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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/cache digest to 5a3ec84
• chore(deps): update actions/checkout digest to 11bd719
• chore(deps): update cachix/cachix-action digest to 1d49a1c
• chore(deps): update cameronraysmith/maximize-build-space digest to c28619d
• chore(deps): update cloudflare/wrangler-action digest to da0e0df
• chore(deps): update determinatesystems/flakehub-push digest to 71f5720
• chore(deps): update docker/login-action digest to 74a5d14
• chore(deps): update docker/metadata-action digest to 902fa8e
• chore(deps): update docker/setup-qemu-action digest to 2910929
• chore(deps): update google-github-actions/auth digest to 6fc4af4
• chore(deps): update google-github-actions/upload-cloud-storage digest to 386ab77
• chore(deps): update mikefarah/yq digest to f03c9dc
• chore(deps): update mxschmitt/action-tmate digest to 7b6a61a
• chore(deps): update prefix-dev/rattler-build-action digest to 5181e19
• chore(deps): update rlespinasse/github-slug-action digest to 955b5ba
• chore(deps): update sequoia-pgp/fast-forward digest to 6f66e12
• chore(deps): update actions/upload-artifact action to v4.6.2
• chore(deps): update codecov/codecov-action action to v5.4.3
• 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 v0.9.7
• chore(deps): update dependency polars to v0.20.31
• chore(deps): update dependency pyensembl to v2.3.13
• chore(deps): update dependency pyfaidx to v0.8.1.4
• chore(deps): update dependency pyright to v1.1.403
• chore(deps): update dependency pyyaml to v6.0.2
• chore(deps): update dependency scvelo to v0.3.3
• chore(deps): update dependency sphinx-markdown-builder to v0.6.8
• chore(deps): update dependency statsmodels to v0.14.5
• chore(deps): update actions/download-artifact action to v4.3.0
• 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 v4.9.0
• chore(deps): update dependency arviz to v0.22.0
• chore(deps): update dependency aspect_bazel_lib to v2.20.0
• chore(deps): update dependency bazel to v7.6.1
• chore(deps): update dependency beartype to v0.21.0
• chore(deps): update dependency click to v8.2.1
• chore(deps): update dependency colorlog to v6.9.0
• chore(deps): update dependency coverage to v7.10.0
• chore(deps): update dependency daft to v0.5.12
• chore(deps): update dependency dataclasses-json to v0.6.7
• chore(deps): update dependency diffrax to v0.7.0
• chore(deps): update dependency dill to v0.4.0
• chore(deps): update dependency duckdb to v1.3.2
• chore(deps): update dependency dulwich to v0.23.2
• chore(deps): update dependency einops to v0.8.1
• chore(deps): update dependency expression to v5.6.0
• chore(deps): update dependency flytekit to v1.16.3
• chore(deps): update dependency frozenlist to v1.7.0
• 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 v2.177.0
• chore(deps): update dependency google-cloud-storage to v2.19.0
• chore(deps): update dependency greenlet to v3.2.3
• chore(deps): update dependency h5py to v3.14.0
• chore(deps): update dependency httpx to v0.28.1
• chore(deps): update dependency hydra-zen to v0.15.0
• chore(deps): update dependency hypothesis to v6.136.4
• chore(deps): update dependency ibis-framework to v9.5.0
• chore(deps): update dependency ipython to v8.37.0
• chore(deps): update dependency jupytext to v1.17.2
• chore(deps): update dependency leidenalg to v0.10.2
• chore(deps): update dependency llvmlite to v0.44.0
• chore(deps): update dependency mashumaro to v3.16
• chore(deps): update dependency matplotlib to v3.10.3
• chore(deps): update dependency mlflow to v2.22.1
• chore(deps): update dependency mypy to v1.17.0
• chore(deps): update dependency nbconvert to v7.16.6
• chore(deps): update dependency nbformat to v5.10.4
• chore(deps): update dependency numpyro to v0.18.0
• chore(deps): update dependency pandas to v2.3.1
• chore(deps): update dependency papermill to v2.6.0
• chore(deps): update dependency pillow to v11.3.0
• chore(deps): update dependency plumbum to v1.9.0
• 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 v3.6.2
• chore(deps): update dependency pydantic to v2.11.7
• chore(deps): update dependency pygments to v2.19.2
• chore(deps): update dependency pyperclip to v1.9.0
• 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 v3.14.1
• chore(deps): update dependency pytest-xdist to v3.8.0
• chore(deps): update dependency python-dotenv to v1.1.1
• chore(deps): update dependency pytorch-lightning to v2.5.2
• 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 v0.26.0
• chore(deps): update dependency rich to v13.9.4
• chore(deps): update dependency rich-click to v1.8.9
• chore(deps): update dependency ruff to v0.12.5
• chore(deps): update dependency rules_python to v0.40.0
• chore(deps): update dependency scanpy to v1.11.3
• chore(deps): update dependency scikit-learn to v1.7.1
• chore(deps): update dependency scipy to >=1.16.0,<1.17.0
• chore(deps): update dependency scvi-tools to v1.3.3
• chore(deps): update dependency sparse to v0.17.0
• 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 v0.34.1
• chore(deps): update dependency torch to v2.7.1
• chore(deps): update dependency torchmetrics to v1.8.0
• chore(deps): update dependency trio to v0.30.0
• chore(deps): update dependency validators to v0.35.0
• chore(deps): update dependency vl-convert-python to v1.8.0
• chore(deps): update mxschmitt/action-tmate action to v3.22
• chore(deps): update nvidia/cuda docker tag to v12.9.1
• chore(deps): update python to v3.13.5
• chore(deps): update r-base docker tag to v4.5.1
• chore(deps): update terraform google to v4.85.0
• chore(deps): update yarn to v4.9.2
• chore(deps): update actions/cache action
• chore(deps): update actions/setup-python action
• chore(deps): update cachix/cachix-action action to v16
• chore(deps): update dependency astropy to v7
• chore(deps): update dependency bazel to v8
• chore(deps): update dependency fsspec to v2025
• chore(deps): update dependency furo to v2025
• chore(deps): update dependency google-cloud-storage to v3
• chore(deps): update dependency ibis-framework to v10
• 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 v4
• 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 v5
• chore(deps): update dependency pyarrow to v21
• chore(deps): update dependency pytest to v8
• chore(deps): update dependency pytest-asyncio to v1
• chore(deps): update dependency pytest-cov to v6
• chore(deps): update dependency rich to v14
• chore(deps): update dependency rules_python to v1
• chore(deps): update dependency sphinx to v8
• chore(deps): update dependency sphinx-autobuild to v2024
• 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 v19
• chore(deps): update docker/build-push-action action to v6
• chore(deps): update docker/setup-buildx-action action to v3
• chore(deps): update docker/setup-qemu-action action to v3
• chore(deps): update google-github-actions/deploy-cloudrun action to v2
• chore(deps): update rlespinasse/github-slug-action action to v5
• chore(deps): update terraform google to v6
• 🔐 Create all rate-limited PRs at once 🔐

