diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index d6384966..00000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,125 +0,0 @@
-name: CI
-
-on:
-  pull_request:
-  push:
-    branches:
-      - main
-
-jobs:
-  # pre-commit:
-  #   name: Lint
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - uses: actions/setup-python@v5
-  #       with:
-  #         python-version: '3.11'
-  #     - uses: pre-commit/action@v3.0.1
-  unit:
-    name: Unit tests
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install '.[dev,debug,inference]'
-
-      - name: Run tests
-        run: |
-          python -m pytest --cov=sc2ts tests/
-      # - name: Upload coverage to Coveralls
-      #   uses: coverallsapp/github-action@v2.3.0
-      #   with:
-      #     github-token: ${{ secrets.GITHUB_TOKEN }}
-      #     # The first coveralls upload will succeed and others seem to fail now.
-      #     # This is a quick workaround for doing a proper "parallel" setup:
-      #     # https://github.com/coverallsapp/github-action
-      #     fail-on-error: false
-
-  end_to_end:
-    name: End to end tests
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install '.[inference]'
-
-      - name: Create basedir
-        run: |
-          mkdir -p testrun
-          gunzip -k tests/data/alignments.fasta.gz
-
-      - name: Import alignments
-        run: |
-          sc2ts import-alignments -i testrun/dataset.zarr tests/data/alignments.fasta
-
-      - name: Import metadata
-        run: |
-          sc2ts import-metadata testrun/dataset.zarr tests/data/metadata.tsv
-
-      - name: Info dataset
-        run: |
-          sc2ts info-dataset testrun/dataset.zarr
-
-      - name: Run inference
-        run: |
-          # doing ~10 days here as this is taking a while
-          sc2ts infer tests/data/testrun-conf.toml --stop 2020-02-03
-
-      - name: Validate
-        run: |
-          sc2ts validate -v --date-field=date testrun/dataset.zarr testrun/results/test/test_2020-02-02.ts
-
-      - name: MatchDB
-        run: |
-          sc2ts info-matches testrun/test.matches.db
-
-  bare_api:
-    name: Bare API tests
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install '.'
-          python -m pip install pytest
-      - name: Run tests
-        run: |
-          # We are careful to pull in the minimum dependencies here
-          # and only operate on files stored in the repo
-          python -m pytest -v -c /dev/null -p no:sc2ts_fixtures tests/test_api.py
-
-  packaging:
-    name: Packaging tests
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install build twine validate-pyproject[all]
-      - name: Check and install package
-        run: |
-          validate-pyproject pyproject.toml
-          python -m build
-          python -m twine check --strict dist/*
-          python -m pip install dist/*.whl
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 928edb3a..a88e0b88 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -1,13 +1,11 @@
-name: Docs
+name: Build docs
 
 on:
   pull_request:
   push:
     branches: [main]
-    tags:
-      - '*'
   merge_group:
 
 jobs:
-  Docs:
-    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
+  docs:
+    uses: tskit-dev/.github/.github/workflows/docs.yml@v14
diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml
new file mode 100644
index 00000000..2c06cb88
--- /dev/null
+++ b/.github/workflows/integration.yml
@@ -0,0 +1,59 @@
+name: Integration tests
+
+on:
+  pull_request:
+  push:
+    branches: [main, test]
+  merge_group:
+
+jobs:
+  end-to-end:
+    name: End to end tests
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.2.2
+      - uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.11"
+          version: "0.8.15"
+      - name: Install dependencies
+        run: uv sync --locked --group test
+
+      - name: Create basedir
+        run: |
+          mkdir -p testrun
+          gunzip -k tests/data/alignments.fasta.gz
+
+      - name: Import alignments
+        run: uv run sc2ts import-alignments -i testrun/dataset.zarr tests/data/alignments.fasta
+
+      - name: Import metadata
+        run: uv run sc2ts import-metadata testrun/dataset.zarr tests/data/metadata.tsv
+
+      - name: Info dataset
+        run: uv run sc2ts info-dataset testrun/dataset.zarr
+
+      - name: Run inference
+        run: |
+          # doing ~10 days here as this is taking a while
+          uv run sc2ts infer tests/data/testrun-conf.toml --stop 2020-02-03
+
+      - name: Validate
+        run: uv run sc2ts validate -v --date-field=date testrun/dataset.zarr testrun/results/test/test_2020-02-02.ts
+
+      - name: MatchDB
+        run: uv run sc2ts info-matches testrun/test.matches.db
+
+  bare-api:
+    name: Bare API tests
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.2.2
+      - uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.11"
+          version: "0.8.15"
+      - name: Run tests
+        run: |
+          # Minimal deps only; avoid picking up conftest and fixtures
+          uv run pytest -v -c /dev/null -p no:sc2ts_fixtures tests/test_api.py
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 00000000..78fa03ca
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,9 @@
+name: Lint
+
+on:
+  pull_request:
+  merge_group:
+
+jobs:
+  lint:
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v14
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 00000000..dcc19989
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,25 @@
+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main, test]
+  merge_group:
+
+jobs:
+  packaging:
+    name: Python packaging
+    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v14
+
+  test:
+    name: Python
+    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v14
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python }}
+      coverage-directory: sc2ts
+    secrets: inherit
+    strategy:
+      matrix:
+        python: [3.11, 3.13]
+        os: [macos-latest, ubuntu-24.04]
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
new file mode 100644
index 00000000..1ca87e43
--- /dev/null
+++ b/.github/workflows/wheels.yml
@@ -0,0 +1,47 @@
+name: Publish Python release
+
+on:
+  push:
+    branches: [test-publish]
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.2.2
+        with:
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.12"
+          version: "0.8.15"
+      - run: uv build
+      - uses: actions/upload-artifact@v4.6.1
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    runs-on: ubuntu-24.04
+    environment: release
+    needs: [build]
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4.2.0
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to Test PyPI
+        if: github.event_name == 'push' && github.ref_name == 'test-publish'
+        uses: pypa/gh-action-pypi-publish@v1.13.0
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+
+      - name: Publish to PyPI
+        if: github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@v1.13.0
diff --git a/docs/Makefile b/docs/Makefile
index fe6c42d1..5fabd25d 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -1,16 +1,6 @@
-# Need to set PYTHONPATH so that we pick up the local sc2ts
-PYPATH=${PWD}/..
-SC2TS_VERSION:=$(shell PYTHONPATH=${PYPATH} \
-   python3 -c 'import sc2ts; print(sc2ts.__version__.split("+")[0])')
 
-dev:
-	PYTHONPATH=${PYPATH} ./build.sh
-
-dist:
-	@echo Building distribution for sc2ts version ${SC2TS_VERSION}
-	sed -i s/__SC2TS_VERSION__/${SC2TS_VERSION}/g _config.yml
-	PYTHONPATH=${PYPATH} ./build.sh
+all:
+	./build.sh
 
 clean:
 	rm -fR _build
-
diff --git a/docs/_config.yml b/docs/_config.yml
index 553428e6..8466510f 100644
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -43,7 +43,7 @@ sphinx:
       navigation_with_keys: false
       pygments_dark_style: monokai
       logo:
-        text: "Version __SC2TS_VERSION__"
+        text: "Version __PKG_VERSION__"
 
     myst_enable_extensions:
       - colon_fence
diff --git a/docs/build.sh b/docs/build.sh
index 50be22cd..a3a3dbf1 100755
--- a/docs/build.sh
+++ b/docs/build.sh
@@ -6,7 +6,7 @@
 
 REPORTDIR=_build/html/reports
 
-jupyter-book build -W . 
+uv run --project=../python --group docs jupyter-book build . -vnW --keep-going
 RETVAL=$?
 if [ $RETVAL -ne 0 ]; then
     if [ -e $REPORTDIR ]; then
@@ -18,4 +18,3 @@ else
     rm -f $REPORTDIR/*
 fi
 exit $RETVAL
-
diff --git a/docs/make_sc2ts_arg_subset.py b/docs/make_sc2ts_arg_subset.py
index a2b01c88..8ebe3cc6 100644
--- a/docs/make_sc2ts_arg_subset.py
+++ b/docs/make_sc2ts_arg_subset.py
@@ -1,5 +1,5 @@
-import tszip
 import numpy as np
+import tszip
 
 ts = tszip.load("sc2ts_viridian_v1.2.trees.tsz")
 
