diff --git a/.bumpversion.cfg b/.bumpversion.cfg
deleted file mode 100644
index fdba9e4f..00000000
--- a/.bumpversion.cfg
+++ /dev/null
@@ -1,8 +0,0 @@
-[bumpversion]
-current_version = 0.0.1
-tag = True
-commit = True
-
-[bumpversion:file:./pyproject.toml]
-search = version = "{current_version}"
-replace = version = "{new_version}"
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 4ee1a57d..7e3a8d75 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -26,30 +26,17 @@ jobs:
             PYTHON: ${{ matrix.python }}
 
         steps:
-            - uses: actions/checkout@v4
+            - uses: actions/checkout@v6
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v5
+              uses: actions/setup-python@v6
               with:
                   python-version: ${{ matrix.python }}
-
-            - name: Get pip cache dir
-              id: pip-cache-dir
-              run: |
-                  echo "::set-output name=dir::$(pip cache dir)"
-            - name: Restore pip cache
-              uses: actions/cache@v4
-              with:
-                  path: ${{ steps.pip-cache-dir.outputs.dir }}
-                  key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
-                  restore-keys: |
-                      pip-${{ runner.os }}-${{ env.pythonLocation }}-
-            - name: Install test dependencies
-              run: |
-                  python -m pip install --upgrade pip wheel
-                  pip install pytest-cov
+                  cache: pip
+                  cache-dependency-path: pyproject.toml
             - name: Install dependencies
               run: |
-                  pip install --pre -e ".[dev,test]"
+                  python -m pip install --upgrade "pip>=25.1" wheel
+                  python -m pip install -e . --group test
 
             - name: Download artifact of test data
               if: matrix.python == '3.13'
@@ -65,7 +52,7 @@ jobs:
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
               run: |
-                  pytest -v --cov --color=yes --cov-report=xml
+                  python -m pytest -v --cov --color=yes --cov-report=xml
             - name: Upload coverage to Codecov
               uses: codecov/codecov-action@v4
               with:
diff --git a/.mypy.ini b/.mypy.ini
deleted file mode 100644
index 1e3bcb54..00000000
--- a/.mypy.ini
+++ /dev/null
@@ -1,27 +0,0 @@
-[mypy]
-python_version = 3.10
-
-ignore_errors = False
-warn_redundant_casts = True
-warn_unused_configs = True
-warn_unused_ignores = True
-
-disallow_untyped_calls = False
-disallow_untyped_defs = True
-disallow_incomplete_defs = True
-disallow_any_generics = True
-
-strict_optional = True
-strict_equality = True
-warn_return_any = True
-warn_unreachable = False
-check_untyped_defs = True
-; because of docrep
-allow_untyped_decorators = True
-no_implicit_optional = True
-no_implicit_reexport = True
-no_warn_no_return = True
-
-show_error_codes = True
-show_column_numbers = True
-error_summary = True
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c2681a9f..0f6f4910 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,15 +6,11 @@ default_stages:
     - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/rbubley/mirrors-prettier
-      rev: v3.8.3
-      hooks:
-          - id: prettier
     - repo: https://github.com/astral-sh/ruff-pre-commit
       rev: v0.15.12
       hooks:
           - id: ruff
-            args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+            args: [--fix, --exit-non-zero-on-fix]
           - id: ruff-format
     - repo: https://github.com/pre-commit/mirrors-mypy
       rev: v1.20.2
@@ -26,11 +22,6 @@ repos:
       rev: v6.0.0
       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: local
       hooks:
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 31d8fef4..f8fcd935 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,15 +1,16 @@
 version: 2
 build:
-    os: ubuntu-24.04
-    tools:
-        python: "3.12"
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
 sphinx:
-    configuration: docs/conf.py
-    fail_on_warning: true
+  configuration: docs/conf.py
+  fail_on_warning: true
+
 python:
-    install:
-        - method: pip
-          path: .
-          extra_requirements:
-              - doc
-              - pre
+  install:
+    - method: uv
+      command: sync
+      groups:
+        - doc
diff --git a/pyproject.toml b/pyproject.toml
index 05c5baa2..34705a5d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,12 +39,11 @@ dependencies = [
     "xmltodict",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
-    # CLI for bumping the version number
-    "bump2version",
-    "pre-commit"
+    "pre-commit",
 ]
+
 doc = [
     "sphinx>=4.5,<9",
     "sphinx-book-theme>=1.0.0",
@@ -53,22 +52,15 @@ doc = [
     "sphinx-autodoc-typehints",
     "sphinx-design",
     "sphinx-click",
-    # For notebooks
     "ipython>=8.6.0",
     "sphinx-copybutton",
 ]
+
 test = [
     "pytest",
     "pytest-cov",
-    # https://github.com/scverse/spatialdata-io/issues/334
     "pyarrow!=22",
-    "pytest-mock"
-]
-# this will be used by readthedocs and will make pip also look for pre-releases, generally installing the latest available version
-# update: readthedocs doens't seem to try to install pre-releases even if when trying to install the pre optional-dependency. For
-# the moment, if needed, let's add the latest pre-release explicitly here.
-pre = [
-    "spatialdata>=0.7.3a0"
+    "pytest-mock",
 ]
 
 [tool.coverage.run]
@@ -85,7 +77,9 @@ addopts = [
 ]
 
 [tool.ruff]
+target-version = "py311"
 line-length = 120
+indent-width = 4
 exclude = [
     ".git",
     ".tox",
@@ -95,7 +89,9 @@ exclude = [
     "dist",
     "setup.py",
 ]
-lint.select = [
+
+[tool.ruff.lint]
+select = [
     "F", # Errors detected by Pyflakes
     "E", # Error detected by Pycodestyle
     "W", # Warning detected by Pycodestyle
@@ -112,7 +108,7 @@ lint.select = [
     # "PTH",  # Use pathlib
     # "S"  # Security
 ]
-lint.ignore = [
+ignore = [
     # Do not catch blind exception: `Exception`
     "BLE001",
     # Errors from function calls in argument defaults. These are fine when the result is immutable.
@@ -140,7 +136,7 @@ lint.ignore = [
     # Missing docstring in __init__
     "D107",
     ## Disable one in each pair of mutually incompatible rules
-    # We don’t want a blank line before a class docstring
+    # We don't want a blank line before a class docstring
     "D203",
     # 1 blank line required after class docstring
     "D204",
@@ -186,11 +182,48 @@ lint.ignore = [
     # Unused imports
     "F401",
 ]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
 [tool.ruff.lint.per-file-ignores]
 "src/spatialdata_io/__init__.py" = ["I001"]
 
-[tool.jupytext]
-formats = "ipynb,md"
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+line-ending = "lf"
+
+[tool.mypy]
+python_version = "3.11"
+
+ignore_errors = false
+warn_redundant_casts = true
+warn_unused_configs = true
+warn_unused_ignores = true
+
+disallow_untyped_calls = false
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+disallow_any_generics = true
+
+strict_optional = true
+strict_equality = true
+warn_return_any = true
+warn_unreachable = false
+check_untyped_defs = true
+
+# because of docrep
+allow_untyped_decorators = true
+
+no_implicit_optional = true
+no_implicit_reexport = true
+no_warn_no_return = true
+
+show_error_codes = true
+show_column_numbers = true
+error_summary = true
+
 
 [tool.hatch.metadata]
 allow-direct-references = true