diff --git a/.codecov.yaml b/.codecov.yaml
new file mode 100644
index 000000000..d0c0e2917
--- /dev/null
+++ b/.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
diff --git a/.cruft.json b/.cruft.json
new file mode 100644
index 000000000..744ae8c70
--- /dev/null
+++ b/.cruft.json
@@ -0,0 +1,43 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
+  "context": {
+    "cookiecutter": {
+      "project_name": "squidpy",
+      "package_name": "squidpy",
+      "project_description": "Spatial Single Cell Analysis in Python",
+      "author_full_name": "Giovanni Palla",
+      "author_email": "giovanni.palla@helmholtz-muenchen.de",
+      "github_user": "giovp",
+      "github_repo": "squidpy",
+      "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
+}
diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 000000000..66678e378
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,15 @@
+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,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 000000000..3ca1ccbde
--- /dev/null
+++ b/.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
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 000000000..5b62547f9
--- /dev/null
+++ b/.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.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 000000000..b11e828fe
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for squidpy
+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
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
new file mode 100644
index 000000000..83e01a1ee
--- /dev/null
+++ b/.github/workflows/build.yaml
@@ -0,0 +1,33 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+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
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 000000000..b4bf7da2a
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,34 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+# 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/squidpy
+    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
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 000000000..0bd76e8cf
--- /dev/null
+++ b/.github/workflows/test.yaml
@@ -0,0 +1,103 @@
+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
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  # Get the test environment from hatch as defined in pyproject.toml.
+  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
+  # run locally and on continuous integration.
+  # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
+  # more details.
+  get-environments:
+    runs-on: ubuntu-latest
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+            | map(
+                select(.key | startswith("hatch-test"))
+                | {
+                    name: .key,
+                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                    python: .value.python
+                  }
+              )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
+  test:
+    needs: get-environments
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+    name: ${{ matrix.env.label }}
+    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.env.python }}
+          cache-dependency-glob: pyproject.toml
+      - name: create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
+      - name: run tests using hatch
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
+      - name: generate coverage report
+        run: |
+          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+          uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
+          uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
+      - name: Upload coverage
+        uses: codecov/codecov-action@v5
+
+  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
+  # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
+  check:
+    name: Tests pass in all hatch environments
+    if: always()
+    needs:
+      - get-environments
+      - test
+    runs-on: ubuntu-latest
+    steps:
+        - uses: re-actors/alls-green@release/v1
+          with:
+            jobs: ${{ toJSON(needs) }}
diff --git a/.gitignore b/.gitignore
index b6e47617d..bd24e4e00 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,129 +1,21 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
+# Temp files
+.DS_Store
+*~
+buck-out/
 
-# C extensions
-*.so
+# Compiled files
+.venv/
+__pycache__/
+.*cache/
 
 # Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
+/dist/
 
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
+# Tests and coverage
+/data/
+/node_modules/
+/.coverage*
 
-# Pyre type checker
-.pyre/
+# docs
+/docs/generated/
+/docs/_build/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 000000000..b9de3fe04
--- /dev/null
+++ b/.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: v2.2.4
+    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: v2.6.0
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.2
+    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]
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 000000000..c3f3f96fb
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,15 @@
+# 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
+    build:
+      html:
+        - uvx hatch run docs:build
+        - mv docs/_build $READTHEDOCS_OUTPUT
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 000000000..caaeb4f73
--- /dev/null
+++ b/.vscode/extensions.json
@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}
diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 000000000..36d187461
--- /dev/null
+++ b/.vscode/launch.json
@@ -0,0 +1,33 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 000000000..e034b91f7
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,18 @@
+{
+    "[python][json][jsonc]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "always",
+            "source.organizeImports": "always",
+        },
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}
diff --git a/biome.jsonc b/biome.jsonc
new file mode 100644
index 000000000..9f8f2208c
--- /dev/null
+++ b/biome.jsonc
@@ -0,0 +1,17 @@
+{
+    "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+    "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "includes": ["./.vscode/*.json", "**/*.jsonc"],
+            "json": {
+                "formatter": { "trailingCommas": "all" },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}
diff --git a/docs/_static/.gitkeep b/docs/_static/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
new file mode 100644
index 000000000..b8c8d47fa
--- /dev/null
+++ b/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;
+}
diff --git a/docs/_templates/.gitkeep b/docs/_templates/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
new file mode 100644
index 000000000..7b4a0cf87
--- /dev/null
+++ b/docs/_templates/autosummary/class.rst
@@ -0,0 +1,61 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. add toctree option to make autodoc generate the pages
+
+.. autoclass:: {{ objname }}
+
+{% block attributes %}
+{% if attributes %}
+Attributes table
+~~~~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in attributes %}
+    ~{{ name }}.{{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block methods %}
+{% if methods %}
+Methods table
+~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in methods %}
+    {%- if item != '__init__' %}
+    ~{{ name }}.{{ item }}
+    {%- endif -%}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block attributes_documentation %}
+{% if attributes %}
+Attributes
+~~~~~~~~~~
+
+{% for item in attributes %}
+
+.. autoattribute:: {{ [objname, item] | join(".") }}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
+
+{% block methods_documentation %}
+{% if methods %}
+Methods
+~~~~~~~
+
+{% for item in methods %}
+{%- if item != '__init__' %}
+
+.. automethod:: {{ [objname, item] | join(".") }}
+{%- endif -%}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
diff --git a/docs/changelog.md b/docs/changelog.md
new file mode 100644
index 000000000..d9e79ba64
--- /dev/null
+++ b/docs/changelog.md
@@ -0,0 +1,3 @@
+```{include} ../CHANGELOG.md
+
+```
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 000000000..3625ea241
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,131 @@
+# Configuration file for the Sphinx documentation builder.