diff --git a/docs/make_viridian_subset.py b/docs/make_viridian_subset.py
index 011cb521..953ad8ce 100644
--- a/docs/make_viridian_subset.py
+++ b/docs/make_viridian_subset.py
@@ -9,4 +9,3 @@
 path = f"viridian_mafft_subset_{k}_v1.vcz"
 ds.copy(path, sample_id=samples)
 sc2ts.Dataset.create_zip(path, path + ".zip")
-
diff --git a/prek.toml b/prek.toml
new file mode 100644
index 00000000..16363167
--- /dev/null
+++ b/prek.toml
@@ -0,0 +1,40 @@
+# The prek configuration defining linting requirements. This
+# setup is optimised for long-term stability and determinism,
+# and therefore only uses either "builtin" rules or "local"
+# rules implementing lint workflows.  We do not use any remote
+# workflow repos.
+
+[[repos]]
+repo = "builtin"
+hooks = [
+    { id = "check-added-large-files" },
+    { id = "check-merge-conflict" },
+    { id = "mixed-line-ending" },
+    { id = "check-case-conflict" },
+    { id = "check-yaml" },
+    { id = "check-toml" },
+]
+
+[[repos]]
+repo = "local"
+hooks = [
+  {
+    id = "ruff-check",
+    name = "ruff check",
+    language = "system",
+    entry = "uv run --only-group lint ruff check --fix --force-exclude",
+    types = ["python"],
+  },
+]
+
+[[repos]]
+repo = "local"
+hooks = [
+  {
+    id = "ruff-format",
+    name = "ruff format",
+    language = "system",
+    entry = "uv run --only-group lint ruff format --force-exclude",
+    types = ["python"],
+  },
+]
diff --git a/pyproject.toml b/pyproject.toml
index 9c0f6740..156077f0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,6 @@ dependencies = [
   "tszip",
   "pandas",
   "tqdm",
-  "zarr<3",
   "click>=8.2",
   # Not strictly needed for base functionality, but easier to include
   # as imported by the CLI
@@ -27,46 +26,71 @@ Documentation = "https://tskit.dev/sc2ts/docs/"
 "Bug Tracker" = "https://github.com/tskit-dev/sc2ts/issues"
 GitHub = "https://github.com/tskit-dev/sc2ts/"
 
-
 [project.scripts]
 sc2ts = "sc2ts.cli:cli"
 
+# NOTE: project.optional-dependencies and the dependency-groups below
+# cannot be deduplicated as they serve different purposes.
 [project.optional-dependencies]
-dev = [
-  "msprime",
-  "sgkit",
-  "pytest",
-  "pytest-coverage",
-  "tomli-w",
-]
 inference = [
   "scipy",
   "biotite",
-  "tsinfer>=0.5",
+  "tsinfer>=0.5,<1",
   "pyfaidx",
   "numba",
+  "zarr<3",
 ]
 debug = [
   "matplotlib",
   "IPython",
 ]
+
+[dependency-groups]
+test = [
+  "msprime",
+  "pytest",
+  "pytest-cov",
+  "pytest-xdist",
+  "xarray",
+  "tomli-w",
+  # inference and debug deps needed by the test suite
+  "scipy",
+  "biotite",
+  "tsinfer>=0.5,<1",
+  "pyfaidx",
+  "numba",
+  "matplotlib",
+  "IPython",
+]
 docs = [
-  "jupyter-book==1.0.4.post1",
+  "jupyter-book<2",
   "sphinx-book-theme",
   "sphinx-copybutton",
   "sphinx-click",
-  "setuptools_scm",
-  "sphinx-argparse==0.5.2",
-  "sphinx-issues==5.0.1",
+  "sphinx-argparse",
+  "sphinx-issues",
   "IPython",
-  # docs requires running the CLI, which means we need to full inference 
-  # requirements also
+  # docs require running the CLI, which means the full inference deps are needed
   "scipy",
   "biotite",
   "tsinfer>=0.5",
   "pyfaidx",
   "numba",
 ]
+lint = [
+  "ruff==0.15.1",
+  "prek==0.3.3",
+]
+packaging = [
+  "twine",
+  "validate-pyproject[all]",
+]
+dev = [
+  {include-group = "docs"},
+  {include-group = "lint"},
+  {include-group = "test"},
+  {include-group = "packaging"},
+]
 
 [build-system]
 requires = [
@@ -84,4 +108,28 @@ write_to = "sc2ts/_version.py"
 
 [tool.pytest.ini_options]
 testpaths = "tests"
-addopts = "--cov=sc2ts --cov-report term-missing"
+
+[tool.ruff]
+target-version = "py311"
+line-length = 89
+
+[tool.ruff.lint]
+select = ["E", "F", "B", "W", "I", "N", "UP", "A", "PT"]
+fixable = ["ALL"]
+
+
+ignore = [
+    "A001", "A002", "RUF",
+    "B905", #Don't add strict=False to zips (B905)
+    "E741", # using 'l' as a variable name
+    "N806", "N802", "N803", # Various nags about uppercase vars
+    "F821", # Undefined name `List`
+    "B006", # Do not use mutable data structures for argument defaults
+    "E721", # Use `is` and `is not` for type comparisons, or `isinstance()`
+    "F841", # Local variable `shape` is assigned to but never
+    "PT018", # Assertion should be broken down into multiple parts
+    "B007", # Loop control variable `j` not used within
+    "PT006", # Wrong type passed to first argument of `pytest.mar
+    "PT007", # Wrong values type in `pytest.mark.parametrize`
+    "PT009", # Use a regular `assert` instead of unittest-style
+]
diff --git a/sc2ts/__init__.py b/sc2ts/__init__.py
index 69a09969..ca55d3a0 100644
--- a/sc2ts/__init__.py
+++ b/sc2ts/__init__.py
@@ -1,6 +1,11 @@
-from .core import __version__
-
 # star imports are fine here as it's just a bunch of constants
-from .core import *
-from .dataset import mask_ambiguous, mask_flanking_deletions, decode_alleles, Dataset, Variant
-from .stats import node_data, mutation_data
+from .core import *  # noqa
+from .core import __version__  # noqa
+from .dataset import (
+    Dataset,  # noqa
+    Variant,  # noqa
+    decode_alleles,  # noqa
+    mask_ambiguous,  # noqa
+    mask_flanking_deletions,  # noqa
+)
+from .stats import mutation_data, node_data  # noqa
diff --git a/sc2ts/__main__.py b/sc2ts/__main__.py
index 0b6a7bb7..91e12cb2 100644
--- a/sc2ts/__main__.py
+++ b/sc2ts/__main__.py
@@ -1,5 +1,4 @@
 from . import cli
 
-
 if __name__ == "__main__":
     cli.cli()
diff --git a/sc2ts/cli.py b/sc2ts/cli.py
index 8df17e68..abbb45ed 100644
--- a/sc2ts/cli.py
+++ b/sc2ts/cli.py
@@ -1,31 +1,22 @@
-import json
 import collections
 import concurrent.futures as cf
+import datetime
+import json
 import logging
-import itertools
 import pathlib
 import sys
-import contextlib
-import dataclasses
-import datetime
-import time
-from typing import List
 
-import tomli
-import numpy as np
-import tqdm
-import tskit
-import tszip
 import click
 import humanize
+import numpy as np
 import pandas as pd
+import tomli
+import tqdm
+import tszip
 
 import sc2ts
-from . import core
-from . import data_import
-from . import tree_ops
-from . import jit
-from . import validation
+
+from . import core, data_import, jit, tree_ops, validation
 from . import inference as si  # sc2ts inference
 
 logger = logging.getLogger(__name__)
@@ -86,7 +77,11 @@ def summarise_usage(ts):
     max_mem = d["max_memory"]
     if max_mem > 0:
         maxmem_str = "; max_memory=" + humanize.naturalsize(max_mem, binary=True)
-    return f"elapsed={wall_time:.2f}m; user={user_time:.2f}m; sys={sys_time:.2f}m{maxmem_str}"
+    return (
+        f"elapsed={wall_time:.2f}m; "
+        f"user={user_time:.2f}m; "
+        f"sys={sys_time:.2f}m{maxmem_str}"
+    )
 
 
 def setup_logging(verbosity, log_file=None, date=None):
@@ -129,8 +124,7 @@ def setup_logging(verbosity, log_file=None, date=None):
     is_flag=True,
     flag_value=True,
     help=(
-        "If true, initialise a new dataset. WARNING! This will erase an existing "
-        "store"
+        "If true, initialise a new dataset. WARNING! This will erase an existing store"
     ),
 )
 @progress
@@ -280,9 +274,7 @@ def _run_extend(out_path, verbose, log_file, **params):
 
 @click.command()
 @click.argument("config_file", type=click.File(mode="rb"))
-@click.option(
-    "--start", default=None, help="Start inference at this date (inclusive). "
-)
+@click.option("--start", default=None, help="Start inference at this date (inclusive). ")
 @click.option(
     "--stop",
     default="3000",
@@ -373,9 +365,7 @@ def infer(config_file, start, stop, force):
 
         base_ts = ts_file_pattern.format(date=date)
         with cf.ProcessPoolExecutor(1) as executor:
-            future = executor.submit(
-                _run_extend, base_ts, log_level, log_file, **params
-            )
+            future = executor.submit(_run_extend, base_ts, log_level, log_file, **params)
             # Block and wait, raising exception if it occured
             future.result()
 
