[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -7,24 +7,24 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v1.9.4
+    rev: v2.4.7
     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
+    rev: v2.19.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.0
+    rev: v0.15.6
     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
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast

pyproject.toml

@@ -24,6 +24,7 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
 ]
 dynamic = [ "version" ]
 dependencies = [
@@ -47,24 +48,20 @@ optional-dependencies.dev = [
   "pre-commit",
   "twine>=4.0.2",
 ]
-
 optional-dependencies.doc = [
   "mkdocs-macros-plugin",
   "mkdocs-material",
   "mkdocstrings[python]",
   "mknotebooks",
   "pymdown-extensions",
 ]
-
 optional-dependencies.mapping = [
   "scarches>=0.6.1",
   "scvi-tools>=1.2",
 ]
-
 optional-dependencies.stats = [
   "decoupler>=1.6",
 ]
-
 optional-dependencies.test = [
   "coverage",
   "igraph>=0.11",
@@ -77,29 +74,21 @@ urls.Documentation = "https://devsystemslab.github.io/HNOCA-tools/"
 urls.Homepage = "https://github.com/devsystemslab/HNOCA-tools"
 urls.Source = "https://github.com/devsystemslab/HNOCA-tools"
 
-[tool.hatch.version]
-source = "vcs"
-
-[tool.hatch.envs.default]
-installer = "uv"
-features = [ "dev" ]
-
-[tool.hatch.envs.hatch-test]
-features = [ "test" ]
-
-[tool.hatch.envs.docs]
-features = [ "doc" ]
-scripts.build = "mkdocs build {args}"
-scripts.serve = "mkdocs serve {args}"
-scripts.clean = "rm -rf docs/*"
+[tool.hatch]
+envs.default.installer = "uv"
+envs.default.features = [ "dev" ]
+envs.docs.features = [ "doc" ]
+envs.docs.scripts.build = "mkdocs build {args}"
+envs.docs.scripts.serve = "mkdocs serve {args}"
+envs.docs.scripts.clean = "rm -rf docs/*"
+envs.hatch-test.features = [ "test" ]
+version.source = "vcs"
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -133,18 +122,18 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
-[tool.pytest.ini_options]
-testpaths = [ "tests" ]
-xfail_strict = true
-addopts = [
+[tool.pytest]
+ini_options.testpaths = [ "tests" ]
+ini_options.xfail_strict = true
+ini_options.addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
 
-[tool.coverage.run]
-source = [ "hnoca" ]
-omit = [
+[tool.coverage]
+run.omit = [
   "**/test_*.py",
 ]
+run.source = [ "hnoca" ]
 
 [tool.cruft]
 skip = [

site/vignettes/reference_mapping.ipynb

@@ -18,11 +18,10 @@
    "source": [
     "import os\n",
     "\n",
+    "import hnoca.map as hmap\n",
     "import scanpy as sc\n",
     "import scvi\n",
     "\n",
-    "import hnoca.map as hmap\n",
-    "\n",
     "os.chdir(\"/home/fleckj/scratch/hnoca/\")"
    ]
   },