026a6aa633fdb11d772146be0bf → [Updates: v4.3.0, v5.0.5]
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48 → [Updates: v3]

.github/workflows/app.yaml (10)

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• docker/setup-qemu-action v2@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7 → [Updates: v4]
• docker/setup-buildx-action v2@885d1462b80bc1c1c7f0b00334ad271f09369c55 → [Updates: v4]
• docker/login-action v3@0d4c9c5ea7693da7b068278f7b52bda2a190a446 → [Updates: v4, v3]
• docker/login-action v3@0d4c9c5ea7693da7b068278f7b52bda2a190a446 → [Updates: v4, v3]
• docker/metadata-action v5@8e5442c4ef9f78752691e2d8f8d19755c6f78e81 → [Updates: v6, v5]
• docker/build-push-action v5@ca052bb54ab0790a636c9b5f226502c73d547a25 → [Updates: v7]
• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• google-github-actions/auth v2@71fee32a0bb7e97b4d33d548e7d957010649d8fa → [Updates: v3, v2]
• google-github-actions/deploy-cloudrun v1@e62f655d5754bec48078a72edc015367b01ee97b → [Updates: v3]

.github/workflows/build-images.yaml (3)

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• rlespinasse/github-slug-action v4@797d68864753cbceedc271349d402da4590e6302 → [Updates: v5]
• mxschmitt/action-tmate v3@a283f9441d2d96eb62436dc46d7014f5d357ac22 → [Updates: v3]

.github/workflows/build-nix-images.yaml (2)

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• mxschmitt/action-tmate v3@a283f9441d2d96eb62436dc46d7014f5d357ac22 → [Updates: v3]

.github/workflows/cid.yaml (29)

• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• mikefarah/yq ratchet:mikefarah/yq@master@d74e70104f379475810a3bf2e20d80732f0cf6dc
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 → [Updates: v4.6.2, v7.0.1]
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• actions/download-artifact v4.1.9@cc203385981b70ca67e1cc392babf9cc229d5806 → [Updates: v4.3.0, v8.0.1]
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48 → [Updates: v3]
• codecov/codecov-action v5.4.0@0565863a31f2c772f9f0395002a31e3f06189574 → [Updates: v5.5.4, v6.0.0]
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• actions/cache v4@d4323d4df104b026a6aa633fdb11d772146be0bf → [Updates: v5, v4]
• actions/cache v4@d4323d4df104b026a6aa633fdb11d772146be0bf → [Updates: v5, v4]
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 → [Updates: v4.6.2, v7.0.1]
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• DeterminateSystems/nix-installer-action v16@e50d5f73bfe71c2dd0aa4218de8f4afa59f8f81d → [Updates: v22]
• cachix/cachix-action ratchet:cachix/cachix-action@master@be5295a636153b6ad194d3245f78f8e0b78dc704
• rlespinasse/github-slug-action v5@aba9f8db6ef36e0733227a62673d6592b1f430ea → [Updates: v5]
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• DeterminateSystems/nix-installer-action v16@e50d5f73bfe71c2dd0aa4218de8f4afa59f8f81d → [Updates: v22]
• cachix/cachix-action ratchet:cachix/cachix-action@master@be5295a636153b6ad194d3245f78f8e0b78dc704
• cihelper/action-semanticrelease-poetry v1@66900ba780321bcdb974891ee82f945a25a870d7
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 → [Updates: v4.6.2, v7.0.1]
• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• DeterminateSystems/nix-installer-action v16@e50d5f73bfe71c2dd0aa4218de8f4afa59f8f81d → [Updates: v22]
• DeterminateSystems/flakehub-push ratchet:DeterminateSystems/flakehub-push@main@c96c7bfc42e46f90c84030706c00b62b8c0f1ef4
• actions/download-artifact v4.1.9@cc203385981b70ca67e1cc392babf9cc229d5806 → [Updates: v4.3.0, v8.0.1]
• pypa/gh-action-pypi-publish release/v1@76f52bc884231f62b9a034ebfe128415bbaabdfc → [Updates: release/v1]
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• actions/upload-pages-artifact v3@56afc609e74202658d3ffba0e8f6dda462b719fa → [Updates: v5]
• actions/deploy-pages v4@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e → [Updates: v5]

.github/workflows/cml-images.yml (13)