@@ -428,9 +418,7 @@ def validate(
     setup_logging(verbose)
 
     ts = tszip.load(ts_file)
-    ds = sc2ts.Dataset(
-        dataset, date_field=date_field, chunk_cache_size=chunk_cache_size
-    )
+    ds = sc2ts.Dataset(dataset, date_field=date_field, chunk_cache_size=chunk_cache_size)
     if genotypes:
         validation.validate_genotypes(ts, ds, deletions_as_missing, show_progress=True)
     if metadata:
@@ -749,9 +737,7 @@ def find_previous_date_path(date, path_pattern):
         if path.exists():
             break
     else:
-        raise ValueError(
-            f"No path exists for pattern {path_pattern} starting at {date}"
-        )
+        raise ValueError(f"No path exists for pattern {path_pattern} starting at {date}")
     return path
 
 
diff --git a/sc2ts/data_import.py b/sc2ts/data_import.py
index fbb1939b..dc14e961 100644
--- a/sc2ts/data_import.py
+++ b/sc2ts/data_import.py
@@ -1,6 +1,6 @@
 import collections.abc
-import pathlib
 import csv
+import pathlib
 
 import numpy as np
 import pyfaidx
@@ -140,4 +140,3 @@ def massage_viridian_metadata(df):
         a[~missing] = np.array(data[~missing], dtype=int)
         df[name] = a
     return df
-
diff --git a/sc2ts/dataset.py b/sc2ts/dataset.py
index 61c89704..d6f1c02c 100644
--- a/sc2ts/dataset.py
+++ b/sc2ts/dataset.py
@@ -2,20 +2,19 @@
 Methods for managing a sc2ts Zarr based dataset.
 """
 
-import dataclasses
-import os.path
-import zipfile
 import collections
+import concurrent.futures as cf
+import dataclasses
 import logging
+import os.path
 import pathlib
-import concurrent.futures as cf
+import zipfile
 
-import tskit
-import tqdm
-import pandas as pd
-import zarr
 import numcodecs
 import numpy as np
+import pandas as pd
+import tqdm
+import zarr
 
 from sc2ts import core
 
@@ -236,6 +235,7 @@ class Variant:
     Represents a single variant, including the genomic position and the integer encoded
     genotypes.
     """
+
     position: int
     genotypes: np.ndarray
     alleles: list
@@ -252,6 +252,7 @@ class Dataset(collections.abc.Mapping):
     :param int chunk_cache_size: Maximum number of chunks to cache for
         alignments and metadata. Defaults to 1.
     """
+
     def __init__(self, path, chunk_cache_size=1, date_field=None):
         logger.info(f"Loading dataset @{path} using {date_field} as date field")
         self.date_field = date_field
diff --git a/sc2ts/debug.py b/sc2ts/debug.py
index 80a76d4f..68545225 100644
--- a/sc2ts/debug.py
+++ b/sc2ts/debug.py
@@ -4,28 +4,24 @@
 included if the "debug"] option is included with the sc2ts
 install.
 """
+
 import collections
-import logging
-import json
-import warnings
 import dataclasses
 import datetime
+import json
+import logging
 import re
-from typing import List
+import warnings
 
-import tskit
-import numpy as np
-from tqdm.auto import tqdm
-import pandas as pd
 import humanize
 import matplotlib.pyplot as plt
-from matplotlib import colors
-from IPython.display import Markdown, HTML
+import numpy as np
+import pandas as pd
+import tskit
+from IPython.display import HTML, Markdown
+from tqdm.auto import tqdm
 
-from . import jit
-from . import core
-from . import inference
-from . import data_import
+from . import core, data_import, inference, jit
 
 logger = logging.getLogger(__name__)
 
@@ -89,7 +85,6 @@ def max_descendant_samples(ts, show_progress=True):
 
 
 class CopyingTable:
-
     default_colours = (  # Chosen to be light enough that black text on top is readable
         "#FC0",  # Gold for de-novo mutations
         "#8D8",  # Copy from first parent: light green
@@ -117,7 +112,7 @@ def line_cell(pos, prev_pos, next_pos):
             dist_to_left = 0
         if dist_to_right > 2:
             dist_to_right = 0
-        return f'<td title="{pos}" class="run-{int(dist_to_left)}-{int(dist_to_right)}"></td>'
+        return f'<td title="{pos}" "class="run-{int(dist_to_left)}-{int(dist_to_right)}"></td>'  # noqa E501
 
     def node_mutations(self):
         muts = {}
@@ -206,10 +201,11 @@ def html(
             matches the first parent, ``colours[2]`` for the second parent, etc.
             Default: None, treated as ``["#FC0", "#8D8", "#6AD", "#B9D", "#A88"]``.
         :param exclude_stylesheet bool:
-            If True, exclude the default stylesheet from the HTML output. This is useful
-            simply to save space if you want to include the copying table in a larger HTML
-            document (e.g. a Jupyter notebook) that already has one copying table shown with
-            the standard stylesheet. If False or None (default), include the default stylesheet.
+            If True, exclude the default stylesheet from the HTML output. This
+            is useful simply to save space if you want to include the copying
+            table in a larger HTML document (e.g. a Jupyter notebook) that
+            already has one copying table shown with the standard stylesheet.
+            If False or None (default), include the default stylesheet.
         :param font_family str:
             The font family to use for the table. Default: None.
         :param css_class str:
@@ -284,7 +280,7 @@ def label(allele, default=""):
                         except IndexError as e:
                             raise ValueError(
                                 "Displaying the copying path only deals with a max of "
-                                f"{len(parent_colours)-1} parents"
+                                f"{len(parent_colours) - 1} parents"
                             ) from e
                     elif parent_allele == var.site.ancestral_state:
                         col = "#DDD"
@@ -310,19 +306,20 @@ def label(allele, default=""):
             runlength_cols = ("white", "red", "orange")
             bg_im_src = (
                 "background-image:linear-gradient(to right, {0} 50%, {1} 50%);"
-                "background-image:-webkit-linear-gradient(left, {0} 50%, {1} 50%);"  # for imgkit/wkhtmltopdf
+                # for imgkit/wkhtmltopdf
+                "background-image:-webkit-linear-gradient(left, {0} 50%, {1} 50%);"
             )
             html += "<style>"
             if font_family is not None:
                 html += f".copying-table {{font-family: '{font_family}'}}"
             html += ".copying-table .position {text-align: center; font-size: 7px}"
-            html += ".copying-table .pattern td {border:0px solid black; text-align: center; width:1em}"
+            html += ".copying-table .pattern td {border:0px solid black; text-align: center; width:1em}"  # noqa: E501
             html += ".copying-table .mut {text-align: center; font-size: 7px}"
             html += ".copying-table .ref {text-align: center; font-size: 9px}"
             html += ".copying-table {border-spacing: 0px; border-collapse: collapse}"
             html += ".copying-table .runlengths {font-size:3px; height:3px;}"
             html += ".copying-table .child-rgt {text-align: left;}"
-            html += ".copying-table .runlengths td {border-style: solid; background: white; border-width:0px 1px; border-color: black}"
+            html += ".copying-table .runlengths td {border-style: solid; background: white; border-width:0px 1px; border-color: black}"  # noqa: E501
             for left in range(len(runlength_cols)):
                 for right in range(len(runlength_cols)):
                     html += (
@@ -350,7 +347,8 @@ def label(allele, default=""):
         html += row_template.format(label=row_lab(child_label), data="".join(child))
         for i, parent in enumerate(parents):
             html += row_template.format(
-                label=row_lab(parent_labels.get(i + 1, f"P{i+1}")), data="".join(parent)
+                label=row_lab(parent_labels.get(i + 1, f"P{i + 1}")),
+                data="".join(parent),
             )
         if not hide_runlengths:
             p = np.concatenate(([-np.inf], positions, [np.inf]))
@@ -391,12 +389,8 @@ def __init__(
         samples = ts.samples()
         self.strain_map = dict(zip(top_level_md["samples_strain"], ts.samples()))
 
-        self.sites_num_mutations = np.bincount(
-            ts.mutations_site, minlength=ts.num_sites
-        )
-        self.nodes_num_mutations = np.bincount(
-            ts.mutations_node, minlength=ts.num_nodes
-        )
+        self.sites_num_mutations = np.bincount(ts.mutations_site, minlength=ts.num_sites)
+        self.nodes_num_mutations = np.bincount(ts.mutations_node, minlength=ts.num_nodes)
         self.nodes_num_parents = np.bincount(ts.edges_child, minlength=ts.num_edges)
 
         # The number of samples per day in time-ago (i.e., the nodes_time units).
@@ -456,9 +450,7 @@ def _preprocess_nodes(self, show_progress):
         self.first_scorpio_sample = {}
 
