Merge pull request #609 from tupui/drop_old_python

Update dependencies

.github/workflows/lint.yml

@@ -5,12 +5,16 @@ on:
  push:
  branches: [main]
 
+concurrency:
+ group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+ cancel-in-progress: true
+
 jobs:
  linter:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v3
- - uses: actions/setup-python@v4
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v5
  with:
- python-version: "3.10"
- - uses: pre-commit/[email protected].0
+ python-version: "3.12"
+ - uses: pre-commit/[email protected].1

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
  runs-on: ubuntu-latest
  strategy:
  matrix:
- python-version: ['3.8', '3.10']
+ python-version: ['3.9', '3.12']
  defaults:
  run:
  shell: bash -l {0}
@@ -50,7 +50,8 @@ jobs:
  id: envcache
 
  - name: Update Conda Environment
- run: mamba env update -n SALib -f environment.yml
+ run: |
+ mamba env update -n SALib -f environment.yml
  if: steps.envcache.outputs.cache-hit != 'true'
 
  - name: Install package
@@ -59,13 +60,13 @@ jobs:
  pip install .[test]
 
  - name: Test
- if: matrix.python-version != '3.10'
+ if: matrix.python-version != '3.12'
  run: |
  conda activate SALib
  pytest
 
  - name: Test with coverage and uploads
- if: matrix.python-version == '3.10'
+ if: matrix.python-version == '3.12'
  run: |
  conda activate SALib
  python -m pip install coveralls

.gitignore

@@ -13,6 +13,8 @@ __pycache__
 .*.swp
 */.ipynb_checkpoints/*
 
+.DS_Store
+
 # Project files
 .ropeproject
 .project

.pre-commit-config.yaml

@@ -1,31 +1,27 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.3.0
+ rev: v4.5.0
  hooks:
  - id: trailing-whitespace
  - id: check-added-large-files
  - id: check-ast
- - id: check-byte-order-marker
+ - id: fix-byte-order-marker
  - id: check-case-conflict
  - id: check-docstring-first
  - id: check-merge-conflict
  - id: detect-private-key
  - id: end-of-file-fixer
 
 - repo: https://github.com/psf/black
- rev: 22.6.0
+ rev: 24.2.0
  hooks:
  - id: black
  exclude: "src/SALib/sample/directions.py"
 
-- repo: https://github.com/PyCQA/flake8
- rev: 6.0.0
- hooks:
- - id: flake8
- exclude: "src/SALib/sample/directions.py"
- args:
- - "--max-line-length=88"
- # whitespace before ':'
- # line too long
- # module level import not at top of file
- - "--extend-ignore=E203,E402"
+- repo: https://github.com/astral-sh/ruff-pre-commit
+ # Ruff version.
+ rev: v0.3.0
+ hooks:
+ # Run the linter.
+ - id: ruff
+ args: [ --fix ]

docs/conf.py

@@ -9,10 +9,11 @@
 # serve to show the default.
 
 from datetime import date
-import os
-import sys
+import importlib.metadata
 import inspect
+import os
 import shutil
+import sys
 
 # -- Path setup --------------------------------------------------------------
 
@@ -106,9 +107,7 @@
 project = "SALib"
 copyright = f"{date.today().year}, Jon Herman, Will Usher and others"
 
-import SALib
-
-version = SALib.__version__
+version = importlib.metadata.version("SALib")
 release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation

environment.yml

@@ -4,11 +4,10 @@ channels:
 dependencies:
  # required
  - numpy>=1.20.3
- - python>=3.8
- - pandas>=1.1.2
- - matplotlib>=3.2.2
- - scipy>=1.7.3
- - pathos>=0.2.5
+ - pandas>=2.0
+ - matplotlib>=3.5
+ - scipy>=1.9.3
+ - pathos>=0.3.2
  # tests
  - pytest
  - pytest-cov
@@ -18,7 +17,7 @@ dependencies:
  # doc
  - sphinx
  - numpydoc
- - pydata-sphinx-theme>=0.10
+ - pydata-sphinx-theme>=0.15.2
  - pip
  - pip:
  - myst_parser

examples/Problem/problem_spec.py

@@ -22,7 +22,6 @@
 
 
 if __name__ == "__main__":
-
  # Create the SALib Problem specification
  sp = ProblemSpec(
  {

pyproject.toml

@@ -1,13 +1,13 @@
 [build-system]
-requires = ["hatchling>=1.8.1"]
+requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
 [project]
 name = "SALib"
 dynamic = ["version"]
 description = "Tools for global sensitivity analysis. Contains Sobol', Morris, FAST, DGSM, PAWN, HDMR, Moment Independent and fractional factorial methods"
 readme = "README.rst"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = "MIT"
 authors = [
  { name = "Jon Herman", email = "[email protected]" },
@@ -20,9 +20,10 @@ maintainers = [
 classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Programming Language :: Python :: 3",
- "Programming Language :: Python :: 3.8",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3.11",
+ "Programming Language :: Python :: 3.12",
  "License :: OSI Approved :: MIT License",
  "Intended Audience :: End Users/Desktop",
  "Intended Audience :: Developers",
@@ -32,15 +33,15 @@ classifiers = [
 
 dependencies = [
  "numpy>=1.20.3",
- "scipy>=1.7.3",
- "matplotlib>=3.2.2",
- "pandas>=1.2",
+ "scipy>=1.9.3",
+ "matplotlib>=3.5",
+ "pandas>=2.0",
  "multiprocess",
 ]
 
