Merge pull request #466 from MC-kit/devel

switch to msgspec from PyPI: not it supports python 3.13

Author: dvp2015

.github/constraints.txt

@@ -1,3 +1,3 @@
-pip==24.1.2
-poetry==1.8.3
+pip==24.3.1
+poetry==1.8.4
 

.github/workflows/tests.yml

@@ -236,4 +236,6 @@ jobs:
           nox --force-color --session=coverage -- xml
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -111,7 +111,7 @@ repos:
       #   exclude: ^notebooks|^extern
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.8.4
     hooks:
       - id: ruff
         exclude: ^notebooks|^extern

docs/requirements.txt

@@ -1,7 +1,7 @@
-sphinx==5.1.1
-sphinx-autobuild==2021.3.14
-sphinx-autodoc-typehints==1.19.2
+sphinx==8.1.3
+sphinx-autobuild==2024.10.3
+sphinx-autodoc-typehints==2.5.0
 sphinx-autorun==1.1.1
 sphinx-click==4.3.0
-sphinx-rtd-theme==1.2.0
+sphinx-rtd-theme==3.0.2
 sphinxcontrib-napoleon==0.7

noxfile.py

@@ -48,7 +48,7 @@ def find_my_name() -> str:
     Raises:
         ValueError: if the pattern is not found.
     """
-    with Path("pyproject.toml").open() as fid:
+    with Path("pyproject.toml").open(encoding="utf8") as fid:
         for line in fid:
             res = NAME_RGX.match(line)
             if res is not None:
@@ -67,7 +67,7 @@ def find_my_name() -> str:
 def _update_hook(hook: Path, virtualenv: str, s: Session) -> None:
     text = hook.read_text()
     bin_dir = repr(s.bin)[1:-1]  # strip quotes
-    if Path("A") == Path("a") and bin_dir.lower() in text.lower() or bin_dir in text:
+    if (Path("A") == Path("a") and bin_dir.lower() in text.lower()) or bin_dir in text:
         lines = text.splitlines()
         if lines[0].startswith("#!") and "python" in lines[0].lower():
             header = dedent(

poetry.lock

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "xpypact"
-version = "0.12.3"
+version = "0.12.4"
 description = "\"Python workflow framework for FISPACT.\""
 authors = ["dvp <[email protected]>"]
 license = "MIT"
@@ -26,9 +26,7 @@ classifiers = [
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Operating System :: OS Independent",
-  "Programming Language :: Python",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3 :: Only",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
@@ -54,10 +52,11 @@ duckdb = ">=1.0.0"
 mckit-nuclides = ">=0.3.2"
 multipledispatch = ">=0.6.0"
 numpy = ">=2.0"
-polars = {version = ">=1.12.0", extras = ["all"]}
+polars = { version = ">=1.12.0", extras = ["all"] }
 pyarrow = ">=18.0.0"
 rich = ">=13.7.0"
-msgspec = {git = "https://github.com/jcrist/msgspec.git", rev = "main"}  # TODO: switch back to PyPI on update to Python 3.13
+msgspec = ">=0.19.0"
+poetry = "^1.8.5"
 
 [tool.poetry.group.dev.dependencies]
 Pygments = ">=2.10.0"
@@ -152,7 +151,7 @@ addopts = '''
 --failed-first
 --xdoctest
 '''
-doctest_optionflags = "ELLIPSIS NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL ALLOW_UNICODE ALLOW_BYTES"
+doctest_optionflags = "ELLIPSIS NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL ALLOW_UNICODE ALLOW_BYTES NUMBER"
 testpaths = ["tests", "src"]
 markers = [
     "slow: marks tests as slow (deselect with '-m \"not slow\"')",
@@ -304,11 +303,23 @@ src = ["src", "tests"]
 
 exclude = [
     "*.egg-info",
+    ".direnv",
     ".cache",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".mypy_cache",
+    ".nox",
+    ".ruff_cache",
+    ".venv",
     "__pycache__",
+    "_build",
     "adhoc",
+    "build",
+    "dist",
     "docs/source/conf.py",
     "notebooks",
+    "venv",
     "wrk",
 ]
 