         # NOTE: keyed by *string* because of JSON
-        exact_matches = ts.metadata["sc2ts"]["cumulative_stats"]["exact_matches"][
-            "node"
-        ]
+        exact_matches = ts.metadata["sc2ts"]["cumulative_stats"]["exact_matches"]["node"]
 
         iterator = tqdm(
             ts.nodes(),
@@ -567,7 +559,10 @@ def _preprocess_mutations(self, show_progress):
             parent = ts.mutations_parent[mut_id]
             if parent != -1:
                 mutations_num_inheritors[parent] -= descendants
-                is_reversion[mut_id] = self.mutations_inherited_state[parent] == self.mutations_derived_state[mut_id]
+                is_reversion[mut_id] = (
+                    self.mutations_inherited_state[parent]
+                    == self.mutations_derived_state[mut_id]
+                )
                 if is_reversion[mut_id] and ts.mutations_node[parent] == tree.parent(
                     mutation_node
                 ):
@@ -579,7 +574,10 @@ def _preprocess_mutations(self, show_progress):
                 parent = ts.mutations_parent[parent]
             mutations_num_parents[mut_id] = num_parents
             # Ts/Tvs
-            key = (self.mutations_inherited_state[mut_id], self.mutations_derived_state[mut_id])
+            key = (
+                self.mutations_inherited_state[mut_id],
+                self.mutations_derived_state[mut_id],
+            )
             mutations_is_transition[mut_id] = key in transitions
             mutations_is_transversion[mut_id] = key in transversions
             site = ts.mutations_site[mut_id]
@@ -612,7 +610,7 @@ def summary(self):
         re_nodes = np.sum(self.ts.nodes_flags == core.NODE_IS_RECOMBINANT)
         exact_matches = np.sum((self.ts.nodes_flags & core.NODE_IS_EXACT_MATCH) > 0)
         imr_nodes = np.sum(
-            (self.ts.nodes_flags == core.NODE_IS_IMMEDIATE_REVERSION_MARKER)
+            self.ts.nodes_flags == core.NODE_IS_IMMEDIATE_REVERSION_MARKER
         )
 
         samples = self.ts.samples()[1:]  # skip reference
@@ -707,10 +705,7 @@ def _node_summary(self, u, child_mutations=True):
             strain = md["strain"]
         else:
             md = md.get("sc2ts", {})
-            if (
-                flags & (core.NODE_IS_MUTATION_OVERLAP | core.NODE_IS_REVERSION_PUSH)
-                > 0
-            ):
+            if flags & (core.NODE_IS_MUTATION_OVERLAP | core.NODE_IS_REVERSION_PUSH) > 0:
                 try:
                     strain = f"{md['date_added']}:{', '.join(md['mutations'])}"
                 except KeyError:
@@ -941,7 +936,8 @@ def node_info(node, label):
             interval_left = interval[0][0]
             if interval_left >= interval_right:
                 logger.warning(
-                    f"RE: {u} interval_right >= interval_left; moving from {interval_left}"
+                    f"RE: {u} interval_right >= interval_left; "
+                    f"moving from {interval_left}"
                     f"to {interval_right - 1}"
                 )
                 interval_left = interval_right - 1
@@ -1510,7 +1506,7 @@ def plot_samples_per_day(
                     first_date = self.nodes_date[self.first_scorpio_sample[col]]
                     first_scorpio_date.append((first_date, col))
                 except KeyError:
-                    warnings.warn(f"No samples for Scorpio {col} present")
+                    warnings.warn(f"No samples for Scorpio {col} present", stacklevel=2)
 
         df_scorpio = df_scorpio[keep_cols]
         ax4.set_title("Scorpio composition of processed samples")
@@ -1629,7 +1625,10 @@ def draw_pango_lineage_subtree(
         appropriate set of samples. See that function for more details.
         """
         return self.draw_subtree(
-            tracked_pango=[pango_lineage], position=position, *args, **kwargs
+            tracked_pango=[pango_lineage],
+            position=position,
+            *args,  # noqa B026
+            **kwargs,
         )
 
     def draw_subtree(
@@ -1764,9 +1763,7 @@ def draw_subtree(
 
         if extra_tracked_samples is not None:
             tn_set = set(tracked_nodes)
-            extra_tracked_samples = [
-                e for e in extra_tracked_samples if e not in tn_set
-            ]
+            extra_tracked_samples = [e for e in extra_tracked_samples if e not in tn_set]
             tracked_nodes = np.concatenate((tracked_nodes, extra_tracked_samples))
         tree = ts.at(position, tracked_samples=tracked_nodes)
         order = np.array(
@@ -1868,7 +1865,7 @@ def draw_subtree(
         re_nodes = np.where(ts.nodes_flags & core.NODE_IS_RECOMBINANT)[0]
         styles.append(
             ",".join([f".node.n{u} > .sym" for u in re_nodes])
-            + f"{{r:{symbol_size/2*1.5:.2f}px; stroke:black; fill:white}}"
+            + f"{{r:{symbol_size / 2 * 1.5:.2f}px; stroke:black; fill:white}}"
         )
         if date_format == "cal":
             if y_ticks is not None:
@@ -1950,7 +1947,7 @@ class DeletionEvent:
     start: int
     node: int
     length: int
-    mutations: List
+    mutations: list
 
 
 def country_abbr(country):
@@ -1971,7 +1968,7 @@ def country_abbr(country):
 @dataclasses.dataclass
 class SampleGroupInfo:
     group_id: str
-    nodes: List[int]
+    nodes: list[int]
     ts: tskit.TreeSequence
     attach_date: None
 
@@ -1989,22 +1986,26 @@ def draw_svg(
         **kwargs,
     ):
         """
-        Draw an SVG representation of the tree of samples that trace to a single origin.
+        Draw an SVG representation of the tree of samples that trace to a
+        single origin.
 
         The default style is to colour mutations such that sites with a single
-        mutation in the tree are dark red, whereas sites with multiple mutations
-        show those mutations in red or magenta (magenta when a mutation immediately
-        reverts its parent mutation). Any identical mutations (from the same inherited
-        to derived state at the same site, i.e. recurrent mutations) have the count of
-        recurrent mutations appended to the label, e.g. "C842T (1/2)".
-
-        If highlight_universal_mutations is set, then mutations in the ancestry of all
-        the samples (i.e. between the root and the MRCA of all the samples) are highlighted
+        mutation in the tree are dark red, whereas sites with multiple
+        mutations show those mutations in red or magenta (magenta when a
+        mutation immediately reverts its parent mutation). Any identical
+        mutations (from the same inherited to derived state at the same site,
+        i.e. recurrent mutations) have the count of recurrent mutations
+        appended to the label, e.g. "C842T (1/2)".
+
+        If highlight_universal_mutations is set, then mutations in the ancestry
+        of all the samples (i.e. between the root and the MRCA of all the
+        samples) are highlighted
         in bold and with thicker symbol lines
 
-        If genetic_regions is set, it should be a dictionary mapping (start, end) tuples
-        to region names. These will be drawn as coloured rectangles on the x-axis. If None,
-        a default selection of SARS-CoV-2 genes will be used.
+        If genetic_regions is set, it should be a dictionary mapping (start,
+        end) tuples to region names. These will be drawn as coloured rectangles
+        on the x-axis. If None, a default selection of SARS-CoV-2 genes will be
+        used.
         """
         if x_regions is None:
             x_regions = {
@@ -2039,7 +2040,7 @@ def draw_svg(
             }
         elif node_labels == "pango+country":
             node_labels = {
-                n.id: f"{n.metadata.get(pango_md, '')}:{country_abbr(n.metadata.get('Country', ''))}"
+                n.id: f"{n.metadata.get(pango_md, '')}:{country_abbr(n.metadata.get('Country', ''))}"  # noqa E501
                 for n in ts.nodes()
                 if pango_md in n.metadata or "Country" in n.metadata
             }
@@ -2081,13 +2082,16 @@ def draw_svg(
                     mutation_labels[label].append(mut.id)
             # If more than one mutation has the same label, add a prefix with the counts
             mutation_labels = {
-                m_id: label + (f" ({i+1}/{len(ids)})" if len(ids) > 1 else "")
+                m_id: label + (f" ({i + 1}/{len(ids)})" if len(ids) > 1 else "")
                 for label, ids in mutation_labels.items()
                 for i, m_id in enumerate(ids)
             }
         # some default styles
         styles = [
-            ".mut .lab {fill: darkred} .mut .sym {stroke: darkred} .background path {fill: white}"
+            (
+                ".mut .lab {fill: darkred} .mut .sym {stroke: darkred} "
+                ".background path {fill: white}"
+            )
         ]
         if len(multiple_mutations) > 0:
             lab_css = ", ".join(f".mut.m{m} .lab" for m in multiple_mutations)
@@ -2112,7 +2116,7 @@ def draw_svg(
         re_nodes = np.where(ts.nodes_flags & core.NODE_IS_RECOMBINANT)[0]
         styles.append(
             ",".join([f".node.n{u} > .sym" for u in re_nodes])
-            + f"{{r: {symbol_size/2*1.5:.2f}px; stroke: black; fill: white}}"
+            + f"{{r: {symbol_size / 2 * 1.5:.2f}px; stroke: black; fill: white}}"
         )
         svg = self.ts.draw_svg(
             size=size,
@@ -2135,14 +2139,20 @@ def draw_svg(
 
