Maintainence fixes abound; updates to support python>=3.11

.pre-commit-config.yaml

@@ -1,26 +1,33 @@
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.6.0
       hooks:
           - id: trailing-whitespace
           - id: end-of-file-fixer
           - id: check-yaml
           - id: check-added-large-files
           - id: check-ast
-    - repo: https://github.com/psf/black
-      rev: 23.3.0
-      hooks:
-          - id: black
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.0.270
+      rev: v0.4.4
       hooks:
           - id: ruff
-            args: [--fix, --exit-non-zero-on-fix]
+          - id: ruff-format
+    - repo: https://github.com/pre-commit/pygrep-hooks
+      rev: v1.10.0
+      hooks:
+        - id: rst-backticks
+        - id: rst-directive-colons
+        - id: rst-inline-touching-normal
+        - id: python-no-log-warn
+        - id: python-check-mock-methods
+
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.9-for-vscode
+      rev: v4.0.0-alpha.8
       hooks:
-          - id: prettier
+        - id: prettier
+          files: 'docs/'
+          types_or: [javascript, ts, tsx, html, css]
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: 'v1.3.0'
+      rev: 'v1.10.0'
       hooks:
           - id: mypy

.prettierrc.toml

@@ -1,3 +1,3 @@
-tabWidth = 4
+tabWidth = 2
 singleQuote = true
 bracketSpacing = false

LICENSE

@@ -0,0 +1,16 @@
+Copyright (c) 2024 Peyton Murray
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to deal in the Software without restriction,
+including without limitation the rights to use, copy, modify, merge, publish, distribute,
+sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial
+portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT
+NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES
+OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

pyproject.toml

@@ -1,16 +1,113 @@
 [build-system]
 requires = [
     "setuptools",
-    "wheel",
-    "bump2version",
+    "setuptools_scm"
 ]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "pyforc"
+dynamic = ["version"]
+authors = [
+  { name="Peyton  Murray" },
+]
+description = "FORC analysis in Python"
+readme = "README.md"
+requires-python = ">=3.11"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy",
+    "scipy",
+    "matplotlib",
+]
+urls = { Homepage = "https://github.com/peytondmurray/pyforc" }
+license = { file = 'LICENSE' }
+
+
 [tool.interrogate]
 ignore-init-method = true
 ignore-init-module = true
 ignore-magic = true
 ignore-module = true
 
+[tool.setuptools_scm]
+
+[tool.isort]
+profile = "black"
+
+[project.optional-dependencies]
+dev = ["pre-commit>=3.6.0"]
+test = ["pytest"]
+doc = ["sphinx", "myst-parser"]
+
 [tool.ruff]
-line-length = 100
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+    # pycodestyle
+    "E",
+    "W",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # pep8 naming
+    "N",
+    # pydocstyle
+    "D",
+    # annotations
+    "ANN",
+    # debugger
+    "T10",
+    # flake8-pytest
+    "PT",
+    # flake8-return
+    "RET",
+    # flake8-unused-arguments
+    "ARG",
+    # flake8-fixme
+    "FIX",
+    # flake8-eradicate
+    "ERA",
+    # pandas-vet
+    "PD",
+    # numpy-specific rules
+    "NPY",
+]
+ignore = [
+    "D104", # Missing docstring in public package
+    "D100", # Missing docstring in public module
+    "D211", # No blank line before class
+    "D213", # Multiline summary second line
+    "PD901", # Avoid using 'df' for pandas dataframes. Perfectly fine in functions with limited scope
+    "ANN201", # Missing return type annotation for public function (makes no sense for NoneType return types...)
+    "ANN101", # Missing type annotation for `self`
+    "ANN204", # Missing return type annotation for special method
+    "ANN002", # Missing type annotation for `*args`
+    "ANN003", # Missing type annotation for `**kwargs`
+    "D105", # Missing docstring in magic method
+    "D107", # Missing docstring in __init__
+    "D203", # 1 blank line before after class docstring
+    "D204", # 1 blank line required after class docstring
+    "D413", # 1 black line after parameters
+    "SIM108", # Simplify if/else to one line; not always clearer
+    "D206", # Docstrings should be indented with spaces; unnecessary when running ruff-format
+    "E501", # Line length too long; unnecessary when running ruff-format
+    "W191", # Indentation contains tabs; unnecessary when running ruff-format
+    "B905", # zip() without an explicit strict=; incompatible with python<3.12
+]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["F401"]
+"test_*.py" = ["ANN001"]

src/pyforc/__init__.py

@@ -0,0 +1 @@
+from . import core

src/pyforc/core/__init__.py

@@ -0,0 +1 @@
+from . import config, coordinates, forc, forcdata, ingester, ops, plot

pyforc/core/config.py → src/pyforc/core/config.py

@@ -1,8 +1,7 @@
 """Class to hold configuration details for creating and analyzing FORC data."""
-from __future__ import annotations
 
 import dataclasses
-from typing import Callable, Optional
+from collections.abc import Callable
 
 from .forcdata import ForcData
 
@@ -13,9 +12,9 @@ class Config:
 
