scib-rapids 0.1.0__tar.gz

scib_rapids-0.1.0/.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

scib_rapids-0.1.0/.editorconfig

@@ -0,0 +1,18 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[.cruft.json]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

scib_rapids-0.1.0/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,33 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+            available datasets or to share a subset of your data.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Version information
+      description: |
+        Please paste below the output of
+
+        ```python
+        import session_info
+        session_info.show(html=False, dependencies=True)
+        ```

scib_rapids-0.1.0/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about "How to do X", please ask them here.

scib_rapids-0.1.0/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for scib-rapids
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

scib_rapids-0.1.0/.github/workflows/build.yaml

@@ -0,0 +1,29 @@
+name: Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip wheel twine build
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check --strict dist/*.whl

scib_rapids-0.1.0/.github/workflows/release.yaml

@@ -0,0 +1,29 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/scib-rapids
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

scib_rapids-0.1.0/.github/workflows/test.yaml

@@ -0,0 +1,62 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.11", "3.12", "3.13"]
+
+    name: Integration
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+
+      - name: Install dependencies
+        run: |
+          pip install ".[dev,test]"
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

scib_rapids-0.1.0/.gitignore

@@ -0,0 +1,34 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+.venv-*/
+__pycache__/
+.mypy_cache/
+.ruff_cache/
+
+# Distribution / packaging
+/build/
+/dist/
+/*.egg-info/
+
+# Tests and coverage
+/.pytest_cache/
+/.cache/
+/data/
+
+# docs
+/docs/generated/
+/docs/_build/
+
+# IDEs
+/.idea/
+/.vscode/
+
+# node
+/node_modules/
+
+docs/notebooks/data/

scib_rapids-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.6
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.9.1
+    hooks:
+      - id: nbstripout

scib_rapids-0.1.0/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.11"
+sphinx:
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: false
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

scib_rapids-0.1.0/CHANGELOG.md

@@ -0,0 +1,20 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/en/1.0.0/
+[semantic versioning]: https://semver.org/spec/v2.0.0.html
+
+## 0.1.0 (unreleased)
+
+### Added
+
+- Initial release with GPU-accelerated metrics using CuPy/RAPIDS.
+- All metrics from scib-metrics ported: silhouette, LISI, kBET, NMI/ARI, graph connectivity, isolated labels, PCR comparison, BRAS.
+- CuPy-based utility functions: cdist, pdist_squareform, PCA, KMeans, silhouette_samples, Simpson index.
+- NeighborsResults dataclass with sparse graph properties.
+- Unit tests validating correctness against scikit-learn.
+- Benchmark test suite comparing runtime against scib-metrics.

scib_rapids-0.1.0/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, Maarten de Vries
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