@@ -317,24 +328,27 @@ exclude = [
 #or run 'ruff linter' to see a brief list
 select = [
     "A", # flake8-builtins
-    "ANN", # flake8-annotations
     "AIR", # Airflow https://airflow.apache.org/docs/apache-airflow/stable/index.html
+    "ANN", # flake8-annotations
     "ARG", # flake8-unused-arguments
     "ASYNC", # flake8-async
     "B", # flake8-bugbear
     "BLE", # flake8-blind-except
     "C4", # flake8-comprehensions
     "C90", # mccabe
     "COM", # flake8-commas
+    # "CPY", # flake8-copyright
     "D", # pydocstyle
     "DJ", # flake8-django
+    "DOC", # pydoclint
     "DTZ", # flake8-datetimez
     "E", # pycodestyle
     "EM", # flake8-errmsg
     "ERA", # eradicate
     "EXE", # flake8-executable
     "F", # Pyflakes
     "FA", # flake8-future-annotations
+    # "FAST", # FastAPI
     "FBT", # flake8-boolean-trap  https://adamj.eu/tech/2021/07/10/python-type-hints-how-to-avoid-the-boolean-trap
     "FIX", # flake8-fixme
     "FLY", # flynt
@@ -381,8 +395,6 @@ select = [
 ignore = [
     "ANN001", # ANN001 Missing type annotation for function argument: doesn't allow to use functools dispatching
     # "ANN002", # ANN002 Missing type annotation for *drop_items: ... as above
-    "ANN101", # ANN101 Missing type annotation for self in method
-    "ANN102", # ANN102 Missing type annotation for cls in classmethod
     # "ANN201", # Missing return type annotation for public function `mesh2com`
     "ANN202", # ANN202 Missing return type annotation for protected function: ... dispatching
     # "ANN204", # ANN204 Missing return type annotation for special method
@@ -483,7 +495,7 @@ ignore = [
 
 
 [tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402"]
+"**/__init__.py" = ["E402"]
 "src/xpypact/fluxes.py" = ["F811"]
 "benchmarks/*" = ["S101"]
 "noxfile.py" = ["ANN"]

pyproject.toml

@@ -13,7 +13,7 @@
 import numpy as np
 
 # noinspection PyUnresolvedReferences
-from xpypact.time_step import TimeStep  # noqa: TCH001  - required for Struct field
+from xpypact.time_step import TimeStep  # noqa: TC001  - required for Struct field
 
 if TYPE_CHECKING:
     from collections.abc import Iterable, Iterator

src/xpypact/inventory.py

@@ -61,8 +61,8 @@ class Nuclide(ms.Struct):  # pylint: disable=too-many-instance-attributes
 
     def __post_init__(self) -> None:
         """Make the values consistent in data from old FISPACT."""
-        if (
-            self.zai == 0 or self.atoms == FLOAT_ZERO and self.grams > FLOAT_ZERO
+        if self.zai == 0 or (
+            self.atoms == FLOAT_ZERO and self.grams > FLOAT_ZERO
         ):  # pragma: no cover
             _z = z(self.element)
             if self.zai == 0:
@@ -91,4 +91,4 @@ def info(self) -> NuclideInfo:
         return NuclideInfo(self.zai, self.element, self.a, self.state, self.half_life)
 
 
-__all__ = ["Avogadro", "Nuclide", "NuclideInfo", "FLOAT_ZERO", "eV", "MeV"]
+__all__ = ["FLOAT_ZERO", "Avogadro", "MeV", "Nuclide", "NuclideInfo", "eV"]

src/xpypact/nuclide.py

@@ -4,7 +4,7 @@
 
 import msgspec as ms
 
-from xpypact.nuclide import Nuclide  # noqa: TCH001  - need for Struct field
+from xpypact.nuclide import Nuclide  # noqa: TC001  - need for Struct field
 
 FLOAT_ZERO = 0.0
 

src/xpypact/time_step.py

@@ -31,7 +31,7 @@ def data() -> Path:
 
 
 @pytest.fixture
-def cd_tmpdir(tmpdir):  # noqa: PT004
+def cd_tmpdir(tmpdir):
     """Temporarily switch to temp directory.
 
     Args:

tests/conftest.py

@@ -18,7 +18,7 @@ reset() {
     local env="${1:-}"
     read -r -a pkgs <<< "$(ls -1 src)"
     local pkg=${pkgs[0]}
-    local last_python="3.13.0"
+    local last_python="3.13.1"
     [[ -z "$env" ]] && env="${pkg//_/-}"
     echo "Installing package $pkg to environment $env with python $last_python."
     eval "$(pyenv init -)"
@@ -34,7 +34,7 @@ reset() {
     poetry lock --no-update
     poetry install
     pyenv deactivate
-    pyenv local "$env" "3.12.7" "3.11.10" "3.10.15" "3.9.20"
+    pyenv local "$env" "3.12.8" "3.11.11" "3.10.16"
     pyenv rehash
     pyenv activate "$env"
     python -c "import ${pkg}; print(${pkg}.__version__)" && success "Environment $env is reset"