[pre-commit.ci] pre-commit autoupdate

.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"]
+__all__ = ["destvi_utils"]

.flake8

@@ -2,4 +2,3 @@
 ignore = E203, E266, E501, W503, W605, N812
 exclude = .git,docs
 max-line-length = 119
-

.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

.pre-commit-config.yaml

@@ -31,7 +31,7 @@ repos:
           )$
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.46.0
+    rev: v0.47.0
     hooks:
       - id: markdownlint-fix
         exclude: |
@@ -41,7 +41,7 @@ repos:
           )$
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.6
+    rev: v0.14.10
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

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.

docs/api/index.rst

@@ -14,4 +14,4 @@ destvi_utils
    automatic_proportion_threshold
    explore_gamma_space
    de_genes
-   plot_de_genes
+   plot_de_genes

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
 

docs/release_notes/index.rst

@@ -9,4 +9,4 @@ Version 0.1
 .. toctree::
    :maxdepth: 2
 
-   v0.1.0
+   v0.1.0

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`.
+Initial release of the utilities functions. Complies with `scvi-tools>=0.15.0`.