+
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+import sys
+from datetime import datetime
+from importlib.metadata import metadata
+from pathlib import Path
+
+HERE = Path(__file__).parent
+sys.path.insert(0, str(HERE / "extensions"))
+
+
+# -- Project information -----------------------------------------------------
+
+# NOTE: If you installed your project in editable mode, this might be stale.
+#       If this is the case, reinstall it to refresh the metadata
+info = metadata("squidpy")
+project_name = info["Name"]
+author = info["Author"]
+copyright = f"{datetime.now():%Y}, {author}."
+version = info["Version"]
+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
+repository_url = urls["Source"]
+
+# The full version, including alpha/beta/rc tags
+release = info["Version"]
+
+bibtex_bibfiles = ["references.bib"]
+templates_path = ["_templates"]
+nitpicky = True  # Warn about broken links
+needs_sphinx = "4.0"
+
+html_context = {
+    "display_github": True,  # Integrate GitHub
+    "github_user": "giovp",
+    "github_repo": project_name,
+    "github_version": "main",
+    "conf_py_path": "/docs/",
+}
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings.
+# They can be extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = [
+    "myst_nb",
+    "sphinx_copybutton",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinxcontrib.bibtex",
+    "sphinx_autodoc_typehints",
+    "sphinx_tabs.tabs",
+    "sphinx.ext.mathjax",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "sphinxext.opengraph",
+    *[p.stem for p in (HERE / "extensions").glob("*.py")],
+]
+
+autosummary_generate = True
+autodoc_member_order = "groupwise"
+default_role = "literal"
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_use_rtype = True  # having a separate entry generally helps readability
+napoleon_use_param = True
+myst_heading_anchors = 6  # create anchors for h1-h6
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "html_image",
+    "html_admonition",
+]
+myst_url_schemes = ("http", "https", "mailto")
+nb_output_stderr = "remove"
+nb_execution_mode = "off"
+nb_merge_streams = True
+typehints_defaults = "braces"
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
+}
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+}
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_book_theme"
+html_static_path = ["_static"]
+html_css_files = ["css/custom.css"]
+
+html_title = project_name
+
+html_theme_options = {
+    "repository_url": repository_url,
+    "use_repository_button": True,
+    "path_to_docs": "docs/",
+    "navigation_with_keys": False,
+}
+
+pygments_style = "default"
+
+nitpick_ignore = [
+    # If building the documentation fails because of a missing link that is outside your control,
+    # you can add an exception to this list.
+    #     ("py:class", "igraph.Graph"),
+]
diff --git a/docs/contributing.md b/docs/contributing.md
new file mode 100644
index 000000000..699d94291
--- /dev/null
+++ b/docs/contributing.md
@@ -0,0 +1,330 @@
+# Contributing guide
+
+This document aims at summarizing the most important information for getting you started on contributing to this project.
+We assume that you are already familiar with git and with making pull requests on GitHub.
+
+For more extensive tutorials, that also cover the absolute basics,
+please refer to other resources such as the [pyopensci tutorials][],
+the [scientific Python tutorials][], or the [scanpy developer guide][].
