enh: add python 3.12, cleanup (#53)

.github/dependabot.yml

@@ -1,8 +1,7 @@
 version: 2
 updates:
-
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       # Check for updates to GitHub Actions monthly
-      interval: "monthly"
+      interval: "quarterly"

.github/workflows/ci.yml

@@ -17,7 +17,14 @@ jobs:
       max-parallel: 8
       fail-fast: False
       matrix:
-        python-version: [ "3.7", "3.8", "3.9", "3.10" , "3.11" ]
+        python-version: [ "3.7", "3.8", "3.9", "3.10" , "3.11", "3.12" ]
+        include:
+          - os: macos-latest
+            python-version: "3.12"
+          - os: windows-latest
+            python-version: "3.12"
+          - os: macos-14  # Apple silicon runner
+            python-version: '3.12'
     name: tests on ubuntu with ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -18,52 +18,57 @@ repos:
 
 
   - repo: https://github.com/myint/docformatter
-    rev: v1.5.0
+    rev: v1.7.5
     hooks:
       - id: docformatter
         args: [ -r, --in-place, --wrap-descriptions, '120', --wrap-summaries, '120', -- ]
 
   - repo: https://github.com/mattlqx/pre-commit-sign
-    rev: v1.1.3
+    rev: v1.2.0
     hooks:
       - id: sign-commit
   - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0 # Use the ref you want to point at
+    rev: v1.10.0 # Use the ref you want to point at
     hooks:
       - id: python-use-type-annotations
       - id: python-check-mock-methods
       - id: rst-directive-colons
 
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.3
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
         args: [ --py36-plus ]
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.2.0
+    rev: v2.5.0
     hooks:
       - id: setup-cfg-fmt
 
   # Notebook formatting
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.5.3
+    rev: 1.8.5
     hooks:
       - id: nbqa-isort
-        additional_dependencies: [ isort==5.6.4 ]
+        additional_dependencies: [ isort ]
 
       - id: nbqa-pyupgrade
-        additional_dependencies: [ pyupgrade==2.7.4 ]
-        args: [ --py37-plus ]
+        additional_dependencies: [ pyupgrade ]
+        args: [ --py36-plus ]
 
   - repo: https://github.com/mgedmin/check-manifest
-    rev: '0.48'
+    rev: '0.49'
     hooks:
       - id: check-manifest
         stages: [ manual ]
 
-  - repo: https://github.com/ambv/black
-    rev: 22.10.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.3.7"
     hooks:
-      - id: black
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix, --unsafe-fixes, --show-fixes , --line-length=120]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

docs/api/conf.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python3
 #
 # yamlloader documentation build configuration file, created by
 # sphinx-quickstart on Wed Dec 13 13:46:00 2017.
@@ -16,10 +15,12 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import os
+from __future__ import annotations
+
 import sys
+from pathlib import Path
 
-sys.path.insert(0, os.path.abspath("../.."))
+sys.path.insert(0, Path("../..").resolve())
 
 
 # -- General configuration ------------------------------------------------
@@ -29,16 +30,16 @@
 # needs_sphinx = '1.0'
 
 # Manually added things
-import os
+
+import sphinx_rtd_theme
 
 import yamlloader
 
-here = os.path.abspath(os.path.dirname(__file__))
+here = Path(__file__).resolve().parent
 
 autoclass_content = "both"  # document modules and packages
 
 # Sphinx theme
-import sphinx_rtd_theme
 
 html_theme = "sphinx_rtd_theme"
 
@@ -59,7 +60,7 @@
     "sphinx.ext.githubpages",
 ]
 
-html_logo = os.path.join(here, "static/img/phynix_logo_medium.png")
+html_logo = here / "static/img/phynix_logo_medium.png"
 
 # Napoleon settings (convert numpy/google docstrings to proper ReST
 napoleon_google_docstring = False

docs/api/tools/change_headline.py

@@ -1,4 +1,7 @@
+from __future__ import annotations
+
 import argparse
+from pathlib import Path
 
 parser = argparse.ArgumentParser(description="replace first two line")
 