---

Warning

Renovate failed to look up the following dependencies: Could not determine new digest for update (github-tags package pypa/gh-action-pypi-publish), Could not determine new digest for update (github-tags package iterative/setup-dvc).

Files affected: .github/workflows/cid.yaml, .github/workflows/deploy-docs-cloudflare.yaml, .github/workflows/manuscript.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 dependency chex to v0.1.90
• chore(deps): update dependency diskcache to v5.6.3
• chore(deps): update dependency ipywidgets to v8.1.7
• chore(deps): update dependency anndata to v0.12.1
• chore(deps): update dependency flax to v0.10.7
• chore(deps): update dependency jax to v0.7.0
• chore(deps): update dependency jaxlib to v0.7.0
• chore(deps): update dependency jaxtyping to v0.3.2
• chore(deps): update dependency xdoctest to v1.2.0
• Click on this checkbox to rebase all open PRs at once

Detected dependencies

bazel-module

MODULE.bazel

• aspect_bazel_lib 2.7.9
• rules_python 0.29.0

bazelisk

.bazelversion

• bazel 7.2.1

devcontainer

.devcontainer/devcontainer.json

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

docker-compose

containers/compose.yaml

dockerfile

.devcontainer/devcontainer.Dockerfile

containers/Dockerfile

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

containers/Dockerfile.app

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

containers/Dockerfile.app.local

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

containers/Dockerfile.conda

• condaforge/mambaforge 23.3.1-1

containers/Dockerfile.conda.cpu

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

containers/dyngen.Dockerfile

• r-base 4.2.3

containers/gpu.Dockerfile

• nvidia/cuda 12.3.0-runtime-ubuntu22.04

containers/nix.Dockerfile

• ghcr.io/pinellolab/pyrovelocity 520-sum

containers/pkg.Dockerfile

• python 3.10.13-slim

github-actions

.github/actions/build_nix_image/action.yml

• docker/setup-qemu-action v3@5927c834f5b4fdf503fca6f4c7eccda82949e1ee
• DeterminateSystems/nix-installer-action v12@7993355175c2765e5733dae74f3e0786fe0e5c4f
• cachix/cachix-action v15@ad2ddac53f961de1989924296a1f236fcfbaa4fc
• rlespinasse/github-slug-action v4@797d68864753cbceedc271349d402da4590e6302