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• docker/setup-qemu-action v2@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7 → [Updates: v4]
• docker/setup-buildx-action v2@885d1462b80bc1c1c7f0b00334ad271f09369c55 → [Updates: v4]
• docker/login-action v3@0d4c9c5ea7693da7b068278f7b52bda2a190a446 → [Updates: v4, v3]
• docker/metadata-action v5@8e5442c4ef9f78752691e2d8f8d19755c6f78e81 → [Updates: v6, v5]
• docker/build-push-action v5@ca052bb54ab0790a636c9b5f226502c73d547a25 → [Updates: v7]
• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• docker/setup-qemu-action v2@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7 → [Updates: v4]
• docker/setup-buildx-action v2@885d1462b80bc1c1c7f0b00334ad271f09369c55 → [Updates: v4]
• docker/login-action v3@0d4c9c5ea7693da7b068278f7b52bda2a190a446 → [Updates: v4, v3]
• docker/login-action v3@0d4c9c5ea7693da7b068278f7b52bda2a190a446 → [Updates: v4, v3]
• docker/metadata-action v5@8e5442c4ef9f78752691e2d8f8d19755c6f78e81 → [Updates: v6, v5]
• docker/build-push-action v5@ca052bb54ab0790a636c9b5f226502c73d547a25 → [Updates: v7]

.github/workflows/cml.yml (10)

• actions/checkout v4 → [Updates: v6]
• iterative/setup-cml v1
• mxschmitt/action-tmate v3
• actions/checkout v4 → [Updates: v6]
• actions/setup-python v4 → [Updates: v6]
• snok/install-poetry v1
• actions/cache v3 → [Updates: v5]
• mxschmitt/action-tmate v3
• mxschmitt/action-tmate v3
• python 3.10 → [Updates: 3.14]

.github/workflows/colab.yml (5)

• cameronraysmith/maximize-build-space ratchet:cameronraysmith/maximize-build-space@print-usage@fdf0c06b18d92be98aa64cb68ae4ea4c9bc4794d
• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• mxschmitt/action-tmate v3@a283f9441d2d96eb62436dc46d7014f5d357ac22 → [Updates: v3]
• google-github-actions/auth v2@71fee32a0bb7e97b4d33d548e7d957010649d8fa → [Updates: v3, v2]
• google-github-actions/upload-cloud-storage v2@22121cd842b0d185e042e28d969925b538c33d77 → [Updates: v3, v2]

.github/workflows/conda.yaml (4)

• cameronraysmith/maximize-build-space ratchet:cameronraysmith/maximize-build-space@print-usage@fdf0c06b18d92be98aa64cb68ae4ea4c9bc4794d
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48 → [Updates: v3]
• prefix-dev/rattler-build-action v0@6f0cd2ff475379a6da7221b22894613bb26a65ab → [Updates: v0]

.github/workflows/deploy-docs-cloudflare.yaml (8)

• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• DeterminateSystems/nix-installer-action v16@e50d5f73bfe71c2dd0aa4218de8f4afa59f8f81d → [Updates: v22]
• cachix/cachix-action ratchet:cachix/cachix-action@master@be5295a636153b6ad194d3245f78f8e0b78dc704
• google-github-actions/auth v2@6fc4af4b145ae7821d527454aa9bd537d1f2dc5f → [Updates: v3, v2]
• iterative/setup-dvc v1@180d52394bc746fb0bb5ca8e9e1a7a49a151742e
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48 → [Updates: v3]
• threeal/setup-yarn-action v2.0.0@ec8c075e62bc497968de40011c2b766f5e8f1ac5
• cloudflare/wrangler-action v3@392082e81ffbcb9ebdde27400634aa004b35ea37 → [Updates: v3]

.github/workflows/labeler.yml (2)

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332 → [Updates: v6, v4]
• crazy-max/ghaction-github-labeler v5.0.0@de749cf181958193cb7debf1a9c5bb28922f3e1b → [Updates: v5.3.0, v6.0.0]

.github/workflows/manuscript.yaml (5)

• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• iterative/setup-dvc v1@180d52394bc746fb0bb5ca8e9e1a7a49a151742e
• quarto-dev/quarto-actions ratchet:quarto-dev/quarto-actions/setup@v2.1.9@9e48da27e184aa238fcb49f5db75469626d43adb
• mxschmitt/action-tmate v3.19@e5c7151931ca95bad1c6f4190c730ecf8c7dde48 → [Updates: v3.23]
• actions/upload-artifact v4.6.2@ea165f8d65b6e75b540449e92b4886f43607fa02 → [Updates: v7.0.1]

