Fix failures from updates to linting tools

- all ruff failures
- newer black
- stricter mypy
- some changes in setuptools packaging normalization
- silence some sphinx warnings that we can't seem to be able to fix
- Run with pypy3.10 instead of 3.8, some packages are not compatible
  anymore
- Add codecov token to allow uploading reports

.github/scripts/summary.py

@@ -5,7 +5,7 @@
 import logging
 from dataclasses import InitVar, dataclass, field
 from typing import Any, Literal
-from xml.etree import ElementTree
+from xml.etree import ElementTree as ET
 
 from tabulate import tabulate
 
@@ -21,7 +21,7 @@ class TestCase:
     summary: str | None
 
     @classmethod
-    def from_junit(cls, tree: ElementTree.Element) -> TestCase:
+    def from_junit(cls, tree: ET.Element) -> TestCase:
         children = tree.getchildren()
         assert len(children) <= 1
 
@@ -75,7 +75,7 @@ def __post_init__(self, total: int) -> None:
         self.successes = total - self.errors - self.failures - self.skipped
 
     @classmethod
-    def from_junit(cls, tree: ElementTree.Element) -> TestSuite:
+    def from_junit(cls, tree: ET.Element) -> TestSuite:
         attrs = tree.attrib
 
         tests = [
@@ -139,9 +139,7 @@ def main() -> None:
     testsuites = [
         TestSuite.from_junit(testsuite)
         for file in files
-        for testsuite in ElementTree.parse(file).findall(  # noqa: S314
-            "testsuite"
-        )
+        for testsuite in ET.parse(file).findall("testsuite")  # noqa: S314
     ]
 
     summary = tabulate(

.github/workflows/ci.yml

@@ -94,7 +94,7 @@ jobs:
           - "3.10"
           - "3.11"
           - "3.12"
-          - "pypy3.8"
+          - "pypy3.10"
         include:
         - os: macos-latest
           python: "3.8"
@@ -205,6 +205,7 @@ jobs:
       - name: Upload coverage to codecov
         uses: codecov/codecov-action@v3
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           files: ./_artifacts/coverage.xml
           fail_ci_if_error: true
           verbose: true

docs/conf.py

@@ -79,6 +79,14 @@
     ("py:class", "dwas._steps.parametrize.T"),
     ("py:class", "dwas._steps.handlers.StepHandler"),
 ]
+suppress_warnings = [
+    # See https://github.com/sphinx-doc/sphinx/issues/12589
+    "autosummary.import_cycle",
+]
+
+linkcheck_ignore = [
+    "https://pypi.org/project/dwas/#history",
+]
 
 # Theme options
 html_theme = "furo"

dwasfile.py

@@ -1,6 +1,7 @@
 """
 Contains the dwas configuration for this project.
 """
+
 from pathlib import Path
 
 import dwas
@@ -10,7 +11,7 @@
 DOCS_REQUIREMENTS = "-rrequirements/requirements-docs.txt"
 TEST_REQUIREMENTS = "-rrequirements/requirements-test.txt"
 TYPES_REQUIREMENTS = "-rrequirements/requirements-types.txt"
-SUPPORTED_PYTHONS = ["3.8", "3.9", "3.10", "3.11", "3.12", "pypy3.8"]
+SUPPORTED_PYTHONS = ["3.8", "3.9", "3.10", "3.11", "3.12", "pypy3.10"]
 OLDEST_SUPPORTED_PYTHON = SUPPORTED_PYTHONS[0]
 PYTHON_FILES = [
     "docs/conf.py",

pyproject.toml

@@ -135,12 +135,12 @@ disable = [
 # Ruff
 [tool.ruff]
 target-version = "py38"
+
+[tool.ruff.lint]
 select = ["ALL"]
 ignore = [
     ##
     # Typing
-    "ANN101",  # Don't annotate 'self'
-    "ANN102",  # Don't annotate 'cls'
     "ANN401",  # Allow typing with ANY
     ##
     # Format
@@ -162,7 +162,6 @@ ignore = [
     "FIX",  # We want to put fixmes longterm
     "TD",  # We want to be able to add todos without issu links
     "INP001",  # Not every .py file is part of a package
-    "PT004",  # Don't add `_` in front of fixtures returning nothing
     "S101",  # Allow asserts
     "TID252",  # We want relative imports
     "PLR2004",  # Disable magic numbers check
@@ -183,7 +182,7 @@ ignore = [
 flake8-pytest-style.parametrize-values-type = "tuple"
 flake8-pytest-style.parametrize-values-row-type = "tuple"
 flake8-pytest-style.fixture-parentheses = false
-lint.isort.known-first-party = ["dwas"]
+isort.known-first-party = ["dwas"]
 