.github/actions/setup_environment/action.yml

• actions/setup-python v5.4.0@42375524e23c412d93fb67b49958b491fce71c38
• r-lib/actions v2
• snok/install-poetry v1@76e04a911780d5b312d89783f7b1cd627778900a
• actions/cache v4.2.2@d4323d4df104b026a6aa633fdb11d772146be0bf
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48

.github/workflows/app.yaml

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

.github/workflows/build-images.yaml

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
• rlespinasse/github-slug-action v4@797d68864753cbceedc271349d402da4590e6302
• mxschmitt/action-tmate v3@a283f9441d2d96eb62436dc46d7014f5d357ac22

.github/workflows/build-nix-images.yaml

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
• mxschmitt/action-tmate v3@a283f9441d2d96eb62436dc46d7014f5d357ac22

.github/workflows/cid.yaml

• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• mikefarah/yq d74e70104f379475810a3bf2e20d80732f0cf6dc
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/download-artifact v4.1.9@cc203385981b70ca67e1cc392babf9cc229d5806
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48
• codecov/codecov-action v5.4.0@0565863a31f2c772f9f0395002a31e3f06189574
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/cache v4@d4323d4df104b026a6aa633fdb11d772146be0bf
• actions/cache v4@d4323d4df104b026a6aa633fdb11d772146be0bf
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• DeterminateSystems/nix-installer-action v16@e50d5f73bfe71c2dd0aa4218de8f4afa59f8f81d
• cachix/cachix-action be5295a636153b6ad194d3245f78f8e0b78dc704
• rlespinasse/github-slug-action v5@aba9f8db6ef36e0733227a62673d6592b1f430ea
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• DeterminateSystems/nix-installer-action v16@e50d5f73bfe71c2dd0aa4218de8f4afa59f8f81d
• cachix/cachix-action be5295a636153b6ad194d3245f78f8e0b78dc704
• cihelper/action-semanticrelease-poetry v1@66900ba780321bcdb974891ee82f945a25a870d7
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1
• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
• DeterminateSystems/nix-installer-action v16@e50d5f73bfe71c2dd0aa4218de8f4afa59f8f81d
• DeterminateSystems/flakehub-push c96c7bfc42e46f90c84030706c00b62b8c0f1ef4
• actions/download-artifact v4.1.9@cc203385981b70ca67e1cc392babf9cc229d5806
• pypa/gh-action-pypi-publish release/v1@76f52bc884231f62b9a034ebfe128415bbaabdfc
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/upload-pages-artifact v3@56afc609e74202658d3ffba0e8f6dda462b719fa
• actions/deploy-pages v4@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e

.github/workflows/cml-images.yml

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
• docker/setup-qemu-action v2@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7
• docker/setup-buildx-action v2@885d1462b80bc1c1c7f0b00334ad271f09369c55
• docker/login-action v3@0d4c9c5ea7693da7b068278f7b52bda2a190a446
• docker/metadata-action v5@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
• docker/build-push-action v5@ca052bb54ab0790a636c9b5f226502c73d547a25
• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
• docker/setup-qemu-action v2@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7
• docker/setup-buildx-action v2@885d1462b80bc1c1c7f0b00334ad271f09369c55
• docker/login-action v3@0d4c9c5ea7693da7b068278f7b52bda2a190a446
• docker/login-action v3@0d4c9c5ea7693da7b068278f7b52bda2a190a446
• docker/metadata-action v5@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
• docker/build-push-action v5@ca052bb54ab0790a636c9b5f226502c73d547a25

.github/workflows/cml.yml

• actions/checkout v4
• iterative/setup-cml v1
• mxschmitt/action-tmate v3
• actions/checkout v4
• actions/setup-python v4
• snok/install-poetry v1
• actions/cache v3
• mxschmitt/action-tmate v3
• mxschmitt/action-tmate v3
• python 3.10

.github/workflows/colab.yml

• cameronraysmith/maximize-build-space fdf0c06b18d92be98aa64cb68ae4ea4c9bc4794d
• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
• mxschmitt/action-tmate v3@a283f9441d2d96eb62436dc46d7014f5d357ac22
• google-github-actions/auth v2@71fee32a0bb7e97b4d33d548e7d957010649d8fa
• google-github-actions/upload-cloud-storage v2@22121cd842b0d185e042e28d969925b538c33d77

