diff --git a/.bumpversion.cfg b/.bumpversion.cfg
deleted file mode 100644
index fdba9e4..0000000
--- a/.bumpversion.cfg
+++ /dev/null
@@ -1,8 +0,0 @@
-[bumpversion]
-current_version = 0.0.1
-tag = True
-commit = True
-
-[bumpversion:file:./pyproject.toml]
-search = version = "{current_version}"
-replace = version = "{new_version}"
diff --git a/.codecov.yaml b/.codecov.yaml
index 829e56c..d0c0e29 100644
--- a/.codecov.yaml
+++ b/.codecov.yaml
@@ -1,17 +1,17 @@
 # Based on pydata/xarray
 codecov:
-    require_ci_to_pass: no
+  require_ci_to_pass: no
 
 coverage:
-    status:
-        project:
-            default:
-                # Require 1% coverage, i.e., always succeed
-                target: 1
-        patch: false
-        changes: false
+  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
+  layout: diff, flags, files
+  behavior: once
+  require_base: no
diff --git a/.cruft.json b/.cruft.json
index 34b6f48..367a8e0 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,23 +1,31 @@
 {
-    "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "7cc5403b05e299d7a4bb169c2bd8c27a2a7676f3",
-    "context": {
-        "cookiecutter": {
-            "project_name": "infercnvpy",
-            "package_name": "infercnvpy",
-            "project_description": "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. ",
-            "author_full_name": "Gregor Sturm",
-            "author_email": "mail@gregor-sturm.de",
-            "github_user": "grst",
-            "project_repo": "https://github.com/icbi-lab/infercnvpy",
-            "license": "BSD 3-Clause License",
-            "_copy_without_render": [
-                ".github/workflows/**.yaml",
-                "docs/_templates/autosummary/**.rst"
-            ],
-            "_template": "https://github.com/scverse/cookiecutter-scverse"
-        }
-    },
-    "directory": null,
-    "checkout": "v0.1.3"
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "497afeaf179fe5c1144c4503046efa494586cc3d",
+  "context": {
+    "cookiecutter": {
+      "project_name": "infercnvpy",
+      "package_name": "infercnvpy",
+      "project_description": "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. ",
+      "author_full_name": "Gregor Sturm",
+      "author_email": "mail@gregor-sturm.de",
+      "github_user": "grst",
+      "github_repo": "infercnvpy",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "497afeaf179fe5c1144c4503046efa494586cc3d"
+    }
+  },
+  "directory": null,
+  "checkout": "test4"
 }
diff --git a/.editorconfig b/.editorconfig
index 2fe0ce0..66678e3 100644
--- a/.editorconfig
+++ b/.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
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 9dfd4ac..3ca1ccb 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,88 +2,93 @@ 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 procecure.
-                * 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: 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: 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
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of packages.
 
-              ```python
-              import session_info
-              session_info.show(html=False, dependencies=True)
-              ```
-          placeholder: |
-              -----
-              anndata             0.8.0rc2.dev27+ge524389
-              session_info        1.0.0
-              -----
-              asttokens           NA
-              awkward             1.8.0
-              backcall            0.2.0
-              cython_runtime      NA
-              dateutil            2.8.2
-              debugpy             1.6.0
-              decorator           5.1.1
-              entrypoints         0.4
-              executing           0.8.3
-              h5py                3.7.0
-              ipykernel           6.15.0
-              jedi                0.18.1
-              mpl_toolkits        NA
-              natsort             8.1.0
-              numpy               1.22.4
-              packaging           21.3
-              pandas              1.4.2
-              parso               0.8.3
-              pexpect             4.8.0
-              pickleshare         0.7.5
-              pkg_resources       NA
-              prompt_toolkit      3.0.29
-              psutil              5.9.1
-              ptyprocess          0.7.0
-              pure_eval           0.2.2
-              pydev_ipython       NA
-              pydevconsole        NA
-              pydevd              2.8.0
-              pydevd_file_utils   NA
-              pydevd_plugins      NA
-              pydevd_tracing      NA
-              pygments            2.12.0
-              pytz                2022.1
-              scipy               1.8.1
-              setuptools          62.5.0
-              setuptools_scm      NA
-              six                 1.16.0
-              stack_data          0.3.0
-              tornado             6.1
-              traitlets           5.3.0
-              wcwidth             0.2.5
-              zmq                 23.1.0
-              -----
-              IPython             8.4.0
-              jupyter_client      7.3.4
-              jupyter_core        4.10.0
-              -----
-              Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
-              Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
-              -----
-              Session information updated at 2022-07-07 17:55
+        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
index 5cad625..5b62547 100644
--- a/.github/ISSUE_TEMPLATE/config.yml
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,5 +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.
+  - 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
index 26123f3..473785f 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -2,10 +2,10 @@ name: Feature request
 description: Propose a new feature for infercnvpy
 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
+  - 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
index 0242943..e822177 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -1,23 +1,32 @@
 name: Check Build
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -e {0} # -e to fail on error
 
