[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.github/workflows/test.yaml.rej

@@ -13,4 +13,4 @@ diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml	(rejected hunks
 +            python: "3.12"
              pip-flags: "--pre"
              name: PRE-RELEASE DEPENDENCIES
- 
+

.pre-commit-config.yaml

@@ -1,80 +1,80 @@
 fail_fast: false
 default_language_version:
-    python: python3
-    node: 16.14.2
+  python: python3
+  node: 16.14.2
 default_stages:
-    - commit
-    - push
+  - commit
+  - push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/psf/black
-      rev: 24.8.0
-      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: 1.18.0
-      hooks:
-          - id: blacken-docs
-    - repo: https://github.com/PyCQA/isort
-      rev: 5.13.2
-      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: v4.6.0
-      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/PyCQA/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: 7.1.1
-      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: v3.17.0
-      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/psf/black
+    rev: 24.8.0
+    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: 1.18.0
+    hooks:
+      - id: blacken-docs
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    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: v4.6.0
+    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/PyCQA/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: 7.1.1
+    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: v3.17.0
+    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$'

.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: false
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: false
 python:
-    install:
-        - method: pip
-          path: .
-          extra_requirements:
-              - doc
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

README.md.rej

@@ -1,10 +1,10 @@
 diff a/README.md b/README.md	(rejected hunks)
 @@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the
- 
+
  ## Installation
- 
+
 -You need to have Python 3.9 or newer installed on your system. If you don't have
 +You need to have Python 3.10 or newer installed on your system. If you don't have
  Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
- 
+
  There are several alternative options to install cellcharter:

docs/conf.py.rej

@@ -1,6 +1,6 @@
 diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
 @@ -36,10 +36,10 @@ needs_sphinx = "4.0"
- 
+
  html_context = {
      "display_github": True,  # Integrate GitHub
 -    "github_user": "marcovarrone",  # Username
@@ -12,5 +12,5 @@ diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
 +    "github_version": "main",
 +    "conf_py_path": "/docs/",
  }
- 
+
  # -- General configuration ---------------------------------------------------

docs/index.md.rej

@@ -1,9 +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
- 
+

src/cellcharter/gr/_utils.py

@@ -1,4 +1,5 @@
 """Graph utilities."""
+
 from __future__ import annotations
 
 from anndata import AnnData

src/cellcharter/tl/_autok.py

@@ -101,9 +101,7 @@ def fit(self, adata: ad.AnnData, use_rep: str = None):
         X = (
             adata.obsm[use_rep]
             if use_rep is not None
-            else adata.obsm["X_cellcharter"]
-            if "X_cellcharter" in adata.obsm
-            else adata.X
+            else adata.obsm["X_cellcharter"] if "X_cellcharter" in adata.obsm else adata.X
         )
 
         set_logging_level(logging.WARNING)
@@ -194,9 +192,7 @@ def predict(self, adata: ad.AnnData, use_rep: str = None, k: int = None) -> pd.C
         X = (
             adata.obsm[use_rep]
             if use_rep is not None
-            else adata.obsm["X_cellcharter"]
-            if "X_cellcharter" in adata.obsm
-            else adata.X
+            else adata.obsm["X_cellcharter"] if "X_cellcharter" in adata.obsm else adata.X
         )
         return pd.Categorical(self.best_models[k].predict(X), categories=np.arange(k))