Merge pull request #319 from MC-kit/devel

Suspend MacOS support, stop supporting Python 3.9

.flake8

@@ -3,6 +3,7 @@ select=ANN,B,B9,BLK,C,D,DAR,E,F,I,N,PD,R,TC,TR,S,W
 max-complexity=15
 max-mccabe-complexity=6
 max-cognitive-complexity=10
+max-expression-complexity=10
 max-line-length=100
 ignore=
     # ANN001 Missing type annotation for function argument: doesn't allow to use functools dispatching

.github/constraints.txt

@@ -1,3 +1,3 @@
-pip==23.3.1
-poetry==1.7.1
+pip==24.1.2
+poetry==1.8.3
 

.github/workflows/clean-workflow-logs.yml

@@ -22,7 +22,7 @@ jobs:
       #          repo: ${{ github.event.repository.name }}
       #          days_old: ${{ github.event.inputs.days_old }}
       - name: Clean workflow runs
-        uses: dmvict/clean-workflow-runs@v1.2.1
+        uses: dmvict/clean-workflow-runs@v1
         with:
           token: ${{ secrets.MCKIT_GITHUB_TOKEN }}
           save_period: 30

.github/workflows/combine-prs.yml

@@ -100,7 +100,7 @@ jobs:
             console.log('Combined: ' + combined);
             return combined
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.1.2
         with:
           fetch-depth: 0
       # Creates a branch with other PR branches merged together

.github/workflows/publish.yml

@@ -18,19 +18,19 @@ jobs:
     strategy:
       matrix:
         # ubuntu-20.04 is required to build wheels for older OS (clusters...)
-        os: [ubuntu-20.04, ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        os: [ubuntu-20.04, ubuntu-latest, windows-latest]
+        python-version: ['3.10', '3.11', '3.12']
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3.5.3
+        uses: actions/checkout@v4.1.2
         with:
           fetch-depth: 1
 
       - name: Checkout submodules
         run: git submodule update --init --recursive --depth=1
 
       - name: Set up Python
-        uses: actions/setup-python@v4.6.1
+        uses: actions/setup-python@v5.1.0
         with:
           python-version: ${{ matrix.python-version }}
           architecture: x64

.github/workflows/tests.yml

@@ -38,7 +38,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  DEFAULT_PYTHON: "3.11"
+  DEFAULT_PYTHON: "3.12"
 
 jobs:
 
@@ -141,8 +141,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+        os: [ ubuntu-latest, windows-latest ]
+        python-version: [ '3.10', '3.11', '3.12' ]
 
     steps:
 
@@ -247,3 +247,5 @@ jobs:
 
       - name: Upload coverage report
         uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -15,7 +15,7 @@
 #     https://github.com/pre-commit/pre-commit  for more information
 #     https://pre-commit.com/hooks.html         for more hooks
 default_language_version:
-  python: python3.11
+  python: python3.12
 
 repos:
 
@@ -29,7 +29,7 @@ repos:
       - id: check-json
       - id: check-merge-conflict
       - id: check-shebang-scripts-are-executable
-        exclude: notebooks
+        exclude: notebooks  # jupytext creates python scripts with shebangs but without permissions
       - id: check-symlinks
       - id: check-toml
       - id: check-yaml
@@ -65,34 +65,38 @@ repos:
         exclude: \.idea|\.cache|^notebooks|^extern
         entry: pyupgrade
         args:
-          - --py39-plus
+          - --py310-plus
         language: system
         types: [ python ]
+        stages: [ manual ]
 
-      # Nicely sort imports
-      - id: isort
-        name: isort
-        exclude: tools|\.idea|\.cache|^notebooks|^extern
-        entry: isort
+      # Security check
+      - id: bandit
+        name: bandit
+        entry: bandit
+        args: ["-c", "pyproject.toml"]
         language: system
         types: [ python ]
+        exclude: ^notebooks|^extern
+        stages: [ manual ]
 
-      # Black, the code formatter, natively supports pre-commit
-      - id: black
-        name: black
-        entry: black
+      # Lint and fix Python code (including import sort)
+      - id: ruff
+        name: ruff
+        entry: ruff check --force-exclude --fix --config pyproject.toml
         language: system
         types: [ python ]
         exclude: ^notebooks|^extern
 