 jobs:
-    package:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v2
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.10"
-            - 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
+  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 0000000..885c3b0
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,33 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+defaults:
+  run:
+    shell: bash -e {0} # -e to fail on error
+
+# 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/infercnvpy
+    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/sync.yaml b/.github/workflows/sync.yaml
deleted file mode 100644
index 5219499..0000000
--- a/.github/workflows/sync.yaml
+++ /dev/null
@@ -1,46 +0,0 @@
-name: Sync Template
-
-on:
-    workflow_dispatch:
-    schedule:
-        - cron: "0 2 * * *" # every night at 2:00 UTC
-
-jobs:
-    sync:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v2
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
-            - name: Install dependencies
-              # for now, pin cookiecutter version, due to https://github.com/cruft/cruft/issues/166
-              run: python -m pip install --upgrade cruft "cookiecutter<2" pre-commit toml
-            - name: Find Latest Tag
-              uses: oprypin/find-latest-tag@v1.1.0
-              id: get-latest-tag
-              with:
-                  repository: scverse/cookiecutter-scverse
-                  releases-only: false
-                  sort-tags: true
-                  regex: '^v\d+\.\d+\.\d+$' # vX.X.X
-            - name: Sync
-              run: |
-                  cruft update --checkout ${{ steps.get-latest-tag.outputs.tag }} --skip-apply-ask --project-dir .
-            - name: Create Pull Request
-              uses: peter-evans/create-pull-request@v4
-              with:
-                  commit-message: Automated template update from cookiecutter-scverse
-                  branch: template-update
-                  title: Automated template update from cookiecutter-scverse
-                  body: |
-                      A new version of the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse/releases)
-                      got released. This PR adds all new changes to your repository and helps to to stay in sync with
-                      the latest best-practice template maintained by the scverse team.
-
-                      **If a merge conflict arised, a `.rej` file with the rejected patch is generated. You'll need to
-                      manually merge these changes.**
-
-                      For more information about the template sync, please refer to the
-                      [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).
diff --git a/.github/workflows/test.yaml.rej b/.github/workflows/test.yaml.rej
new file mode 100644
index 0000000..a1d93b3
--- /dev/null
+++ b/.github/workflows/test.yaml.rej
@@ -0,0 +1,115 @@
+diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml	(rejected hunks)
+@@ -1,62 +1,58 @@
+ name: Test
+ 
+ on:
+-    push:
+-        branches: [main]
+-    pull_request:
+-        branches: [main]
++  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:
++    shell: bash -e {0} # -e to fail on error
+ 
+ jobs:
+-    test:
+-        runs-on: ${{ matrix.os }}
+-        defaults:
+-            run:
+-                shell: bash -e {0} # -e to fail on error
+-
+-        strategy:
+-            fail-fast: false
+-            matrix:
+-                python: ["3.8", "3.10"]
+-                os: [ubuntu-latest]
++  test:
++    runs-on: ${{ matrix.os }}
++
++    strategy:
++      fail-fast: false
++      matrix:
++        include:
++          - os: ubuntu-latest
++            python: "3.10"
++          - os: ubuntu-latest
++            python: "3.12"
++          - os: ubuntu-latest
++            python: "3.12"
++            pip-flags: "--pre"
++            name: PRE-RELEASE DEPENDENCIES
++
++    name: ${{ matrix.name }} Python ${{ matrix.python }}
++
++    env:
++      OS: ${{ matrix.os }}
++      PYTHON: ${{ matrix.python }}
+ 
++    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: run tests using hatch
+         env:
+-            OS: ${{ matrix.os }}
+-            PYTHON: ${{ matrix.python }}
+-
+-        steps:
+-            - uses: actions/checkout@v2
+-            - name: Set up Python ${{ matrix.python }}
+-              uses: actions/setup-python@v2
+-              with:
+-                  python-version: ${{ matrix.python }}
+-
+-            - name: Get pip cache dir
+-              id: pip-cache-dir
+-              run: |
+-                  echo "::set-output name=dir::$(pip cache dir)"
+-            - name: Restore pip cache
+-              uses: actions/cache@v2
+-              with:
+-                  path: ${{ steps.pip-cache-dir.outputs.dir }}
+-                  key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
+-                  restore-keys: |
+-                      pip-${{ runner.os }}-${{ env.pythonLocation }}-
+-            - name: Install test dependencies
+-              run: |
+-                  python -m pip install --upgrade pip wheel
+-                  pip install codecov
+-            - name: Install dependencies
+-              run: |
+-                  pip install ".[dev,test]"
+-            - name: Test
+-              env:
+-                  MPLBACKEND: agg
+-                  PLATFORM: ${{ matrix.os }}
+-                  DISPLAY: :42
+-              run: |
+-                  pytest -v --cov --color=yes
+-            - name: Upload coverage
+-              env:
+-                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
+-              run: |
+-                  codecov --required --flags=unittests
++          MPLBACKEND: agg
++          PLATFORM: ${{ matrix.os }}
++          DISPLAY: :42
++        run: uvx hatch test --cover --python ${{ matrix.python }}
++      - name: Upload coverage
++        uses: codecov/codecov-action@v4
diff --git a/.gitignore b/.gitignore
index 7bb0bd5..31e10b3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,24 +1,20 @@
 # 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/
 
