From 984e2a3dd61e35d95e27dd14870666d1b369ef60 Mon Sep 17 00:00:00 2001 From: Miles Smith Date: Sat, 4 Nov 2023 11:25:11 -0500 Subject: [PATCH] Update deps --- .vscode/settings.json | 3 +- CHANGELOG.md | 35 +- poetry.lock | 1785 ++++++++++++++++++-------------------- pyproject.toml | 136 ++- src/pysmooth/__init__.py | 2 +- src/pysmooth/__main__.py | 36 +- src/pysmooth/_smooth.py | 90 +- 7 files changed, 1056 insertions(+), 1031 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index d28782b..bc7eb72 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -3,5 +3,6 @@ "python.linting.mypyEnabled": true, "python.linting.enabled": true, "restructuredtext.confPath": "${workspaceFolder}/docs", - "restructuredtext.languageServer.disabled": true + "restructuredtext.languageServer.disabled": true, + "esbonio.sphinx.confDir": "${workspaceFolder}/docs" } diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f6fb71..abf795b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,64 +5,73 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [1.3.0] +* [1.4.0] + +## Changed + +- Code cleanup. +- Make Python 3.9 the minimum version +- Update dependencies + +# [1.3.0] ## Changed - Altered the maximum allowed Python version so that newer versions of 3.10.* are not excluded -## [1.1.4] +# [1.1.4] -### Changed +## Changed - Miscellaneous fixes for mypy and passing tests - Add `smooth` to `__all__` for explicit export of the symbol -### Removed +## Removed - Custom `Numeric` type for type hinting in lieu of following PEP 484 and the Numeric Tower -## [1.1.3] +# [1.1.3] -### Changed +## Changed - Renamed `smooth` submodule so that it does not conflict with the `smooth()` function. - Updated README.rst to include requirements and example usage -## [1.1.2] +# [1.1.2] Version bump for pypi -## [1.1.1] +# [1.1.1] -### Changed +## Changed - Decreased required vesions of numpy to 1.20.3 so that it does not conflict with numba -## [1.1.0] +# [1.1.0] -### Added +## Added - Added unit test to `sm_3` for a 2-element list -### Changed +## Changed - Removed click, typer, and rich requirements - Moved hypothesis and nox-poetry to dev requirements -### Removed +## Removed - `main` function, as it was unused and `pysmooth` is not intended to be a cli application +[1.4.0]: https://github.com/olivierlacan/keep-a-changelog/compare/1.3.0...1.4.0 [1.3.0]: https://github.com/olivierlacan/keep-a-changelog/compare/1.2.0...1.3.0 [1.2.0]: https://github.com/olivierlacan/keep-a-changelog/compare/1.1.3...1.2.0 [1.1.3]: https://github.com/olivierlacan/keep-a-changelog/compare/1.1.2...1.1.3 diff --git a/poetry.lock b/poetry.lock index 5cb7b54..9a94f9e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "alabaster" -version = "0.7.12" +version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" optional = false -python-versions = "*" +python-versions = ">=3.6" files = [ - {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"}, - 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"dee140c8cfce11986417aee55ab0f17771bcd418a15fb8c0e655f2245fca3215" +python-versions = "^3.9,<3.11" +content-hash = "39a58035ff95b586ee5aa1148a2c18704bdea7563a4cce77686f0fc4b59b4dc0" diff --git a/pyproject.toml b/pyproject.toml index 6e98dba..d417ddd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,37 +16,28 @@ classifiers = [ Changelog = "https://github.com/milescsmith/pysmooth/releases" [tool.poetry.dependencies] -python = "^3.8,<3.11" -numpy = "^1.22" +python = "^3.9,<3.11" +numpy = "^1.26" -[tool.poetry.dev-dependencies] -hypothesis = "^6.49.0" -nox-poetry = "^1.0.1" +[tool.poetry.group.dev.dependencies] +hypothesis = "^6.88" +nox-poetry = "^1.0.3" pytest = "^7.4.3" -coverage = {extras = ["toml"], version = "^6.4"} -safety = "^1.10.3" -mypy = "^0.931" -typeguard = "^2.13.3" -xdoctest = {extras = ["colors"], version = "^1.0.0"} -sphinx = "^5.3.0" +coverage = {extras = ["toml"], version = "^7.3"} +safety = "^2.3.5" +mypy = "^1.6" +typeguard = "^4.1" +xdoctest = {extras = ["colors"], version = "^1.1"} +sphinx = "^7.2" sphinx-autobuild = "^2021.3.14" -pre-commit = "^2.19.0" -flake8 = "^4.0.1" -black = "^21.12b0" -flake8-bandit = "^2.1.2" -flake8-bugbear = "^21.9.2" -flake8-docstrings = "^1.6.0" -flake8-rst-docstrings = "^0.2.6" -pep8-naming = "^0.12.1" -darglint = "^1.8.1" -reorder-python-imports = "^3.0.1" -pre-commit-hooks = "^4.0.1" -sphinx-rtd-theme = "^1.0.0" -sphinx-click = "^3.0.2" -Pygments = "^2.12.0" -ipython = "^7.31.1" -isort = "^5.10.1" -types-decorator = "^5.1.7" +pre-commit = "^3.5" +black = "^23" +pre-commit-hooks = "^4.5" +sphinx-rtd-theme = "^1.3.0" +sphinx-click = "^5.0" +Pygments = "^2.16" +ipython = "^8.17.2" +ruff = "^0.1.3" [tool.coverage.paths] source = ["src", "*/site-packages"] @@ -62,3 +53,92 @@ fail_under = 100 [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" + +[tool.isort] +known_typing = "typing,types,typing_extensions,mypy,mypy_extensions" +sections = "FUTURE,TYPING,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER" +include_trailing_comma = true +default_section = "FIRSTPARTY" +multi_line_output = 3 +indent = 4 +force_grid_wrap = 0 +use_parentheses = true +line_length = 80 + +[tool.black] +line-length = 120 +target-version = ["py309"] +skip-string-normalization = true + +[tool.ruff] +target-version = "py309" +line-length = 120 +select = [ + "A", + "ARG", + "B", + "C", + "DTZ", + "E", + "EM", + "F", + "FBT", + "I", + "I001", + "ICN", + "ISC", + "N", + "PLC", + "PLE", + "PLR", + "PLW", + "Q", + "RUF", + "S", + "T", + "TID", + "UP", + "W", + "YTT", +] +ignore = [ + "B027", + "FBT003", + "S105", + "S106", + "S107", + "C901", + "PLR0911", + "PLR0912", + "PLR0913", + "PLR0915", +] +unfixable = [ + "F401", + "UP007", +] +exclude = [ + ".git", + ".hg", + "__pycache__", + "_bin/*", + "_build/*", + "_ig_fbcode_wheel/*", + "buck-out/*", + "third-party-buck/*", + "third-party2/*", + "dist", + ".venv", + ".nox", + ".mypy_cache", + ".pytype", + ".svn", + "__pypackages__", +] +src = ["src"] + +[tool.ruff.mccabe] +max-complexity = 50 + +[tool.ruff.flake8-tidy-imports] +ban-relative-imports = "all" \ No newline at end of file diff --git a/src/pysmooth/__init__.py b/src/pysmooth/__init__.py index 8be6ddc..c0e4318 100644 --- a/src/pysmooth/__init__.py +++ b/src/pysmooth/__init__.py @@ -1,4 +1,4 @@ """Pysmoother.""" -from .__main__ import smooth +from pysmooth.