.github/workflows/conda.yaml

• cameronraysmith/maximize-build-space fdf0c06b18d92be98aa64cb68ae4ea4c9bc4794d
• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48
• prefix-dev/rattler-build-action v0@6f0cd2ff475379a6da7221b22894613bb26a65ab

.github/workflows/deploy-docs-cloudflare.yaml

• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• DeterminateSystems/nix-installer-action v16@e50d5f73bfe71c2dd0aa4218de8f4afa59f8f81d
• cachix/cachix-action be5295a636153b6ad194d3245f78f8e0b78dc704
• google-github-actions/auth v2@6fc4af4b145ae7821d527454aa9bd537d1f2dc5f
• iterative/setup-dvc v1@180d52394bc746fb0bb5ca8e9e1a7a49a151742e
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48
• threeal/setup-yarn-action v2.0.0@ec8c075e62bc497968de40011c2b766f5e8f1ac5
• cloudflare/wrangler-action v3@392082e81ffbcb9ebdde27400634aa004b35ea37

.github/workflows/labeler.yml

• actions/checkout v4@692973e3d937129bcbf40652eb9f2f61becf3332
• crazy-max/ghaction-github-labeler v5.0.0@de749cf181958193cb7debf1a9c5bb28922f3e1b

.github/workflows/manuscript.yaml

• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• iterative/setup-dvc v1@180d52394bc746fb0bb5ca8e9e1a7a49a151742e
• quarto-dev/quarto-actions v2.1.9
• mxschmitt/action-tmate v3.19@e5c7151931ca95bad1c6f4190c730ecf8c7dde48
• actions/upload-artifact v4.6.2@ea165f8d65b6e75b540449e92b4886f43607fa02

.github/workflows/pr-check.yaml

• sequoia-pgp/fast-forward 042cd23fbf9d5ed1400497a106c8abe4b45408ab

.github/workflows/pr-merge.yaml

• sequoia-pgp/fast-forward 042cd23fbf9d5ed1400497a106c8abe4b45408ab

.github/workflows/run-workflow.yaml

• actions/checkout v4.2.2@11bd71901bbe5b1630ceea73d27597364c9af683
• actions/download-artifact v4.1.9@cc203385981b70ca67e1cc392babf9cc229d5806
• mxschmitt/action-tmate v3@e5c7151931ca95bad1c6f4190c730ecf8c7dde48
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1
• actions/upload-artifact v4.6.1@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1

npm

package.json

• prettier ^3.1.0
• node >=18
• yarn 4.5.0

pep621

pyproject.toml

• poetry-core >=1.6.0,<2

pip_requirements

docs/requirements.txt

reproducibility/figures/fig3/requirements.txt

reproducibility/figures/suppfig2/requirements.txt

requirements-cpu.txt

requirements-main.txt

poetry

pyproject.toml

• python >=3.11, <3.13
• adjusttext >=1.1.1
• altair >=5.3.0
• anndata >=0.10.5
• anyio >=4.3.0
• appdirs >=1.4.4
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• fsspec >=2024.3.0
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• httpx >=0.27.0
• h5py >=3.9.0
• ibis-framework >=9.2.0
• jax >=0.4.23
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• jaxtyping >=0.2.25
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• llvmlite >=0.41.1
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• rich >=13.7.1
• scanpy >=1.10.1
• scikit-learn >=1.3.1
• scipy >=1.10.1,<1.14.0
• scvelo >=0.3.2
• scvi-tools >=1.1.1
• seaborn >=0.13.2
• sparse >=0.15.4
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• sympy >=1.12
• termcolor >=2.2.0
• tiledb >=0.31.1
• torch >=2.1.2
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• trio >=0.26.0
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• vegafusion >=1.6.9
• vegafusion-python-embed >=1.6.9
• vl-convert-python >=1.6.0
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• pre-commit-hooks >=4.1.0
• pyensembl >=2.3.12
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• sphinx-markdown-builder >=0.6.6
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• myst-parser >=2.0.0
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• sphinx-copybutton >=0.5.2
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• sphinx >=7.0.1
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• dataclasses-json >=0.5.7
• dulwich >=0.21.7
• flytekit >=1.13.0
• google-api-python-client >=2.79.0
• google-cloud-storage >=2.14.0
• hydra-core >=1.3.2
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• nbformat >=5.9.2
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• pyperclip >=1.8.2
• python-dotenv >=1.0.0
• rich-click >=1.7.3
• pyensembl >=2.3.12
• pyfaidx >=0.8.1.1

terraform

reproducibility/environment/main.tf

• google 4.41.0

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