             # Find SVG positions of the X axis
             m = re.search(
-                r'class="x-axis".*?class="ax-line" x1="([\d\.]+)" x2="([\d\.]+)" y1="([\d\.]+)"',
+                r'class="x-axis".*?class="ax-line" x1="([\d\.]+)" x2="([\d\.]+)" y1="([\d\.]+)"',  # noqa E501
                 svg,
             )
             assert m is not None
             x1, x2, y1 = float(m.group(1)), float(m.group(2)), float(m.group(3))
             xdiff = x2 - x1
-            x_box_svg = '<rect fill="yellow" stroke="black" x="{x}" width="{w}" y="{y}" height="{h}" />'
-            x_name_svg = '<text text-anchor="middle" alignment-baseline="hanging" x="{x}" y="{y}">{name}</text>'
+            x_box_svg = (
+                '<rect fill="yellow" stroke="black" x="{x}" '
+                'width="{w}" y="{y}" height="{h}" />'
+            )
+            x_name_svg = (
+                '<text text-anchor="middle" alignment-baseline="hanging" '
+                'x="{x}" y="{y}">{name}</text>'
+            )
             x_scale = xdiff / ts.sequence_length
             x_boxes = [
                 x_box_svg.format(
diff --git a/sc2ts/inference.py b/sc2ts/inference.py
index 575e63f7..9d89f17c 100644
--- a/sc2ts/inference.py
+++ b/sc2ts/inference.py
@@ -1,37 +1,31 @@
 from __future__ import annotations
+
 import bz2
-import logging
-import datetime
-import dataclasses
 import collections
-import concurrent.futures as cf
+import dataclasses
+import datetime
+import hashlib
 import inspect
-import time
 import json
-import pickle
-import hashlib
-import sqlite3
+import logging
+import os
 import pathlib
+import pickle
 import random
-import os
+import sqlite3
 import threading
+import time
 
-import tqdm
-import tskit
-import tszip
 import _tsinfer
-import tsinfer
-import numpy as np
-import zarr
-import numba
 import humanize
+import numpy as np
 import pandas as pd
+import tqdm
+import tsinfer
+import tskit
+import tszip
 
-from . import core
-from . import data_import
-from . import jit
-from . import stats
-from . import tree_ops
+from . import core, data_import, jit, stats, tree_ops
 from . import dataset as _dataset
 
 logger = logging.getLogger(__name__)
@@ -227,7 +221,7 @@ def initialise(db_path):
         with sqlite3.connect(db_path) as conn:
             conn.execute(sql)
             conn.execute(
-                "CREATE INDEX [ix_samples_match_date] on 'samples' " "([match_date]);"
+                "CREATE INDEX [ix_samples_match_date] on 'samples' ([match_date]);"
             )
         logger.info(f"Created new MatchDb at {db_path}")
         return MatchDb(db_path)
@@ -270,7 +264,9 @@ def mirror_ts_coordinates(ts):
     return tables.tree_sequence()
 
 
-def initial_ts(problematic_sites=list()):
+def initial_ts(problematic_sites=None):
+    if problematic_sites is None:
+        problematic_sites = []
     reference = data_import.get_reference_sequence()
     L = core.REFERENCE_SEQUENCE_LENGTH
     assert L == len(reference)
@@ -461,7 +457,7 @@ def match_samples(
         deletions_as_missing=deletions_as_missing,
         show_progress=show_progress,
         progress_title=date,
-        progress_phase=f"match(F)",
+        progress_phase="match(F)",
     )
 
 
@@ -497,9 +493,7 @@ def preprocess(
         # Do we need to do this here? Would be easier to do later, maybe
         sample.haplotype = _dataset.mask_ambiguous(a)
         counts = collections.Counter(a)
-        sample.alignment_composition = {
-            alleles[k]: count for k, count in counts.items()
-        }
+        sample.alignment_composition = {alleles[k]: count for k, count in counts.items()}
         samples.append(sample)
     return samples
 
@@ -706,7 +700,7 @@ def _extend(
 
         ts = add_exact_matches(ts=ts, match_db=match_db, date=date)
 
-        logger.info(f"Update ARG with low-cost samples")
+        logger.info("Update ARG with low-cost samples")
         ts, _ = add_matching_results(
             f"match_date=='{date}' and hmm_cost>0 and hmm_cost<={hmm_cost_threshold}",
             ts=ts,
@@ -735,8 +729,7 @@ def _extend(
     )
     for group in groups:
         logger.warning(
-            f"Add retro group {group.summary()}:"
-            f"{group.tree_quality_metrics.summary()}"
+            f"Add retro group {group.summary()}:{group.tree_quality_metrics.summary()}"
         )
 
     return update_top_level_metadata(ts, date, groups, samples)
@@ -746,7 +739,6 @@ def update_top_level_metadata(ts, date, retro_groups, samples):
     tables = ts.dump_tables()
     md = tables.metadata
     md["sc2ts"]["date"] = date
-    num_samples = len(samples)
     samples_strain = md["sc2ts"]["samples_strain"]
     new_samples = ts.samples()[len(samples_strain) :]
     inserted_samples = set()
@@ -823,7 +815,6 @@ def match_path_ts(group):
     tables.nodes.metadata_schema = tskit.MetadataSchema.permissive_json()
     tables.mutations.metadata_schema = tskit.MetadataSchema.permissive_json()
     site_id_map = {}
-    first_sample = len(tables.nodes)
     root = len(group)
     group_id = group.sample_hash
     for sample in group:
@@ -1064,7 +1055,8 @@ def add_matching_results(
                 continue
             if tqm.mean_mutations_per_sample > max_mutations_per_sample:
                 logger.debug(
-                    f"Skipping mean_mutations_per_sample={tqm.mean_mutations_per_sample} "
+                    "Skipping "
+                    f"mean_mutations_per_sample={tqm.mean_mutations_per_sample} "
                     f"exceeds threshold {group.summary()}"
                 )
                 continue
@@ -1544,9 +1536,6 @@ def summary(self):
             f"={self.mutation_summary()}"
         )
 
-    def compute_cost(self, num_mismatches):
-        self.cost = num_mismatches * (len(self.path) - 1) + len(self.mutations)
-
     @property
     def breakpoints(self):
         breakpoints = [seg.left for seg in self.path]
@@ -1654,9 +1643,7 @@ def get_closest_mutation(node, site_id):
                     closest_mutation.inherited_state == mutation.derived_state
                 )
                 if mutation.is_reversion:
-                    mutation.is_immediate_reversion = (
-                        closest_mutation.node == seg.parent
-                    )
+                    mutation.is_immediate_reversion = closest_mutation.node == seg.parent
     logger.debug(f"Characterised {num_mutations} mutations")
 
 
@@ -1720,9 +1707,7 @@ def attach_tree(
     tree = child_ts.first()
     has_root_mutations = np.any(child_ts.mutations_node == tree.root)
     condition = (
-        has_root_mutations
-        or len(attach_path) > 1
-        or len(group.immediate_reversions) > 0
+        has_root_mutations or len(attach_path) > 1 or len(group.immediate_reversions) > 0
     )
     if condition:
         child_ts = add_root_edge(child_ts)
@@ -2225,8 +2210,7 @@ def rewire_long_branch_splits(ts, rematch_results):
         logger.info(f"Rewiring for {rematch.recombinant}")
         for seg in rematch.original_match.path:
             e = np.where(
-                (ts.edges_child == rematch.recombinant)
-                & (ts.edges_parent == seg.parent)
+                (ts.edges_child == rematch.recombinant) & (ts.edges_parent == seg.parent)
             )[0]
             assert ts.edges_left[e] == seg.left
             assert ts.edges_right[e] == seg.right
@@ -2304,8 +2288,7 @@ def rewire_long_branch_splits(ts, rematch_results):
         tables.nodes[rematch.recombinant] = row.replace(flags=0)
 
     logger.info(
-        f"Deleting {len(edges_to_delete)} edges and "
-        f"{len(mutations_to_delete)} mutations"
+        f"Deleting {len(edges_to_delete)} edges and {len(mutations_to_delete)} mutations"
     )
 
     return tree_ops.update_tables(tables, edges_to_delete, mutations_to_delete)
@@ -2442,7 +2425,7 @@ def map_parsimony(ts, ds, sites=None, *, show_progress=False):
 
     added_mutations = len(tables.mutations) - ts.num_mutations
     logger.info(
-        f"Added in {added_mutations} mutations at " f"{len(sites)} sites with parsimony"
+        f"Added in {added_mutations} mutations at {len(sites)} sites with parsimony"
     )
 
     keep_mutations = np.append(keep_mutations, np.ones(added_mutations, dtype=bool))
diff --git a/sc2ts/jit.py b/sc2ts/jit.py
index eaed6e47..dfaf75a7 100644
--- a/sc2ts/jit.py
+++ b/sc2ts/jit.py
@@ -1,10 +1,10 @@
 import dataclasses
 import logging
 
-import numpy as np
 import numba
-import tskit.jit.numba as tskit_numba
+import numpy as np
 import tskit
+import tskit.jit.numba as tskit_numba
 
 NODE_IS_SAMPLE = tskit.NODE_IS_SAMPLE
 
diff --git a/sc2ts/stats.py b/sc2ts/stats.py
index eb857d3d..a20ba4be 100644
--- a/sc2ts/stats.py
+++ b/sc2ts/stats.py
@@ -1,9 +1,9 @@
-from . import core
-
 import numpy as np
 import pandas as pd
 import tskit
 
+from . import core
+
 
 def convert_date(ts, time_array):
     time_zero_date = ts.metadata["time_zero_date"]
diff --git a/sc2ts/tree_ops.py b/sc2ts/tree_ops.py
index bb831d36..6e22fba8 100644
--- a/sc2ts/tree_ops.py
+++ b/sc2ts/tree_ops.py
@@ -4,21 +4,18 @@
 objects.
 """
 