.github/workflows/pr-check.yaml (1)

• sequoia-pgp/fast-forward ratchet:sequoia-pgp/fast-forward@main@042cd23fbf9d5ed1400497a106c8abe4b45408ab

.github/workflows/pr-merge.yaml (1)

• sequoia-pgp/fast-forward ratchet:sequoia-pgp/fast-forward@main@042cd23fbf9d5ed1400497a106c8abe4b45408ab

.github/workflows/run-workflow.yaml (5)

• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683 → [Updates: v4.3.1, v6.0.2]
• actions/download-artifact v4.1.9@cc203385981b70ca67e1cc392babf9cc229d5806 → [Updates: v4.3.0, v8.0.1]
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48 → [Updates: v3]
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 → [Updates: v4.6.2, v7.0.1]
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 → [Updates: v4.6.2, v7.0.1]

npm (1)

package.json (3)

• prettier ^3.1.0 → [Updates: ^3.1.0]
• node >=18
• yarn 4.5.0 → [Updates: 4.13.0]

pip_requirements (5)

docs/requirements.txt

reproducibility/figures/fig3/requirements.txt

reproducibility/figures/suppfig2/requirements.txt

requirements-cpu.txt

requirements-main.txt

poetry (1)

pyproject.toml (163)

• poetry-core >=1.6.0,<2 → [Updates: >=2.3.2,<3]
• python >=3.11, <3.13 → [Updates: >=3.14, <3.15]
• adjusttext >=1.1.1 → [Updates: >=1.1.1]
• altair >=5.3.0 → [Updates: >=5.3.0]
• anndata >=0.10.5 → [Updates: >=0.10.5]
• anyio >=4.3.0 → [Updates: >=4.3.0]
• appdirs >=1.4.4
• arviz >=0.17.1 → [Updates: >=0.17.1]
• astropy >=6.1.2 → [Updates: >=6.1.2]
• beartype >=0.18.5 → [Updates: >=0.18.5]
• chex >=0.1.7 → [Updates: >=0.1.7]
• click >=8.1.7 → [Updates: >=8.1.7]
• colorlog >=6.7.0 → [Updates: >=6.7.0]
• daft >=0.1.2 → [Updates: >=0.1.2]
• diffrax >=0.5.0 → [Updates: >=0.5.0]
• dill >=0.3.8 → [Updates: >=0.3.8]
• diskcache >=5.6.1 → [Updates: >=5.6.1]
• duckdb >=1.0.0 → [Updates: >=1.0.0]
• einops >=0.7.0 → [Updates: >=0.7.0]
• expression >=5.0.2 → [Updates: >=5.0.2]
• flax >=0.8.1 → [Updates: >=0.8.1]
• frozenlist >=1.1.1 → [Updates: >=1.1.1]
• fsspec >=2024.3.0 → [Updates: >=2024.3.0]
• greenlet >=3.0.3 → [Updates: >=3.0.3]
• httpx >=0.27.0 → [Updates: >=0.27.0]
• h5py >=3.9.0 → [Updates: >=3.9.0]
• ibis-framework >=9.2.0 → [Updates: >=9.2.0]
• jax >=0.4.23 → [Updates: >=0.4.23]
• jaxlib >=0.4.23 → [Updates: >=0.4.23]
• jaxtyping >=0.2.25 → [Updates: >=0.2.25]
• leidenalg >=0.9.1 → [Updates: >=0.9.1]
• llvmlite >=0.41.1 → [Updates: >=0.41.1]
• matplotlib >=3.9.1 → [Updates: >=3.9.1]
• mlflow >=2.13.0 → [Updates: >=2.13.0]
• numpyro >=0.15.0 → [Updates: >=0.15.0]
• pandas >=2.0.0 → [Updates: >=2.0.0]
• pillow >=10.1.0 → [Updates: >=10.1.0]
• plumbum >=1.8.2 → [Updates: >=1.8.2]
• polars >=0.20.17 → [Updates: >=0.20.17]