 [tool.ruff.lint.per-file-ignores]
 "docs/*" = ["D"]

src/dwas/__init__.py

@@ -9,6 +9,7 @@
 
     While ``dwas`` is not at version 1.0.0, it does not guarantee API stability.
 """
+
 from ._config import Config
 from ._exceptions import BaseDwasException
 from ._steps import (
@@ -34,23 +35,23 @@
 # XXX: The order here is important, it declares the order in which the entries
 #      are documented in the public docs.
 __all__ = [
-    "StepRunner",
+    "BaseDwasException",
+    "Config",
+    "DefaultsAlreadySetException",
+    "MismatchedNumberOfParametersException",
+    "ParameterConflictException",
     "Step",
-    "StepWithSetup",
-    "StepWithDependentSetup",
+    "StepRunner",
     "StepWithArtifacts",
     "StepWithCleanup",
-    "Config",
-    "register_step",
-    "register_managed_step",
-    "register_step_group",
-    "step",
+    "StepWithDependentSetup",
+    "StepWithSetup",
+    "build_parameters",
     "managed_step",
     "parametrize",
-    "build_parameters",
+    "register_managed_step",
+    "register_step",
+    "register_step_group",
     "set_defaults",
-    "BaseDwasException",
-    "DefaultsAlreadySetException",
-    "MismatchedNumberOfParametersException",
-    "ParameterConflictException",
+    "step",
 ]

src/dwas/_config.py

@@ -157,7 +157,10 @@ def __init__(
         self.n_jobs = n_jobs
 
         self.is_interactive = (
-            sys.__stdout__.isatty() and sys.__stderr__.isatty()
+            sys.__stdout__ is not None
+            and sys.__stdout__.isatty()
+            and sys.__stderr__ is not None
+            and sys.__stderr__.isatty()
         )
 
         self.environ = {

src/dwas/_frontend.py

@@ -93,6 +93,9 @@ def __init__(self, summary: StepSummary) -> None:
         self._summary = summary
 
         def _refresh_in_context() -> None:
+            assert sys.__stdout__ is not None
+            assert sys.__stderr__ is not None
+
             with _io.redirect_streams(
                 sys.__stdout__, sys.__stderr__
             ), _io.log_file(None):

src/dwas/_logging.py

@@ -20,7 +20,7 @@ class ColorFormatter(logging.Formatter):
         {
             logging.DEBUG: Fore.CYAN,
             logging.INFO: "",
-            logging.WARN: Fore.YELLOW,
+            logging.WARNING: Fore.YELLOW,
             logging.ERROR: Fore.RED + Style.BRIGHT,
             logging.FATAL: Back.RED + Fore.WHITE + Style.BRIGHT,
         }
@@ -32,8 +32,10 @@ def formatMessage(self, record: logging.LogRecord) -> str:
 
     def formatException(
         self,
-        ei: tuple[type[BaseException], BaseException, TracebackType | None]
-        | tuple[None, None, None],
+        ei: (
+            tuple[type[BaseException], BaseException, TracebackType | None]
+            | tuple[None, None, None]
+        ),
     ) -> str:
         output = super().formatException(ei)
         return f"{Fore.CYAN}\ndwas > " + "\ndwas > ".join(output.splitlines())

src/dwas/_pipeline.py

@@ -228,9 +228,9 @@ def compute_replacement(requirements: list[str]) -> list[str]:
                         replacements.append(requirement)
                     else:
                         if requirement not in except_replacements:
-                            except_replacements[
-                                requirement
-                            ] = compute_replacement(graph[requirement])
+                            except_replacements[requirement] = (
+                                compute_replacement(graph[requirement])
+                            )
                         replacements.extend(except_replacements[requirement])
 
                 return replacements
@@ -264,10 +264,10 @@ def compute_only_replacement(
                 replacements = []
                 for requirement in requirements:
                     if requirement not in only_replacements:
-                        only_replacements[
-                            requirement
-                        ] = compute_only_replacement(
-                            requirement, graph[requirement]
+                        only_replacements[requirement] = (
+                            compute_only_replacement(
+                                requirement, graph[requirement]
+                            )
                         )
                     replacements.extend(only_replacements[requirement])
 
