From 72d26b59990a58c5eb1bcb808585c5c6313f4ce9 Mon Sep 17 00:00:00 2001
From: Andreas Kloeckner <inform@tiker.net>
Date: Mon, 1 Jul 2024 14:08:37 -0500
Subject: [PATCH] Switch to pyproject, ruff, fix ruff-flagged issues
---
.github/workflows/ci.yml | 14 ++--
.gitlab-ci.yml | 6 +-
pyproject.toml | 97 ++++++++++++++++++++++++++++
pytools/__init__.py | 50 +++++++++-----
pytools/debug.py | 4 +-
pytools/graph.py | 22 +++++--
pytools/persistent_dict.py | 31 ++++++---
pytools/prefork.py | 9 ++-
pytools/py_codegen.py | 5 +-
pytools/tag.py | 10 ++-
pytools/test/test_persistent_dict.py | 12 +++-
pytools/test/test_pytools.py | 17 +++--
pytools/version.py | 12 +++-
setup.cfg | 23 -------
setup.py | 53 ---------------
15 files changed, 228 insertions(+), 137 deletions(-)
create mode 100644 pyproject.toml
delete mode 100644 setup.cfg
delete mode 100644 setup.py
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2476207..4bbe8c3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -10,20 +10,16 @@ on:
- cron: '17 3 * * 0'
jobs:
- flake8:
- name: Flake8
+ ruff:
+ name: Ruff
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- -
- uses: actions/setup-python@v5
- with:
- # matches compat target in setup.py
- python-version: '3.8'
+ - uses: actions/setup-python@v5
- name: "Main Script"
run: |
- curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/prepare-and-run-flake8.sh
- . ./prepare-and-run-flake8.sh "$(basename $GITHUB_REPOSITORY)"
+ pip install ruff
+ ruff check
validate_cff:
name: Validate CITATION.cff
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6726e28..7f23c64 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -42,10 +42,10 @@ Pytest without Numpy:
Flake8:
script:
- - curl -L -O https://gitlab.tiker.net/inducer/ci-support/raw/main/prepare-and-run-flake8.sh
- - . ./prepare-and-run-flake8.sh "$CI_PROJECT_NAME"
+ - pipx install ruff
+ - ruff check
tags:
- - python3
+ - docker-runner
except:
- tags
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..b0b8bc9
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,97 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+ "setuptools>=63",
+]
+
+[project]
+name = "pytools"
+version = "2024.1.6"
+description = "A collection of tools for Python"
+readme = "README.rst"
+license = { text = "MIT" }
+requires-python = "~=3.8"
+authors = [
+ { name = "Andreas Kloeckner", email = "inform@tiker.net" },
+]
+classifiers = [
+ "Development Status :: 4 - Beta",
+ "Intended Audience :: Developers",
+ "Intended Audience :: Other Audience",
+ "Intended Audience :: Science/Research",
+ "License :: OSI Approved :: MIT License",
+ "Natural Language :: English",
+ "Programming Language :: Python",
+ "Programming Language :: Python :: 3",
+ "Topic :: Scientific/Engineering",
+ "Topic :: Scientific/Engineering :: Information Analysis",
+ "Topic :: Scientific/Engineering :: Mathematics",
+ "Topic :: Scientific/Engineering :: Visualization",
+ "Topic :: Software Development :: Libraries",
+ "Topic :: Utilities",
+]
+dependencies = [
+ "platformdirs>=2.2.0",
+ "typing_extensions>=4.0; python_version<'3.11'",
+]
+
+[project.optional-dependencies]
+numpy = [
+ "numpy>=1.6.0",
+]
+
+test = [
+ "mypy",
+ "pytest",
+ "ruff",
+]
+
+[project.urls]
+Homepage = "https://github.com/inducer/pytools/"
+Documentation = "https://documen.tician.de/pytools/"