• pyarrow >=14.0.2 → [Updates: >=14.0.2]
• pydantic >=2.8.0 → [Updates: >=2.8.0]
• pyro-ppl >=1.9.1
• lightning >=2.0.0 → [Updates: >=2.0.0]
• pytorch-lightning >=2.0.0 → [Updates: >=2.0.0]
• pyyaml >=6.0.1 → [Updates: >=6.0.1]
• returns >=0.23.0 → [Updates: >=0.23.0]
• rich >=13.7.1 → [Updates: >=13.7.1]
• scanpy >=1.10.1 → [Updates: >=1.10.1]
• scikit-learn >=1.3.1 → [Updates: >=1.3.1]
• scipy >=1.10.1,<1.14.0 → [Updates: >=1.17.1,<1.18.0]
• scvelo >=0.3.2 → [Updates: >=0.3.2]
• scvi-tools >=1.1.1 → [Updates: >=1.1.1]
• seaborn >=0.13.2
• sparse >=0.15.4 → [Updates: >=0.15.4]
• statsmodels >=0.14.2 → [Updates: >=0.14.2]
• sympy >=1.12 → [Updates: >=1.12]
• termcolor >=2.2.0 → [Updates: >=2.2.0]
• tiledb >=0.31.1 → [Updates: >=0.31.1]
• torch >=2.1.2 → [Updates: >=2.1.2]
• torchmetrics >=1.2.1 → [Updates: >=1.2.1]
• trio >=0.26.0 → [Updates: >=0.26.0]
• validators >=0.33.0 → [Updates: >=0.33.0]
• vegafusion >=1.6.9 → [Updates: >=1.6.9]
• vegafusion-python-embed >=1.6.9
• vl-convert-python >=1.6.0 → [Updates: >=1.6.0]
• zstandard >=0.23.0 → [Updates: >=0.23.0]
• black >=23.3.0 → [Updates: >=23.3.0]
• coverage >=6.2 → [Updates: >=6.2]
• dataclasses-json >=0.5.7 → [Updates: >=0.5.7]
• dulwich >=0.21.7 → [Updates: >=0.21.7]
• flytekit >=1.13.3 → [Updates: >=1.13.3]
• furo >=2023.5.20 → [Updates: >=2023.5.20]
• google-api-python-client >=2.79.0 → [Updates: >=2.79.0]
• hydra-core >=1.3.2
• hydra-zen >=0.12.1 → [Updates: >=0.12.1]
• hypothesis >=6.71.0 → [Updates: >=6.71.0]
• ipdb >=0.13.13
• ipython >=8.11.0 → [Updates: >=8.11.0]
• ipywidgets >=8.0.0 → [Updates: >=8.0.0]
• jupyter-cache >=0.6.1 → [Updates: >=0.6.1]
• jupyterlab >=4.0.9 → [Updates: >=4.0.9]
• jupytext >=1.16.0 → [Updates: >=1.16.0]
• mashumaro >=3.10 → [Updates: >=3.10]
• matplotlib-venn >=0.11.9 → [Updates: >=0.11.9]
• mypy >=0.930 → [Updates: >=0.930]
• myst-parser >=2.0.0 → [Updates: >=2.0.0]
• nbconvert >=7.14.0 → [Updates: >=7.14.0]
• nbformat >=5.9.2 → [Updates: >=5.9.2]
• nbsphinx >=0.9.3 → [Updates: >=0.9.3]
• omegaconf >=2.3.0
• papermill >=2.4.0 → [Updates: >=2.4.0]
• pre-commit >=2.16.0 → [Updates: >=2.16.0]
• pre-commit-hooks >=4.1.0 → [Updates: >=4.1.0]
• pyensembl >=2.3.12 → [Updates: >=2.3.12]
• pyfaidx >=0.8.1.1 → [Updates: >=0.8.1.1]
• pygments >=2.15.0 → [Updates: >=2.15.0]
• pytest >=6.2.5 → [Updates: >=6.2.5]
• pytest-asyncio >=0.21.1 → [Updates: >=0.21.1]
• pytest-cov >=4.0.0 → [Updates: >=4.0.0]
• pytest-mock >=3.10.0 → [Updates: >=3.10.0]
• pytest-xdist >=3.1.0 → [Updates: >=3.1.0]
• python-dotenv >=1.0.0 → [Updates: >=1.0.0]
• rich-click >=1.7.3 → [Updates: >=1.7.3]
• ruff >=0.1.5 → [Updates: >=0.1.5]