 # docs
 /docs/generated/
 /docs/_build/
-
-# IDEs
-/.idea/
-/.vscode/
diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej
new file mode 100644
index 0000000..88a5d7d
--- /dev/null
+++ b/.pre-commit-config.yaml.rej
@@ -0,0 +1,123 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -1,79 +1,47 @@
+ fail_fast: false
+ default_language_version:
+-    python: python3
++  python: python3
+ default_stages:
+-    - pre-commit
+-    - pre-push
++  - pre-commit
++  - pre-push
+ minimum_pre_commit_version: 2.16.0
+ repos:
+-    - repo: https://github.com/psf/black
+-      rev: 25.1.0
+-      hooks:
+-          - id: black
+-    - repo: https://github.com/pre-commit/mirrors-prettier
+-      rev: v4.0.0-alpha.8
+-      hooks:
+-          - id: prettier
+-    - repo: https://github.com/asottile/blacken-docs
+-      rev: 1.19.1
+-      hooks:
+-          - id: blacken-docs
+-    - repo: https://github.com/PyCQA/isort
+-      rev: 6.0.1
+-      hooks:
+-          - id: isort
+-    - repo: https://github.com/asottile/yesqa
+-      rev: v1.5.0
+-      hooks:
+-          - id: yesqa
+-            additional_dependencies:
+-                - flake8-tidy-imports
+-                - flake8-docstrings
+-                - flake8-rst-docstrings
+-                - flake8-comprehensions
+-                - flake8-bugbear
+-                - flake8-blind-except
+-    - repo: https://github.com/pre-commit/pre-commit-hooks
+-      rev: v5.0.0
+-      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
+-    - repo: https://github.com/myint/autoflake
+-      rev: v2.3.1
+-      hooks:
+-          - id: autoflake
+-            args:
+-                - --in-place
+-                - --remove-all-unused-imports
+-                - --remove-unused-variable
+-                - --ignore-init-module-imports
+-    - repo: https://github.com/PyCQA/flake8
+-      rev: 7.2.0
+-      hooks:
+-          - id: flake8
+-            additional_dependencies:
+-                - flake8-tidy-imports
+-                - flake8-docstrings
+-                - flake8-rst-docstrings
+-                - flake8-comprehensions
+-                - flake8-bugbear
+-                - flake8-blind-except
+-    - repo: https://github.com/asottile/pyupgrade
+-      rev: v3.19.1
+-      hooks:
+-          - id: pyupgrade
+-            args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+-    - 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$'
++  - repo: https://github.com/biomejs/pre-commit
++    rev: v1.9.4
++    hooks:
++      - id: biome-format
++        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
++  - repo: https://github.com/tox-dev/pyproject-fmt
++    rev: v2.5.1
++    hooks:
++      - id: pyproject-fmt
++  - repo: https://github.com/astral-sh/ruff-pre-commit
++    rev: v0.11.2
++    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: v5.0.0
++    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$'
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 9e5d5fa..69897c3 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,16 +1,16 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-    os: ubuntu-20.04
-    tools:
-        python: "3.10"
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
 sphinx:
-    configuration: docs/conf.py
-    # disable this for more lenient docs builds
-    fail_on_warning: true
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: true
 python:
-    install:
-        - method: pip
-          path: .
-          extra_requirements:
-              - doc
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 0000000..caaeb4f
--- /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 0000000..36d1874
--- /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/CHANGELOG.md.rej b/CHANGELOG.md.rej
new file mode 100644
index 0000000..512112b
--- /dev/null
+++ b/CHANGELOG.md.rej
@@ -0,0 +1,7 @@
+diff a/CHANGELOG.md b/CHANGELOG.md	(rejected hunks)
+@@ -12,4 +12,4 @@ and this project adheres to [Semantic Versioning][].
+ 
+ ### Added
+ 
+--   Basic tool, preprocessing and plotting functions
++- Basic tool, preprocessing and plotting functions
diff --git a/README.md.rej b/README.md.rej
new file mode 100644
index 0000000..9b39424
--- /dev/null
+++ b/README.md.rej
@@ -0,0 +1,69 @@
+diff a/README.md b/README.md	(rejected hunks)
+@@ -1,29 +1,27 @@
+ # infercnvpy
+ 
+-[![Tests][badge-tests]][link-tests]
+-[![Documentation][badge-docs]][link-docs]
++[![Tests][badge-tests]][tests]
++[![Documentation][badge-docs]][documentation]
+ 
+ [badge-tests]: https://img.shields.io/github/actions/workflow/status/grst/infercnvpy/test.yaml?branch=main
+-[link-tests]: https://github.com/icbi-lab/infercnvpy/actions/workflows/test.yml
+ [badge-docs]: https://img.shields.io/readthedocs/infercnvpy
+ 
+ Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. 
+ 
+ ## Getting started
+ 
+-Please refer to the [documentation][link-docs]. In particular, the
+-
+--   [API documentation][link-api].
++Please refer to the [documentation][],
++in particular, the [API documentation][].
+ 
+ ## Installation
+ 
+-You need to have Python 3.8 or newer installed on your system. If you don't have
+-Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
++You need to have Python 3.10 or newer installed on your system.
++If you don't have Python installed, we recommend installing [uv][].
+ 
+ There are several alternative options to install infercnvpy:
+ 
+ <!--
+-1) Install the latest release of `infercnvpy` from `PyPI <https://pypi.org/project/infercnvpy/>`_:
++1) Install the latest release of `infercnvpy` from [PyPI][]:
+ 
+ ```bash
+ pip install infercnvpy
+@@ -38,19 +36,22 @@ pip install git+https://github.com/grst/infercnvpy.git@main
+ 
+ ## Release notes
+ 
+-See the [changelog][changelog].
++See the [changelog][].
+ 
+ ## Contact
+ 
+-For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
+-If you found a bug, please use the [issue tracker][issue-tracker].
++For questions and help requests, you can reach out in the [scverse discourse][].
++If you found a bug, please use the [issue tracker][].
+ 
+ ## Citation
+ 
+ > t.b.a
+ 
+-[scverse-discourse]: https://discourse.scverse.org/
+-[issue-tracker]: https://github.com/grst/infercnvpy/issues
+-[changelog]: https://infercnvpy.readthedocs.io/latest/changelog.html
+-[link-docs]: https://infercnvpy.readthedocs.io
+-[link-api]: https://infercnvpy.readthedocs.io/latest/api.html
++[uv]: https://github.com/astral-sh/uv
++[scverse discourse]: https://discourse.scverse.org/
++[issue tracker]: https://github.com/grst/infercnvpy/issues
++[tests]: https://github.com/grst/infercnvpy/actions/workflows/test.yaml
++[documentation]: https://infercnvpy.readthedocs.io
++[changelog]: https://infercnvpy.readthedocs.io/en/latest/changelog.html
++[api documentation]: https://infercnvpy.readthedocs.io/en/latest/api.html
++[pypi]: https://pypi.org/project/infercnvpy
diff --git a/biome.jsonc b/biome.jsonc
new file mode 100644
index 0000000..2175c16
--- /dev/null
+++ b/biome.jsonc
@@ -0,0 +1,16 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "json": {
+                "formatter": { "trailingCommas": "all" },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
new file mode 100644
index 0000000..b8c8d47
--- /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/autosummary/class.rst b/docs/_templates/autosummary/class.rst
index 17dc123..7b4a0cf 100644
--- a/docs/_templates/autosummary/class.rst
+++ b/docs/_templates/autosummary/class.rst
@@ -9,11 +9,11 @@
 {% block attributes %}
 {% if attributes %}
 Attributes table
-~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~
 
 .. autosummary::
 {% for item in attributes %}
-    ~{{ fullname }}.{{ item }}
+    ~{{ name }}.{{ item }}
 {%- endfor %}
 {% endif %}
 {% endblock %}
@@ -26,7 +26,7 @@ Methods table
 .. autosummary::
 {% for item in methods %}
     {%- if item != '__init__' %}
-    ~{{ fullname }}.{{ item }}
+    ~{{ name }}.{{ item }}
     {%- endif -%}
 {%- endfor %}
 {% endif %}
@@ -35,13 +35,10 @@ Methods table
 {% block attributes_documentation %}
 {% if attributes %}
 Attributes
-~~~~~~~~~~~
+~~~~~~~~~~
 
 {% for item in attributes %}
 
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. autoattribute:: {{ [objname, item] | join(".") }}
 {%- endfor %}
 
@@ -56,9 +53,6 @@ Methods
 {% for item in methods %}
 {%- if item != '__init__' %}
 
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. automethod:: {{ [objname, item] | join(".") }}
 {%- endif -%}
 {%- endfor %}
diff --git a/docs/conf.py b/docs/conf.py
index 7e9d672..c70069e 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,5 +1,5 @@
 # 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
@@ -16,12 +16,15 @@
 
 # -- 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("infercnvpy")
 project_name = info["Name"]
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}."
 version = info["Version"]
-repository_url = f"https://github.com/grst/{project_name}"
+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"]
@@ -52,8 +55,10 @@
     "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")],
 ]
 
@@ -65,7 +70,7 @@
 napoleon_include_init_with_doc = False
 napoleon_use_rtype = True  # having a separate entry generally helps readability
 napoleon_use_param = True
-myst_heading_anchors = 3  # create anchors for h1-h3
+myst_heading_anchors = 6  # create anchors for h1-h6
 myst_enable_extensions = [
     "amsmath",
     "colon_fence",
@@ -116,11 +121,15 @@
 #
 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"
diff --git a/docs/conf.py.rej b/docs/conf.py.rej
new file mode 100644
index 0000000..33fb48d
--- /dev/null
+++ b/docs/conf.py.rej
@@ -0,0 +1,45 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -33,10 +36,10 @@ needs_sphinx = "4.0"
+ 
+ html_context = {
+     "display_github": True,  # Integrate GitHub
+-    "github_user": "grst",  # Username
+-    "github_repo": project_name,  # Repo name
+-    "github_version": "main",  # Version
+-    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
++    "github_user": "grst",
++    "github_repo": project_name,
++    "github_version": "main",
++    "conf_py_path": "/docs/",
+ }
+ 
+ # -- General configuration ---------------------------------------------------
+@@ -87,7 +92,9 @@ source_suffix = {
+ }
+ 
+ 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),
+ }
+ 
+@@ -118,18 +129,3 @@ nitpick_ignore = [
+     # you can add an exception to this list.
+     #     ("py:class", "igraph.Graph"),
+ ]
+-
+-
+-def setup(app):
+-    """App setup hook."""
+-    app.add_config_value(
+-        "recommonmark_config",
+-        {
+-            "auto_toc_tree_section": "Contents",
+-            "enable_auto_toc_tree": True,
+-            "enable_math": True,
+-            "enable_inline_math": False,
+-            "enable_eval_rst": True,
+-        },
+-        True,
+-    )
diff --git a/docs/contributing.md b/docs/contributing.md
index 8155b9c..45b9636 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -1,27 +1,49 @@
 # Contributing guide
 
-Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this repo, too.
-This document will not reproduce the entire content from there. Instead, it aims at summarizing the most important
-information to get you started on contributing.
+Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
+This document will not reproduce the entire content from there.
+Instead, it aims at summarizing the most important information to get you started on contributing.
 
-We assume that you are already familiar with git and with making pull requests on GitHub. If not, please refer
-to the [scanpy developer guide][].
+We assume that you are already familiar with git and with making pull requests on GitHub.
+If not, please refer to the [scanpy developer guide][].
+
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
 
 ## Installing dev dependencies
 
-In addition to the packages needed to _use_ this package, you need additional python packages to _run tests_ and _build
-the documentation_. It's easy to install them using `pip`:
+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
+The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+```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]
+```
+
+::::
+
+::::{group-tab} Pip
+If you prefer managing environments manually, you can use `pip`:
 