__main__ import smooth __all__ = ["smooth"] diff --git a/src/pysmooth/__main__.py b/src/pysmooth/__main__.py index e933073..3a1283d 100644 --- a/src/pysmooth/__main__.py +++ b/src/pysmooth/__main__.py @@ -1,18 +1,16 @@ """Command-line interface.""" -from typing import List - import numpy as np -from ._smooth import sm_3, sm_3R, sm_3RS3R, sm_3RSR, sm_3RSS, sm_split3 +from pysmooth._smooth import sm_3, sm_3R, sm_3RS3R, sm_3RSR, sm_3RSS, sm_split3 def smooth( - x: List[float], + x: list[float], kind: str = "3RS3R", - twiceit: bool = False, + twiceit: bool = False, # noqa FBT001 endrule: str = "Tukey", - do_ends: bool = False, -) -> List[float]: + do_ends: bool = False, # noqa FBT001 +) -> list[float]: """Tukey's smoothers, translated from the `smooth` function found in the R module {stats}. Parameters @@ -40,25 +38,27 @@ def smooth( number of iterations required to reach stable smoothing """ if kind not in ("3RS3R", "3RSS", "3RSR", "3R", "3", "S"): - raise RuntimeError("An invalid kind of smoother was selected") + msg = "An invalid kind of smoother was selected" + raise RuntimeError(msg) if endrule == "copy": iend = 1 elif endrule == "Tukey": iend = 2 else: - raise RuntimeError( - f"endrule must be either 'copy' or 'Tukey', but {endrule} was passed" - ) + msg = f"endrule must be either 'copy' or 'Tukey', but {endrule} was passed" + raise RuntimeError(msg) if any(np.isnan(np.array(x, dtype=np.float64))): - raise ValueError( + msg = ( "The sequence to be smoothed contains NAs/nans. This algorithm " "is unable to accomodate NAs." ) + raise ValueError(msg) - if not all([np.issubdtype(type(_), np.number) for _ in x]): - raise ValueError("The sequence contains non-float values.") + if not all(np.issubdtype(type(_), np.number) for _ in x): + msg = "The sequence contains non-float values." + raise ValueError(msg) if kind.startswith("3RS") and not do_ends: iend = -iend @@ -66,12 +66,12 @@ def smooth( iend = int(bool(do_ends)) n: int = len(x) - y: List[float] = np.zeros(n, dtype=np.float64).tolist() + y: list[float] = np.zeros(n, dtype=np.float64).tolist() split_ends = True if iend < 0 else False if kind != "S": - z: List[float] = np.zeros(n, dtype=np.float64).tolist() - w: List[float] = np.zeros(n, dtype=np.float64).tolist() + z: list[float] = np.zeros(n, dtype=np.float64).tolist() + w: list[float] = np.zeros(n, dtype=np.float64).tolist() if kind == "3RS3R": _, x, y, z, w = sm_3RS3R(x, y, z, w, n, abs(iend), split_ends) elif kind == "3RSS": @@ -87,7 +87,7 @@ def smooth( _, x, y = sm_split3(x, y, n, bool(iend)) if twiceit: - r: List[float] = smooth( + r: list[float] = smooth( x=y, kind=kind, twiceit=False, endrule=endrule, do_ends=do_ends ) y += r diff --git a/src/pysmooth/_smooth.py b/src/pysmooth/_smooth.py index af40e5d..ceceb25 100644 --- a/src/pysmooth/_smooth.py +++ b/src/pysmooth/_smooth.py @@ -5,10 +5,19 @@ https://github.com/wch/r-source/blob/trunk/src/library/stats/src/smooth.c """ +from enum import Enum from statistics import median -from typing import List, Tuple +class EndRule(int, Enum): + sm_no_endrule = 0 + sm_copy_endrule = 1 + sm_tukey_endrule = 2 + + +N_CUTOFF = 2 + +# TODO: reimplement this in rust def med3(u: float, v: float, w: float) -> float: """Find the median of three numbers. @@ -52,12 +61,12 @@ def imed3(u: float, v: float, w: float) -> int: def sm_3( - x: List[float], y: List[float], n: int, end_rule: int -) -> Tuple[bool, List[float], List[float]]: + x: list[float], y: list[float], n: int, end_rule: int +) -> tuple[bool, list[float], list[float]]: chg = False - if n <= 2: + if n <= N_CUTOFF: for i in range(n): y[i] = x[i] return False, x, y @@ -73,35 +82,36 @@ def sm_3( def sm_do_endrule( - y: List[float], - x: List[float], + y: list[float], + x: list[float], n: int, - chg: bool, + chg: bool, # noqa FBT001 end_rule: int, -) -> Tuple[bool, List[float], List[float]]: - if end_rule == 0: # "sm_NO_ENDRULE" +) -> tuple[bool, list[float], list[float]]: + if end_rule == EndRule.sm_no_endrule: pass - elif end_rule == 1: # "sm_COPY_ENDRULE" + elif end_rule == EndRule.sm_copy_endrule: y[0] = x[0] y[n - 1] = x[n - 1] - elif end_rule == 2: # "sm_TUKEY_ENDRULE" + elif end_rule == EndRule.sm_tukey_endrule: y[0] = median([3 * y[1] - 2 * y[2], x[0], y[1]]) chg = chg or (y[0] != x[0]) y[n - 1] = median([y[n - 2], x[n - 1], 3 * y[n - 2] - 2 * y[n - 3]]) chg = chg or (y[n - 1] != x[n - 1]) else: - raise RuntimeError(f"invalid end-rule for running median of 3: {end_rule}") + msg = f"invalid end-rule for running median of 3: {end_rule}" + raise RuntimeError(msg) return chg, y, x -def sm_3R( - x: List[float], - y: List[float], - z: List[float], +def sm_3R( # noqa N802 + x: list[float], + y: list[float], + z: list[float], n: int, end_rule: int, -) -> Tuple[int, List[float], List[float], List[float]]: +) -> tuple[int, list[float], list[float], list[float]]: chg, x, y = sm_3(x, y, n, 1) # "sm_COPY_ENDRULE" it = int(chg) @@ -122,7 +132,7 @@ def sm_3R( return int(chg), x, y, z -def sptest(x: List[float], i: int) -> bool: +def sptest(x: list[float], i: int) -> bool: if x[i] != x[i + 1]: return False elif (x[i - 1] <= x[i] and x[i + 1] <= x[i + 2]) or ( @@ -134,8 +144,8 @@ def sptest(x: List[float], i: int) -> bool: def sm_split3( - x: List[float], y: List[float], n: int, do_ends: bool -) -> Tuple[bool, List[float], List[float]]: + x: list[float], y: list[float], n: int, do_ends: bool # noqa FBT001 +) -> tuple[bool, list[float], list[float]]: # y[] := S(x[]) where S() = "sm_split3" chg = False @@ -177,15 +187,15 @@ def sm_split3( return chg, x, y -def sm_3RS3R( - x: List[float], - y: List[float], - z: List[float], - w: List[float], +def sm_3RS3R( # noqa N802 + x: list[float], + y: list[float], + z: list[float], + w: list[float], n: int, end_rule: int, - split_ends: bool, -) -> Tuple[int, List[float], List[float], List[float], List[float]]: + split_ends: bool, # noqa FBT001 +) -> tuple[int, list[float], list[float], list[float], list[float]]: # y[1:n] := "3R S 3R"(x[1:n]); z = "work"; it, x, y, z = sm_3R(x, y, z, n, end_rule) @@ -202,14 +212,14 @@ def sm_3RS3R( return (it + chg), x, y, z, w -def sm_3RSS( - x: List[float], - y: List[float], - z: List[float], +def sm_3RSS( # noqa 802 + x: list[float], + y: list[float], + z: list[float], n: int, end_rule: int, - split_ends: bool, -) -> Tuple[int, List[float], List[float], List[float]]: + split_ends: bool, # noqa FBT001 +) -> tuple[int, list[float], list[float], list[float]]: # y[1:n] := "3RSS"(x[1:n]); z = "work" it, x, y, z = sm_3R(x, y, z, n, end_rule) @@ -220,15 +230,15 @@ def sm_3RSS( return (it + int(chg)), x, y, z -def sm_3RSR( - x: List[float], - y: List[float], - z: List[float], - w: List[float], +def sm_3RSR( # noqa 802 + x: list[float], + y: list[float], + z: list[float], + w: list[float], n: int, end_rule: int, - split_ends: bool, -) -> Tuple[int, List[float], List[float], List[float], List[float]]: + split_ends: bool, # noqa FBT001 +) -> tuple[int, list[float], list[float], list[float], list[float]]: # y[1:n] := "3RSR"(x[1:n]); z := residuals; w = "work";