From 63559609c9fbecf40aee91d0202deb2a04eb04da Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Mar 2026 21:04:48 +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/igorshubovych/markdownlint-cli: v0.46.0 → v0.48.0](https://github.com/igorshubovych/markdownlint-cli/compare/v0.46.0...v0.48.0)
- [github.com/astral-sh/ruff-pre-commit: v0.14.6 → v0.15.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.6...v0.15.5)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4f032c7..97741e6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -31,7 +31,7 @@ repos:
           )$
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.46.0
+    rev: v0.48.0
     hooks:
       - id: markdownlint-fix
         exclude: |
@@ -41,7 +41,7 @@ repos:
           )$
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.6
+    rev: v0.15.5
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

From 5f7221e6de1964cb979e93d6347b87bc1f4201a4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Mar 2026 21:11:10 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .editorconfig                    |  4 +--
 .flake8                          |  1 -
 .github/workflows/test.yml       | 47 ++++++++++++++++----------------
 README.md                        |  6 ++--
 docs/api/index.rst               |  2 +-
 docs/extensions/typed_returns.py |  2 +-
 docs/release_notes/index.rst     |  2 +-
 docs/release_notes/v0.1.0.rst    |  2 +-
 8 files changed, 32 insertions(+), 34 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index de025f3..e63add8 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -3,7 +3,7 @@ import logging
 from rich.console import Console
 from rich.logging import RichHandler
 
-from ._destvi_utils import 
+from ._destvi_utils import
 
 try:
     import importlib.metadata as importlib_metadata
@@ -29,4 +29,4 @@ logger.addHandler(ch)
 # this prevents double outputs
 logger.propagate = False
 
-__all__ = ["destvi_utils"]
\ No newline at end of file
+__all__ = ["destvi_utils"]
diff --git a/.flake8 b/.flake8
index 460d241..1caef0c 100644
--- a/.flake8
+++ b/.flake8
@@ -2,4 +2,3 @@
 ignore = E203, E266, E501, W503, W605, N812
 exclude = .git,docs
 max-line-length = 119
-
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d76492f..8a164ab 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -11,35 +11,34 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: [3.11, 3.12, 3.13]
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python }}
-        cache: "pip"
-        cache-dependency-path: "**/pyproject.toml"
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
 
-    - name: Install dependencies
-      run: |
-        pip install pytest-cov
-        pip install .[dev]
-    - name: Lint with flake8
-      run: |
-        flake8
-    - name: Format with black
-      run: |
-        black --check .
-    - name: Test with pytest
-      run: |
-        pytest --cov-report=xml --cov=destvi_utils
-    - name: After success
-      run: |
-        bash <(curl -s https://codecov.io/bash)
-        pip list
+      - name: Install dependencies
+        run: |
+          pip install pytest-cov
+          pip install .[dev]
+      - name: Lint with flake8
+        run: |
+          flake8
+      - name: Format with black
+        run: |
+          black --check .
+      - name: Test with pytest
+        run: |
+          pytest --cov-report=xml --cov=destvi_utils
+      - name: After success
+        run: |
+          bash <(curl -s https://codecov.io/bash)
+          pip list
diff --git a/README.md b/README.md
index 31d2f64..6a7291f 100644
--- a/README.md
+++ b/README.md
@@ -13,11 +13,11 @@ Implementation of the automatic pipeline for downstream analysis of DestVI's res
 ```
 pip install git+https://github.com/yoseflab/destvi_utils.git
 ```
-Please be sure to install a version of [PyTorch](https://pytorch.org/) that is compatible with your GPU (if applicable).
 
+Please be sure to install a version of [PyTorch](https://pytorch.org/) that is compatible with your GPU (if applicable).
 
 # Resources
 
--   API reference, and installation guides are available in
+- API reference, and installation guides are available in
     the [documentation](https://destvi-utils.readthedocs.io/en/latest/).
--   Please use the [issues](https://github.com/yoseflab/destvi_utils_/issues) to submit bug reports.
+- Please use the [issues](https://github.com/yoseflab/destvi_utils_/issues) to submit bug reports.
diff --git a/docs/api/index.rst b/docs/api/index.rst
index 45fe654..3552665 100644
--- a/docs/api/index.rst
+++ b/docs/api/index.rst
@@ -14,4 +14,4 @@ destvi_utils
    automatic_proportion_threshold
    explore_gamma_space
    de_genes
-   plot_de_genes
\ No newline at end of file
+   plot_de_genes
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
index d4e1d26..56a8779 100644
--- a/docs/extensions/typed_returns.py
+++ b/docs/extensions/typed_returns.py
@@ -11,7 +11,7 @@ def process_return(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"]}`)'
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
         else:
             yield line
 
diff --git a/docs/release_notes/index.rst b/docs/release_notes/index.rst
index ffffd7f..5a70257 100644
--- a/docs/release_notes/index.rst
+++ b/docs/release_notes/index.rst
@@ -9,4 +9,4 @@ Version 0.1
 .. toctree::
    :maxdepth: 2
 
-   v0.1.0
\ No newline at end of file
+   v0.1.0
diff --git a/docs/release_notes/v0.1.0.rst b/docs/release_notes/v0.1.0.rst
index 08d094d..c3acbdc 100644
--- a/docs/release_notes/v0.1.0.rst
+++ b/docs/release_notes/v0.1.0.rst
@@ -1,3 +1,3 @@
 New in 0.1.0 (2022-04-02)
 -------------------------
-Initial release of the utilities functions. Complies with `scvi-tools>=0.15.0`.
\ No newline at end of file
+Initial release of the utilities functions. Complies with `scvi-tools>=0.15.0`.