 ```bash
 cd infercnvpy
+python3 -m venv .venv
+source .venv/bin/activate
 pip install -e ".[dev,test,doc]"
 ```
 
+::::
+:::::
+
+[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+
 ## Code-style
 
-This template 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. See [pre-commit checks](template_usage.md#pre-commit-checks) for
-a full list of checks enabled for this repository.
+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
 
@@ -29,10 +51,11 @@ To enable pre-commit locally, simply run
 pre-commit install
 ```
 
-in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
+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.
+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
 
@@ -43,155 +66,149 @@ 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 [black][black-editors]
-and [prettier][prettier-editors].
+Finally, most editors have an _autoformat on save_ feature.
+Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
 
-[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html
-[prettier-editors]: https://prettier.io/docs/en/editors.html
+[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)=
 
-```{note}
-Remember to first install the package with `pip install '-e[dev,test]'`
-```
+## Writing tests
 
-This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
-to the package.
+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. Alternatively, you can run all tests from the
-command line by executing
+Most IDEs integrate with pytest and provide a GUI to run tests.
+Just point yours to one of the environments returned by
 
 ```bash
-pytest
+hatch env create hatch-test  # create test environments for all supported versions
+hatch env find hatch-test  # list all possible test environment paths
 ```
 
-in the root of the repository. Continuous integration will automatically run the tests on all pull requests.
-
-[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
+Alternatively, you can run all tests from the command line by executing
 