@@ -7,15 +10,13 @@
 
 n_files = 0
 for rest_file in parsed_args.files:
-    with open(rest_file) as f:
+    with Path(rest_file).open() as f:
         first_word = f.readline().strip().split()[0]
         if "." not in first_word:
             continue
         replacement = first_word.split(".")[-1]
         underline = f.readline()[0] * len(replacement)
         lower_file = f.read()
-    with open(rest_file, "w") as f:
+    with Path(rest_file).open("w") as f:
         f.write("\n".join((replacement, underline, lower_file)))
     n_files += 1
-
-print(f"finished successfully parsing {n_files} files")

pyproject.toml

@@ -7,3 +7,57 @@ requires = [
 ]
 
 build-backend = "setuptools.build_meta"
+
+[tool.ruff]
+#src = ["src"]
+line-length = 120
+exclude = [
+    ".tox/*",
+    "*/test*",
+    "*/__init__.py",
+    "*/_version.py",
+]
+[tool.ruff.lint]
+extend-select = [
+    "B",        # flake8-bugbear
+    "I",        # isort
+    "ARG",      # flake8-unused-arguments
+    "C4",       # flake8-comprehensions
+    "EM",       # flake8-errmsg
+    "ICN",      # flake8-import-conventions
+    "G",        # flake8-logging-format
+    "PGH",      # pygrep-hooks
+    "PIE",      # flake8-pie
+    "PL",       # pylint
+    "PT",       # flake8-pytest-style
+    "PTH",      # flake8-use-pathlib
+    "RET",      # flake8-return
+    "RUF",      # Ruff-specific
+    "SIM",      # flake8-simplify
+    "T20",      # flake8-print
+    "UP",       # pyupgrade
+    "YTT",      # flake8-2020
+    "EXE",      # flake8-executable
+    "NPY",      # NumPy specific rules
+    "PD",       # pandas-vet
+]
+ignore = [
+    "UP007",    # type annotation upgrade, breaks pydantic for Python 3.9 (remove once above)
+    "PLR09",    # Too many <...>
+    "PLR2004",  # Magic value used in comparison
+    "ISC001",   # Conflicts with formatter
+    "RET505",   # This is sometimes wanted, protets against accidental intendation
+    "PD901",    # "avoid using `df[...].values`" -> no, this is a very good name if there is only one df
+    "PD011",    # "replace `df[...].values` with `df[...].to_numpy()`" -> not yet, it's not deprecated.
+    # Prefer to have a single way to access the data if we don't care about whether it's a numpy array or not.
+    "PLW0603",  # updating global variables with a function is bad, but we use it for
+    "PLW2901",  # "for loop overwritten by assignment" -> we use this to update the loop variable
+    "PD013",    # "melt over stack": df function, but triggers on tensors
+    "NPY002",   # "Use rnd generator in numpy" -> we use np.random for some legacy stuff but do use the new one where we can
+
+]
+isort.required-imports = ["from __future__ import annotations"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["T20"]
+"noxfile.py" = ["T20"]

setup.py

@@ -1,16 +1,18 @@
-import os
+from __future__ import annotations
+
+from pathlib import Path
 
 from setuptools import setup
 
-here = os.path.abspath(os.path.dirname(__file__))
+here = Path(__file__).resolve().parent
 
-with open(os.path.join(here, "requirements.txt")) as f:
+with (here / "requirements.txt").open() as f:
     requirements = f.read().split("\n")
 
 
 def long_description():
     """Load README.rst."""
-    with open("README.rst", encoding="utf-8") as f:
+    with Path("README.rst").open(encoding="utf-8") as f:
         return f.read()
 
 
@@ -41,6 +43,8 @@ def long_description():
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Topic :: Software Development :: Libraries",
         "Topic :: Utilities",
     ],
     packages=["yamlloader", "yamlloader.ordereddict"],

yamlloader/ordereddict/dumpers.py

@@ -1,5 +1,7 @@
 """Dumpers for `:py:class:~collections.OrderedDict`."""
 
+from __future__ import annotations
+
 from collections import OrderedDict
 
 import yaml

yamlloader/ordereddict/loaders.py

@@ -1,5 +1,7 @@
 """Loaders for `:py:class:~collections.OrderedDict`."""
 
+from __future__ import annotations
+
 from collections import OrderedDict
 
 import yaml
@@ -30,12 +32,13 @@ def construct_mapping(self, node, deep=False):
         try:
             hash(key)
         except TypeError as err:
+            msg = "while constructing a mapping"
             raise yaml.constructor.ConstructorError(
-                "while constructing a mapping",
+                msg,
                 node.start_mark,
                 f"found unacceptable key ({err})",
                 key_node.start_mark,
-            )
+            ) from err
         value = self.construct_object(value_node, deep=deep)
         mapping[key] = value
     return mapping

yamlloader/settings.py

@@ -1,3 +1,5 @@
 """Global settings for the behavior of the module."""
 
+from __future__ import annotations
+
 ALLOW_NON_C_FALLBACK = True