From 2471d6e4f01f0a4dc087959b44e7d26b7ba68fc6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 26 Oct 2026 18:15:15 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/biomejs/pre-commit: v2.5.3 → v2.6.3](https://github.com/biomejs/pre-commit/compare/v2.5.3...v2.6.3)
- [github.com/tox-dev/pyproject-fmt: v2.25.3 → v2.30.3](https://github.com/tox-dev/pyproject-fmt/compare/v2.25.3...v2.30.3)
- [github.com/astral-sh/ruff-pre-commit: v0.15.21 → v0.17.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.21...v0.17.2)
- [github.com/pre-commit/mirrors-mypy: v2.1.0 → v2.4.0](https://github.com/pre-commit/mirrors-mypy/compare/v2.1.0...v2.4.0)
- [github.com/zizmorcore/zizmor-pre-commit: v1.24.1 → v1.31.1](https://github.com/zizmorcore/zizmor-pre-commit/compare/v1.24.1...v1.31.1)
---
 .pre-commit-config.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7f4f5560..63ce91b6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.5.3
+    rev: v2.6.3
     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: v2.25.3
+    rev: v2.30.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.21
+    rev: v0.17.2
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
@@ -38,7 +38,7 @@ repos:
         args: [--assume-in-merge]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v2.1.0
+    rev: v2.4.0
     hooks:
       - id: mypy
         pass_filenames: false
@@ -46,7 +46,7 @@ repos:
         additional_dependencies: [pandas-stubs, scipy-stubs]
 
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.24.1
+    rev: v1.31.1
     hooks:
       - id: zizmor
         args: [--no-progress, --fix]

From 907ea447656ae845227478f3633c5c5082f30c6e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 26 Oct 2026 18:16:15 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .codecov.yaml                              |  22 +--
 .github/ISSUE_TEMPLATE/bug_report.yml      | 166 +++++++++---------
 .github/ISSUE_TEMPLATE/config.yml          |   6 +-
 .github/ISSUE_TEMPLATE/feature_request.yml |  14 +-
 .github/PULL_REQUEST_TEMPLATE.md           |   1 +
 .github/dependabot.yml                     |  20 +--
 .github/workflows/build.yaml               |  42 ++---
 .github/workflows/release.yaml             |  50 +++---
 .github/workflows/test.yaml                | 194 ++++++++++-----------
 .pre-commit-config.yaml                    |  90 +++++-----
 .readthedocs.yaml                          |  26 +--
 CODE_OF_CONDUCT.md                         |   3 +-
 CONTRIBUTING.md                            |   7 +-
 README.md                                  |  14 +-
 pyproject.toml                             |   7 +-
 15 files changed, 331 insertions(+), 331 deletions(-)

diff --git a/.codecov.yaml b/.codecov.yaml
index d0c0e291..829e56c0 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/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index cc32eda8..0a883e8b 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,92 +2,92 @@ 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.
-          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
+    - 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.
+                * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
 
-  - 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: Versions
-      description: |
-        Which version of packages.
+    - 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.
+              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)
-        ```
+              ```python
+              In[1]: import session_info2; session_info2.session_info(dependencies=True)
+              ```
 
-        Alternatively, run this in a console:
+              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
+              ```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 5b62547f..5cad625d 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 c6bb2bb3..be387899 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 PyDESeq2
 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/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 6222fe20..65985ffc 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -5,6 +5,7 @@ Make sure that you have added unit tests if applicable.
 -->
 
 #### Reference Issue or PRs
+
 <!--
 If this PR is related to an existing issue or PR please reference it, eg:
 Fixes #1234.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 914ad69d..0c21fed3 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -1,12 +1,12 @@
 version: 2
 updates:
-  - package-ecosystem: github-actions
-    directory: /
-    schedule:
-      interval: weekly
-    cooldown:
-      default-days: 7
-    groups:
-      actions-deps:
-        patterns:
-          - "*"
+    - package-ecosystem: github-actions
+      directory: /
+      schedule:
+          interval: weekly
+      cooldown:
+          default-days: 7
+      groups:
+          actions-deps:
+              patterns:
+                  - "*"
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 539a9809..3dff1b9a 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -1,30 +1,30 @@
 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
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
 
 permissions:
-  contents: read
+    contents: read
 
 jobs:
-  package:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-        with:
-          filter: blob:none
-          fetch-depth: 0
-          persist-credentials: false
-      - name: Install uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
-      - name: Build package
-        run: uv build
-      - name: Check package
-        run: uvx twine check --strict dist/*.whl
+    package:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  filter: blob:none
+                  fetch-depth: 0
+                  persist-credentials: false
+            - name: Install uv
+              uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+            - 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
index 4cee8a96..ff6ae819 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -1,33 +1,33 @@
 name: Release
 
 on:
-  release:
-    types: [published]
+    release:
+        types: [published]
 
 # Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
 permissions: {}
 
 jobs:
-  release:
-    name: Upload release to PyPI
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/pydeseq2
-    permissions:
-      contents: read
-      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-        with:
-          filter: blob:none
-          fetch-depth: 0
-          persist-credentials: false
-      - name: Install uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
-        with:
-          enable-cache: false
-      - name: Build package
-        run: uv build
-      - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2
+    release:
+        name: Upload release to PyPI
+        runs-on: ubuntu-latest
+        environment:
+            name: pypi
+            url: https://pypi.org/p/pydeseq2
+        permissions:
+            contents: read
+            id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+        steps:
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  filter: blob:none
+                  fetch-depth: 0
+                  persist-credentials: false
+            - name: Install uv
+              uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+              with:
+                  enable-cache: false
+            - name: Build package
+              run: uv build
+            - name: Publish package distributions to PyPI
+              uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index b98363e6..d2c06b58 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -1,111 +1,111 @@
 name: Test
 
 on:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
-  schedule:
-    - cron: "0 5 1,15 * *"
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+    schedule:
+        - cron: "0 5 1,15 * *"
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
 
 permissions:
-  contents: read
+    contents: read
 
 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-slim
-    outputs:
-      envs: ${{ steps.get-envs.outputs.envs }}
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-        with:
-          filter: blob:none
-          fetch-depth: 0
-          persist-credentials: false
-      - name: Install uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
-      - name: Get test environments
-        id: get-envs
-        run: |
-          ENVS_JSON=$(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
+    # 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-slim
+        outputs:
+            envs: ${{ steps.get-envs.outputs.envs }}
+        steps:
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  filter: blob:none
+                  fetch-depth: 0
+                  persist-credentials: false
+            - name: Install uv
+              uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+            - name: Get test environments
+              id: get-envs
+              run: |
+                  ENVS_JSON=$(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
-    permissions:
-       id-token: write  # for codecov OIDC
-       contents: read
+    # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
+    test:
+        needs: get-environments
+        permissions:
+            id-token: write # for codecov OIDC
+            contents: read
 
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest]
-        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [ubuntu-latest]
+                env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
 
-    name: ${{ matrix.env.label }}
-    runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
+        name: ${{ matrix.env.label }}
+        runs-on: ${{ matrix.os }}
+        continue-on-error: ${{ contains(matrix.env.name, 'pre') }} # make "all-green" pass even if pre-release job fails
 
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-        with:
-          filter: blob:none
-          fetch-depth: 0
-          persist-credentials: false
-      - name: Install uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
-        with:
-          python-version: ${{ matrix.env.python }}
-      - name: create hatch environment
-        run: uvx hatch env create ${{ matrix.env.name }}
-      - name: list all all installed package versions
-        run: uvx hatch run ${{ matrix.env.name }}:uv pip list
-      - 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/page/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@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
-        with:
-          fail_ci_if_error: true
-          use_oidc: true
+        steps:
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  filter: blob:none
+                  fetch-depth: 0
+                  persist-credentials: false
+            - name: Install uv
+              uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+              with:
+                  python-version: ${{ matrix.env.python }}
+            - name: create hatch environment
+              run: uvx hatch env create ${{ matrix.env.name }}
+            - name: list all all installed package versions
+              run: uvx hatch run ${{ matrix.env.name }}:uv pip list
+            - 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/page/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@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
+              with:
+                  fail_ci_if_error: true
+                  use_oidc: true
 
-  # 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@b5b5b37504aa4183270bd3d855c52a67f212be35 # v1.3.0
-          with:
-            jobs: ${{ toJSON(needs) }}
+    # 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@b5b5b37504aa4183270bd3d855c52a67f212be35 # v1.3.0
+              with:
+                  jobs: ${{ toJSON(needs) }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 63ce91b6..9a9a1ccb 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,52 +1,52 @@
 fail_fast: false
 default_language_version:
-  python: python3
+    python: python3
 default_stages:
-  - pre-commit
-  - pre-push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/biomejs/pre-commit
-    rev: v2.6.3
-    hooks:
-      - id: biome-format
-        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
-  - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.30.3
-    hooks:
-      - id: pyproject-fmt
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.17.2
-    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]
+    - repo: https://github.com/biomejs/pre-commit
+      rev: v2.6.3
+      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: v2.30.3
+      hooks:
+          - id: pyproject-fmt
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.17.2
+      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]
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v2.4.0
-    hooks:
-      - id: mypy
-        pass_filenames: false
-        args: [src/pydeseq2, --ignore-missing-imports]
-        additional_dependencies: [pandas-stubs, scipy-stubs]
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v2.4.0
+      hooks:
+          - id: mypy
+            pass_filenames: false
+            args: [src/pydeseq2, --ignore-missing-imports]
+            additional_dependencies: [pandas-stubs, scipy-stubs]
 