+
+[tool.setuptools.package-data]
+pytools = [
+ "py.typed",
+]
+
+[tool.ruff]
+target-version = "py38"
+line-length = 85
+
+preview = true
+[tool.ruff.lint]
+extend-select = [
+ "B", # flake8-bugbear
+ "C", # flake8-comprehensions
+ "E", # pycodestyle
+ "F", # pyflakes
+ "I", # flake8-isort
+ "N", # pep8-naming
+ "NPY", # numpy
+ "Q", # flake8-quotes
+ "W", # pycodestyle
+]
+extend-ignore = [
+ "C90", # McCabe complexity
+ "E221", # multiple spaces before operator
+ "E226", # missing whitespace around arithmetic operator
+ "E402", # module-level import not at top of file
+]
+[tool.ruff.lint.flake8-quotes]
+docstring-quotes = "double"
+inline-quotes = "double"
+multiline-quotes = "double"
+
+[tool.ruff.lint.isort]
+combine-as-imports = true
+
+known-local-folder = [
+ "pytools",
+]
+lines-after-imports = 2
+
+[tool.mypy]
+ignore_missing_imports = true
+warn_unused_ignores = true
+
diff --git a/pytools/__init__.py b/pytools/__init__.py
index 2304462..b09bf03 100644
--- a/pytools/__init__.py
+++ b/pytools/__init__.py
@@ -36,8 +36,24 @@ import sys
from functools import reduce, wraps
from sys import intern
from typing import (
- Any, Callable, ClassVar, Dict, Generic, Hashable, Iterable, Iterator, List,
- Mapping, Optional, Sequence, Set, Tuple, Type, TypeVar, Union)
+ Any,
+ Callable,
+ ClassVar,
+ Dict,
+ Generic,
+ Hashable,
+ Iterable,
+ Iterator,
+ List,
+ Mapping,
+ Optional,
+ Sequence,
+ Set,
+ Tuple,
+ Type,
+ TypeVar,
+ Union,
+)
try:
@@ -528,7 +544,8 @@ class Reference:
def get(self):
from warnings import warn
- warn("Reference.get() is deprecated -- use ref.value instead")
+ warn("Reference.get() is deprecated -- use ref.value instead. "
+ "This will stop working in 2025.", stacklevel=2)
return self.value
def set(self, value):
@@ -607,7 +624,7 @@ def one(iterable: Iterable[T]) -> T:
try:
v = next(it)
except StopIteration:
- raise ValueError("empty iterable passed to 'one()'")
+ raise ValueError("empty iterable passed to 'one()'") from None
def no_more():
try:
@@ -629,7 +646,7 @@ def is_single_valued(
try:
first_item = next(it)
except StopIteration:
- raise ValueError("empty iterable passed to 'single_valued()'")
+ raise ValueError("empty iterable passed to 'single_valued()'") from None
for other_item in it:
if not equality_pred(other_item, first_item):
@@ -656,7 +673,7 @@ def single_valued(
try:
first_item = next(it)
except StopIteration:
- raise ValueError("empty iterable passed to 'single_valued()'")
+ raise ValueError("empty iterable passed to 'single_valued()'") from None
def others_same():
for other_item in it:
@@ -1241,7 +1258,7 @@ def argmin2(iterable, return_value=False):
try:
current_argmin, current_min = next(it)
except StopIteration:
- raise ValueError("argmin of empty iterable")
+ raise ValueError("argmin of empty iterable") from None
for arg, item in it:
if item < current_min:
@@ -1259,7 +1276,7 @@ def argmax2(iterable, return_value=False):
try:
current_argmax, current_max = next(it)
except StopIteration:
- raise ValueError("argmax of empty iterable")
+ raise ValueError("argmax of empty iterable") from None
for arg, item in it:
if item > current_max:
@@ -1326,7 +1343,7 @@ def average(iterable):
s = next(it)
count = 1
except StopIteration:
- raise ValueError("empty average")
+ raise ValueError("empty average") from None
