Switch linting to Ruff

.pre-commit-config.yaml

@@ -17,32 +17,10 @@ repos:
     - id: clang-format
       exclude: dev-tools|examples
       verbose: true
-  - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.12.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.5
     hooks:
-      - id: reorder-python-imports
-        args: [--application-directories=python,
-               --unclassifiable-application-module=_tskit]
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
-    hooks:
-      - id: pyupgrade
-        args: [--py3-plus, --py38-plus]
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-      - id: black
-        language_version: python3
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        args: [--config=python/.flake8]
-        additional_dependencies: ["flake8-bugbear==23.9.16", "flake8-builtins==2.1.0"]
-  - repo: https://github.com/asottile/blacken-docs
-    rev: 1.16.0
-    hooks:
-      - id: blacken-docs
-        args: [--skip-errors]
-        additional_dependencies: [black==22.3.0]
-        language_version: python3
+      - id: ruff
+        args: [  "--fix", "--config", "python/ruff.toml" ]
+      - id: ruff-format
+        args: [ "--config", "python/ruff.toml" ]

python/benchmark/run-for-all-releases.py

@@ -1,9 +1,9 @@
 import json
 import subprocess
+from distutils.version import StrictVersion
 from urllib.request import urlopen
 
 import tqdm
-from distutils.version import StrictVersion
 
 
 def versions(package_name):

python/benchmark/run.py

@@ -14,9 +14,10 @@
 
 tskit_dir = Path(__file__).parent.parent
 sys.path.append(str(tskit_dir))
-import tskit  # noqa: E402
 import msprime  # noqa: E402
 
+import tskit  # noqa: E402
+
 with open("config.yaml") as f:
     config = yaml.load(f, Loader=yaml.FullLoader)
 

python/lwt_interface/dict_encoding_testlib.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2022 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -26,6 +26,7 @@
 compiled module exporting the LightweightTableCollection class.
 See the test_example_c_module file for an example.
 """
+
 import copy
 
 import kastore
@@ -98,7 +99,7 @@ def full_ts():
 
 # The ts above is used for the whole test session, but our tests need fresh tables to
 # modify
-@pytest.fixture
+@pytest.fixture()
 def tables(full_ts):
     return full_ts.dump_tables()
 
@@ -183,9 +184,7 @@ def test_example(self, tables):
                     {
                         "codec": "struct",
                         "type": "object",
-                        "properties": {
-                            table: {"type": "string", "binaryFormat": "50p"}
-                        },
+                        "properties": {table: {"type": "string", "binaryFormat": "50p"}},
                     }
                 )
 
@@ -459,9 +458,7 @@ def verify_optional_column(self, tables, table_len, table_name, col_name):
             out[table_name][col_name], np.zeros(table_len, dtype=np.int32) - 1
         )
 
-    def verify_offset_pair(
-        self, tables, table_len, table_name, col_name, required=False
-    ):
+    def verify_offset_pair(self, tables, table_len, table_name, col_name, required=False):
         offset_col = col_name + "_offset"
 
         if not required:
@@ -544,9 +541,7 @@ def test_individuals(self, tables):
         self.verify_offset_pair(
             tables, len(tables.individuals), "individuals", "location"
         )
-        self.verify_offset_pair(
-            tables, len(tables.individuals), "individuals", "parents"
-        )
+        self.verify_offset_pair(tables, len(tables.individuals), "individuals", "parents")
         self.verify_offset_pair(
             tables, len(tables.individuals), "individuals", "metadata"
         )
@@ -578,9 +573,7 @@ def test_migrations(self, tables):
         self.verify_required_columns(
             tables, "migrations", ["left", "right", "node", "source", "dest", "time"]
         )
-        self.verify_offset_pair(
-            tables, len(tables.migrations), "migrations", "metadata"
-        )
+        self.verify_offset_pair(tables, len(tables.migrations), "migrations", "metadata")
         self.verify_optional_column(tables, len(tables.nodes), "nodes", "individual")
         self.verify_metadata_schema(tables, "migrations")
 
@@ -674,9 +667,7 @@ def get_refseq(d):
         assert get_refseq(d).is_null()
 
         # All empty strings is the same thing
-        d["reference_sequence"] = dict(
-            data="", url="", metadata_schema="", metadata=b""
-        )
+        d["reference_sequence"] = dict(data="", url="", metadata_schema="", metadata=b"")
         assert get_refseq(d).is_null()
 
         del refseq_dict["metadata_schema"]  # handled above

python/lwt_interface/setup.py

@@ -1,17 +1,15 @@
 import os.path
 import platform
 
-from setuptools import Extension
-from setuptools import setup
+from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext
 
-
 IS_WINDOWS = platform.system() == "Windows"
 
 
 # Obscure magic required to allow numpy be used as a 'setup_requires'.
 # Based on https://stackoverflow.com/questions/19919905
-class local_build_ext(build_ext):
+class local_build_ext(build_ext):  # noqa: N801
     def finalize_options(self):
         build_ext.finalize_options(self)
         import builtins

python/ruff.toml

@@ -0,0 +1,12 @@
+line-length = 90
+
+[lint]
+select = ["E", "F", "B", "W", "I", "N", "UP", "A", "RUF", "PT", "NPY"]
+# N803,806,802 Allow capital varnames
+# E741 Allow "l" as var name
+# PT011 allow pytest raises without match
+ignore = ["N803", "N806", "N802", "E741", "PT011", "PT009"]
+
+[lint.isort]
+section-order = ["future", "standard-library", "third-party", "first-party", "local-folder"]
+known-first-party = ["tskit", "_tskit"]

python/setup.py

@@ -1,17 +1,15 @@
 import os.path
 import platform
 
-from setuptools import Extension
-from setuptools import setup
+from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext
 