scib_rapids-0.1.0/PKG-INFO

@@ -0,0 +1,155 @@
+Metadata-Version: 2.4
+Name: scib-rapids
+Version: 0.1.0
+Summary: GPU-accelerated single-cell integration benchmarking metrics using RAPIDS (cuML, CuPy)
+Project-URL: Documentation, https://scib-rapids.readthedocs.io/
+Project-URL: Source, https://github.com/maarten-devries/scib-rapids
+Project-URL: Home-page, https://github.com/maarten-devries/scib-rapids
+Author: Maarten de Vries
+Maintainer: Maarten de Vries
+License: BSD 3-Clause License
+        
+        Copyright (c) 2026, Maarten de Vries
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Requires-Python: >=3.11
+Requires-Dist: anndata
+Requires-Dist: cupy-cuda12x>=13.0
+Requires-Dist: igraph>0.9.0
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pynndescent
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: umap-learn>=0.5.0
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: twine>=4.0.2; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: ipykernel; extra == 'doc'
+Requires-Dist: ipython; extra == 'doc'
+Requires-Dist: myst-nb; extra == 'doc'
+Requires-Dist: pybtex-docutils>=1.0.0; extra == 'doc'
+Requires-Dist: scanpydoc[typehints]>=0.7.4; extra == 'doc'
+Requires-Dist: sphinx-book-theme>=1.0; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinx>=4; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex>=2.6; extra == 'doc'
+Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: harmonypy; extra == 'test'
+Requires-Dist: joblib; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: scib-metrics>=0.5; extra == 'test'
+Description-Content-Type: text/markdown
+
+# scib-rapids
+
+[![PyPI][badge-pypi]][link-pypi]
+[![Docs][badge-docs]][link-docs]
+[![Build][badge-build]][link-build]
+[![Coverage][badge-cov]][link-cov]
+[![Discourse][badge-discourse]][link-discourse]
+[![Chat][badge-zulip]][link-zulip]
+
+[badge-pypi]: https://img.shields.io/pypi/v/scib-rapids.svg
+[link-pypi]: https://pypi.org/project/scib-rapids
+[badge-docs]: https://readthedocs.org/projects/scib-rapids/badge/?version=latest
+[link-docs]: https://scib-rapids.readthedocs.io/en/latest/?badge=latest
+[badge-build]: https://github.com/maarten-devries/scib-rapids/actions/workflows/test.yaml/badge.svg
+[link-build]: https://github.com/maarten-devries/scib-rapids/actions/workflows/test.yaml/
+[badge-cov]: https://codecov.io/gh/maarten-devries/scib-rapids/branch/main/graph/badge.svg
+[link-cov]: https://codecov.io/gh/maarten-devries/scib-rapids
+[badge-discourse]: https://img.shields.io/discourse/posts?color=yellow&logo=discourse&server=https%3A%2F%2Fdiscourse.scverse.org
+[link-discourse]: https://discourse.scverse.org/
+[badge-zulip]: https://img.shields.io/badge/zulip-join_chat-brightgreen.svg
+[link-zulip]: https://scverse.zulipchat.com/
+
+GPU-accelerated metrics for benchmarking single-cell integration outputs using RAPIDS (cuML, CuPy).
+
+This package provides the same metrics as [scib-metrics](https://github.com/YosefLab/scib-metrics) but replaces JAX with [RAPIDS](https://rapids.ai/) (CuPy, cuML) for GPU acceleration. All implementations leverage CuPy for device-level computation on NVIDIA GPUs.
+
+## Metrics
+
+- **Silhouette**: `silhouette_label`, `silhouette_batch`, `bras`
+- **LISI**: `lisi_knn`, `ilisi_knn`, `clisi_knn`
+- **kBET**: `kbet`, `kbet_per_label`
+- **Clustering**: `nmi_ari_cluster_labels_kmeans`, `nmi_ari_cluster_labels_leiden`
+- **Graph connectivity**: `graph_connectivity`
+- **Isolated labels**: `isolated_labels`
+- **PCR comparison**: `pcr_comparison`
+
+## Getting started
+
+Please refer to the [documentation][link-docs].
+
+## Installation
+
+You need to have Python 3.11 or newer and a CUDA-capable GPU. We recommend installing in a [conda](https://docs.conda.io/en/latest/miniconda.html) environment with RAPIDS pre-installed.
+
+1. Install the latest release on PyPI:
+
+```bash
+pip install scib-rapids
+```
+
+2. Install the latest development version:
+
+```bash
+pip install git+https://github.com/maarten-devries/scib-rapids.git@main
+```
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+For questions and help requests, you can reach out in the [scverse Discourse][link-discourse].
+If you found a bug, please use the [issue tracker][issue-tracker].
+
+## Citation
+
+If you use `scib-rapids`, please cite the original single-cell integration benchmarking work:
+
+```bibtex
+@article{luecken2022benchmarking,
+  title={Benchmarking atlas-level data integration in single-cell genomics},
+  author={Luecken, Malte D and B{\"u}ttner, Maren and Chaichoompu, Kridsadakorn and Danese, Anna and Interlandi, Marta and M{\"u}ller, Michaela F and Strobl, Daniel C and Zappia, Luke and Dugas, Martin and Colom{\'e}-Tatch{\'e}, Maria and others},
+  journal={Nature methods},
+  volume={19},
+  number={1},
+  pages={41--50},
+  year={2022},
+  publisher={Nature Publishing Group}
+}
+```
+
+[issue-tracker]: https://github.com/maarten-devries/scib-rapids/issues
+[changelog]: https://scib-rapids.readthedocs.io/en/latest/changelog.html