-import time
 import collections
-import logging
 import dataclasses
-from typing import List
+import logging
 
-import tskit
-import tqdm
+import biotite.sequence.phylo as bsp
 import numpy as np
-import scipy.spatial.distance
 import scipy.cluster.hierarchy
-import biotite.sequence.phylo as bsp
+import scipy.spatial.distance
+import tqdm
+import tskit
 
-from . import core
-from . import stats
+from . import core, stats
 
 logger = logging.getLogger(__name__)
 
@@ -647,8 +644,6 @@ def split_branch(ts, node, mutations):
     return tables.tree_sequence()
 
 
-
-
 def drop_vestigial_root_edge(ts):
     """
     Drop the edge joining 1 (the reference) to the vestigial root, needed
diff --git a/sc2ts/validation.py b/sc2ts/validation.py
index 3c7c83c1..356e7809 100644
--- a/sc2ts/validation.py
+++ b/sc2ts/validation.py
@@ -1,13 +1,13 @@
 import logging
 import unittest
 
-import numpy as np
 import numpy.testing as nt
 import tqdm
 
+import sc2ts
+
 logger = logging.getLogger(__name__)
 
-import sc2ts
 
 MISSING = -1
 DELETION = sc2ts.IUPAC_ALLELES.index("-")
diff --git a/tests/data/make_ba2_recomb.py b/tests/data/make_ba2_recomb.py
index 0987237e..f091f078 100644
--- a/tests/data/make_ba2_recomb.py
+++ b/tests/data/make_ba2_recomb.py
@@ -1,16 +1,14 @@
-import tskit
+import pathlib
+
 import numpy as np
 import pandas as pd
-
-import pathlib
+import tskit
 
 prefix = pathlib.Path("/home/jk/work/github/sc2ts-paper")
 
 orig_ts = tskit.load(prefix / "inference/results/v1-beta1/v1-beta1_2023-02-21.ts")
 recomb_df = pd.read_csv(prefix / "data/recombinants.csv").set_index("sample_id")
-strain2nodeid = dict(
-    zip(orig_ts.metadata["sc2ts"]["samples_strain"], orig_ts.samples())
-)
+strain2nodeid = dict(zip(orig_ts.metadata["sc2ts"]["samples_strain"], orig_ts.samples()))
 ba_2_sample = "SRR17461792"
 re_node = recomb_df.loc[ba_2_sample, "recombinant"]
 re_node_children = orig_ts.edges_child[orig_ts.edges_parent == re_node]
diff --git a/tests/sc2ts_fixtures.py b/tests/sc2ts_fixtures.py
index e68a3b48..087ef973 100644
--- a/tests/sc2ts_fixtures.py
+++ b/tests/sc2ts_fixtures.py
@@ -1,25 +1,26 @@
 import dataclasses
+import gzip
+import os
 import pathlib
 import shutil
-import gzip
-import tskit
 
 import numpy as np
 import pandas as pd
 import pytest
+import tskit
 
 import sc2ts
-from sc2ts import cli
-from sc2ts import data_import
-from sc2ts import jit
+from sc2ts import data_import, jit
 from sc2ts import inference as si
 
 
 @pytest.fixture
 def fx_data_cache():
-    cache_path = pathlib.Path("tests/data/cache")
-    if not cache_path.exists():
-        cache_path.mkdir()
+    # This the simplest way to avoid race conditions between parallel
+    # pytest workers - we just make a cache per worker
+    worker = os.environ.get("PYTEST_XDIST_WORKER", "main")
+    cache_path = pathlib.Path("tests/data/cache") / worker
+    cache_path.mkdir(parents=True, exist_ok=True)
     return cache_path
 
 
@@ -103,9 +104,7 @@ def fx_dataset(tmp_path, fx_data_cache, fx_alignments_fasta, fx_metadata_df):
         # Use an awkward chunk size here to make sure we're hitting across
         # chunk stuff by default
         sc2ts.Dataset.new(fs_path, samples_chunk_size=7)
-        sc2ts.Dataset.append_alignments(
-            fs_path, encoded_alignments(fx_alignments_fasta)
-        )
+        sc2ts.Dataset.append_alignments(fs_path, encoded_alignments(fx_alignments_fasta))
         sc2ts.Dataset.add_metadata(fs_path, fx_metadata_df)
         sc2ts.Dataset.create_zip(fs_path, cache_path)
     return sc2ts.Dataset(cache_path, date_field="date")
@@ -171,7 +170,8 @@ def fx_ts_map(tmp_path, fx_data_cache, fx_dataset, fx_match_db):
                 **extra_kwargs,
             )
             print(
-                f"INFERRED {date} nodes={last_ts.num_nodes} mutations={last_ts.num_mutations}"
+                f"INFERRED {date} nodes={last_ts.num_nodes} "
+                f"mutations={last_ts.num_mutations}"
             )
             cache_path = fx_data_cache / f"{date}.ts"
             last_ts.dump(cache_path)
@@ -290,7 +290,8 @@ def recombinant_example_2(tmp_path, fx_ts_map, fx_dataset, ds_path):
     ts_path = tmp_path / "intermediate.ts"
     ts.dump(ts_path)
 
-    # Now run again with the recombinant of these two, encoding the interval in the # name
+    # Now run again with the recombinant of these two, encoding the interval
+    # in the name
     date = "2020-03-02"
     left = start + 3 + 1
     right = end - 3 + 1
@@ -368,7 +369,8 @@ def recombinant_example_3(tmp_path, fx_ts_map, fx_dataset, ds_path):
     ts_path = tmp_path / "intermediate.ts"
     ts.dump(ts_path)
 
-    # Now run again with the recombinant of these three, encoding the intervals in the name
+    # Now run again with the recombinant of these three, encoding the intervals
+    # in the name
     date = "2020-03-02"
     left = start + 3 + 1
     right = end - 3 + 1
diff --git a/tests/test_api.py b/tests/test_api.py
index 3789ef10..414f4482 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -15,7 +15,6 @@ def fx_ds_v1():
 
 
 class TestStatFuncs:
-
     def test_top_level_md(self, fx_ts_v1):
         ts = fx_ts_v1
         assert ts.metadata == {"time_zero_date": "2020-02-15"}
@@ -32,7 +31,6 @@ def test_mutation_data(self, fx_ts_v1):
 
 
 class TestDataset:
-
     def test_basics(self, fx_ds_v1):
         ds = fx_ds_v1
         G = ds["call_genotype"][:].squeeze()
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 584f699e..a2a6d7eb 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,23 +1,20 @@
 import io
 import json
-import collections
 
+import click.testing as ct
 import numpy as np
 import numpy.testing as nt
-import click.testing as ct
+import pandas as pd
 import pytest
-import tskit
 import tomli_w
-import pandas as pd
+import tskit
 
 import sc2ts
-from sc2ts import __main__ as main
 from sc2ts import cli
 from sc2ts import inference as si
 
 
 class TestImportAlignments:
-
     def test_init(self, tmp_path, fx_alignments_fasta):
         ds_path = tmp_path / "ds.zarr"
         runner = ct.CliRunner()
@@ -61,7 +58,10 @@ def test_suite_data(self, tmp_path, fx_metadata_tsv, fx_alignments_fasta):
 
         result = runner.invoke(
             cli.cli,
-            f"import-metadata {ds_path} {fx_metadata_tsv} --field-descriptions={fields_path}",
+            (
+                f"import-metadata {ds_path} {fx_metadata_tsv} "
+                f"--field-descriptions={fields_path}"
+            ),
             catch_exceptions=False,
         )
         ds = sc2ts.Dataset(ds_path)
@@ -87,7 +87,6 @@ def test_viridian_metadata(
 
 
 class TestRunHmm:
-
     def test_single_defaults(self, tmp_path, fx_ts_map, fx_dataset):
         strain = "ERR4206593"
         ts = fx_ts_map["2020-02-04"]
@@ -159,7 +158,6 @@ def test_single_options(self, tmp_path, fx_ts_map, fx_dataset):
 
 
 class TestInfer:
-
     def make_config(
         self,
         tmp_path,
@@ -379,7 +377,6 @@ def test_multiple_override(self, tmp_path, fx_ts_map, fx_dataset):
 
 
 class TestPostprocess:
-
     def test_example(self, tmp_path, fx_ts_map, fx_match_db):
         ts = fx_ts_map["2020-02-13"]
         out_ts_path = tmp_path / "ts.ts"
@@ -399,7 +396,6 @@ def test_example(self, tmp_path, fx_ts_map, fx_match_db):
 
