Update pre-commit

jeromekelleher · May 3, 2024 · d32d63f · d32d63f
1 parent 1b84b63
commit d32d63f
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Showing 21 changed files with 78 additions and 62 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
@@ -24,17 +24,17 @@ repos:
         args: [--application-directories=python,
                --unclassifiable-application-module=_tskit]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py38-plus]
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.4.2
     hooks:
       - id: black
         language_version: python3
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         args: [--config=python/.flake8]

diff --git a/c/tests/test_core.c b/c/tests/test_core.c
@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2021 Tskit Developers
+ * Copyright (c) 2019-2024 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

diff --git a/c/tests/testlib.h b/c/tests/testlib.h
@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2023 Tskit Developers
+ * Copyright (c) 2019-2024 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

diff --git a/c/tskit/core.c b/c/tskit/core.c
@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2023 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  * Copyright (c) 2015-2018 University of Oxford
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy

diff --git a/c/tskit/core.h b/c/tskit/core.h
@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2023 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  * Copyright (c) 2015-2018 University of Oxford
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy

diff --git a/python/_tskitmodule.c b/python/_tskitmodule.c
@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2023 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  * Copyright (c) 2015-2018 University of Oxford
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy

diff --git a/python/stress_lowlevel.py b/python/stress_lowlevel.py
@@ -1,7 +1,3 @@
-"""
-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
@@ -13,6 +9,11 @@
 
 import pytest
 
+"""
+Code to stress the low-level API as much as possible to expose
+any memory leaks or error handling issues.
+"""
+
 
 def main(stdscr):
     if len(sys.argv) > 1:

diff --git a/python/tests/simplify.py b/python/tests/simplify.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2019-2022 Tskit Developers
+# Copyright (c) 2019-2024 Tskit Developers
 # Copyright (c) 2015-2018 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy

diff --git a/python/tests/test_genotype_matching.py b/python/tests/test_genotype_matching.py
@@ -366,9 +366,9 @@ def update_probabilities(self, site, genotype_state):
 
         for st1 in T:
             if st1.tree_node != -1:
-                normalisation_factor_inner[
-                    st1.tree_node
-                ] = self.compute_normalisation_factor_inner_dict(st1.tree_node)
+                normalisation_factor_inner[st1.tree_node] = (
+                    self.compute_normalisation_factor_inner_dict(st1.tree_node)
+                )
 
         for st1 in T:
             if st1.tree_node != -1:
@@ -506,9 +506,9 @@ def process_site(
 
             for st1 in self.T:
                 if st1.tree_node != -1:
-                    normalisation_factor_inner[
-                        st1.tree_node
-                    ] = self.compute_normalisation_factor_inner_dict(st1.tree_node)
+                    normalisation_factor_inner[st1.tree_node] = (
+                        self.compute_normalisation_factor_inner_dict(st1.tree_node)
+                    )
 
             for st1 in self.T:
                 if st1.tree_node != -1:

diff --git a/python/tests/test_ibd.py b/python/tests/test_ibd.py
@@ -1,6 +1,3 @@
-"""
-Tests of IBD finding algorithms.
-"""
 import collections
 import io
 import itertools
@@ -15,6 +12,10 @@
 import tskit
 from tests.test_highlevel import get_example_tree_sequences
 
+"""
+Tests of IBD finding algorithms.
+"""
+
 
 # ↑ See https://github.com/tskit-dev/tskit/issues/1804 for when
 # we can remove this. The example_ts here is intended to be the

diff --git a/python/tests/test_intervals.py b/python/tests/test_intervals.py
@@ -1,7 +1,7 @@
 # MIT License
 #
-# Copyright (c) 2023 Tskit Developers
-# Copyright (C) 2020-2021 University of Oxford
+# Copyright (c) 2023-2024 Tskit Developers
+# Copyright (C) 2020-2022 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/python/tests/test_lowlevel.py b/python/tests/test_lowlevel.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2023 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 # Copyright (c) 2015-2018 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy

diff --git a/python/tests/test_table_transforms.py b/python/tests/test_table_transforms.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2022 Tskit Developers
+# Copyright (c) 2022-2024 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

diff --git a/python/tests/test_tables.py b/python/tests/test_tables.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2023 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 # Copyright (c) 2017 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -102,12 +102,20 @@ def make_transposed_input_data(self, num_rows):
         cols = self.make_input_data(num_rows)
         return [
             {
-                col: data[j]
-                if len(data) == num_rows
-                else (
-                    bytes(data[cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]])
-                    if "metadata" in col
-                    else data[cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]]
+                col: (
+                    data[j]
+                    if len(data) == num_rows
+                    else (
+                        bytes(
+                            data[
+                                cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]
+                            ]
+                        )
+                        if "metadata" in col
+                        else data[
+                            cols[f"{col}_offset"][j] : cols[f"{col}_offset"][j + 1]
+                        ]
+                    )
                 )
                 for col, data in cols.items()
                 if "offset" not in col

