multigrate 0.0.2__tar.gz → 1.0.1__tar.gz

multigrate-1.0.1/.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

multigrate-1.0.1/.cruft.json

@@ -0,0 +1,43 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
+  "context": {
+    "cookiecutter": {
+      "project_name": "multigrate",
+      "package_name": "multigrate",
+      "project_description": "Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases",
+      "author_full_name": "Anastasia Litinetskaya",
+      "author_email": "alitinet@gmail.com",
+      "github_user": "theislab",
+      "github_repo": "multigrate",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
+    }
+  },
+  "directory": null
+}

{multigrate-0.0.2 → multigrate-1.0.1}/.editorconfig

@@ -8,5 +8,8 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
 [Makefile]
 indent_style = tab

multigrate-1.0.1/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,94 @@
+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: Versions
+      description: |
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+      placeholder: |
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47

multigrate-1.0.1/.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.

multigrate-1.0.1/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for multigrate
+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

multigrate-1.0.1/.github/workflows/build.yaml

@@ -0,0 +1,28 @@
+name: Check 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
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

multigrate-1.0.1/.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/multigrate
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

multigrate-1.0.1/.github/workflows/test.yaml

@@ -0,0 +1,61 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.12", "3.13"]
+        prerelease: [false]
+        include:
+          - python-version: "3.13"
+            prerelease: true
+            os: ubuntu-latest
+
+    name: Python ${{ matrix.python-version }}${{ matrix.prerelease && ' (pre-release)' || '' }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-glob: uv.lock
+      - name: Install dependencies
+        run: uv sync --group test
+        env:
+          UV_PRERELEASE: ${{ matrix.prerelease && 'allow' || 'disallow' }}
+      - name: Run tests
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+        run: uv run pytest --cov --cov-report=xml -v
+      - name: Upload coverage
+        uses: codecov/codecov-action@v5
+
+  check:
+    name: Tests pass
+    if: always()
+    needs: [test]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: re-actors/alls-green@release/v1
+        with:
+          jobs: ${{ toJSON(needs) }}

{multigrate-0.0.2 → multigrate-1.0.1}/.gitignore

@@ -1,30 +1,24 @@
 # Temp files
 .DS_Store
 *~
+buck-out/
 
 # Compiled files
+.venv/
 __pycache__/
+.*cache/
 
 # Distribution / packaging
-/build/
 /dist/
-/*.egg-info/
 
 # Tests and coverage
-/.pytest_cache/
-/.cache/
 /data/
+/node_modules/
+/.coverage*
 
 # docs
 /docs/generated/
 /docs/_build/
-
-# IDEs
-/.idea/
-/.vscode/
-
-# data
-*.h5ad
-
-# jupyter checkpoints
-.ipynb_checkpoints
+/docs/notebooks/data/
+/docs/notebooks/totalvi_test.ipynb
+/docs/notebooks/*.h5ad

multigrate-1.0.1/.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+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/biomejs/pre-commit
+    rev: v2.3.10
+    hooks:
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.11.1
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.14
+    hooks:
+      - id: ruff-check
+        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]

multigrate-1.0.1/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+      - uv sync --group doc
+    build:
+      html:
+        - uv run sphinx-build -M html docs docs/_build -W
+        - mv docs/_build $READTHEDOCS_OUTPUT

multigrate-1.0.1/.vscode/extensions.json

@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}

multigrate-1.0.1/.vscode/launch.json

@@ -0,0 +1,33 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}

multigrate-1.0.1/.vscode/settings.json

@@ -0,0 +1,18 @@
+{
+    "[python][json][jsonc]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "always",
+            "source.organizeImports": "always",
+        },
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}

multigrate-1.0.1/CHANGELOG.md

@@ -0,0 +1,35 @@
+# 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
+
+## [1.0.1] - 2026-06-14
+
+### Fixed
+
+- `MultiVAE(losses=None)` no longer raises `TypeError: argument of type 'NoneType' is not iterable`. `losses=None` (the documented default, meaning MSE for all modalities) now works correctly in both the model wrapper (`_multivae.py`) and the torch module (`_multivae_torch.py`).
+- `MultiVAE.load_query_data` no longer raises `AttributeError` when the reference model was trained with `integrate_on` but without an nb/zinb loss (i.e. `theta` is `None`).
+- `StratifiedSampler` (used when `integrate_on` is set) no longer silently produces zero training batches on small datasets. Training will now always produce at least one batch per group, and raises a clear `ValueError` if the batch size is too large for the data.
+- `organize_multimodal_anndatas` now preserves `.var` metadata from each modality. When the same column name appears in multiple modalities it is suffixed with the modality index (e.g. `mean_0`, `mean_1`). Fixes [#4](https://github.com/theislab/multigrate/issues/4).
+- Defensive `.get("columns", [])` in the continuous-covariate registry lookup prevents a `KeyError` with certain scvi-tools versions. Fixes [#45](https://github.com/theislab/multigrate/issues/45).
+- Removed deprecated `dtype=` argument from `anndata.AnnData()` call (anndata 0.12+).
+
+### Changed
+
+- Requires Python ≥ 3.12 (aligned with scvi-tools 1.4.3 minimum).
+- Bumped core dependencies: `scvi-tools>=1.4.3`, `anndata>=0.12`; removed `numpy<2` and `jax<0.6` upper-bound pins.
+- Migrated developer tooling from hatch to native [uv](https://docs.astral.sh/uv/). Dependency groups (`dev`, `test`, `doc`) are now declared via PEP 735 `[dependency-groups]` in `pyproject.toml`.
+- CI rewritten to use `uv sync --group test` + `uv run pytest` against Python 3.12 and 3.13.
+- ReadTheDocs build updated to use `uv sync --group doc` + `uv run sphinx-build`.
+- How the masks for missing modalities are calculated: now assume that the modality is missing when all features are zero instead of the sum over all features being <= 0 previously (only makes a difference when the input can be negative, which doesn't happen with standard single-cell modalities)
+
+### Added
+
+- support for scvi-tools >= 1.0 ([#37](https://github.com/theislab/multigrate/pull/37))
+- support for multiple NB lossed ([#34](https://github.com/theislab/multigrate/pull/34))
+- tests