-
 IS_WINDOWS = platform.system() == "Windows"
 
 
 # Obscure magic required to allow numpy be used as a 'setup_requires'.
 # Based on https://stackoverflow.com/questions/19919905
-class local_build_ext(build_ext):
+class local_build_ext(build_ext):  # noqa: N801
     def finalize_options(self):
         build_ext.finalize_options(self)
         import builtins

python/tests/__init__.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2023 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -22,6 +22,7 @@
 import base64
 
 import tskit
+
 from . import tsutil
 from .simplify import *  # NOQA
 
@@ -195,9 +196,7 @@ def trees(self):
             pt.left = left
             pt.right = right
             # Add in all the sites
-            pt.site_list = [
-                site for site in self._sites if left <= site.position < right
-            ]
+            pt.site_list = [site for site in self._sites if left <= site.position < right]
             yield pt
             pt.index += 1
         pt.index = -1

python/tests/conftest.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2022 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -38,9 +38,9 @@ def test_something(self, ts_fixture):
 Note that fixtures have a "scope" for example `ts_fixture` below is only created once
 per test session and re-used for subsequent tests.
 """
+
 import msprime
 import pytest
-from pytest import fixture
 
 from . import tsutil
 
@@ -81,45 +81,45 @@ def pytest_collection_modifyitems(config, items):
                 item.add_marker(skip_slow)
 
 
-@fixture
+@pytest.fixture()
 def overwrite_viz(request):
     return request.config.getoption("--overwrite-expected-visualizations")
 
 
-@fixture
+@pytest.fixture()
 def draw_plotbox(request):
     return request.config.getoption("--draw-svg-debug-box")
 
 
-@fixture(scope="session")
+@pytest.fixture(scope="session")
 def simple_degree1_ts_fixture():
     return msprime.simulate(10, random_seed=42)
 
 
-@fixture(scope="session")
+@pytest.fixture(scope="session")
 def simple_degree2_ts_fixture():
     ts = msprime.simulate(10, recombination_rate=0.2, random_seed=42)
     assert ts.num_trees == 2
     return ts
 
 
-@fixture(scope="session")
+@pytest.fixture(scope="session")
 def ts_fixture():
     """
     A tree sequence with data in all fields
     """
     return tsutil.all_fields_ts()
 
 
-@fixture(scope="session")
+@pytest.fixture(scope="session")
 def ts_fixture_for_simplify():
     """
     A tree sequence with data in all fields execpt edge metadata and migrations
     """
     return tsutil.all_fields_ts(edge_metadata=False, migrations=False)
 
 
-@fixture(scope="session")
+@pytest.fixture(scope="session")
 def replicate_ts_fixture():
     """
     A list of tree sequences

python/tests/ibd.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2020-2022 Tskit Developers
+# Copyright (c) 2020-2024 Tskit Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -22,6 +22,7 @@
 """
 Python implementation of the IBD-finding algorithms.
 """
+
 import argparse
 import collections
 
@@ -46,9 +47,7 @@ def __init__(self, left=None, right=None, node=None, next_seg=None):
         self.next = next_seg
 
     def __str__(self):
-        s = "({}-{}->{}:next={})".format(
-            self.left, self.right, self.node, repr(self.next)
-        )
+        s = f"({self.left}-{self.right}->{self.node}:next={self.next!r})"
         return s
 
     def __repr__(self):

python/tests/simplify.py

@@ -23,6 +23,7 @@
 """
 Python implementation of the simplify algorithm.
 """
+
 import sys
 
 import numpy as np
@@ -82,9 +83,7 @@ def __init__(self, left=None, right=None, node=None, next_segment=None):
         self.next = next_segment
 
     def __str__(self):
-        s = "({}-{}->{}:next={})".format(
-            self.left, self.right, self.node, repr(self.next)
-        )
+        s = f"({self.left}-{self.right}->{self.node}:next={self.next!r})"
         return s
 
     def __repr__(self):
@@ -305,7 +304,8 @@ def merge_labeled_ancestors(self, S, input_id):
         if is_sample:
             # Free up the existing ancestry mapping.
             x = self.A_tail[input_id]
-            assert x.left == 0 and x.right == self.sequence_length
+            assert x.left == 0
+            assert x.right == self.sequence_length
             self.A_tail[input_id] = None
             self.A_head[input_id] = None
 
@@ -333,8 +333,7 @@ def merge_labeled_ancestors(self, S, input_id):
                 # Fill in any gaps in the ancestry for the sample
                 self.add_ancestry(input_id, prev_right, left, output_id)
             if self.keep_unary or (
-                self.keep_unary_in_individuals
-                and self.ts.node(input_id).individual >= 0
+                self.keep_unary_in_individuals and self.ts.node(input_id).individual >= 0
             ):
                 ancestry_node = output_id
             self.add_ancestry(input_id, left, right, ancestry_node)
@@ -637,9 +636,7 @@ def process_parent_edges(self, edges):
             x = self.A_head[edge.child]
             while x is not None:
                 if x.right > edge.left and edge.right > x.left:
-                    y = Segment(
-                        max(x.left, edge.left), min(x.right, edge.right), x.node
-                    )
+                    y = Segment(max(x.left, edge.left), min(x.right, edge.right), x.node)
                     S.append(y)
                 x = x.next
         self.merge_labeled_ancestors(S, parent)
@@ -654,7 +651,8 @@ def merge_labeled_ancestors(self, S, input_id):
         if is_sample:
             # Free up the existing ancestry mapping.
             x = self.A_tail[input_id]
-            assert x.left == 0 and x.right == self.sequence_length
+            assert x.left == 0
+            assert x.right == self.sequence_length
             self.A_tail[input_id] = None
             self.A_head[input_id] = None