@@ -665,7 +665,7 @@ def _compute_slowest_chains(
         total_time_per_step: dict[str, tuple[list[str], timedelta]] = {}
 
         def compute_chain(step: str) -> tuple[list[str], timedelta]:
-            precomputed_result = total_time_per_step.get(step, None)
+            precomputed_result = total_time_per_step.get(step)
             if precomputed_result is not None:
                 return precomputed_result
 

src/dwas/_steps/__init__.py

@@ -23,21 +23,21 @@
 )
 
 __all__ = [
+    "DefaultsAlreadySetException",
+    "MismatchedNumberOfParametersException",
+    "ParameterConflictException",
+    "Step",
+    "StepRunner",
+    "StepWithArtifacts",
+    "StepWithCleanup",
+    "StepWithDependentSetup",
+    "StepWithSetup",
+    "build_parameters",
     "managed_step",
     "parametrize",
-    "build_parameters",
     "register_managed_step",
     "register_step",
     "register_step_group",
     "set_defaults",
     "step",
-    "Step",
-    "StepRunner",
-    "StepWithDependentSetup",
-    "StepWithSetup",
-    "StepWithArtifacts",
-    "StepWithCleanup",
-    "DefaultsAlreadySetException",
-    "MismatchedNumberOfParametersException",
-    "ParameterConflictException",
 ]

src/dwas/_steps/parametrize.py

@@ -90,17 +90,15 @@ def parametrize(
     arg_names: str,
     args_values: Sequence[Any],
     ids: Sequence[str | None] | None = None,
-) -> Callable[[T], T]:
-    ...
+) -> Callable[[T], T]: ...
 
 
 @overload
 def parametrize(
     arg_names: Sequence[str],
     args_values: Sequence[Sequence[Any]],
     ids: Sequence[str | None] | None = None,
-) -> Callable[[T], T]:
-    ...
+) -> Callable[[T], T]: ...
 
 
 def parametrize(

src/dwas/_steps/steps.py

@@ -3,7 +3,7 @@
 
 from __future__ import annotations
 
-from pathlib import Path  # noqa: TCH003  required for Sphinx
+from pathlib import Path  # noqa: TC003  required for Sphinx
 from typing import TYPE_CHECKING, Any, Callable, Protocol, runtime_checkable
 
 if TYPE_CHECKING:

src/dwas/_subproc.py

@@ -114,9 +114,9 @@ def _run() -> subprocess.CompletedProcess[None]:
                 stdout_reader.join()
                 stderr_reader.join()
 
-            ret: subprocess.CompletedProcess[
-                None
-            ] = subprocess.CompletedProcess(command, proc.returncode)
+            ret: subprocess.CompletedProcess[None] = (
+                subprocess.CompletedProcess(command, proc.returncode)
+            )
             self._remove(proc)
             ret.check_returncode()
             return ret

src/dwas/predefined/_sphinx.py

@@ -2,7 +2,7 @@
 
 import shutil
 from contextlib import suppress
-from pathlib import Path  # noqa: TCH003 required for sphinx documentation
+from pathlib import Path  # noqa: TC003 required for sphinx documentation
 
 from .. import Step, StepRunner, build_parameters, set_defaults
 

tests/predefined/test_package.py

@@ -17,7 +17,7 @@ def test_exposes_sdists_and_wheels(self, cache_path):
         cli(cache_path=cache_path, steps=["output_artifacts"])
         artifacts = json.loads(Path("artifacts.json").read_text("utf-8"))
         assert list(artifacts.keys()) == ["sdists", "wheels"]
-        assert Path(artifacts["sdists"][0]).name == "test-package-0.0.0.tar.gz"
+        assert Path(artifacts["sdists"][0]).name == "test_package-0.0.0.tar.gz"
         assert (
             Path(artifacts["wheels"][0]).name
             == "test_package-0.0.0-py3-none-any.whl"