• sphinx >=7.0.1 → [Updates: >=7.0.1]
• sphinx-autobuild >=2021.3.14 → [Updates: >=2021.3.14]
• sphinx-autodoc-typehints >=1.23.3 → [Updates: >=1.23.3]
• sphinx-click >=4.4.0 → [Updates: >=4.4.0]
• sphinx-copybutton >=0.5.2
• sphinx-markdown-builder >=0.6.6 → [Updates: >=0.6.6]
• quartodoc >=0.7.2 → [Updates: >=0.7.2]
• xdoctest >=0.15.10 → [Updates: >=0.15.10]
• black >=23.3.0 → [Updates: >=23.3.0]
• mypy >=1.5.1 → [Updates: >=1.5.1]
• pre-commit >=2.16.0 → [Updates: >=2.16.0]
• pre-commit-hooks >=4.1.0 → [Updates: >=4.1.0]
• pyright >=1.1.347 → [Updates: >=1.1.347]
• ruff >=0.1.5 → [Updates: >=0.1.5]
• docformatter >=1.7.5 → [Updates: >=1.7.5]
• coverage >=6.2 → [Updates: >=6.2]
• hypothesis >=6.72.1 → [Updates: >=6.72.1]
• ipdb >=0.13.13
• ipython >=8.11.0 → [Updates: >=8.11.0]
• pygments >=2.15.0 → [Updates: >=2.15.0]
• pytest >=7.3.1 → [Updates: >=7.3.1]
• pytest-asyncio >=0.21.1 → [Updates: >=0.21.1]
• pytest-cov >=4.0.0 → [Updates: >=4.0.0]
• pytest-mock >=3.10.0 → [Updates: >=3.10.0]
• pytest-xdist >=3.1.0 → [Updates: >=3.1.0]
• requests-mock >=1.11.0 → [Updates: >=1.11.0]
• xdoctest >=1.1.1 → [Updates: >=1.1.1]
• furo >=2023.5.20 → [Updates: >=2023.5.20]
• jupyter-cache >=0.6.1 → [Updates: >=0.6.1]
• jupyterlab >=4.0.9 → [Updates: >=4.0.9]
• jupytext >=1.16.0 → [Updates: >=1.16.0]
• myst-parser >=2.0.0 → [Updates: >=2.0.0]
• nbsphinx >=0.9.3 → [Updates: >=0.9.3]
• sphinx-autobuild >=2021.3.14 → [Updates: >=2021.3.14]
• sphinx-autodoc-typehints >=1.23.3 → [Updates: >=1.23.3]
• sphinx-click >=4.4.0 → [Updates: >=4.4.0]
• sphinx-copybutton >=0.5.2
• sphinx-markdown-builder >=0.6.6 → [Updates: >=0.6.6]
• sphinx >=7.0.1 → [Updates: >=7.0.1]
• quartodoc >=0.7.2 → [Updates: >=0.7.2]
• dataclasses-json >=0.5.7 → [Updates: >=0.5.7]
• dulwich >=0.21.7 → [Updates: >=0.21.7]
• flytekit >=1.13.0 → [Updates: >=1.13.0]
• google-api-python-client >=2.79.0 → [Updates: >=2.79.0]
• google-cloud-storage >=2.14.0 → [Updates: >=2.14.0]
• hydra-core >=1.3.2
• hydra-zen >=0.12.1 → [Updates: >=0.12.1]
• ipywidgets >=8.0.0 → [Updates: >=8.0.0]
• jupytext >=1.16.0 → [Updates: >=1.16.0]
• mashumaro >=3.10 → [Updates: >=3.10]
• nbconvert >=7.14.0 → [Updates: >=7.14.0]
• nbformat >=5.9.2 → [Updates: >=5.9.2]
• omegaconf >=2.3.0
• papermill >=2.4.0 → [Updates: >=2.4.0]
• pyperclip >=1.8.2 → [Updates: >=1.8.2]
• python-dotenv >=1.0.0 → [Updates: >=1.0.0]
• rich-click >=1.7.3 → [Updates: >=1.7.3]
• pyensembl >=2.3.12 → [Updates: >=2.3.12]
• pyfaidx >=0.8.1.1 → [Updates: >=0.8.1.1]

terraform (1)

reproducibility/environment/main.tf (1)

• google 4.41.0 → [Updates: 4.85.0, 7.27.0]

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