+
+[pyopensci tutorials]: https://www.pyopensci.org/learn.html
+[scientific Python tutorials]: https://learn.scientific-python.org/development/tutorials/
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+
+:::{tip} The *hatch* project manager
+
+We highly recommend to familiarize yourself with [`hatch`][hatch].
+Hatch is a Python project manager that
+
+- manages virtual environments, separately for development, testing and building the documentation.
+  Separating the environments is useful to avoid dependency conflicts.
+- allows to run tests locally in different environments (e.g. different python versions)
+- allows to run tasks defined in `pyproject.toml`, e.g. to build documentation.
+
+While the project is setup with `hatch` in mind,
+it is still possible to use different tools to manage dependencies, such as `uv` or `pip`.
+
+:::
+
+[hatch]: https://hatch.pypa.io/latest/
+
+## Installing dev dependencies
+
+In addition to the packages needed to _use_ this package,
+you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
+
+:::::{tabs}
+::::{group-tab} Hatch
+
+On the command line, you typically interact with hatch through its command line interface (CLI).
+Running one of the following commands will automatically resolve the environments for testing and
+building the documentation in the background:
+
+```bash
+hatch test  # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
+hatch run docs:build  # defined in the table [tool.hatch.envs.docs]
+```
+
+When using an IDE such as VS Code,
+you’ll have to point the editor at the paths to the virtual environments manually.
+The environment you typically want to use as your main development environment is the `hatch-test`
+environment with the latest Python version.
+
+To get a list of all environments for your projects, run
+
+```bash
+hatch env show -i
+```
+
+This will list “Standalone” environments and a table of “Matrix” environments like the following:
+
+```
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+| Name       | Type    | Envs                     | Features | Dependencies                    | Scripts     |
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+| hatch-test | virtual | hatch-test.py3.10-stable | dev      | coverage-enable-subprocess==1.0 | cov-combine |
+|            |         | hatch-test.py3.13-stable | test     | coverage[toml]~=7.4             | cov-report  |
+|            |         | hatch-test.py3.13-pre    |          | pytest-mock~=3.12               | run         |
+|            |         |                          |          | pytest-randomly~=3.15           | run-cov     |
+|            |         |                          |          | pytest-rerunfailures~=14.0      |             |
+|            |         |                          |          | pytest-xdist[psutil]~=3.5       |             |
+|            |         |                          |          | pytest~=8.1                     |             |
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+```
+
+From the `Envs` column, select the environment name you want to use for development.
+In this example, it would be `hatch-test.py3.13-stable`.
+
+Next, create the environment with
+
+```bash
+hatch env create hatch-test.py3.13-stable
+```
+
+Then, obtain the path to the environment using
+
+```bash
+hatch env find hatch-test.py3.13-stable
+```
+
+In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
+Choose `Enter Interpreter Path` and paste the path to the virtual environment from above.
+
+In this future, this may become easier through a hatch vscode extension.
+
+::::
+
+::::{group-tab} uv
+
+A popular choice for managing virtual environments is [uv][].
+The main disadvantage compared to hatch is that it supports only a single environment per project at a time,
+which requires you to mix the dependencies for running tests and building docs.
+This can have undesired side-effects,
+such as requiring to install a lower version of a library your project depends on,
+only because an outdated sphinx plugin pins an older version.
+
+To initalize a virtual environment in the `.venv` directory of your project, simply run
+
+```bash
+uv sync --all-extras
+```
+
+The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
+
+::::
+
+::::{group-tab} Pip
+
+Pip is nowadays mostly superseded by environment manager such as [hatch][].
+However, for the sake of completeness, and since it’s ubiquitously available,
+we describe how you can manage environments manually using `pip`:
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev,test,doc]"
+```
+
+The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
+
+::::
+:::::
+
+[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+[uv]: https://docs.astral.sh/uv/
+
+## Code-style
+
+This package uses [pre-commit][] to enforce consistent code-styles.
+On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message.
+
+To enable pre-commit locally, simply run
+
+```bash
+pre-commit install
+```
+
+in the root of the repository.
+Pre-commit will automatically download all dependencies when it is run for the first time.
+
+Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
+If you didn’t run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+
+If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
+
+```bash
+git pull --rebase
+```
+
+to integrate the changes into yours.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
+
+Finally, most editors have an _autoformat on save_ feature.
+Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
+
+[pre-commit]: https://pre-commit.com/
+[pre-commit.ci]: https://pre-commit.ci/
+[ruff-editors]: https://docs.astral.sh/ruff/integrations/
+[biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
+
+(writing-tests)=
+
+## Writing tests
+
+This package uses [pytest][] for automated testing.