for value in it:
s = s + value
@@ -1441,7 +1458,7 @@ def generate_decreasing_nonnegative_tuples_summing_to(
yield ()
elif length == 1:
if n <= max_value:
- #print "MX", n, max_value
+ # print "MX", n, max_value
yield (n,)
else:
return
@@ -1450,7 +1467,7 @@ def generate_decreasing_nonnegative_tuples_summing_to(
max_value = n
for i in range(min_value, max_value+1):
- #print "SIG", sig, i
+ # print "SIG", sig, i
for remainder in generate_decreasing_nonnegative_tuples_summing_to(
n-i, length-1, min_value, i):
yield (i,) + remainder
@@ -1502,7 +1519,7 @@ def generate_permutations(original):
else:
for perm_ in generate_permutations(original[1:]):
for i in range(len(perm_)+1):
- #nb str[0:1] works in both string and list contexts
+ # nb str[0:1] works in both string and list contexts
yield perm_[:i] + original[0:1] + perm_[i:]
@@ -1527,7 +1544,7 @@ def enumerate_basic_directions(dimensions):
# {{{ graph algorithms
-from pytools.graph import a_star as a_star_moved
+from pytools.graph import a_star as a_star_moved # noqa: E402
a_star = MovedFunctionDeprecationWrapper(a_star_moved)
@@ -1808,7 +1825,7 @@ def string_histogram( # pylint: disable=too-many-arguments,too-many-locals
for value in iterable:
if max_value is not None and value > max_value or value < bin_starts[0]:
from warnings import warn
- warn("string_histogram: out-of-bounds value ignored")
+ warn("string_histogram: out-of-bounds value ignored", stacklevel=2)
else:
bin_nr = bisect(bin_starts, value)-1
try:
@@ -2425,7 +2442,7 @@ def find_git_revision(tree_root): # pylint: disable=too-many-locals
assert retcode is not None
if retcode != 0:
from warnings import warn
- warn("unable to find git revision")
+ warn("unable to find git revision", stacklevel=1)
return None
return git_rev
@@ -2704,7 +2721,8 @@ def natsorted(iterable, key=None, reverse=False):
.. versionadded:: 2020.1
"""
if key is None:
- key = lambda x: x
+ def key(x):
+ return x
return sorted(iterable, key=lambda y: natorder(key(y)), reverse=reverse)
# }}}
diff --git a/pytools/debug.py b/pytools/debug.py
index 71e08d2..b4923f6 100644
--- a/pytools/debug.py
+++ b/pytools/debug.py
@@ -51,7 +51,7 @@ def open_unique_debug_file(stem, extension=""):
# {{{ refcount debugging ------------------------------------------------------
-class RefDebugQuit(Exception):
+class RefDebugQuit(Exception): # noqa: N818
pass
@@ -159,7 +159,7 @@ def setup_readline():
e = sys.exc_info()[1]
from warnings import warn
- warn(f"Error opening readline history file: {e}")
+ warn(f"Error opening readline history file: {e}", stacklevel=2)
readline.parse_and_bind("tab: complete")
diff --git a/pytools/graph.py b/pytools/graph.py
index 9fd6f26..09db7aa 100644
--- a/pytools/graph.py
+++ b/pytools/graph.py
@@ -65,8 +65,20 @@ Type Variables Used
"""
from typing import (
- Any, Callable, Collection, Dict, Hashable, Iterator, List, Mapping, MutableSet,
- Optional, Set, Tuple, TypeVar)
+ Any,
+ Callable,
+ Collection,
+ Dict,
+ Hashable,
+ Iterator,
+ List,
+ Mapping,
+ MutableSet,
+ Optional,
+ Set,
+ Tuple,
+ TypeVar,
+)
try:
@@ -437,10 +449,12 @@ def as_graphviz_dot(graph: GraphT[NodeT],
from pytools.graphviz import dot_escape
if node_labels is None:
- node_labels = lambda x: str(x)
+ def node_labels(x):
+ return str(x)
if edge_labels is None:
- edge_labels = lambda x, y: ""
