diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
deleted file mode 100644
index 4ef58869c..000000000
--- a/.github/workflows/pre-release.yml
+++ /dev/null
@@ -1,69 +0,0 @@
-name: Pre-release checks
-
-on:
-  push:
-    branches:
-      - master
-  pull_request:
-    branches:
-      - master
-
-defaults:
-  run:
-    shell: bash
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
-permissions:
-  contents: read
-
-jobs:
-  pre-release:
-    # Check pre-releases of dependencies on stable Python
-    runs-on: ${{ matrix.os }}
-    continue-on-error: true
-    strategy:
-      matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11', '3.12']
-        install: ['pip']
-        check: ['tests']
-        pip-flags: ['PRE_PIP_FLAGS']
-    env:
-      INSTALL_TYPE: ${{ matrix.install }}
-      CHECK_TYPE: ${{ matrix.check }}
-      EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
-      OS_TYPE: ${{ matrix.os }}
-
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: recursive
-          fetch-depth: 0
-      - name: Install dependencies
-        run: .maint/ci/install_dependencies.sh
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
-      - name: Create virtual environment
-        run: .maint/ci/create_venv.sh
-      - name: Build archive
-        run: |
-          source .maint/ci/build_archive.sh
-          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
-      - name: Install fMRIPrep
-        run: .maint/ci/install.sh
-      - name: Install extras
-        run: .maint/ci/install_extras.sh
-      - name: Run tests
-        run: .maint/ci/check.sh
-      - uses: codecov/codecov-action@v4
-        with:
-          file: coverage.xml
-          token: ${{ secrets.CODECOV_TOKEN }}
-        if: ${{ always() }}
diff --git a/.github/workflows/stable.yml b/.github/workflows/test.yml
similarity index 60%
rename from .github/workflows/stable.yml
rename to .github/workflows/test.yml
index b67aecaa4..53bcc4026 100644
--- a/.github/workflows/stable.yml
+++ b/.github/workflows/test.yml
@@ -16,6 +16,10 @@ defaults:
   run:
     shell: bash
 
+# Force tox and pytest to use color
+env:
+  FORCE_COLOR: true
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -24,47 +28,49 @@ permissions:
   contents: read
 
 jobs:
-  stable:
+  test:
     # Check each OS, all supported Python, minimum versions and latest releases
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: ['ubuntu-latest']
         python-version: ['3.10', '3.11', '3.12']
-        install: ['pip']
-        check: ['tests']
-        pip-flags: ['']
+        dependencies: ['latest', 'pre']
+        include:
+          - os: ubuntu-latest
+            python-version: '3.10'
+            dependencies: 'min'
+
     env:
-      INSTALL_TYPE: ${{ matrix.install }}
-      CHECK_TYPE: ${{ matrix.check }}
-      EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
-      OS_TYPE: ${{ matrix.os }}
+      DEPENDS: ${{ matrix.dependencies }}
 