-## Publishing a release
-
-### Updating the version number
-
-Before making a release, you need to update the version number. 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.
-
-We use [bump2version][] to automatically update the version number in all places and automatically create a git tag.
-Run one of the following commands in the root of the repository
+:::::{tabs}
+::::{group-tab} Hatch
 
 ```bash
-bump2version patch
-bump2version minor
-bump2version major
+hatch test  # test with the highest supported Python version
+# or
+hatch test --all  # test with all supported Python versions
 ```
 
-Once you are done, run
-
-```
-git push --tags
-```
+::::
 
-to publish the created tag on GitHub.
+::::{group-tab} Pip
 
-[bump2version]: https://github.com/c4urself/bump2version
+```bash
+source .venv/bin/activate
+pytest
+```
 
-### Building and publishing the package on PyPI
+::::
+:::::
 
-Python packages are not distributed as source code, but as _distributions_. The most common distribution format is the so-called _wheel_. To build a _wheel_, run
+in the root of the repository.
 
-```bash
-python -m build
-```
+[pytest]: https://docs.pytest.org/
 
-This command creates a _source archive_ and a _wheel_, which are required for publishing your package to [PyPI][]. These files are created directly in the root of the repository.
+### Continuous integration
 
-Before uploading them to [PyPI][] you can check that your _distribution_ is valid by running:
+Continuous integration will automatically run the tests on all pull requests and test
+against the minimum and maximum supported Python version.
 
-```bash
-twine check dist/*
-```
+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.
 
-and finally publishing it with:
+## Publishing a release
 
-```bash
-twine upload dist/*
-```
+### Updating the version number
 
-Provide your username and password when requested and then go check out your package on [PyPI][]!
+Before making a release, you need to update the version number in the `pyproject.toml` file.
+Please adhere to [Semantic Versioning][semver], in brief
 
-For more information, follow the [Python packaging tutorial][].
+> 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.
 
-It is possible to automate this with GitHub actions, see also [this feature request][pypi-feature-request]
-in the cookiecutter-scverse template.
+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][].
 