-      # Lint and fix Python code
+      # Format Python code
       - id: ruff
-        name: ruff
-        entry: ruff --force-exclude --fix --config pyproject.toml
+        name: ruff-format
+        entry: ruff format --force-exclude --config pyproject.toml
         language: system
         types: [ python ]
         exclude: ^notebooks|^extern
 
+
   # CMake formatting
   - repo: https://github.com/cheshirekow/cmake-format-precommit
     rev: "v0.6.13"
@@ -102,16 +106,16 @@ repos:
         types: [ file ]
         files: (\.cmake|CMakeLists.txt)(.in)?$
 
-  # Check for common shell mistakes
-  - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: "v0.9.0.6"
-    hooks:
-      - id: shellcheck
-        stages: [ manual ]
-
   # Clang format the codebase automatically
   - repo: https://github.com/pre-commit/mirrors-clang-format
     rev: "v17.0.6"
     hooks:
       - id: clang-format
         types_or: [ c++, c, cuda ]
+
+  # Check for common shell mistakes
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.9.0.6"
+    hooks:
+      - id: shellcheck
+        stages: [ manual ]

.readthedocs.yml

@@ -10,10 +10,9 @@ sphinx:
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.11"
 
 python:
-  version: "3.8"
   install:
     - requirements: docs/requirements.txt
     - path: .

README.rst

@@ -16,6 +16,10 @@
 .. image:: https://img.shields.io/github/license/MC-kit/mckit
    :target: https://github.com/MC-kit/mckit
 
+.. image:: https://img.shields.io/badge/security-bandit-yellow.svg
+    :target: https://github.com/PyCQA/bandit
+    :alt: Security Status
+
 
 MCKIT: MCNP model and results processing utilities
 ==================================================

adhoc/ep11/verify_co05_volumes.py

@@ -22,13 +22,12 @@
 
 import dotenv
 import numpy as np
+import pandas as pd
+import typer
 
 from loguru import logger
 from tqdm import tqdm
 
-import pandas as pd
-import typer
-
 from mckit.geometry import EX, EY, EZ, Box
 from mckit.parser import ParseResult, from_file
 

benchmarks/mckit_utils.py

@@ -4,37 +4,22 @@
 
 from mckit.utils import get_decades, significant_digits
 
-# def run_digits_in_fraction(a: np.ndarray) -> None:
-#     map(digits_in_fraction_for_str, a)
-#
-#
-# def test_digits_in_fraction(benchmark):
-#     values = (np.random.rand(1000) - 0.5) * 1000.0
-#     benchmark(run_digits_in_fraction, values)
-
-# Name (time in ns)                Min       Max      Mean   StdDev    Median     IQR    Outliers  OPS (Mops/s)  Rounds  Iterations
-# test_digits_in_fraction     186.9630  720.5936  194.0950  26.6555  190.4080  1.2957  3901;10481        5.1521  192753          27
-
 
 def run_significant_digits(a: np.ndarray) -> None:
     map(significant_digits, a)
 
 
 def test_significant_digits(benchmark):
-    values = (np.random.rand(1000) - 0.5) * 1000.0
+    values = (np.random.default_rng().random(1000) - 0.5) * 1000.0
     benchmark(run_significant_digits, values)
 
 
-# Name (time in ns)                Min       Max      Mean   StdDev    Median      IQR   Outliers  OPS (Mops/s)  Rounds  Iterations
-# test_significant_digits     185.8118  811.3717  200.8212  30.4897  190.1493  21.4075  2785;2766        4.9796  193839          27
-
-
 def run_get_decades(a: np.ndarray) -> None:
     return np.fromiter(map(get_decades, a), np.int16)
 
 
 def test_get_decades(benchmark):
-    values = (np.random.rand(1000) - 0.5) * 1000.0
+    values = (np.random.default_rng().random(1000) - 0.5) * 1000.0
     benchmark(run_get_decades, values)
 
 

build.py

@@ -82,7 +82,6 @@ def copy_files(src_dir: Path, dest_dir: Path, pattern: str) -> None:
             distutils_log.info(f"copied {src} to {dest}")
 
 
-#
 def save_setup_kwargs(setup_kwargs: dict[str, Any]) -> None:
     """Save resulting setup_kwargs for examining."""
     kwargs_path = Path(__file__).parent / "poetry_setup_kwargs.txt"