+ def edge_labels(x, y):
+ return ""
node_to_id = {}
diff --git a/pytools/persistent_dict.py b/pytools/persistent_dict.py
index 89ef3a8..ed4fce9 100644
--- a/pytools/persistent_dict.py
+++ b/pytools/persistent_dict.py
@@ -39,8 +39,18 @@ import sys
from dataclasses import fields as dc_fields, is_dataclass
from enum import Enum
from typing import (
- TYPE_CHECKING, Any, Callable, FrozenSet, Iterator, Mapping, Optional, Protocol,
- Tuple, TypeVar, cast)
+ TYPE_CHECKING,
+ Any,
+ Callable,
+ FrozenSet,
+ Iterator,
+ Mapping,
+ Optional,
+ Protocol,
+ Tuple,
+ TypeVar,
+ cast,
+)
if TYPE_CHECKING:
@@ -224,7 +234,7 @@ class KeyBuilder:
if not isinstance(key, type):
try:
# pylint:disable=protected-access
- object.__setattr__(key, "_pytools_persistent_hash_digest", digest)
+ object.__setattr__(key, "_pytools_persistent_hash_digest", digest)
except AttributeError:
pass
except TypeError:
@@ -418,7 +428,7 @@ def __getattr__(name: str) -> Any:
if name in ("NoSuchEntryInvalidKeyError",
"NoSuchEntryInvalidContentsError"):
from warnings import warn
- warn(f"pytools.persistent_dict.{name} has been removed.")
+ warn(f"pytools.persistent_dict.{name} has been removed.", stacklevel=2)
return NoSuchEntryError
raise AttributeError(name)
@@ -517,7 +527,8 @@ class _PersistentDictBase(Mapping[K, V]):
"that they're often indicative of a broken hash key "
"implementation (that is not considering some elements "
"relevant for equality comparison)",
- CollisionWarning
+ CollisionWarning,
+ stacklevel=3
)
# This is here so we can step through equality comparison to
@@ -551,7 +562,7 @@ class _PersistentDictBase(Mapping[K, V]):
if n % 20 == 0:
from warnings import warn
warn(f"PersistentDict: database '{self.filename}' busy, {n} "
- "retries")
+ "retries", stacklevel=3)
else:
break
@@ -696,12 +707,12 @@ class WriteOncePersistentDict(_PersistentDictBase[K, V]):
if hasattr(e, "sqlite_errorcode"):
if e.sqlite_errorcode == sqlite3.SQLITE_CONSTRAINT_PRIMARYKEY:
raise ReadOnlyEntryError("WriteOncePersistentDict, "
- "tried overwriting key")
+ "tried overwriting key") from e
else:
raise
else:
raise ReadOnlyEntryError("WriteOncePersistentDict, "
- "tried overwriting key")
+ "tried overwriting key") from e
def _fetch_uncached(self, keyhash: str) -> Tuple[K, V]:
# This method is separate from fetch() to allow for LRU caching
@@ -719,8 +730,8 @@ class WriteOncePersistentDict(_PersistentDictBase[K, V]):
try:
stored_key, value = self._fetch(keyhash)
- except KeyError:
- raise NoSuchEntryError(key)
+ except KeyError as err:
+ raise NoSuchEntryError(key) from err
else:
self._collision_check(key, stored_key)
return value
diff --git a/pytools/prefork.py b/pytools/prefork.py
index c2ed6d3..aa76c6b 100644
--- a/pytools/prefork.py
+++ b/pytools/prefork.py
@@ -23,7 +23,8 @@ class DirectForker:
try:
return spcall(cmdline, cwd=cwd)
except OSError as e:
- raise ExecError("error invoking '{}': {}".format(" ".join(cmdline), e))
+ raise ExecError(
+ "error invoking '{}': {}".format(" ".join(cmdline), e)) from e
def call_async(self, cmdline, cwd=None):
from subprocess import Popen
@@ -36,7 +37,8 @@ class DirectForker:
return self.count
except OSError as e:
- raise ExecError("error invoking '{}': {}".format(" ".join(cmdline), e))
+ raise ExecError(
+ "error invoking '{}': {}".format(" ".join(cmdline), e)) from e
@staticmethod