scib_rapids-0.1.0/README.md

@@ -0,0 +1,84 @@
+# scib-rapids
+
+[![PyPI][badge-pypi]][link-pypi]
+[![Docs][badge-docs]][link-docs]
+[![Build][badge-build]][link-build]
+[![Coverage][badge-cov]][link-cov]
+[![Discourse][badge-discourse]][link-discourse]
+[![Chat][badge-zulip]][link-zulip]
+
+[badge-pypi]: https://img.shields.io/pypi/v/scib-rapids.svg
+[link-pypi]: https://pypi.org/project/scib-rapids
+[badge-docs]: https://readthedocs.org/projects/scib-rapids/badge/?version=latest
+[link-docs]: https://scib-rapids.readthedocs.io/en/latest/?badge=latest
+[badge-build]: https://github.com/maarten-devries/scib-rapids/actions/workflows/test.yaml/badge.svg
+[link-build]: https://github.com/maarten-devries/scib-rapids/actions/workflows/test.yaml/
+[badge-cov]: https://codecov.io/gh/maarten-devries/scib-rapids/branch/main/graph/badge.svg
+[link-cov]: https://codecov.io/gh/maarten-devries/scib-rapids
+[badge-discourse]: https://img.shields.io/discourse/posts?color=yellow&logo=discourse&server=https%3A%2F%2Fdiscourse.scverse.org
+[link-discourse]: https://discourse.scverse.org/
+[badge-zulip]: https://img.shields.io/badge/zulip-join_chat-brightgreen.svg
+[link-zulip]: https://scverse.zulipchat.com/
+
+GPU-accelerated metrics for benchmarking single-cell integration outputs using RAPIDS (cuML, CuPy).
+
+This package provides the same metrics as [scib-metrics](https://github.com/YosefLab/scib-metrics) but replaces JAX with [RAPIDS](https://rapids.ai/) (CuPy, cuML) for GPU acceleration. All implementations leverage CuPy for device-level computation on NVIDIA GPUs.
+
+## Metrics
+
+- **Silhouette**: `silhouette_label`, `silhouette_batch`, `bras`
+- **LISI**: `lisi_knn`, `ilisi_knn`, `clisi_knn`
+- **kBET**: `kbet`, `kbet_per_label`
+- **Clustering**: `nmi_ari_cluster_labels_kmeans`, `nmi_ari_cluster_labels_leiden`
+- **Graph connectivity**: `graph_connectivity`
+- **Isolated labels**: `isolated_labels`
+- **PCR comparison**: `pcr_comparison`
+
+## Getting started
+
+Please refer to the [documentation][link-docs].
+
+## Installation
+
+You need to have Python 3.11 or newer and a CUDA-capable GPU. We recommend installing in a [conda](https://docs.conda.io/en/latest/miniconda.html) environment with RAPIDS pre-installed.
+
+1. Install the latest release on PyPI:
+
+```bash
+pip install scib-rapids
+```
+
+2. Install the latest development version:
+
+```bash
+pip install git+https://github.com/maarten-devries/scib-rapids.git@main
+```
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+For questions and help requests, you can reach out in the [scverse Discourse][link-discourse].
+If you found a bug, please use the [issue tracker][issue-tracker].
+
+## Citation
+
+If you use `scib-rapids`, please cite the original single-cell integration benchmarking work:
+
+```bibtex
+@article{luecken2022benchmarking,
+  title={Benchmarking atlas-level data integration in single-cell genomics},
+  author={Luecken, Malte D and B{\"u}ttner, Maren and Chaichoompu, Kridsadakorn and Danese, Anna and Interlandi, Marta and M{\"u}ller, Michaela F and Strobl, Daniel C and Zappia, Luke and Dugas, Martin and Colom{\'e}-Tatch{\'e}, Maria and others},
+  journal={Nature methods},
+  volume={19},
+  number={1},
+  pages={41--50},
+  year={2022},
+  publisher={Nature Publishing Group}
+}
+```
+
+[issue-tracker]: https://github.com/maarten-devries/scib-rapids/issues
+[changelog]: https://scib-rapids.readthedocs.io/en/latest/changelog.html

scib_rapids-0.1.0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

scib_rapids-0.1.0/docs/_static/css/custom.css

@@ -0,0 +1,4 @@
+/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
+div.cell_output table.dataframe {
+    font-size: 0.8em;
+}