 
 class TestMinimiseMetadata:
-
     def test_example(self, tmp_path, fx_ts_map):
         ts = fx_ts_map["2020-02-13"]
         out_ts_path = tmp_path / "ts.ts"
@@ -411,9 +407,7 @@ def test_example(self, tmp_path, fx_ts_map):
         )
         assert result.exit_code == 0
         out = tskit.load(out_ts_path)
-        ts.tables.assert_equals(
-            out.tables, ignore_metadata=True, ignore_provenance=True
-        )
+        ts.tables.assert_equals(out.tables, ignore_metadata=True, ignore_provenance=True)
         dfn = sc2ts.node_data(out, inheritance_stats=False)
         assert "sample_id" in dfn
         # Check we've kept the vestigial root edge
@@ -447,16 +441,13 @@ def test_example_args(self, tmp_path, fx_ts_map):
         )
         assert result.exit_code == 0
         out = tskit.load(out_ts_path)
-        ts.tables.assert_equals(
-            out.tables, ignore_metadata=True, ignore_provenance=True
-        )
+        ts.tables.assert_equals(out.tables, ignore_metadata=True, ignore_provenance=True)
         dfn = sc2ts.node_data(out, inheritance_stats=False)
         assert "sample_id" in dfn
         assert "pango" in dfn
 
 
 class TestMapParsimony:
-
     def test_example(self, tmp_path, fx_ts_map, fx_dataset):
         ts = fx_ts_map["2020-02-13"]
         out_ts_path = tmp_path / "ts.ts"
@@ -494,9 +485,7 @@ def test_example_no_report(self, tmp_path, fx_ts_map, fx_dataset):
         )
         assert result.exit_code == 0
         out = tskit.load(out_ts_path)
-        ts.tables.assert_equals(
-            out.tables, ignore_metadata=True, ignore_provenance=True
-        )
+        ts.tables.assert_equals(out.tables, ignore_metadata=True, ignore_provenance=True)
 
     def test_example_no_sites(self, tmp_path, fx_ts_map, fx_dataset):
         ts = fx_ts_map["2020-02-13"]
@@ -516,7 +505,6 @@ def test_example_no_sites(self, tmp_path, fx_ts_map, fx_dataset):
 
 
 class TestApplyParsimonyHeuristics:
-
     def test_example(self, tmp_path, fx_ts_map):
         ts = fx_ts_map["2020-02-13"]
         out_ts_path = tmp_path / "out.ts"
@@ -537,7 +525,6 @@ def test_example(self, tmp_path, fx_ts_map):
 
 
 class TestRematchRecombinant:
-
     def test_recombinant_example_1(self, fx_recombinant_example_1_info):
         info = fx_recombinant_example_1_info
 
@@ -555,7 +542,6 @@ def test_recombinant_example_1(self, fx_recombinant_example_1_info):
 
 
 class TestRematchRecombinantLbs:
-
     def test_recombinant_example_1(self, fx_recombinant_example_1_info):
         info = fx_recombinant_example_1_info
 
@@ -595,7 +581,6 @@ def test_ba2_example(self, tmp_path):
 
 
 class TestValidate:
-
     @pytest.mark.parametrize("date", ["2020-01-01", "2020-02-11"])
     def test_date(self, tmp_path, fx_ts_map, fx_dataset, date):
         ts = fx_ts_map[date]
diff --git a/tests/test_dataset.py b/tests/test_dataset.py
index 253ff690..10d8ad8e 100644
--- a/tests/test_dataset.py
+++ b/tests/test_dataset.py
@@ -1,19 +1,24 @@
 import itertools
 
 import numpy as np
-import pytest
 import numpy.testing as nt
+import pytest
+import xarray as xr
 import xarray.testing as xt
-import sgkit
 
 import sc2ts
-from sc2ts import jit
-from sc2ts import data_import
+from sc2ts import data_import, jit
+
+
+# Partial copy of the load_dataset function.
+def load_dataset(store):
+    ds = xr.open_zarr(store, concat_characters=False)
+    return ds
 
 
 def assert_datasets_equal(ds1, ds2):
-    sg_ds1 = sgkit.load_dataset(ds1.path)
-    sg_ds2 = sgkit.load_dataset(ds2.path)
+    sg_ds1 = load_dataset(ds1.path)
+    sg_ds2 = load_dataset(ds2.path)
     xt.assert_equal(sg_ds1, sg_ds2)
 
 
@@ -36,11 +41,10 @@ def test_massaged_viridian_metadata(fx_raw_viridian_metadata_df):
 
 
 class TestCreateDataset:
-
     def test_new(self, tmp_path):
         path = tmp_path / "dataset.vcz"
         sc2ts.Dataset.new(path)
-        sg_ds = sgkit.load_dataset(path)
+        sg_ds = load_dataset(path)
         assert dict(sg_ds.sizes) == {
             "variants": 29903,
             "samples": 0,
@@ -71,7 +75,7 @@ def test_single_append_alignments(
 
         sc2ts.Dataset.append_alignments(path, alignments)
 
-        sg_ds = sgkit.load_dataset(path)
+        sg_ds = load_dataset(path)
         assert dict(sg_ds.sizes) == {
             "variants": 29903,
             "samples": num_samples,
@@ -119,7 +123,7 @@ def test_multi_append_alignments(
         for k, v in alignments.items():
             sc2ts.Dataset.append_alignments(path, {k: v})
 
-        sg_ds = sgkit.load_dataset(path)
+        sg_ds = load_dataset(path)
         assert dict(sg_ds.sizes) == {
             "variants": 29903,
             "samples": num_samples,
@@ -142,7 +146,7 @@ def test_add_metadata(self, tmp_path, fx_encoded_alignments, fx_metadata_df):
             path, fx_metadata_df, field_descriptions=field_descriptions
         )
 
-        sg_ds = sgkit.load_dataset(path)
+        sg_ds = load_dataset(path)
         assert dict(sg_ds.sizes) == {
             "variants": 29903,
             "samples": len(fx_encoded_alignments),
@@ -183,8 +187,8 @@ def test_copy_reorder(self, tmp_path, fx_dataset):
         path = tmp_path / "dataset.vcz"
         sample_id = fx_dataset.sample_id[::-1]
         fx_dataset.copy(path, sample_id=sample_id)
-        sg_ds2 = sgkit.load_dataset(path).set_index({"samples": "sample_id"})
-        sg_ds1 = sgkit.load_dataset(fx_dataset.path).set_index({"samples": "sample_id"})
+        sg_ds2 = load_dataset(path).set_index({"samples": "sample_id"})
+        sg_ds1 = load_dataset(fx_dataset.path).set_index({"samples": "sample_id"})
         permuted = sg_ds1.sel(samples=sample_id)
         xt.assert_equal(permuted, sg_ds2)
 
@@ -220,14 +224,13 @@ def test_copy_reorder(self, tmp_path, fx_dataset):
     def test_copy_subset(self, tmp_path, fx_dataset, sample_id):
         path = tmp_path / "dataset.vcz"
         fx_dataset.copy(path, sample_id=sample_id)
-        sg_ds2 = sgkit.load_dataset(path).set_index({"samples": "sample_id"})
-        sg_ds1 = sgkit.load_dataset(fx_dataset.path).set_index({"samples": "sample_id"})
+        sg_ds2 = load_dataset(path).set_index({"samples": "sample_id"})
+        sg_ds1 = load_dataset(fx_dataset.path).set_index({"samples": "sample_id"})
         permuted = sg_ds1.sel(samples=sample_id)
         xt.assert_equal(permuted, sg_ds2)
 
 
 class TestDatasetFasta:
-
     def test_write_fasta_all(self, tmp_path, fx_dataset, fx_alignments_fasta):
         path = tmp_path / "export.fa"
         with open(path, "w") as f:
@@ -288,7 +291,6 @@ def test_write_fasta_subset(
 
 
 class TestDatasetVariants:
-
     def test_all(self, fx_dataset):
         G = fx_dataset["call_genotype"][:].squeeze()
         pos = fx_dataset["variant_position"][:]
@@ -351,7 +353,6 @@ def test_sample_slice(self, fx_dataset, start, stop):
 
 
 class TestDatasetMethods:
-
     def test_zarr_mapping(self, fx_dataset):
         assert len(fx_dataset) == len(fx_dataset.root)
         assert list(fx_dataset) == list(fx_dataset.root)
@@ -382,7 +383,6 @@ def test_repr_markdown(self, fx_dataset):
 
 
 class TestMafftAlignments:
-
     def test_import(self, tmp_path, fx_encoded_alignments_mafft):
         path = tmp_path / "dataset.vcz"
         sc2ts.Dataset.new(path)
@@ -398,7 +398,6 @@ def test_import(self, tmp_path, fx_encoded_alignments_mafft):
 
 
 class TestDatasetAlignments:
-
     def test_fetch_known(self, fx_dataset):
         a = fx_dataset.alignment["SRR11772659"]
         assert a.shape == (sc2ts.REFERENCE_SEQUENCE_LENGTH - 1,)
@@ -449,7 +448,6 @@ def test_chunk_size_cache_size(
 
 
 class TestDatasetMetadata:
-
     def test_len(self, fx_dataset):
         assert len(fx_dataset.metadata) == 55
 
@@ -602,7 +600,6 @@ def test_too_large(self, a):
 
 
 class TestMaskFlankingDeletions:
-
     @pytest.mark.parametrize(
         ["nucs", "expected"],
         [
diff --git a/tests/test_debug.py b/tests/test_debug.py
index ce47e466..4f79e264 100644
--- a/tests/test_debug.py
+++ b/tests/test_debug.py
@@ -1,18 +1,13 @@
-import datetime
 import inspect
 