+Please write {doc}`scanpy:dev/testing` for every function added to the package.
+
+Most IDEs integrate with pytest and provide a GUI to run tests.
+Just point yours to one of the environments returned by
+
+```bash
+hatch env create hatch-test  # create test environments for all supported versions
+hatch env find hatch-test  # list all possible test environment paths
+```
+
+Alternatively, you can run all tests from the command line by executing
+
+:::::{tabs}
+::::{group-tab} Hatch
+
+```bash
+hatch test  # test with the highest supported Python version
+# or
+hatch test --all  # test with all supported Python versions
+```
+
+::::
+
+::::{group-tab} uv
+
+```bash
+uv run pytest
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
+pytest
+```
+
+::::
+:::::
+
+in the root of the repository.
+
+[pytest]: https://docs.pytest.org/
+
+### Continuous integration
+
+Continuous integration via GitHub actions will automatically run the tests on all pull requests and test
+against the minimum and maximum supported Python version.
+
+Additionally, there’s a CI job that tests against pre-releases of all dependencies (if there are any).
+The purpose of this check is to detect incompatibilities of new package versions early on and
+gives you time to fix the issue or reach out to the developers of the dependency before the package
+is released to a wider audience.
+
+The CI job is defined in `.github/workflows/test.yaml`,
+however the single point of truth for CI jobs is the Hatch test matrix defined in `pyproject.toml`.
+This means that local testing via hatch and remote testing on CI tests against the same python versions and uses the same environments.
+
+## Publishing a release
+
+### Updating the version number
+
+Before making a release, you need to update the version number in the `pyproject.toml` file.
+Please adhere to [Semantic Versioning][semver], in brief
+
+> Given a version number MAJOR.MINOR.PATCH, increment the:
+>
+> 1. MAJOR version when you make incompatible API changes,
+> 2. MINOR version when you add functionality in a backwards compatible manner, and
+> 3. PATCH version when you make backwards compatible bug fixes.
+>
+> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
+
+Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
+Specify `vX.X.X` as a tag name and create a release.
+For more information, see [managing GitHub releases][].
+This will automatically create a git tag and trigger a Github workflow that creates a release on [PyPI][].
+
+[semver]: https://semver.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
+[pypi]: https://pypi.org/
+
+## Writing documentation
+
+Please write documentation for new or changed features and use-cases.
+This project uses [sphinx][] with the following features:
+
+- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+
+See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
+
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
+
+### Tutorials with myst-nb and jupyter notebooks
+
+The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
+Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
+It is your responsibility to update and re-run the notebook whenever necessary.
+
+If you are interested in automatically running notebooks as part of the continuous integration,
+please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
+
+[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
+
+#### Hints
+
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`.
+  Only if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control,
+  you can add an entry to the `nitpick_ignore` list in `docs/conf.py`
+
+(docs-building)=
+
+### Building the docs locally
+
+:::::{tabs}
+::::{group-tab} Hatch
+
+```bash
+hatch run docs:build
+hatch run docs:open
+```
+
+::::
+
+::::{group-tab} uv
+
+```bash
+cd docs
+uv run sphinx-build -M html . _build -W
+(xdg-)open _build/html/index.html
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
+cd docs
+sphinx-build -M html . _build -W
+(xdg-)open _build/html/index.html
+```
+
+::::
+:::::
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
new file mode 100644
index 000000000..0fbffefe3
--- /dev/null
+++ b/docs/extensions/typed_returns.py
@@ -0,0 +1,32 @@
+# code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
+# with some minor adjustment
+from __future__ import annotations
+
+import re
+from collections.abc import Generator, Iterable
+
+from sphinx.application import Sphinx
+from sphinx.ext.napoleon import NumpyDocstring
+
+
+def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
+    for line in lines:
+        if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
+        else:
+            yield line
+
+
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
+    lines_raw = self._dedent(self._consume_to_next_section())
+    if lines_raw[0] == ":":
+        del lines_raw[0]
+    lines = self._format_block(":returns: ", list(_process_return(lines_raw)))
+    if lines and lines[-1]:
+        lines.append("")
+    return lines
+
+
+def setup(app: Sphinx):
+    """Set app."""