diff --git a/python/tests/test_text_formats.py b/python/tests/test_text_formats.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2021-2022 Tskit Developers
+# Copyright (c) 2021-2024 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

diff --git a/python/tskit/__init__.py b/python/tskit/__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

diff --git a/python/tskit/combinatorics.py b/python/tskit/combinatorics.py
@@ -1,7 +1,7 @@
 #
 # 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

diff --git a/python/tskit/metadata.py b/python/tskit/metadata.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2020-2023 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
@@ -263,18 +263,18 @@ def required_validator(validator, required, instance, schema):
     "type": "string",
     "pattern": r"^([cbB\?hHiIlLqQfd]|\d*[spx])$",
 }
-struct_meta_schema["definitions"]["root"]["properties"][
-    "binaryFormat"
-] = struct_meta_schema["properties"]["binaryFormat"]
+struct_meta_schema["definitions"]["root"]["properties"]["binaryFormat"] = (
+    struct_meta_schema["properties"]["binaryFormat"]
+)
 # arrayLengthFormat matches regex and has default
 struct_meta_schema["properties"]["arrayLengthFormat"] = {
     "type": "string",
     "pattern": r"^[BHILQ]$",
     "default": "L",
 }
-struct_meta_schema["definitions"]["root"]["properties"][
-    "arrayLengthFormat"
-] = struct_meta_schema["properties"]["arrayLengthFormat"]
+struct_meta_schema["definitions"]["root"]["properties"]["arrayLengthFormat"] = (
+    struct_meta_schema["properties"]["arrayLengthFormat"]
+)
 # index is numeric
 struct_meta_schema["properties"]["index"] = {"type": "number"}
 struct_meta_schema["definitions"]["root"]["properties"]["index"] = struct_meta_schema[
@@ -285,14 +285,14 @@ def required_validator(validator, required, instance, schema):
     "type": "string",
     "default": "utf-8",
 }
-struct_meta_schema["definitions"]["root"]["properties"][
-    "stringEncoding"
-] = struct_meta_schema["properties"]["stringEncoding"]
+struct_meta_schema["definitions"]["root"]["properties"]["stringEncoding"] = (
+    struct_meta_schema["properties"]["stringEncoding"]
+)
 # nullTerminated is a boolean
 struct_meta_schema["properties"]["nullTerminated"] = {"type": "boolean"}
-struct_meta_schema["definitions"]["root"]["properties"][
-    "nullTerminated"
-] = struct_meta_schema["properties"]["nullTerminated"]
+struct_meta_schema["definitions"]["root"]["properties"]["nullTerminated"] = (
+    struct_meta_schema["properties"]["nullTerminated"]
+)
 # noLengthEncodingExhaustBuffer is a boolean
 struct_meta_schema["properties"]["noLengthEncodingExhaustBuffer"] = {"type": "boolean"}
 struct_meta_schema["definitions"]["root"]["properties"][

diff --git a/python/tskit/text_formats.py b/python/tskit/text_formats.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2021-2022 Tskit Developers
+# Copyright (c) 2021-2024 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
@@ -356,9 +356,11 @@ def dump_text(
                 ).format(
                     site=mutation.site,
                     node=mutation.node,
-                    time="unknown"
-                    if util.is_unknown_time(mutation.time)
-                    else mutation.time,
+                    time=(
+                        "unknown"
+                        if util.is_unknown_time(mutation.time)
+                        else mutation.time
+                    ),
                     derived_state=mutation.derived_state,
                     parent=mutation.parent,
                     metadata=metadata,

diff --git a/python/tskit/trees.py b/python/tskit/trees.py
@@ -4283,9 +4283,11 @@ def __str__(self):
                         name.capitalize(),
                         table.num_rows,
                         util.naturalsize(table.nbytes),
-                        "Yes"
-                        if hasattr(table, "metadata") and len(table.metadata) > 0
-                        else "No",
+                        (
+                            "Yes"
+                            if hasattr(table, "metadata") and len(table.metadata) > 0
+                            else "No"
+                        ),
                     ]
                 ]
             )

diff --git a/python/tskit/util.py b/python/tskit/util.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
@@ -457,10 +457,12 @@ def unicode_table(
 def html_table(rows, *, header):
     headers = "".join(f"<th>{h}</th>" for h in header)
     rows = (
-        f'<td style="text-align: center;" colspan="{len(headers)}"><em>{row[11:]}'
-        f" rows skipped (tskit.set_print_options)</em></td>"
-        if "__skipped__" in row
-        else "".join(f"<td>{cell}</td>" for cell in row)
+        (
+            f'<td style="text-align: center;" colspan="{len(headers)}"><em>{row[11:]}'
+            f" rows skipped (tskit.set_print_options)</em></td>"
+            if "__skipped__" in row
+            else "".join(f"<td>{cell}</td>" for cell in row)
+        )
         for row in rows
     )
     rows = "".join(f"<tr>{row}</tr>\n" for row in rows)