+import matplotlib
 import numpy as np
 import numpy.testing as nt
 import pandas as pd
-import matplotlib
 import pytest
 
-import msprime
-import tskit
-
 import sc2ts
 from sc2ts import debug
-from sc2ts import inference as si
 
 
 @pytest.fixture
@@ -161,12 +156,6 @@ def test_summary(self, fx_ti_2020_02_15):
         assert df.loc["sample_groups"].value == 27
         assert df.loc["retro_sample_groups"].value == 1
 
-    def test_summary(self, fx_ti_2020_02_15):
-        df = fx_ti_2020_02_15.summary()
-        assert df.loc["samples"].value == 43
-        assert df.loc["sample_groups"].value == 27
-        assert df.loc["retro_sample_groups"].value == 1
-
     def test_recombinants_summary_example_1(self, fx_ti_recombinant_example_1):
         df = fx_ti_recombinant_example_1.recombinants_summary()
         assert df.shape[0] == 1
@@ -263,7 +252,6 @@ def test_draw_svg(self, fx_ti_2020_02_13):
 
 
 class TestDataFuncsEquivalant:
-
     def test_example_node(self, fx_ts_min_2020_02_15, fx_ti_2020_02_15):
         ts = fx_ts_min_2020_02_15
         ti = fx_ti_2020_02_15
diff --git a/tests/test_inference.py b/tests/test_inference.py
index 685787ff..0f429372 100644
--- a/tests/test_inference.py
+++ b/tests/test_inference.py
@@ -1,22 +1,16 @@
 import dataclasses
-import collections
 import hashlib
-import logging
 import json
 
+import msprime
 import numpy as np
 import numpy.testing as nt
+import pandas as pd
 import pytest
-import tsinfer
 import tskit
-import msprime
-import pandas as pd
 
 import sc2ts
-from sc2ts import debug
-from sc2ts import jit
-from sc2ts import tree_ops
-from sc2ts import validation
+from sc2ts import debug, jit, tree_ops, validation
 from sc2ts import inference as si
 
 
@@ -85,7 +79,6 @@ def test_get_group_strains(fx_ts_map):
 
 
 class TestRecombinantHandling:
-
     def test_get_recombinant_strains_ex1(self, fx_recombinant_example_1):
         d = si.get_recombinant_strains(fx_recombinant_example_1)
         assert d == {55: ["recombinant_example_1_0", "recombinant_example_1_1"]}
@@ -529,9 +522,7 @@ def test_2020_02_02_max_missing_sites(
 
         assert np.sum(ts.nodes_time[ts.samples()] == 0) == new_samples
         for u in ts.samples()[-new_samples:]:
-            assert (
-                ts.node(u).metadata["sc2ts"]["num_missing_sites"] <= max_missing_sites
-            )
+            assert ts.node(u).metadata["sc2ts"]["num_missing_sites"] <= max_missing_sites
 
     @pytest.mark.parametrize(
         ["strain", "start", "length"],
@@ -754,8 +745,7 @@ def test_2020_02_14_skip_max_mutations(
             retro_groups = ts.metadata["sc2ts"]["retro_groups"]
             assert len(retro_groups) == 0
             assert (
-                "Skipping mean_mutations_per_sample=1.0 exceeds threshold"
-                in caplog.text
+                "Skipping mean_mutations_per_sample=1.0 exceeds threshold" in caplog.text
             )
 
     def test_2020_02_14_skip_root_mutations(
@@ -980,7 +970,6 @@ def test_exact_matches(self, fx_ts_map, strain, parent):
 
 
 class TestSyntheticAlignments:
-
     def test_exact_match(self, tmp_path, fx_ts_map, fx_dataset):
         # Pick two unique strains and we should match exactly with them
         strains = ["SRR11597218", "ERR4204459"]
@@ -1252,7 +1241,6 @@ def test_match_recombinant(self, fx_ts_map):
 
 
 class TestRunHmm:
-
     @pytest.mark.parametrize("direction", ["F", "R", "forwards", "backwards", "", None])
     def test_bad_direction(self, fx_dataset, fx_ts_map, direction):
         strain = "SRR11597164"
@@ -1272,7 +1260,6 @@ def test_no_strains(self, fx_dataset, fx_ts_map):
 
 
 class TestCharacteriseRecombinants:
-
     def test_example_1(self, fx_ts_map):
         ts, s = recombinant_example_1(fx_ts_map)
 
@@ -1389,7 +1376,6 @@ def test_example_3_way_same_parent(self, fx_recombinant_example_3):
 
 
 class TestExtractHaplotypes:
-
     @pytest.mark.parametrize(
         ["samples", "result"],
         [
@@ -1536,9 +1522,7 @@ def test_validate(self, fx_ts_map, fx_dataset):
         ts = fx_ts_map["2020-02-13"]
         sites = [1547, 3951, 3952, 3953]
         result = si.map_parsimony(ts, fx_dataset, sites)
-        validation.validate(
-            result.tree_sequence, fx_dataset, deletions_as_missing=False
-        )
+        validation.validate(result.tree_sequence, fx_dataset, deletions_as_missing=False)
 
     def test_provenance(self, fx_ts_map, fx_dataset):
         ts = fx_ts_map["2020-02-13"]
@@ -1614,13 +1598,10 @@ def test_provenance(self, fx_ts_map, fx_match_db):
 
 
 class TestMinimiseMetadata:
-
     def test_equivalent(self, fx_ts_map):
         ts = fx_ts_map["2020-02-13"]
         tsp = si.minimise_metadata(ts)
-        ts.tables.assert_equals(
-            tsp.tables, ignore_metadata=True, ignore_provenance=True
-        )
+        ts.tables.assert_equals(tsp.tables, ignore_metadata=True, ignore_provenance=True)
 
     def test_properties(self, fx_ts_map):
         ts = fx_ts_map["2020-02-13"]
@@ -1672,7 +1653,6 @@ def test_provenance(self, fx_ts_map):
 
 
 class TestPushUpRecombinantMutations:
-
     def test_no_recombinants(self, fx_ts_map):
         ts = fx_ts_map["2020-02-13"]
         tsp = si.push_up_unary_recombinant_mutations(ts)
@@ -1811,7 +1791,6 @@ def test_ba2_recombinant(self):
 
 
 class TestRematchRecombinantsLbs:
-
     def test_bad_node(self, fx_recombinant_example_1_info):
         info = fx_recombinant_example_1_info
         base_ts = tskit.load(info.base_ts)
diff --git a/tests/test_jit.py b/tests/test_jit.py
index cb088a33..b633469f 100644
--- a/tests/test_jit.py
+++ b/tests/test_jit.py
@@ -1,7 +1,7 @@
-import numpy as np
 import msprime
-import tskit
+import numpy as np
 import numpy.testing as nt
+import tskit
 
 from sc2ts import jit
 
@@ -63,7 +63,6 @@ def multiple_trees_example_ts():
 
 
 class TestArgCounts:
-
     def test_single_tree_example(self):
         ts = single_tree_example_ts()
         c = jit.count(ts)
diff --git a/tests/test_tree_ops.py b/tests/test_tree_ops.py
index f6982f52..c8bb5bdf 100644
--- a/tests/test_tree_ops.py
+++ b/tests/test_tree_ops.py
@@ -1,13 +1,11 @@
+import biotite.sequence.phylo as bsp
+import msprime
 import numpy as np
+import numpy.testing as nt
 import pytest
 import tskit
-import msprime
-import biotite.sequence.phylo as bsp
-import numpy.testing as nt
 
-import sc2ts
-from sc2ts import tree_ops
-from sc2ts import inference
+from sc2ts import inference, tree_ops
 
 
 def all_trees_ts(n):
@@ -73,7 +71,6 @@ def prepare(tables):
 
 
 class TestSplitBranch:
-
     def test_root(self):
         # 2.00┊    6    ┊
         #     ┊  ┏━┻━┓  ┊
@@ -658,7 +655,6 @@ def test_simulation(self, n, mutation_rate):
 
 
 class TestFullSpanSibs:
-
     @pytest.mark.parametrize(
         ["nodes", "sibs"],
         [
@@ -707,7 +703,6 @@ def test_all_trees_ts(self, nodes):
 
 
 class TestInferBinary:
-
     def check_properties(self, ts):
         assert ts.num_trees == 1
         tree = ts.first()
@@ -777,7 +772,6 @@ def test_simulation_root_mutations(self, n, num_mutations):
 
 
 class TestFromBiotite:
-
     def check_round_trip(self, tsk_tree):
         node_labels = {u: f"{u}" for u in tsk_tree.tree_sequence.samples()}
         nwk = tsk_tree.as_newick(node_labels=node_labels)
@@ -798,7 +792,6 @@ def test_comb(self, n):
 
 
 class TestRerooting:
-
     def check_properties(self, before, after, root):
         assert after.num_trees == 1
         assert before.sequence_length == after.sequence_length
@@ -924,7 +917,6 @@ def test_example_same_root(self):
 
 
 class TestDropVestigialRootEdge:
-
     def test_example(self, fx_ts_map):
         ts = fx_ts_map["2020-02-13"]
         e = ts.edge(-1)
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