def call_capture_output(cmdline, cwd=None, error_on_nonzero=True):
@@ -55,7 +57,8 @@ class DirectForker:
return popen.returncode, stdout_data, stderr_data
except OSError as e:
- raise ExecError("error invoking '{}': {}".format(" ".join(cmdline), e))
+ raise ExecError(
+ "error invoking '{}': {}".format(" ".join(cmdline), e)) from e
def wait(self, aid):
proc = self.apids.pop(aid)
diff --git a/pytools/py_codegen.py b/pytools/py_codegen.py
index 4e08239..887497c 100644
--- a/pytools/py_codegen.py
+++ b/pytools/py_codegen.py
@@ -25,7 +25,10 @@ from importlib.util import MAGIC_NUMBER as BYTECODE_VERSION
from types import FunctionType, ModuleType
from pytools.codegen import ( # noqa
- CodeGenerator as CodeGeneratorBase, Indentation, remove_common_indentation)
+ CodeGenerator as CodeGeneratorBase,
+ Indentation,
+ remove_common_indentation,
+)
class PythonCodeGenerator(CodeGeneratorBase):
diff --git a/pytools/tag.py b/pytools/tag.py
index 7e4f32f..2130e04 100644
--- a/pytools/tag.py
+++ b/pytools/tag.py
@@ -30,7 +30,15 @@ Internal stuff that is only here because the documentation tool wants it
from dataclasses import dataclass
from typing import ( # noqa: F401
- Any, FrozenSet, Iterable, Set, Tuple, Type, TypeVar, Union)
+ Any,
+ FrozenSet,
+ Iterable,
+ Set,
+ Tuple,
+ Type,
+ TypeVar,
+ Union,
+)
from pytools import memoize, memoize_method
diff --git a/pytools/test/test_persistent_dict.py b/pytools/test/test_persistent_dict.py
index 2f6812c..b0e050e 100644
--- a/pytools/test/test_persistent_dict.py
+++ b/pytools/test/test_persistent_dict.py
@@ -8,8 +8,14 @@ from typing import Any, Dict
import pytest
from pytools.persistent_dict import (
- CollisionWarning, KeyBuilder, NoSuchEntryCollisionError, NoSuchEntryError,
- PersistentDict, ReadOnlyEntryError, WriteOncePersistentDict)
+ CollisionWarning,
+ KeyBuilder,
+ NoSuchEntryCollisionError,
+ NoSuchEntryError,
+ PersistentDict,
+ ReadOnlyEntryError,
+ WriteOncePersistentDict,
+)
from pytools.tag import Tag, tag_dataclass
@@ -495,7 +501,7 @@ def test_ABC_hashing() -> None: # noqa: N802
keyb = KeyBuilder()
- class MyABC(ABC):
+ class MyABC(ABC): # noqa: B024
pass
assert keyb(MyABC) != keyb(ABC)
diff --git a/pytools/test/test_pytools.py b/pytools/test/test_pytools.py
index 9e393a7..8bcd9af 100644
--- a/pytools/test/test_pytools.py
+++ b/pytools/test/test_pytools.py
@@ -23,6 +23,7 @@ THE SOFTWARE.
import logging
import sys
+from typing import FrozenSet
import pytest
@@ -30,7 +31,6 @@ from pytools import Record
logger = logging.getLogger(__name__)
-from typing import FrozenSet
def test_memoize_method_clear():
@@ -223,8 +223,10 @@ def test_memoize_frozen() -> None:
def test_spatial_btree(dims, do_plot=False):
pytest.importorskip("numpy")
import numpy as np
+
+ rng = np.random.default_rng()
nparticles = 2000
- x = -1 + 2*np.random.rand(dims, nparticles)
+ x = -1 + 2*rng.uniform(size=(dims, nparticles))
x = np.sign(x)*np.abs(x)**1.9
x = (1.4 + x) % 2 - 1
@@ -360,8 +362,6 @@ def test_eoc():
# {{{ test invalid inputs
- import numpy as np
-
eoc = EOCRecorder()
# scalar inputs are fine
@@ -500,7 +500,12 @@ def test_obj_array_vectorize(c=1):
def test_tag():
from pytools.tag import (
- NonUniqueTagError, Tag, Taggable, UniqueTag, check_tag_uniqueness)
+ NonUniqueTagError,
+ Tag,
+ Taggable,
+ UniqueTag,
+ check_tag_uniqueness,
+ )