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: recursive
           fetch-depth: 0
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/templateflow
+          key: templateflow-v1
       - name: Install dependencies
-        run: .maint/ci/install_dependencies.sh
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends graphviz
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
-      - name: Create virtual environment
-        run: .maint/ci/create_venv.sh
-      - name: Build archive
+      - name: Install tox
         run: |
-          source .maint/ci/build_archive.sh
-          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
-      - name: Install fMRIPrep
-        run: .maint/ci/install.sh
-      - name: Install extras
-        run: .maint/ci/install_extras.sh
-      - name: Run tests
-        run: .maint/ci/check.sh
+          python -m pip install --upgrade pip
+          python -m pip install tox tox-gh-actions
+      - name: Show tox config
+        run: tox c
+      - name: Run tox
+        run: tox -v --exit-and-dump-after 1200
       - uses: codecov/codecov-action@v4
         with:
           file: coverage.xml
diff --git a/.maint/ci/activate.sh b/.maint/ci/activate.sh
deleted file mode 100644
index 567e13a67..000000000
--- a/.maint/ci/activate.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-if [ -e virtenv/bin/activate ]; then
-    source virtenv/bin/activate
-elif [ -e virtenv/Scripts/activate ]; then
-    source virtenv/Scripts/activate
-else
-    echo Cannot activate virtual environment
-    ls -R virtenv
-    false
-fi
diff --git a/.maint/ci/build_archive.sh b/.maint/ci/build_archive.sh
deleted file mode 100755
index 6e8be6fb9..000000000
--- a/.maint/ci/build_archive.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-echo "Building archive"
-
-source .maint/ci/activate.sh
-
-set -eu
-
-# Required dependencies
-echo "INSTALL_TYPE = $INSTALL_TYPE"
-
-set -x
-
-if [ "$INSTALL_TYPE" = "sdist" -o "$INSTALL_TYPE" = "wheel" ]; then
-    python -m build
-elif [ "$INSTALL_TYPE" = "archive" ]; then
-    ARCHIVE="/tmp/package.tar.gz"
-    git archive -o $ARCHIVE HEAD
-fi
-
-if [ "$INSTALL_TYPE" = "sdist" ]; then
-    ARCHIVE=$( ls $PWD/dist/*.tar.gz )
-elif [ "$INSTALL_TYPE" = "wheel" ]; then
-    ARCHIVE=$( ls $PWD/dist/*.whl )
-elif [ "$INSTALL_TYPE" = "pip" ]; then
-    ARCHIVE="$PWD"
-fi
-
-if [ "$INSTALL_TYPE" = "sdist" -o "$INSTALL_TYPE" = "wheel" ]; then
-    python -m pip install twine
-    python -m twine check $ARCHIVE
-fi
-
-set +eux
diff --git a/.maint/ci/check.sh b/.maint/ci/check.sh
deleted file mode 100755
index d693e7086..000000000
--- a/.maint/ci/check.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/bin/bash
-
-echo Running tests
-
-source .maint/ci/activate.sh
-
-set -eu
-
-# Required variables
-echo CHECK_TYPE = $CHECK_TYPE
-
-set -x
-
-if [ "${CHECK_TYPE}" == "doc" ]; then
-    cd doc
-    make html && make doctest
-elif [ "${CHECK_TYPE}" == "tests" ]; then
-    pytest --doctest-modules --cov fmriprep --cov-report xml \
-        --junitxml=test-results.xml -v fmriprep
-else
-    false
-fi
-
-set +eux
-
-echo Done running tests
diff --git a/.maint/ci/create_venv.sh b/.maint/ci/create_venv.sh
deleted file mode 100755
index 6b6822e27..000000000
--- a/.maint/ci/create_venv.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-
-echo Creating isolated virtual environment
-
-source .maint/ci/env.sh
-
-set -eu
-
-# Required variables
-echo SETUP_REQUIRES = $SETUP_REQUIRES
-
-set -x
-
-python -m pip install --upgrade pip virtualenv
-virtualenv --python=python virtenv
-source .maint/ci/activate.sh
-python --version
-python -m pip install -U $SETUP_REQUIRES
-which python
-which pip
-
-set +eux
-
-echo Done creating isolated virtual environment
diff --git a/.maint/ci/env.sh b/.maint/ci/env.sh
deleted file mode 100644
index 65e148b60..000000000
--- a/.maint/ci/env.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-SETUP_REQUIRES="pip build"
-
-# Numpy and scipy upload nightly/weekly/intermittent wheels
-NIGHTLY_WHEELS="https://pypi.anaconda.org/scipy-wheels-nightly/simple"
-STAGING_WHEELS="https://pypi.anaconda.org/multibuild-wheels-staging/simple"
-PRE_PIP_FLAGS="--pre --extra-index-url $NIGHTLY_WHEELS --extra-index-url $STAGING_WHEELS --prefer-binary"
diff --git a/.maint/ci/install.sh b/.maint/ci/install.sh
deleted file mode 100755
index e58e3fb15..000000000
--- a/.maint/ci/install.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-echo Installing fmriprep
-
-source .maint/ci/activate.sh
-source .maint/ci/env.sh
-
-set -eu
-
-# Required variables
-echo INSTALL_TYPE = $INSTALL_TYPE
-echo CHECK_TYPE = $CHECK_TYPE
-echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
-
-set -x
-
-if [ -n "$EXTRA_PIP_FLAGS" ]; then
-    EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
-fi
-
-pip install $EXTRA_PIP_FLAGS $ARCHIVE
-
-# Basic import check
-python -c 'import fmriprep; print(fmriprep.__version__)'
-
-if [ "$CHECK_TYPE" == "skiptests" ]; then
-    exit 0
-fi
-
-pip install $EXTRA_PIP_FLAGS "fmriprep[$CHECK_TYPE]"
-
-set +eux
-
-echo Done installing fmriprep
diff --git a/.maint/ci/install_dependencies.sh b/.maint/ci/install_dependencies.sh
deleted file mode 100755
index 7e0e33fe7..000000000
--- a/.maint/ci/install_dependencies.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-
-echo "Installing dependencies"
-
-set -eu
-
-# Required variables
-echo OS_TYPE = $OS_TYPE
-
-if [ "$OS_TYPE" = "ubuntu-latest" ]; then
-    sudo apt update
-    sudo apt install -y graphviz
-elif  [ "$OS_TYPE" = "macos-latest" ]; then
-    brew install graphviz
-else
-    echo "Unknown OS_TYPE: $OS_TYPE"
-fi
-
-set +eux
-
-echo Done installing dependencies
diff --git a/.maint/ci/install_extras.sh b/.maint/ci/install_extras.sh
deleted file mode 100755
index 725adb65b..000000000
--- a/.maint/ci/install_extras.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-
-echo Installing dependencies
-
-source .maint/ci/activate.sh
-source .maint/ci/env.sh
-
-set -eu
-
-# Required variables
-echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
-echo CHECK_TYPE = $CHECK_TYPE
-
-set -x
-
-if [ -n "$EXTRA_PIP_FLAGS" ]; then
-    EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
-fi
-
-pip install $EXTRA_PIP_FLAGS "fmriprep[$CHECK_TYPE]"
-
-set +eux
-
-echo Done installing dependencies
diff --git a/pyproject.toml b/pyproject.toml
index 80412448d..cbace0737 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -75,10 +75,11 @@ telemetry = [
     "sentry-sdk >= 1.3",
 ]
 test = [
-    "coverage",
+    "coverage[toml]",
     "pytest",
     "pytest-cov",
     "pytest-env",
+    "pytest-xdist",
 ]
 maint = [
     "fuzzywuzzy",
@@ -127,11 +128,21 @@ exclude = ".*"
 