-[python packaging tutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives
-[pypi-feature-request]: https://github.com/scverse/cookiecutter-scverse/issues/88
+[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:
+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
+- 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 the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
-on how to write documentation.
+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 reponsibility to update and re-run the notebook whenever necessary.
+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](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
-repository.
+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`
+- 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} Pip
+
+```bash
+source .venv/bin/activate
 cd docs
 make html
-open _build/html/index.html
+(xdg-)open _build/html/index.html
 ```
 
-<!-- Links -->
-
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
-[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
-[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
-[codecov]: https://about.codecov.io/sign-up/
-[codecov docs]: https://docs.codecov.com/docs
-[codecov bot]: https://docs.codecov.com/docs/team-bot
-[codecov app]: https://github.com/apps/codecov
-[pre-commit.ci]: https://pre-commit.ci/
-[readthedocs.org]: https://readthedocs.org/
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[jupytext]: https://jupytext.readthedocs.io/en/latest/
-[pre-commit]: https://pre-commit.com/
-[anndata]: https://github.com/scverse/anndata
-[mudata]: https://github.com/scverse/mudata
-[pytest]: https://docs.pytest.org/
-[semver]: https://semver.org/
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[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
-[pypi]: https://pypi.org/
+::::
+:::::
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
index 9447813..0fbffef 100644
--- a/docs/extensions/typed_returns.py
+++ b/docs/extensions/typed_returns.py
@@ -1,24 +1,27 @@
 # 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):
+def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
     for line in lines:
-        m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
-        if m:
-            # Once this is in scanpydoc, we can use the fancy hover stuff
-            yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+        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, section):
-    lines_raw = list(_process_return(self._dedent(self._consume_to_next_section())))
-    lines = self._format_block(":returns: ", lines_raw)
+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
diff --git a/docs/index.md.rej b/docs/index.md.rej
new file mode 100644
index 0000000..14a8d31
--- /dev/null
+++ b/docs/index.md.rej
@@ -0,0 +1,9 @@
+diff a/docs/index.md b/docs/index.md	(rejected hunks)
+@@ -8,7 +8,6 @@
+ 
+ api.md
+ changelog.md
+-template_usage.md
+ contributing.md
+ references.md
+ 
diff --git a/docs/make.bat b/docs/make.bat
deleted file mode 100644
index 954237b..0000000
--- a/docs/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/docs/template_usage.md b/docs/template_usage.md
deleted file mode 100644
index 25c5601..0000000
--- a/docs/template_usage.md
+++ /dev/null
@@ -1,322 +0,0 @@
-# Using this template
-
-Welcome to the developer guidelines! This document is split into two parts:
-
-1.  The [repository setup](#setting-up-the-repository). This section is relevant primarily for the repository maintainer and shows how to connect
-    continuous integration services and documents initial set-up of the repository.
-2.  The [contributor guide](contributing.md#contributing-guide). It contains information relevant to all developers who want to make a contribution.
-
-## Setting up the repository
-
-### First commit
-
-If you are reading this, you should have just completed the repository creation with :
-
-```bash
-cruft create https://github.com/scverse/cookiecutter-scverse
-```
-
-and you should have
-
-```
-cd infercnvpy
-```
-
-into the new project directory. Now that you have created a new repository locally, the first step is to push it to github. To do this, you'd have to create a **new repository** on github.
-You can follow the instructions directly on [github quickstart guide][].
-Since `cruft` already populated the local repository of your project with all the necessary files, we suggest to _NOT_ initialize the repository with a `README.md` file or `.gitignore`, because you might encounter git conflicts on your first push.
-If you are familiar with git and knows how to handle git conflicts, you can go ahead with your preferred choice.
-
-:::{note}
-If you are looking at this document in the [cookiecutter-scverse-instance][] repository documentation, throughout this document the name of the project is `cookiecutter-scverse-instance`. Otherwise it should be replaced by your new project name: `infercnvpy`.
-:::
-
-Now that your new project repository has been created on github at `https://github.com/grst/infercnvpy` you can push your first commit to github.
-To do this, simply follow the instructions on your github repository page or a more verbose walkthrough here:
-
-Assuming you are in `/your/path/to/infercnvpy`. Add all files and commit.
-
-```bash
-# stage all files of your new repo
-git add --all
-# commit
-git commit -m "first commit"
-```
-
-You'll notice that the command `git commit` installed a bunch of packages and triggered their execution: those are pre-commit! To read more about what they are and what they do, you can go to the related section [Pre-commit checks](#pre-commit-checks) in this document.
-
-:::{note}
-There is a chance that `git commit -m "first commit"` fails due to the `prettier` pre-commit formatting the file `.cruft.json`. No problem, you have just experienced what pre-commit checks do in action. Just go ahead and re-add the modified file and try to commit again:
-
-```bash
- git add -u # update all tracked file
- git commit -m "first commit"
-```
-
-:::
-
-Now that all the files of the newly created project have been committed, go ahead with the remaining steps:
-
-```bash
-# update the `origin` of your local repo with the remote github link
-git remote add origin https://github.com/grst/infercnvpy.git
-# rename the default branch to main
-git branch -M main
-# push all your files to remote
-git push -u origin main
-```
-
-Your project should be now available at `https://github.com/grst/infercnvpy`. While the repository at this point can be directly used, there are few remaining steps that needs to be done in order to achieve full functionality.
-
-### Coverage tests with _Codecov_
-
-Coverage tells what fraction of the code is "covered" by unit tests, thereby encouraging contributors to
-[write tests](contributing.md#writing-tests).
-To enable coverage checks, head over to [codecov][] and sign in with your GitHub account.
-You'll find more information in "getting started" section of the [codecov docs][].
-
-In the `Actions` tab of your projects' github repository, you can see that the workflows are failing due to the **Upload coverage** step. The error message in the workflow should display something like:
-
-```
-...
-    Retrying 5/5 in 2s..
-    {'detail': ErrorDetail(string='Could not find a repository, try using repo upload token', code='not_found')}
-Error: 404 Client Error: Not Found for url:
-...
-```
-
-While [codecov docs][] has a very extensive documentation on how to get started, _if_ you are using the default settings of this template we can assume that you are using [codecov][] in a github action workflow and hence you can make use of the [codecov bot][].
-
-To set it up, simply go to the [codecov app][] page and follow the instructions to activate it for your repository.