+    NumpyDocstring._parse_returns_section = _parse_returns_section
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..9e8740c51
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,154 @@
+[build-system]
+build-backend = "hatchling.build"
+requires = [ "hatchling" ]
+
+[project]
+name = "squidpy"
+version = "0.0.1"
+description = "Spatial Single Cell Analysis in Python"
+readme = "README.md"
+license = { file = "LICENSE" }
+maintainers = [
+  { name = "Giovanni Palla", email = "giovanni.palla@helmholtz-muenchen.de" },
+]
+authors = [
+  { name = "Giovanni Palla" },
+]
+requires-python = ">=3.10"
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+  "anndata",
+  # for debug logging (referenced from the issue template)
+  "session-info2",
+]
+optional-dependencies.dev = [
+  "pre-commit",
+  "twine>=4.0.2",
+]
+optional-dependencies.doc = [
+  "docutils>=0.8,!=0.18.*,!=0.19.*",
+  "ipykernel",
+  "ipython",
+  "myst-nb>=1.1",
+  "pandas",
+  # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+  "setuptools",
+  "sphinx>=8.1",
+  "sphinx-autodoc-typehints",
+  "sphinx-book-theme>=1",
+  "sphinx-copybutton",
+  "sphinx-tabs",
+  "sphinxcontrib-bibtex>=1",
+  "sphinxext-opengraph",
+]
+optional-dependencies.test = [
+  "coverage>=7.10",
+  "pytest",
+  "pytest-cov",     # For VS Code’s coverage functionality
+]
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://squidpy.readthedocs.io/"
+urls.Homepage = "https://github.com/giovp/squidpy"
+urls.Source = "https://github.com/giovp/squidpy"
+
+[tool.hatch.envs.default]
+installer = "uv"
+features = [ "dev" ]
+
+[tool.hatch.envs.docs]
+features = [ "doc" ]
+scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
+scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+scripts.clean = "git clean -fdX -- {args:docs}"
+
+# Test the lowest and highest supported Python versions with normal deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "stable" ]
+python = [ "3.10", "3.13" ]
+
+# Test the newest supported Python version also with pre-release deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "pre" ]
+python = [ "3.13" ]
+
+[tool.hatch.envs.hatch-test]
+features = [ "dev", "test" ]
+
+[tool.hatch.envs.hatch-test.overrides]
+# If the matrix variable `deps` is set to "pre",
+# set the environment variable `UV_PRERELEASE` to "allow".
+matrix.deps.env-vars = [
+  { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+]
+
+[tool.ruff]
+line-length = 120
+src = [ "src" ]
+extend-include = [ "*.ipynb" ]
+
+format.docstring-code-format = true
+
+lint.select = [
+  "B",      # flake8-bugbear
+  "BLE",    # flake8-blind-except
+  "C4",     # flake8-comprehensions
+  "D",      # pydocstyle
+  "E",      # Error detected by Pycodestyle
+  "F",      # Errors detected by Pyflakes
+  "I",      # isort
+  "RUF100", # Report unused noqa directives
+  "TID",    # flake8-tidy-imports
+  "UP",     # pyupgrade
+  "W",      # Warning detected by Pycodestyle
+]
+lint.ignore = [
+  "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
+  "D100", # Missing docstring in public module
+  "D104", # Missing docstring in public package
+  "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
+  "D107", # Missing docstring in __init__
+  # Disable one in each pair of mutually incompatible rules
+  "D203", # We don’t want a blank line before a class docstring
+  "D213", # <> We want docstrings to start immediately after the opening triple quote
+  "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
+  "D401", # First line should be in imperative mood; try rephrasing
+  "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
+  "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+  "E741", # allow I, O, l as variable names -> I is the identity matrix
+]
+lint.per-file-ignores."*/__init__.py" = [ "F401" ]
+lint.per-file-ignores."docs/*" = [ "I" ]
+lint.per-file-ignores."tests/*" = [ "D" ]
+lint.pydocstyle.convention = "numpy"
+
+[tool.pytest.ini_options]
+testpaths = [ "tests" ]
+xfail_strict = true
+addopts = [
+  "--import-mode=importlib", # allow using test files with same name
+]
+
+[tool.coverage.run]
+source = [ "squidpy" ]
+patch = [ "subprocess" ]
+omit = [
+  "**/test_*.py",
+]
+
+[tool.cruft]
+skip = [
+  "tests",
+  "src/**/__init__.py",
+  "src/**/basic.py",
+  "docs/api.md",
+  "docs/changelog.md",
+  "docs/references.bib",
+  "docs/references.md",
+  "docs/notebooks/example.ipynb",
+]