From 615c7bee2f1db2b3ec35cb96ba467ba6629707aa Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 24 Aug 2026 20:10:31 +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: v1.9.4 → v2.5.10](https://github.com/biomejs/pre-commit/compare/v1.9.4...v2.5.10)
- [github.com/tox-dev/pyproject-fmt: v2.5.1 → v2.28.1](https://github.com/tox-dev/pyproject-fmt/compare/v2.5.1...v2.28.1)
- [github.com/astral-sh/ruff-pre-commit: v0.11.0 → v0.16.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.0...v0.16.4)
- [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v5.0.0...v6.0.0)
---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index de542ee..7fff591 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: v1.9.4
+    rev: v2.5.10
     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: v2.28.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.0
+    rev: v0.16.4
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
@@ -24,7 +24,7 @@ repos:
       - 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

From a7faa1c8176f4fc6e09cea041caed6b3ee980847 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 24 Aug 2026 20:10:46 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyproject.toml                         | 45 ++++++++++----------------
 site/vignettes/reference_mapping.ipynb |  3 +-
 2 files changed, 18 insertions(+), 30 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 192366e..c1ce981 100644
--- a/pyproject.toml
+++ b/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 = [
@@ -47,7 +48,6 @@ optional-dependencies.dev = [
   "pre-commit",
   "twine>=4.0.2",
 ]
-
 optional-dependencies.doc = [
   "mkdocs-macros-plugin",
   "mkdocs-material",
@@ -55,16 +55,13 @@ optional-dependencies.doc = [
   "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]
+version.source = "vcs"
+envs.default.installer = "uv"
+envs.default.features = [ "dev" ]
+envs.docs.features = [ "doc" ]
+envs.docs.scripts.build = "mkdocs build {args}"
+envs.docs.scripts.clean = "rm -rf docs/*"
+envs.docs.scripts.serve = "mkdocs serve {args}"
+envs.hatch-test.features = [ "test" ]
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -133,16 +122,16 @@ 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.addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
+ini_options.xfail_strict = true
 
-[tool.coverage.run]
-source = [ "hnoca" ]
-omit = [
+[tool.coverage]
+run.source = [ "hnoca" ]
+run.omit = [
   "**/test_*.py",
 ]
 
diff --git a/site/vignettes/reference_mapping.ipynb b/site/vignettes/reference_mapping.ipynb
index 50a0950..02f491a 100644
--- a/site/vignettes/reference_mapping.ipynb
+++ b/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/\")"
    ]
   },