 [project.optional-dependencies]
 distributed = [
- "pathos>=0.2.5",
+ "pathos>=0.3.2",
 ]
 
 test = [
@@ -53,7 +54,7 @@ doc = [
  "sphinx",
  "myst_parser",
  "numpydoc",
- "pydata-sphinx-theme>=0.10"
+ "pydata-sphinx-theme>=0.15.2"
 ]
 
 dev = [
@@ -72,7 +73,7 @@ Documentation = "https://salib.readthedocs.io"
 "Source code" = "https://github.com/SALib/SALib"
 
 [tool.hatch]
-version.path = "src/SALib/__init__.py"
+version.source = "vcs"
 build.targets.sdist.exclude = [
  ".github",
  "docs",

src/SALib/__init__.py

@@ -1,5 +1,3 @@
 from SALib.util import ProblemSpec
 
-__version__ = "1.4.7"
-
 __all__ = ["ProblemSpec"]

src/SALib/analyze/enhanced_hdmr.py

@@ -581,9 +581,11 @@ def _core_params(
  "S_sum_conf",
  )
  Si = ResultDict(
- (k, np.zeros((hdmr.nc_t, bootstrap)))
- if k in ("S", "Sa", "Sb", "Signf")
- else (k, np.zeros(hdmr.nc_t))
+ (
+ (k, np.zeros((hdmr.nc_t, bootstrap)))
+ if k in ("S", "Sa", "Sb", "Signf")
+ else (k, np.zeros(hdmr.nc_t))
+ )
  for k in keys
  )
  Si["Term"] = problem["names"]

src/SALib/analyze/morris.py

@@ -395,7 +395,6 @@ def _compute_elementary_effects(
  difference = _calc_results_difference(result_increased, result_decreased)
 
  if scaling:
-
  # calculate the scaled value of delta (step size)
  dx_trajectory = _calculate_step_size_x(input_matrix)
 

src/SALib/plotting/hdmr.py

@@ -6,6 +6,7 @@
 This submodule produces two different figures: (1) emulator vs simulator,
 (2) regression lines of first order component functions
 """
+
 import matplotlib.pyplot as plt
 import numpy as np
 

src/SALib/plotting/morris.py

@@ -17,6 +17,7 @@
  p = SALib.plotting.morris.horizontal_bar_plot(ax, Si, {'marker':'x'})
  p.show()
 """
+
 import numpy as np
 
 
@@ -53,7 +54,7 @@ def horizontal_bar_plot(ax, Si, opts=None, sortby="mu_star", unit=""):
  xerr=mu_star_conf_sorted,
  align="center",
  ecolor="black",
- **opts
+ **opts,
  )
 
  ax.set_yticks(y_pos)
@@ -135,7 +136,7 @@ def sample_histograms(fig, input_sample, problem, opts=None):
  bins=num_levels,
  density=False,
  label=None,
- **opts
+ **opts,
  )
  )
 

src/SALib/sample/latin.py

@@ -60,7 +60,6 @@ def sample(problem, N, seed=None):
  )
 
  for group in range(num_groups):
-
  np.random.shuffle(temp[:, group])
 
  for sample in range(num_samples):

src/SALib/sample/morris/brute.py

@@ -1,5 +1,5 @@
-"""
-"""
+""" """
+
 from SALib.sample.morris.strategy import Strategy
 from scipy.special import comb as nchoosek # type: ignore
 from itertools import combinations, islice
@@ -136,9 +136,7 @@ def mappable(combos, pairwise, distance_matrix):
  # Create a list of all pairwise combination for each combo in combos
  combo_list = combos[
  :,
- pairwise[
- :,
- ],
+ pairwise[:,],
  ]
 
  addresses = (combo_list[:, :, 1], combo_list[:, :, 0])
@@ -181,7 +179,7 @@ def nth(iterable, n, default=None):
  The default value to return
  """
 
- if type(n) != int:
+ if not isinstance(n, int):
  raise TypeError("n is not an integer")
 
  return next(islice(iterable, n, None), default)

src/SALib/sample/morris/local.py

@@ -1,5 +1,5 @@
-"""
-"""
+""" """
+
 from itertools import combinations
 import numpy as np # type: ignore
 from typing import List, Tuple, Union

src/SALib/sample/morris/strategy.py

@@ -10,6 +10,7 @@
 >>> context = SampleMorris(localoptimisation)
 >>> context.sample(input_sample, num_samples, num_params, k_choices, groups)
 """
+
 import abc
 
 import numpy as np # type: ignore

src/SALib/sample/saltelli.py

@@ -162,7 +162,6 @@ def sample(
  index = 0
 
  for i in range(skip_values, N + skip_values):
-
  # Copy matrix "A"
  for j in range(D):
  saltelli_sequence[index, j] = base_sequence[i, j]

src/SALib/scripts/salib.py

@@ -1,4 +1,5 @@
 """Command-line utility for SALib"""
+
 import importlib
 import argparse
 from SALib import analyze, sample

src/SALib/test_functions/oakley2004.py

@@ -29,7 +29,6 @@ def evaluate(X: np.ndarray, A: np.ndarray, M: np.ndarray) -> np.ndarray:
 
 
 if __name__ == "__main__":
-
  # Raw values taken from: http:https://www.jeremy-oakley.staff.shef.ac.uk/psa_example.txt
  M = np.array(
  [

src/SALib/util/__init__.py

@@ -1,6 +1,5 @@
-"""A set of utility functions
+"""A set of utility functions"""
 
-"""
 from collections import OrderedDict
 from typing import Dict, Tuple
 import warnings