-Once the activation is completed, go back to the `Actions` tab and re-run the failing workflows.
-
-The workflows should now succeed and you will be able to find the code coverage at this link: `https://app.codecov.io/gh/grst/infercnvpy`. You might have to wait couple of minutes and the coverage of this repository should be ~60%.
-
-If your repository is private, you will have to specify an additional token in the repository secrets. In brief, you need to:
-
-1. Generate a Codecov Token by clicking _setup repo_ in the codecov dashboard.
-    - If you have already set up codecov in the repository by following the previous steps, you can directly go to the codecov repo webpage.
-2. Go to _Settings_ and copy **only** the token `_______-____-...`.
-3. Go to _Settings_ of your newly created repository on GitHub.
-4. Go to _Security > Secrets > Actions_.
-5. Create new repository secret with name `CODECOV_TOKEN` and paste the token generated by codecov.
-6. Past these additional lines in `/.github/workflows.test.yaml` under the **Upload coverage** step:
-    ```bash
-    - name: Upload coverage
-      uses: codecov/codecov-action@v3
-      with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-    ```
-7. Go back to github `Actions` page an re-run previously failed jobs.
-
-### Documentation on _readthedocs_
-
-We recommend using [readthedocs.org][] (RTD) to build and host the documentation for your project.
-To enable readthedocs, head over to [their website][readthedocs.org] and sign in with your GitHub account.
-On the RTD dashboard choose "Import a Project" and follow the instructions to add your repository.
-
--   Make sure to choose the correct name of the default branch. On GitHub, the name of the default branch should be `main` (it has
-    recently changed from `master` to `main`).
--   We recommend to enable documentation builds for pull requests (PRs). This ensures that a PR doesn't introduce changes
-    that break the documentation. To do so, got to `Admin -> Advanced Settings`, check the
-    `Build pull requests for this projects` option, and click `Save`. For more information, please refer to
-    the [official RTD documentation](https://docs.readthedocs.io/en/stable/pull-requests.html).
--   If you find the RTD builds are failing, you can disable the `fail_on_warning` option in `.readthedocs.yaml`.
-
-If your project is private, there are ways to enable docs rendering on [readthedocs.org][] but it is more cumbersome and requires a different subscription for read the docs. See a guide [here](https://docs.readthedocs.io/en/stable/guides/importing-private-repositories.html).
-
-### Pre-commit checks
-
-[Pre-commit][] checks are fast programs that
-check code for errors, inconsistencies and code styles, before the code
-is committed.
-
-We recommend setting up [pre-commit.ci][] to enforce consistency checks on every commit
-and pull-request.
-
-To do so, head over to [pre-commit.ci][] and click "Sign In With GitHub". Follow
-the instructions to enable pre-commit.ci for your account or your organization. You
-may choose to enable the service for an entire organization or on a per-repository basis.
-
-Once authorized, pre-commit.ci should automatically be activated.
-
-#### Overview of pre-commit hooks used by the template
-
-The following pre-commit checks are for code style and format:
-
--   [black](https://black.readthedocs.io/en/stable/): standard code
-    formatter in Python.
--   [isort](https://pycqa.github.io/isort/): sort module imports into
-    sections and types.
--   [prettier](https://prettier.io/docs/en/index.html): standard code
-    formatter for non-Python files (e.g. YAML).
--   [blacken-docs](https://github.com/asottile/blacken-docs): black on
-    python code in docs.
-
-The following pre-commit checks are for errors and inconsistencies:
-
--   [flake8](https://flake8.pycqa.org/en/latest/): standard check for errors in Python files.
-    -   [flake8-tidy-imports](https://github.com/adamchainz/flake8-tidy-imports):
-        tidy module imports.
-    -   [flake8-docstrings](https://github.com/PyCQA/flake8-docstrings):
-        pydocstyle extension of flake8.
-    -   [flake8-rst-docstrings](https://github.com/peterjc/e8-rst-docstrings):
-        extension of `flake8-docstrings` for `rst` docs.
-    -   [flake8-comprehensions](https://github.com/adamchainz/e8-comprehensions):
-        write better list/set/dict comprehensions.
-    -   [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear):
-        find possible bugs and design issues in program.
-    -   [flake8-blind-except](https://github.com/elijahandrews/flake8-blind-except):
-        checks for blind, catch-all `except` statements.
--   [yesqa](https://github.com/asottile/yesqa):
-    remove unneccesary `# noqa` comments, follows additional dependencies listed above.
--   [autoflake](https://github.com/PyCQA/autoflake):
-    remove unused imports and variables.
--   [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks.
-    -   **detect-private-key**: checks for the existence of private keys.
-    -   **check-ast**: check whether files parse as valid python.
-    -   **end-of-file-fixer**:check files end in a newline and only a newline.
-    -   **mixed-line-ending**: checks mixed line ending.
-    -   **trailing-whitespace**: trims trailing whitespace.
-    -   **check-case-conflict**: check files that would conflict with case-insensitive file systems.
--   [pyupgrade](https://github.com/asottile/pyupgrade):
-    upgrade syntax for newer versions of the language.
--   **forbid-to-commit**: Make sure that `*.rej` files cannot be commited. These files are created by the
-    [automated template sync](#automated-template-sync) if there's a merge conflict and need to be addressed manually.
-
-### How to disable or add pre-commit checks
-
--   To ignore lint warnigs from **flake8**, see [Ignore certain lint warnings](#how-to-ignore-certain-lint-warnings).
--   You can add or remove pre-commit checks by simply deleting relevant lines in the `.pre-commit-config.yaml` file.
-    Some pre-commit checks have additional options that can be specified either in the `pyproject.toml` or tool-specific
-    config files, such as `.prettierrc.yml` for **prettier** and `.flake8` for **flake8**.
-
-### How to ignore certain lint warnings
-
-The [pre-commit checks](#pre-commit-checks) include [flake8](https://flake8.pycqa.org/en/latest/) which checks
-for errors in Python files, including stylistic errors.
-
-In some cases it might overshoot and you may have good reasons to ignore certain warnings.
-
-To ignore an specific error on a per-case basis, you can add a comment `# noqa` to the offending line. You can also
-specify the error ID to ignore, with e.g. `# noqa: E731`. Check the [flake8 guide][] for reference.
-
-Alternatively, you can disable certain error messages for the entire project. To do so, edit the `.flake8`
-file in the root of the repository. Add one line per linting code you wish to ignore and don't forget to add a comment.
-
-```toml
-...
-# line break before a binary operator -> black does not adhere to PEP8
-W503
-# line break occured after a binary operator -> black does not adhere to PEP8
-W504
-...
-```
-
-[flake8 guide]: https://flake8.pycqa.org/en/3.1.1/user/ignoring-errors.html
-
-### API design
-
-Scverse ecosystem packages should operate on [AnnData][] and/or [MuData][] data structures and typically use an API
-as originally [introduced by scanpy][scanpy-api] with the following submodules:
-
--   `pp` for preprocessing
--   `tl` for tools (that, compared to `pp` generate interpretable output, often associated with a corresponding plotting
-    function)
--   `pl` for plotting functions
-
