Update pre-commit

Author: benjeffery

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
@@ -14,22 +14,22 @@ repos:
       exclude: argtable3
       verbose: true
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.12.0
+    rev: v3.14.0
     hooks:
       - id: reorder-python-imports
         args: [--unclassifiable-application-module=_msprime]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.19.1
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 25.1.0
     hooks:
       - id: black
         language_version: python3
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.1.2
     hooks:
       - id: flake8
         args: [--config=.flake8]

algorithms.py

@@ -1,6 +1,4 @@
-"""
-Python version of the simulation algorithm.
-"""
+# Python version of the simulation algorithm.
 from __future__ import annotations
 
 import argparse

data/run_old_msprime.py

@@ -1,8 +1,6 @@
-"""
-Runs the parameters for a given simulation in an input
-pickle file and writes the output tree sequence to
-an output file.
-"""
+# Runs the parameters for a given simulation in an input
+# pickle file and writes the output tree sequence to
+# an output file.
 import pickle
 import sys
 

msp_dev.py

@@ -1,6 +1,4 @@
-"""
-Simple shim for msp development.
-"""
+# Simple shim for msp development.
 import msprime.cli
 
 if __name__ == "__main__":

mspms_dev.py

@@ -1,6 +1,4 @@
-"""
-Simple shim for mspms development.
-"""
+# Simple shim for mspms development.
 import msprime.cli
 
 if __name__ == "__main__":

stress_lowlevel.py

@@ -1,7 +1,5 @@
-"""
-Code to stress the low-level API as much as possible to expose
-any memory leaks or error handling issues.
-"""
+# Code to stress the low-level API as much as possible to expose
+# any memory leaks or error handling issues.
 import curses
 import os
 import random

tests/test_algorithms.py

@@ -1,6 +1,4 @@
-"""
-Tests for the algorithms.py script.
-"""
+# Tests for the algorithms.py script.
 import pathlib
 import platform
 import tempfile

tests/test_dict_encoding.py

@@ -1,7 +1,5 @@
-"""
-Test cases for the low-level dictionary encoding used to move
-data around in C.
-"""
+# Test cases for the low-level dictionary encoding used to move
+# data around in C.
 import lwt_interface.dict_encoding_testlib
 
 from msprime import _msprime

tests/test_mutations.py

@@ -2141,9 +2141,11 @@ def populate_tables(self, tables):
                     parent=parent_id,
                     metadata=mutation.metadata,
                     # Not sure why, but sometimes the time is a single-element array
-                    time=mutation.time[0]
-                    if isinstance(mutation.time, np.ndarray)
-                    else mutation.time,
+                    time=(
+                        mutation.time[0]
+                        if isinstance(mutation.time, np.ndarray)
+                        else mutation.time
+                    ),
                 )
                 assert mutation_id > parent_id
                 mutation.id = mutation_id

verification.py

@@ -1,57 +1,40 @@
-"""
-Script to automate verification of msprime against known statistical
-results and benchmark programs such as ms and Seq-Gen.
-
-Tests are structured in a similar way to Python unittests. Tests
-are organised into classes of similar tests. Ideally, each test
-in the class is a simple call to a general method with
-different parameters (this is called ``_run``, by convention).
-Tests must be *independent* and not depend on any shared
-state within the test class, other than the ``self.output_dir``
-variable which is guaranteed to be set when the method is called.
-
-The output directory is <output-dir>/<class name>/<test name>.
-Each test should output one or more diagnostic plots, which have
-a clear interpretation as "correct" or "incorrect". QQ-plots
-are preferred, where possible. Numerical results can also be
-output by using ``logging.debug()``, where appropriate; to
-view these, append ``--debug`` to the comand line running
-your tests.
-
-Test classes must be a subclass of the ``Test`` class defined
-in this module.
-
-To run the tests, first get some help from the CLI:
-
-    python3 verification.py --help
-
-This will output some basic help on the tests. Use
-
-    python3 verification.py --list
-
-to show all the available tests.
-
-If you run without any arguments, this will run all the tests
-sequentially. The progress bar and output behaviour can be
-controlled using command line parameters, and running over
-multiple processes is possible.
-
-If you wish to run a specific tests, you can provide the
-test names as positional arguments, i.e.,
-
-    python3 verification.py test_msdoc_outgroup_sequence test_msdoc_recomb_ex
-
-will just run these two specific tests.
-
-Using the ``-c`` option allows you to run all tests in a
-given class.
-
-Gotchas:
-- Any test superclasses must be abstract. That is, you cannot
-  inherit from a test class that contains any tests.
-- Test method names must be unique across *all* classes.
-
-"""
+# Script to automate verification of msprime against known statistical
+# results and benchmark programs such as ms and Seq-Gen.
+# Tests are structured in a similar way to Python unittests. Tests
+# are organised into classes of similar tests. Ideally, each test
+# in the class is a simple call to a general method with
+# different parameters (this is called ``_run``, by convention).
+# Tests must be *independent* and not depend on any shared
+# state within the test class, other than the ``self.output_dir``
+# variable which is guaranteed to be set when the method is called.
+# The output directory is <output-dir>/<class name>/<test name>.
+# Each test should output one or more diagnostic plots, which have
+# a clear interpretation as "correct" or "incorrect". QQ-plots
+# are preferred, where possible. Numerical results can also be
+# output by using ``logging.debug()``, where appropriate; to
+# view these, append ``--debug`` to the comand line running
+# your tests.
+# Test classes must be a subclass of the ``Test`` class defined
+# in this module.
+# To run the tests, first get some help from the CLI:
+#     python3 verification.py --help
+# This will output some basic help on the tests. Use
+#     python3 verification.py --list
+# to show all the available tests.
+# If you run without any arguments, this will run all the tests
+# sequentially. The progress bar and output behaviour can be
+# controlled using command line parameters, and running over
+# multiple processes is possible.
+# If you wish to run a specific tests, you can provide the
+# test names as positional arguments, i.e.,
+#     python3 verification.py test_msdoc_outgroup_sequence test_msdoc_recomb_ex
+# will just run these two specific tests.
+# Using the ``-c`` option allows you to run all tests in a
+# given class.
+# Gotchas:
+# - Any test superclasses must be abstract. That is, you cannot
+#   inherit from a test class that contains any tests.
+# - Test method names must be unique across *all* classes.
 import argparse
 import ast
 import collections
@@ -5643,9 +5626,10 @@ def _run_seq_gen(self, tree, args, model, alleles, num_sites, mutation_rate, Q):
         newick = tree.newick()
         cmd = self._seq_gen_executable + args
         num_sequences = 2 * ts.num_samples - 1
-        with tempfile.TemporaryFile("w+") as in_file, tempfile.TemporaryFile(
-            "w+"
-        ) as out_file:
+        with (
+            tempfile.TemporaryFile("w+") as in_file,
+            tempfile.TemporaryFile("w+") as out_file,
+        ):
             in_file.write(newick)
             in_file.seek(0)
             subprocess.call(cmd, stdin=in_file, stdout=out_file)