diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 90c277e197..98bd4e1ff6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,6 +11,7 @@ repos:
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-json
+      - id: check-toml
       - id: check-ast
       - id: check-added-large-files
       - id: check-case-conflict
@@ -48,7 +49,7 @@ repos:
     rev: 7.1.1
     hooks:
       - id: flake8
-        args: [--config=tools/schemacode/setup.cfg]
+        args: [--config=tools/schemacode/.flake8]
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:
@@ -61,6 +62,11 @@ repos:
       - id: yamllint
         args: [-f=standard, -c=.yamllint.yml]
         files: src/schema/.*/.*\.yaml
+  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.14.0
+    hooks:
+      - id: pretty-format-toml
+        args: [--autofix, --indent, '4', --no-sort]
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
diff --git a/tools/schemacode/.flake8 b/tools/schemacode/.flake8
new file mode 100644
index 0000000000..57d01f9d11
--- /dev/null
+++ b/tools/schemacode/.flake8
@@ -0,0 +1,7 @@
+[flake8]
+max-line-length = 99
+exclude = *build/
+ignore = E203,E402,E722,W503
+per-file-ignores =
+    */__init__.py : F401
+docstring-convention = numpy
diff --git a/tools/schemacode/pyproject.toml b/tools/schemacode/pyproject.toml
index c0a581cd85..9068e6d471 100644
--- a/tools/schemacode/pyproject.toml
+++ b/tools/schemacode/pyproject.toml
@@ -1,10 +1,82 @@
 [build-system]
-requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
+requires = ["setuptools"]
+
+[project]
+name = "bidsschematools"
+description = " Python tools for working with the BIDS schema."
+authors = [{name = "bids-standard developers"}]
+maintainers = [{name = "bids-standard developers", email = " bids.maintenance@gmail.com"}]
+license = {text = "MIT"}
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = [
+    "click",
+    "pyyaml",
+    "jsonschema"
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: MIT License",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13"
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+expressions = ["pyparsing"]
+render = [
+    "tabulate",
+    "pandas",
+    "markdown-it-py"
+]
+tests = [
+    "bidsschematools[expressions,render]",
+    "codecov",
+    "coverage[toml]",
+    "flake8",
+    "flake8-black",
+    "flake8-isort",
+    "pytest>6",
+    "pytest-cov"
+]
+doc = [
+    "sphinx>=1.5.3",
+    "sphinx_rtd_theme"
+]
+all = [
+    "bidsschematools[doc,tests]"
+]
+
+[project.scripts]
+bst = "bidsschematools.__main__:cli"
+
+[project.urls]
+Homepage = "https://github.com/bids-standard/bids-specification"
+
+[tool.setuptools.dynamic]
+version = {file = "bidsschematools/data/schema/SCHEMA_VERSION"}
+
+[tool.setuptools.package-data]
+bidsschematools = [
+    "data/metaschema.json",
+    "data/schema/BIDS_VERSION",
+    "data/schema/SCHEMA_VERSIO",
+    "data/schema/**/*.yaml",
+    "tests/data/**/*",
+    "tests/data/**/.bidsignore"
+]
+
+[tool.setuptools.packages.find]
+include = ["bidsschematools*"]
 
 [tool.black]
 line-length = 99
-target-version = ['py39']
 include = '\.pyi?$'
 exclude = '''
 (
@@ -21,18 +93,23 @@ exclude = '''
 )
 '''
 
+[tool.coverage.run]
+omit = [
+    "*/*/tests/*",
+    "**/tests/*"
+]
+parallel = true
+
 [tool.isort]
-profile = "black"
 multi_line_output = 3
+profile = "black"
 
 [tool.pytest.ini_options]
+addopts = "-ra --strict-markers --strict-config"
+log_cli = true
+log_cli_level = "INFO"
 markers = [
-  "validate_schema: tests that validate the schema itself",
-]
-
-[tool.coverage.run]
-parallel = true
-omit = [
-  "*/*/tests/*",
-  "**/tests/*"
+    "validate_schema: tests that validate the schema itself"
 ]
+minversion = "6.0"
+xfail_strict = true
diff --git a/tools/schemacode/setup.cfg b/tools/schemacode/setup.cfg
deleted file mode 100644
index 01f4f2c726..0000000000
--- a/tools/schemacode/setup.cfg
+++ /dev/null
@@ -1,79 +0,0 @@
-[metadata]
-name = bidsschematools
-version = file:bidsschematools/data/schema/SCHEMA_VERSION
-url = https://github.com/bids-standard/bids-specification
-author = bids-standard developers
-author_email = bids.maintenance@gmail.com
-description = Python tools for working with the BIDS schema.
-long_description = file:README.md
-long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
-license = MIT
-classifiers =
-    Development Status :: 4 - Beta
-    Intended Audience :: Science/Research
-    Topic :: Scientific/Engineering :: Information Analysis
-    License :: OSI Approved :: MIT License
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.11
-    Programming Language :: Python :: 3.12
-    Programming Language :: Python :: 3.13
-
-[options]
-python_requires = >=3.9
-install_requires =
-    click
-    pyyaml
-    importlib_resources; python_version < "3.9"
-    jsonschema
-packages = find:
-include_package_data = false
-zip_safe = false
-
-[options.extras_require]
-doc =
-    sphinx>=1.5.3
-    sphinx_rtd_theme
-render =
-    tabulate
-    pandas
-    markdown-it-py
-expressions =
-    pyparsing
-tests =
-    codecov
-    coverage[toml]
-    flake8
-    flake8-black
-    flake8-isort
-    pytest
-    pytest-cov
-all =
-    %(doc)s
-    %(render)s
-    %(tests)s
-    %(expressions)s
-
-[options.package_data]
-bidsschematools =
-    data/metaschema.json
-    data/schema/BIDS_VERSION
-    data/schema/SCHEMA_VERSION
-    data/schema/**/*.yaml
-    tests/data/**/*
-    tests/data/**/.bidsignore
-
-[options.entry_points]
-console_scripts =
-    bst=bidsschematools.__main__:cli
-
-[flake8]
-max-line-length = 99
-exclude = *build/
-ignore = E203,E402,E722,W503
-per-file-ignores =
-    */__init__.py : F401
-docstring-convention = numpy
-
-[tool:pytest]
-log_cli = true