-You may add additional submodules as appropriate. While we encourage to follow a scanpy-like API for ecosystem packages,
-there may also be good reasons to choose a different approach, e.g. using an object-oriented API.
-
-[scanpy-api]: https://scanpy.readthedocs.io/en/stable/usage-principles.html
-
-### Using VCS-based versioning
-
-By default, the template uses hard-coded version numbers that are set in `pyproject.toml` and [managed with
-bump2version](contributing.md#publishing-a-release). If you prefer to have your project automatically infer version numbers from git
-tags, it is straightforward to switch to vcs-based versioning using [hatch-vcs][].
-
-In `pyproject.toml` add the following changes, and you are good to go!
-
-```diff
---- a/pyproject.toml
-+++ b/pyproject.toml
-@@ -1,11 +1,11 @@
- [build-system]
- build-backend = "hatchling.build"
--requires = ["hatchling"]
-+requires = ["hatchling", "hatch-vcs"]
-
-
- [project]
- name = "infercnvpy"
--version = "0.3.1dev"
-+dynamic = ["version"]
-
-@@ -60,6 +60,9 @@
-+[tool.hatch.version]
-+source = "vcs"
-+
- [tool.coverage.run]
- source = ["infercnvpy"]
- omit = [
-```
-
-Don't forget to update the [Making a release section](contributing.md#publishing-a-release) in this document accordingly, after you are done!
-
-[hatch-vcs]: https://pypi.org/project/hatch-vcs/
-
-### Automated template sync
-
-Automated template sync is enabled by default. This means that every night, a GitHub action runs [cruft][] to check
-if a new version of the `scverse-cookiecutter` template got released. If there are any new changes, a pull request
-proposing these changes is created automatically. This helps keeping the repository up-to-date with the latest
-coding standards.
-
-It may happen that a template sync results in a merge conflict. If this is the case a `*.ref` file with the
-diff is created. You need to manually address these changes and remove the `.rej` file when you are done.
-The pull request can only be merged after all `*.rej` files have been removed.
-
-:::{tip}
-The following hints may be useful to work with the template sync:
-
--   GitHub automatically disables scheduled actions if there has been not activity to the repository for 60 days.
-    You can re-enable or manually trigger the sync by navigating to `Actions` -> `Sync Template` in your GitHub repository.
--   If you want to ignore certain files from the template update, you can add them to the `[tool.cruft]` section in the
-    `pyproject.toml` file in the root of your repository. More details are described in the
-    [cruft documentation][cruft-update-project].
--   To disable the sync entirely, simply remove the file `.github/workflows/sync.yaml`.
-
-:::
-
-[cruft]: https://cruft.github.io/cruft/
-[cruft-update-project]: https://cruft.github.io/cruft/#updating-a-project
-
-## Moving forward
-
-You have reached the end of this document. Congratulations! You have successfully set up your project and are ready to start.
-For everything else related to documentation, code style, testing and publishing your project ot pypi, please refer to the [contributing docs](contributing.md#contributing-guide).
-
-<!-- Links -->
-
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
-[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
-[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
-[codecov]: https://about.codecov.io/sign-up/
-[codecov docs]: https://docs.codecov.com/docs
-[codecov bot]: https://docs.codecov.com/docs/team-bot
-[codecov app]: https://github.com/apps/codecov
-[pre-commit.ci]: https://pre-commit.ci/
-[readthedocs.org]: https://readthedocs.org/
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[jupytext]: https://jupytext.readthedocs.io/en/latest/
-[pre-commit]: https://pre-commit.com/
-[anndata]: https://github.com/scverse/anndata
-[mudata]: https://github.com/scverse/mudata
-[pytest]: https://docs.pytest.org/
-[semver]: https://semver.org/
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[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
diff --git a/pyproject.toml.rej b/pyproject.toml.rej
new file mode 100644
index 0000000..a13e303
--- /dev/null
+++ b/pyproject.toml.rej
@@ -0,0 +1,213 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -1,104 +1,135 @@
+ [build-system]
+ build-backend = "hatchling.build"
+-requires = ["hatchling"]
+-
++requires = [ "hatchling" ]
+ 
+ [project]
+ name = "infercnvpy"
+ version = "0.0.1"
+ description = "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. "
+ readme = "README.md"
+-requires-python = ">=3.8"
+-license = {file = "LICENSE"}
++license = { file = "LICENSE" }
++maintainers = [
++  { name = "Gregor Sturm", email = "mail@gregor-sturm.de" },
++]
+ authors = [
+-    {name = "Gregor Sturm"},
++  { name = "Gregor Sturm" },
+ ]
+-maintainers = [
+-    {name = "Gregor Sturm", email = "mail@gregor-sturm.de"},
++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",
+ ]
+-urls.Documentation = "https://infercnvpy.readthedocs.io/"
+-urls.Source = "https://github.com/icbi-lab/infercnvpy"
+-urls.Home-page = "https://github.com/icbi-lab/infercnvpy"
+ dependencies = [
+-    "anndata",
+-    # for debug logging (referenced from the issue template)
+-    "session-info"
++  "anndata",
++  # for debug logging (referenced from the issue template)
++  "session-info2",
+ ]
+-
+-[project.optional-dependencies]
+-dev = [
+-    # CLI for bumping the version number
+-    "bump2version",
+-    "pre-commit",
+-    "twine>=4.0.2"
++optional-dependencies.dev = [
++  "pre-commit",
++  "twine>=4.0.2",
+ ]
+-doc = [
+-    "sphinx>=4",
+-    "sphinx-book-theme>=0.3.3",
+-    "myst-nb",
+-    "sphinxcontrib-bibtex>=1.0.0",
+-    "sphinx-autodoc-typehints",
+-    # For notebooks
+-    "ipykernel",
+-    "ipython",
+-    "sphinx-copybutton",
++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>=4",
++  "sphinx-autodoc-typehints",
++  "sphinx-book-theme>=1",
++  "sphinx-copybutton",
++  "sphinx-tabs",
++  "sphinxcontrib-bibtex>=1",
++  "sphinxext-opengraph",
+ ]
+-test = [
+-    "pytest",
+-    "pytest-cov",
++optional-dependencies.test = [
++  "coverage",
++  "pytest",
+ ]
++# https://docs.pypi.org/project_metadata/#project-urls
++urls.Documentation = "https://infercnvpy.readthedocs.io/"
++urls.Homepage = "https://github.com/grst/infercnvpy"
++urls.Source = "https://github.com/grst/infercnvpy"
+ 
+-[tool.coverage.run]
+-source = ["infercnvpy"]
+-omit = [
+-    "**/test_*.py",
++[tool.hatch.envs.default]
++installer = "uv"
++features = [ "dev" ]
++
++[tool.hatch.envs.docs]
++features = [ "doc" ]
++scripts.build = "sphinx-build -M html docs docs/_build {args}"
++scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
++scripts.clean = "git clean -fdX -- {args:docs}"
++
++[tool.hatch.envs.hatch-test]
++features = [ "test" ]
++
++[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"]
++testpaths = [ "tests" ]
+ xfail_strict = true
+ addopts = [
+-    "--import-mode=importlib",  # allow using test files with same name
++  "--import-mode=importlib", # allow using test files with same name
+ ]
+ 
+-[tool.isort]
+-include_trailing_comma = true
+-multi_line_output = 3
+-profile = "black"
+-skip_glob = ["docs/*"]
+-
+-[tool.black]
+-line-length = 120
+-target-version = ['py38']
+-include = '\.pyi?$'
+-exclude = '''
+-(
+-  /(
+-      \.eggs
+-    | \.git
+-    | \.hg
+-    | \.mypy_cache
+-    | \.tox
+-    | \.venv
+-    | _build
+-    | buck-out
+-    | build
+-    | dist
+-  )/
+-)
+-'''
+-
+-[tool.jupytext]
+-formats = "ipynb,md"
++[tool.coverage.run]
++source = [ "infercnvpy" ]
++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"
++  "tests",
++  "src/**/__init__.py",
++  "src/**/basic.py",
++  "docs/api.md",
++  "docs/changelog.md",
++  "docs/references.bib",
++  "docs/references.md",
++  "docs/notebooks/example.ipynb",
+ ]