-  - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.31.1
-    hooks:
-      - id: zizmor
-        args: [--no-progress, --fix]
+    - repo: https://github.com/zizmorcore/zizmor-pre-commit
+      rev: v1.31.1
+      hooks:
+          - id: zizmor
+            args: [--no-progress, --fix]
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 67eb948d..3a1054e4 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,16 +1,16 @@
 # https://docs.readthedocs.io/page/config-file/v2.html
 version: 2
 build:
-  os: ubuntu-24.04
-  tools:
-    python: "3.14"
-    nodejs: latest
-  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
+    os: ubuntu-24.04
+    tools:
+        python: "3.14"
+        nodejs: latest
+    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/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
index 6cd2fe26..5d9a8e16 100644
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
@@ -1,5 +1,4 @@
-Code of Conduct
----------------
+## Code of Conduct
 
 We want everyone in the community of users and contributors to PyDeseq2 to feel welcomed.
 
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 4469d02f..e4d45f58 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,14 +1,11 @@
-
-Contributing to PyDeseq2
-========================
+# Contributing to PyDeseq2
 
 Please check out the current version of the contributing guidelines in:
 `docs/contributing.md`, or in the `PyDeseq2` Documentation at:
 
 https://pydeseq2.readthedocs.io/en/latest/contributing.html
 
-Code of Conduct
----------------
+## Code of Conduct
 
 `PyDeseq2` follows the code of conduct defined by
 the Python Software Foundation: https://www.python.org/psf/codeofconduct/.
diff --git a/README.md b/README.md
index c006cf07..479893e3 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,7 @@
 <img src="docs/_static/pydeseq2_logo_green.png" width="600">
 
 #
+
 [![pypi version](https://img.shields.io/pypi/v/pydeseq2)](https://pypi.org/project/pydeseq2)
 [![pypiDownloads](https://static.pepy.tech/badge/pydeseq2)](https://pepy.tech/project/pydeseq2)
 [![condaDownloads](https://img.shields.io/conda/dn/bioconda/pydeseq2?logo=Anaconda)](https://anaconda.org/bioconda/pydeseq2)
@@ -19,6 +20,7 @@ We plan to implement more in the future.
 In case there is a feature you would particularly like to be implemented, feel free to open an issue.
 
 ## Table of Contents
+
 - [PyDESeq2](#pydeseq2)
   - [Table of Contents](#table-of-contents)
   - [Installation](#installation)
@@ -150,14 +152,14 @@ In Dec 2025, the maintenance of PyDESeq2 was taken over by the scverse community
 ## References
 
 [1] Love, M. I., Huber, W., & Anders, S. (2014). "Moderated estimation of fold
-        change and dispersion for RNA-seq data with DESeq2." Genome biology, 15(12), 1-21.
-        <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8>
+change and dispersion for RNA-seq data with DESeq2." Genome biology, 15(12), 1-21.
+<https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8>
 
 [2] Zhu, A., Ibrahim, J. G., & Love, M. I. (2019).
-        "Heavy-tailed prior distributions for sequence count data:
-        removing the noise and preserving large differences."
-        Bioinformatics, 35(12), 2084-2092.
-        <https://academic.oup.com/bioinformatics/article/35/12/2084/5159452>
+"Heavy-tailed prior distributions for sequence count data:
+removing the noise and preserving large differences."
+Bioinformatics, 35(12), 2084-2092.
+<https://academic.oup.com/bioinformatics/article/35/12/2084/5159452>
 
 ## License
 
diff --git a/pyproject.toml b/pyproject.toml
index 894c8568..12a04fb8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,6 +22,7 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
+  "Programming Language :: Python :: 3.15",
 ]
 dynamic = [ "version" ]
 dependencies = [
@@ -87,6 +88,8 @@ envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
 envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
 envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 envs.docs.dependency-groups = [ "doc" ]
+envs.hatch-check-types.scripts.check = [ "mypy src/pydeseq2 --ignore-missing-imports" ]
+envs.hatch-check-types.dependency-groups = [ "typecheck", "test" ]
 envs.hatch-test.matrix = [
   # Test the lowest and highest supported Python versions with normal deps
   { deps = [ "stable" ], python = [ "3.12", "3.14" ] },
@@ -99,8 +102,6 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
   { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
 envs.hatch-test.dependency-groups = [ "dev", "test" ]
-envs.hatch-check-types.scripts.check = [ "mypy src/pydeseq2 --ignore-missing-imports" ]
-envs.hatch-check-types.dependency-groups = [ "typecheck", "test" ]
 
 [tool.ruff]
 line-length = 89
@@ -151,11 +152,11 @@ ini_options.filterwarnings = [
 ]
 
 [tool.coverage]
+run.source = [ "pydeseq2" ]
 run.omit = [
   "**/test_*.py",
 ]
 run.patch = [ "subprocess" ]
-run.source = [ "pydeseq2" ]
 
 [tool.cruft]
 skip = [