     Parameters
     ----------
-    file_name: str
+    file_name: str | None
         Name of the file containing FORC data
-    step: Optional[float]
+    step: float | None
         Step size to be used for the interpolated dataset; if None, step size is determined from the
         step size used for the measurement
     interpolation: str
@@ -38,12 +37,12 @@ class Config:
         Smoothing factor to use for calculating the FORC distribution
     """
 
-    file_name: Optional[str] = None
-    step: Optional[float] = None
+    file_name: str | None = None
+    step: float | None = None
     interpolation: str = "cubic"
     drift_correction: bool = True
     drift_kernel_size: int = 4
     drift_density: int = 3
-    pipeline: Optional[list[Callable[[ForcData, Config], ForcData]]] = None
+    pipeline: list[Callable[[ForcData, "Config"], ForcData]] | None = None
     h_sat: float = 0
     smoothing_factor: int = 3

pyforc/core/coordinates.py → src/pyforc/core/coordinates.py

@@ -1,18 +1,15 @@
 """Coordinate transformations for FORC data."""
-from __future__ import annotations
-
-import typing
 
 import matplotlib.transforms as transforms
 
 
 class Coordinates(transforms.Affine2D):
     """Base class for coordinates."""
 
-    name: typing.Optional[str] = None
+    name: str | None = None
 
     @staticmethod
-    def from_str(name: str) -> Coordinates:
+    def from_str(name: str) -> "Coordinates":
         """Get the appropriate Coordinates class instance by name.
 
         Parameters

pyforc/core/forc.py → src/pyforc/core/forc.py

@@ -1,13 +1,11 @@
 """Classes for storing, extracting, and processing FORC data."""
-from typing import Type
 
 from .config import Config
 from .ingester import IngesterBase
 
 
 class Forc:
-    """
-    Generic for storing, extracting, and processing FORC data.
+    """Generic container for extracting and processing FORC data.
 
     Parameters
     ----------
@@ -17,7 +15,7 @@ class Forc:
         Config instance holding the ingester configuration details
     """
 
-    def __init__(self, ingester: Type[IngesterBase], config: Config):
+    def __init__(self, ingester: type[IngesterBase], config: Config):
         self.config = config
         self.ingester = ingester(self.config)
         self.data = self.ingester.run()

pyforc/core/forcdata.py → src/pyforc/core/forcdata.py

@@ -1,6 +1,4 @@
 """Containers for holding FORC data as arrays."""
-from __future__ import annotations
-from typing import Optional
 
 import numpy as np
 
@@ -34,9 +32,9 @@ class ForcData:
 
     def __init__(
         self,
-        h_raw: Optional[list[np.ndarray]] = None,
-        m_raw: Optional[list[np.ndarray]] = None,
-        t_raw: Optional[list[np.ndarray]] = None,
+        h_raw: list[np.ndarray] | None = None,
+        m_raw: list[np.ndarray] | None = None,
+        t_raw: list[np.ndarray] | None = None,
         m_drift: np.ndarray = None,
         h: np.ndarray = None,
         hr: np.ndarray = None,
@@ -68,17 +66,17 @@ def get_step(self) -> float:
 
     @staticmethod
     def from_existing(
-        data: ForcData,
-        h_raw: Optional[list[np.ndarray]] = None,
-        m_raw: Optional[list[np.ndarray]] = None,
-        t_raw: Optional[list[np.ndarray]] = None,
+        data: "ForcData",
+        h_raw: list[np.ndarray] | None = None,
+        m_raw: list[np.ndarray] | None = None,
+        t_raw: list[np.ndarray] | None = None,
         m_drift: np.ndarray = None,
         h: np.ndarray = None,
         hr: np.ndarray = None,
         m: np.ndarray = None,
         t: np.ndarray = None,
         rho: np.ndarray = None,
-    ) -> ForcData:
+    ) -> "ForcData":
         """Generate a new ForcData instance from the input, but override fields with the kwargs.
 
         Parameters