# Need a subclass that defines the copy function in order to test.
class TaggableWithCopy(Taggable):
@@ -840,7 +845,7 @@ def test_record():
assert str(r) == "SimpleRecord(a=1, b=2, c=3, d=4, e=5)"
with pytest.raises(AttributeError):
- r.ff
+ r.ff # noqa: B018
# Test pickling
import pickle
diff --git a/pytools/version.py b/pytools/version.py
index 87424d5..67a7511 100644
--- a/pytools/version.py
+++ b/pytools/version.py
@@ -1,3 +1,9 @@
-VERSION = (2024, 1, 6)
-VERSION_STATUS = ""
-VERSION_TEXT = ".".join(str(x) for x in VERSION) + VERSION_STATUS
+import re
+from importlib import metadata
+
+
+VERSION_TEXT = metadata.version("pytools")
+_match = re.match("^([0-9.]+)([a-z0-9]*?)$", VERSION_TEXT)
+assert _match is not None
+VERSION_STATUS = _match.group(2)
+VERSION = tuple(int(nr) for nr in _match.group(1).split("."))
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 6f288f8..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,23 +0,0 @@
-[flake8]
-ignore = E126,E127,E128,E123,E226,E241,E242,E265,E402,W503,E731,N818
-max-line-length=85
-
-inline-quotes = "
-docstring-quotes = "
-multiline-quotes = """
-
-# enable-flake8-bugbear
-# enable-isort
-
-[isort]
-line_length = 85
-lines_after_imports = 2
-combine_as_imports = True
-multi_line_output = 4
-
-[wheel]
-universal = 1
-
-[mypy]
-ignore_missing_imports = True
-warn_unused_ignores = true
diff --git a/setup.py b/setup.py
deleted file mode 100644
index f082237..0000000
--- a/setup.py
+++ /dev/null
@@ -1,53 +0,0 @@
-#! /usr/bin/env python
-
-from setuptools import find_packages, setup
-
-
-ver_dic = {}
-version_file = open("pytools/version.py")
-try:
- version_file_contents = version_file.read()
-finally:
- version_file.close()
-
-exec(compile(version_file_contents, "pytools/version.py", "exec"), ver_dic)
-
-setup(name="pytools",
- version=ver_dic["VERSION_TEXT"],
- description="A collection of tools for Python",
- long_description=open("README.rst").read(),
- classifiers=[
- "Development Status :: 4 - Beta",
- "Intended Audience :: Developers",
- "Intended Audience :: Other Audience",
- "Intended Audience :: Science/Research",
- "License :: OSI Approved :: MIT License",
- "Natural Language :: English",
- "Programming Language :: Python",
- "Programming Language :: Python :: 3",
- "Topic :: Scientific/Engineering",
- "Topic :: Scientific/Engineering :: Information Analysis",
- "Topic :: Scientific/Engineering :: Mathematics",
- "Topic :: Scientific/Engineering :: Visualization",
- "Topic :: Software Development :: Libraries",
- "Topic :: Utilities",
- ],
-
- python_requires="~=3.8",
-
- install_requires=[
- "platformdirs>=2.2.0",
- "typing_extensions>=4.0; python_version<'3.11'",
- ],
-
- package_data={"pytools": ["py.typed"]},
-
- extras_require={
- "numpy": ["numpy>=1.6.0"],
- },
-
- author="Andreas Kloeckner",
- url="http://pypi.python.org/pypi/pytools",
- author_email="inform@tiker.net",
- license="MIT",
- packages=find_packages())
--
GitLab