 [tool.pytest.ini_options]
 minversion = "6"
-testpaths = ["fmriprep/tests"]
+testpaths = ["fmriprep"]
 log_cli_level = "INFO"
 xfail_strict = true
 norecursedirs = [".git"]
-addopts = ["-svx", "-ra", "--strict-config", "--strict-markers", "--doctest-modules"]
+addopts = [
+  "-svx",
+  "-ra",
+  "--strict-config",
+  "--strict-markers",
+  "--doctest-modules",
+  # Config pytest-cov
+  "--cov=fmriprep",
+  "--cov-report=xml",
+  "--cov-config=pyproject.toml",
+]
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
@@ -181,3 +192,15 @@ inline-quotes = "single"
 
 [tool.ruff.format]
 quote-style = "single"
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/_version.py"
+]
+
+[tool.coverage.paths]
+source = [
+  "fmriprep",
+  "**/site-packages/fmriprep"
+]
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 000000000..7b9fb6821
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,113 @@
+[tox]
+requires =
+  tox>=4
+envlist =
+  py3{10,11,12}-latest
+  py310-min
+  py3{10,11,12}-pre
+skip_missing_interpreters = true
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+  3.10: py310
+  3.11: py311
+  3.12: py312
+
+[gh-actions:env]
+DEPENDS =
+  min: min
+  latest: latest
+  pre: pre
+
+[testenv]
+description = Pytest with coverage
+labels = test
+pip_pre =
+  pre: true
+pass_env =
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+  PYTHON_GIL
+extras = test
+setenv =
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+deps =
+  min: nibabel == 4.0.1
+  min: nipype == 1.8.5
+  min: nitransforms == 21.0.0
+  min: numpy == 1.22
+  min: psutil == 5.4
+  min: pybids == 0.15.2
+  min: tedana == 23.0.2
+  min: templateflow == 24.1.0
+
+commands_pre =
+  python scripts/fetch_templates.py
+commands =
+  pytest --cov-report term-missing --durations=20 --durations-min=1.0 {posargs:-n auto}
+
+[testenv:style]
+description = Check our style guide
+labels = check
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --diff
+  ruff format --diff
+
+[testenv:style-fix]
+description = Auto-apply style guide to the extent possible
+labels = pre-release
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --fix
+  ruff format
+  ruff check --select ISC001
+
+[testenv:spellcheck]
+description = Check spelling
+labels = check
+deps =
+  codespell[toml]
+skip_install = true
+commands =
+  codespell . {posargs}
+
+[testenv:build{,-strict}]
+labels =
+  check
+  pre-release
+deps =
+  build
+  twine
+skip_install = true
+set_env =
+  # Ignore specific known warnings:
+  # https://github.com/pypa/pip/issues/11684
+  # https://github.com/pypa/pip/issues/12243
+  strict: PYTHONWARNINGS=error,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists
+commands =
+  python -m build
+  python -m twine check dist/*
+
+[testenv:publish]
+depends = build
+labels = release
+deps =
+  twine
+skip_install = true
+commands =
+  python -m twine upload dist/*