{multigrate-0.0.2 → multigrate-1.0.1}/LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2022, Anastasia Litinetskaya
+Copyright (c) 2024, Anastasia Litinetskaya
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

multigrate-1.0.1/PKG-INFO

@@ -0,0 +1,157 @@
+Metadata-Version: 2.4
+Name: multigrate
+Version: 1.0.1
+Summary: Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
+Project-URL: Documentation, https://multigrate.readthedocs.io/
+Project-URL: Homepage, https://github.com/theislab/multigrate
+Project-URL: Source, https://github.com/theislab/multigrate
+Author: Anastasia Litinetskaya
+Maintainer-email: Anastasia Litinetskaya <alitinet@gmail.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, Anastasia Litinetskaya
+        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
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.12
+Requires-Dist: anndata>=0.12
+Requires-Dist: jax
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: requests
+Requires-Dist: scanpy
+Requires-Dist: scvi-tools>=1.4.3
+Requires-Dist: session-info2
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: twine>=4.0.2; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
+Requires-Dist: ipykernel; extra == 'doc'
+Requires-Dist: ipython; extra == 'doc'
+Requires-Dist: myst-nb>=1.1; extra == 'doc'
+Requires-Dist: pandas; extra == 'doc'
+Requires-Dist: setuptools; extra == 'doc'
+Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
+Requires-Dist: sphinx-book-theme>=1; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinx-tabs; extra == 'doc'
+Requires-Dist: sphinx>=8.1; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex>=1; extra == 'doc'
+Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: test
+Requires-Dist: coverage>=7.10; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Provides-Extra: tutorials
+Requires-Dist: gdown; extra == 'tutorials'
+Requires-Dist: igraph; extra == 'tutorials'
+Requires-Dist: ipywidgets; extra == 'tutorials'
+Requires-Dist: jupyterlab; extra == 'tutorials'
+Requires-Dist: leidenalg; extra == 'tutorials'
+Requires-Dist: muon; extra == 'tutorials'
+Description-Content-Type: text/markdown
+
+# Multigrate: multiomic data integration for single-cell genomics
+
+[![Tests][badge-tests]][link-tests]
+[![Documentation][badge-docs]][link-docs]
+
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/multigrate/test.yaml?branch=main
+[link-tests]: https://github.com/theislab/multigrate/actions/workflows/test.yml
+[badge-docs]: https://img.shields.io/readthedocs/multigrate
+[badge-colab]: https://colab.research.google.com/assets/colab-badge.svg
+
+## Getting started
+
+Please refer to the [documentation][link-docs]. In particular, the
+
+- [API documentation][link-api]
+
+and the tutorials:
+
+- [Paired integration and query-to-reference mapping](https://multigrate.readthedocs.io/en/latest/notebooks/paired_integration_cite-seq.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multigrate/blob/main/docs/notebooks/paired_integration_cite-seq.ipynb)
+- [Trimodal integration and query-to-reference mapping](https://multigrate.readthedocs.io/en/latest/notebooks/trimodal_integration.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multigrate/blob/main/docs/notebooks/trimodal_integration.ipynb)
+
+See the paired integration tutorial for advice on which distributions and losses to use for which modalities.
+
+## Installation
+
+You need to have Python 3.12 or newer installed on your system.
+
+### Quick start
+
+To install the latest release of `multigrate` from [PyPI][link-pypi]:
+
+```bash
+pip install multigrate
+```
+
+Or install the latest development version:
+
+```bash
+pip install git+https://github.com/theislab/multigrate.git@main
+```
+
+### Development setup
+
+For development, we recommend using [`uv`](https://docs.astral.sh/uv/) for fast dependency management:
+
+```bash
+# Clone the repository
+git clone https://github.com/theislab/multigrate.git
+cd multigrate
+
+# Install in development mode with all optional dependencies
+uv sync --all-groups
+```
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+If you found a bug, please use the [issue tracker][issue-tracker].
+
+## Citation
+
+> Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, and Fabian Theis. 2022. "Integration and querying of multimodal single-cell data with PoE-VAE." _bioRxiv_. https://doi.org/10.1101/2022.03.16.484643.
+
+## Reproducibility
+
+Code and notebooks to reproduce the results from the paper are available at https://github.com/theislab/multigrate_reproducibility.
+
+[issue-tracker]: https://github.com/theislab/multigrate/issues
+[changelog]: https://multigrate.readthedocs.io/latest/changelog.html
+[link-docs]: https://multigrate.readthedocs.io
+[link-api]: https://multigrate.readthedocs.io/latest/api.html
+[link-pypi]: https://pypi.org/project/multigrate